- Feb 2023
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors convincingly show that their reconstructed ancestral nitrogenases are active both in vivo and in vitro, and show similar inhibitory effects as extant/wild-type enzymes.
The conclusion that, evolutionarily, there is a "single available mechanism for dinitrogen reduction" is not well explored in the paper. This suggests a limitation of using ancestral sequence reconstruction in this instance.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this paper, Kliesmete et al. analyze the protein and regulatory evolution of TRNP1, linking it to the evolution of brain size in mammals. We feel that this is very interesting and the conclusions are generally supported, with one concern.
The comparison of dN/dS (omega) values to 125 control proteins is helpful, but an important factor was not controlled. The fraction of a protein in an intrinsically disordered region (IDR) is potentially even more important in affecting dN/dS than the protein length or number of exons. We suggest comparing dN/dS of TRNP1 to another control set, preferably at least ~500 proteins, which have similar % IDR.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Nutrigenomics has advanced in recent years, with studies identifying how the food environment influences gene expression in multiple model organisms. The molecular mechanisms mediating these food-gene interactions are poorly understood. Previous work identified the enzyme O-GlcNAC (OGT) in mediating the decreased sensitivity in sweet-taste cells when exposed to a high-sugar diet. The present study, using fly gustatory neurons as a model, provides mechanistic insight into how nutrigenomic signaling encodes nutritional information into cellular changes. The authors expand previous work by showing that OGT is associated with neural chromatin at introns and transcriptional start sites, and that diet-induced changes in chromatin accessibility were amplified at loci with presence of both OGT and PRC2.1. The work also identifies Mitogen Activated Kinase as a critical mediator in this pathway. This is an elegant group of experiments revealing mechanisms for how nutrigenomic signaling triggers cellular responses to nutrients.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors address a very old question: what is the mechanism that controls genetic exchanges (crossovers) between the maternal and paternal chromosomes during sexual reproduction (meiosis). Specifically, what could account for two crucial aspects of the non-random distribution of crossovers: the lower-than-expected rate of non-exchange chromosomes, and the larger-than-expected distance between adjacent crossovers on the same chromosome. Despite the great progress that was made in the last few decades in understanding the molecular details crossover formation, the mechanism accounting for their non-random distribution remains a matter of heated debate. Hence, an ability to provide new insight into this question will be of interest to the wide chromosome biology community.
In this work, the authors combine two important findings/resources. The first is their own modeling of a biophysical framework called 'coarsening'. Coarsening relates to the well-described behavior of liquid compartments, which tend to get larger with time, at the expense of smaller compartments. As the authors note, their coarsening work builds on research by many labs, and on the recent understanding of the role of condensates in cell biology in general, and the liquid nature of the synaptonemal complex - a conserved meiotic chromosomal interface. In their previous paper, the authors found that coarsening could account for multiple cytological aspects of crucial regulators of crossovers - a conserved protein called HEI10. Their modeling was able to recapitulate temporal changes in HEI10 distribution and to account for changes that occur upon changes to HEI10 expression levels (halving of expression and over-expression). The second is the recent analysis of plant strains lacking the synaptonemal complex (zyp1). In that mutant, crossovers do occur (this is different than in some organisms), but the non-random distribution of crossovers is mostly lost: both crossover interference and the paucity of non-exchange chromosomes fit mostly random distribution.
Here, the authors combine these resources and adjust their modeling to account for the lack of the synaptonemal complex. A crucial difference is that instead of diffusing inside the SC (which spans each chromosome pair end-to-end), HEI10 now diffuses in the nucleoplasm. With this modified simulation they mostly account for crossover distribution in zyp1 mutants, using both published and new data they have acquired.
Despite the very limited amount of new data included in this manuscript, the clever combination of these two sources of data manages to add yet another layer of evidence to the idea that coarsening can explain crossover distribution. The main concern regarding the manuscript is that most of the aspects of crossover distribution that the model reproduces are quite trivial - for example, the resulting random distribution of the number of crossovers per chromosome. Some of the non-trivial aspects of the distribution - for example, the telomere enrichment - were built into the simulation as an explicit parameter. The only aspect that would be considered truly non-trivial is the narrower-than-expected number of total crossovers, despite the random distribution of crossovers per chromosome (Fig. 2A). Indeed, the modeling recapitulates this parameter, albeit to a much stronger degree than the in vivo data.
The ability of the model to recreate one non-trivial aspect of the crossover distribution is not sufficient to rule out other possible models, which would be necessary to consider this work a significant advance. However, if the authors are able to provide additional, non-trivial predictions relating to this and to other experimental conditions, this would dramatically elevate their ability to claim that a coarsening-based mechanism is indeed the most plausible one to explain crossover distribution. Some of these conditions could involve experimental perturbation of key parameters in the model: HEI10 levels, the number of DSBs or recombination intermediates (the 'substrate' that ends up resulting in crossovers), the length of time coarsening is allowed to proceed, or the volume of the nucleus.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
There is a lot of interest in how cells transfer materials (proteins, RNA, organelles) by extracellular vesicles (EV) and tunneling nanotubes (TNTs). Here, Zhang and Schekman developed quantitative assays, based on two different reporters, to measure EV and direct contact-dependent mediated transfer. The first assay is based on transfer of Cas9, which then edits a luciferase gene, whose enzymatic activity is then measured. The second assay is based on a split-GFP system. The experiments on EV trafficking convincingly show that purified exosomes, or any other diffusible agent, are unable to transfer functional Cas9 (either EV-tethered or untethered) and induce significant luciferase activity in acceptor cells. The authors suggest a plausible model by which Cas9 (with the gRNA?) gets "stuck" in such vesicles and is thus unable to enter the nucleus to edit the gene.
To test alternative pathways of transfer, e.g. by direct cell-cell contact, the authors co-cultured donor and acceptor cells and detect significant luciferase activity. The split GFP assay also showed successful transfer. The authors further characterize this process by biochemical, genetic and imaging approaches. They conclude that a small percentage of cells in the population produce open-ended membrane tubules (which are wider and distinct from TNTs) that can transfer material between cells. This process depends on actin polymerization but not endocytosis or trogocytosis. The process also seems to depend on endogenously expressed Syncytin proteins - fusogens which could be responsible for the membrane fusion leading to the open ends of the tubules.
The paper provides additional solid evidence to what is already known about the inefficiency of EV-mediated protein transport. Importantly, it provides an interesting new mechanism for contact-dependent transport of cellular material and assigns valuable new information about the possible function of Syncytins. However, the evidence that the proteins and vesicles transfer through the tubules is incomplete and a few more experiments are required. In addition, certain inconsistencies within the paper and with previous literature need to be resolved. Finally, some parts of the text, methods and the figures require re-writing or additional information for clarity.
Major comments<br /> 1. In Figure 1F, the authors compare the function of exosome-transported SBP-Cas9-GFP vs. transient transfection of SBP-Cas9-GFP. It is not clear if the cells in the transiently transfected culture also express the myc-str-CD63 and were treated with biotin. It is important to determine if CD63-tethering itself affects Cas9 function.<br /> 2. The authors do not rule out that TNTs are a mode of transfer in any of their experiments. Their actin polymerization inhibition experiments are also in-line with a TNT role in transfer. This possibility is not discussed in the discussion section.<br /> 3. Issues with the Split GFP assay:<br /> a. On page 4, line 176, the authors claim that "A mixture of cells before co-culture should not exhibit a GFP signal". However, this result is not presented.<br /> b. The authors show in Figure 2C and F that in MBA/HEK co-culture or only HEK293T co-culture, there are dual-labeled, CFP-mCherry, cells. First - what is the % of this sub-population? Second, the authors dismiss this population as cell adhesion (Page 5, line 192) - but in the methods section they claim they gated for single particles (page 17, line 642), supposedly excluding such events. There is a simple way to resolve this - sort these dual labeled cells and visualize under the microscope. Finally - why do the authors think that the GFP halves can transfer but not the mature CFP or mCherry?<br /> c. In the Cas9 experiments - the authors detect an increase in Nluc activity similar in order of magnitude that that of transient transfection with the Cas9 plasmid - suggesting most acceptor cells now express Nluc. However, only 6% of the cells are GFP positive in the split-GFP assay. Can the authors explain why the rate is so low in the split-GFP assay? One possibility (related to item #2 above) is that the split-GFP is transferred by TNTs.<br /> 4. The membrane tubules, the membrane fusion and the transfer process are not well characterized:<br /> a. The suggested tubules are distinct from TNTs by diameter and (I presume, based on the images) that they are still attached to the surface - whereas TNTs are detached. However, how are these structures different from filopodia except that they (rarely) fuse?<br /> b. Figure 5E shows that the acceptor cells send out a tubule of its own to meet and fuse. Is this the case in all 8 open-ended tubules that were imaged? Is this structure absent in the closed-ended tubules (e.g. as seen in Figures 6 & 8)?<br /> c. The authors suggest a model for transport of the proteins tethered to vesicles (via CD63 tethering). However, the data is incomplete.<br /> i. They show only a single example of this type of transport, without quantification. How frequent is this event?<br /> ii. Furthermore, the labeling does not conclusively show that these are vesicles and not protein aggregates. Labeling of the vesicle - by dye or protein marker will be useful to determine if these are indeed vesicles, and which type.<br /> iii. The data from Figure 2 suggest (if I understand correctly) transfer of the CD63-tethered half-GFP, further strengthening the idea of vesicular transfer. However, the authors also show efficient transfer of untethered Cas9 protein (Figure 2A and other figures). Does this mean that free protein can diffuse through these tubules? The Cas9 has an NLS so the un-tethered versions should be concentrated in the nucleus of donor cells. How, then, do they transfer? The authors do not provide visual evidence for this and I think it is important they would.<br /> iv. In Figures 6 & 8, where transfer is diminished, there are still red granules in acceptors cells (representing CD63-mcherry). Does this mean that vesicles do transfer, just not those with Cas9-GFP? Is this background of the imaging? The latter case would suggest that the red granule moving from donor to acceptor cells in figure 4 could also be "background". This matter needs to be resolved.<br /> 5. Why do HEK293T do not transfer to HEK293T?<br /> a. A major inexplicable result is that HEK293T express high levels of both Syncytin proteins (Figure 7 - supp figure 1A) yet ectopic expression of mouse Syncytin increases transfer (Figure 7E). Why would that be? In addition, Fig 3A shows high transfer rates to A549 cells - which express the least amount of Syncytin. The authors suggest in the discussion that Syncytin in HEK293T might not be functional without real evidence.<br /> b. In addition - previous publications (e.g. PMID: 35596004; 31735710) show that over expression of syncytin-1 or -2 in HEK293T cells causes massive cell-cell fusion. The authors do not provide images of the cells, to rule out cell-cell fusion in this particular case.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
To explore their dataset, the authors first identify all eligible women (n = 4673) in the database queried and use propensity score matching (PSM) to match group A (not infected by HPV) with group B (infected by HPV) for several covariates thought to affect bone mineral density (e.g.: age, smoking, alcohol). After PSM, no significant difference for selected covariates can be detected between the two groups.
Because they add matched their groups for relevant covariates possibly affecting bone mineral density, the authors then use Welch two-sample t-test to compare bone mineral densities of leg and lumbar spine between group A and group B, and detect significantly lower bone mineral densities for participants infected by HPV, group B. Here, the statistical approach chose by the author seems limited, and although PSM had been applied to match group earlier in the analysis pipeline, the reader could expect the statistical approach to be more robust, i.e. accounting for other covariates, like a linear mixed model.
Then, the authors analyse each HPV subtype independently and use Kendall's tau-b correlation test to estimate a correlation between a given HPV subtype and bone mineral density. To apply this test, the authors had to transform the bone mineral density to a binary variable, i.e. greater or equal to 1. Here again, the statistical approach does not control for any of the bone mineral density potentially affecting covariates. Also, the authors' study performed 32 Kendall's tau-b correlation tests and did not seem to correct for multiple testing.
Finally, the authors use the Restricted cubic spline model to establish a non-linear relationship between the number of infected HPV subtypes and bone mineral density.
The authors had set the aim to explore the association between HPV and bone mineral density. Unfortunately, due to possibly not high enough robustness of statistical approaches used in this manuscript, it does not seem sufficient to establish a clear association between HPV infection status and a lower bone mineral density. However, given the database the authors have created, it is believed that they have all the tools needed to pursue their aim.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This study investigates whether frequency tuning in the avian auditory midbrain is changed by the reliability of a key sound localization cue (Interaural Time Differences, ITDs) during development. It tests whether auditory neurons become more sensitive to sound frequencies that provide more reliable information about ITDs.
To manipulate the reliability of ITDs in a frequency-specific way, the authors removed the facial ruff of barn owls during development, which alters the acoustical input available to the animal in a number of important ways. When these animals reached adulthood, electrophysiological recordings were performed in the external nucleus of the inferior colliculus (ICx). Compared to control animals, these recordings revealed a weaker relationship between the best-frequency and best-ITD of individual neurons. A similarly weak relationship was observed in young animals whose ruff had not yet fully developed.
These results arise partly because animals without a facial ruff possess neurons with a best ITD of 0 that are tuned to unusually low frequencies. Having considered a number of possible explanations, the authors argue that this occurs because facial ruff removal reduces the reliability of high-frequency ITDs for frontal locations. Consequently, neurons tuned to frontal locations shift their frequency sensitivity to lower frequencies, which provides more reliable information about ITD. This shift toward lower frequencies is also thought to partly explain changes in tuning width that are observed in the absence of a facial ruff.
The study concludes that these results collectively provide evidence that the brain learns to implement probabilistic coding of sound location during development. However, although the study clearly shows changes in neural tuning in the absence of a fully developed facial ruff, the causal link with ITD reliability is complicated by a number of technical issues. The most important of these include a tendency to ignore the rear hemifield for some analyses but not others, the complex acoustical effects of facial ruff removal, and a model of IPD reliability that may or may not accurately reflect real-world listening. Nevertheless, the study presents an interesting set of results and shows an innovative approach in a number of places.
ACOUSTICS: A key strength of the study is its attempt to quantify the reliability of ITDs, which forms the foundation for the rest of the study. However, it is not entirely clear whether the method used for calculating ITD reliability is the most appropriate, and the way the data are presented raises a number of questions.<br /> 1) Why is IPD variability plotted instead of ITD variability (or indeed spatial reliability)? The relationship between these measures is likely to vary across frequency, which makes it difficult to compare ITD variability across frequency when IPDs are plotted. Normalizing data across frequencies also makes it difficult to compare different locations and acoustical conditions. For example, in Fig.1a and Fig.1b, the data shown for 3 kHz at ~160 degrees seems quantitatively and visually quite different, but the difference (in Fig.1c) appears to be negligible.
2) How well do the measures of ITD reliability used reflect real-world listening? For example, the model used to calculate ITD reliability appears to assume the same (flat) spectral profile for targets and distractors, which are presented simultaneously with the same temporal envelope, and a uniform spatial distribution of sounds across space. It is therefore unclear how robust the study's results are to violations of these assumptions.
3) Does facial ruff removal produce an isolated effect on ITD variability or does it also produce changes in directional gain, and the relationship between spatial cues and sound location? Although the study considers this issue in some places (e.g. Fig.2, Fig.5), a clearer presentation of the acoustical effects of facial ruff removal and their implications (for all locations, not just those to the front), as well as an attempt to understand how these acoustical changes lead to the observed changes in ITD reliability, would greatly strengthen the study. In addition, Fig.1 shows average ITD reliability across owls, but it would be helpful to know how consistent these measures are across owls, given individual variability in Head-Related Transfer Functions (HRTFs). This potentially has implications for the electrophysiological experiments, if the HRTFs of those animals were not measured. One specific question that is potentially very relevant is whether the facial ruff attenuates sounds presented behind the animal and whether it does so in a frequency-dependent way. In addition, if facial ruff removal enables ILDs to be used for azimuth, then ITDs may also become less necessary at higher frequencies, even if their reliability remains unchanged.
ELECTROPHYSIOLOGY: The electrophysiological recordings in young owls are impressive, particularly since they were done longitudinally (although the follow-up data in adults is not shown). The decision to look at the relationship between different tuning properties following different types of developmental experience (e.g. relationship between best ITD and best frequency in the absence/presence of a fully developed facial ruff) is also a major strength, particularly in light of the very interesting results observed. The authors have succeeded in identifying clear evidence for the importance of acoustical input for determining frequency-tuning properties in the auditory midbrain. However, a number of points remain unclear.
1) It is unclear why some analyses (Fig.5, Fig.7) are focused on frontal locations and frontally-tuned neurons. It is also unclear why neurons with a best ITDs of 0 are described as frontally tuned since locations behind the animal produce an ITD of 0 also. Related to this, in Fig.1, facial ruff removal appears to reduce IPD variability at low frequencies for locations to the rear (~160 degrees), where the ITD is likely to be close to 0. Neurons with a best ITD of 0 might therefore be expected to adjust their frequency tuning in opposite directions depending on whether they are tuned to frontal or rearward locations.
2) The study suggests that information about high-frequency ITDs is not passed on to the ICX if the ICX does not contain neurons that have a high best frequency. However, neurons might be sensitive to ITDs at frequencies other than the best frequency, particularly if their frequency tuning is broader. It is also unclear whether the best frequency of a neuron always corresponds to the frequency that provides the most reliable ITD information, which the study implicitly assumes.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Octopuses are known for their abilities in solving complex tasks and numerous apparently complex cognitive behaviours such as astonishment at octopuses learning how to open jars by watching others and the mind-boggling camouflage. They are very clever molluscs. The octopus shows the famously advanced brain plan but it is one that has little research progress due to its large size and structural complexity. This was originally recognised by the work of BB Boycott, JZ Young, EG Gray, and others in mid last century. Since then, however, little progress has been achieved towards a modern-day description of the octopus neural network particularly in the higher-order brain lobe, despite intense interest and indeed research progress concerning their complex behavioural and cognitive abilities.
This study applied a combination of EM-based imaging, neural tracing, and analyses to start revealing a further detailed view of a part of the lateral gyrus of the vertical lobe (learning and memory centre) of the common European octopus. It is a long overdue contribution and starts to bring octopus neuroscience a step close to the details of some vertebrates achieved. The new findings of neurons and the associated network provide new insights into this very complex but unfamiliar brain, allowing to propose a functional network that may link to the octopus memory formation. Also, this work could be of potential interest to a broad audience of neuroscientists and marine biologists as well as those in bio-imaging and deep-learning fields.
Strengths:<br /> Current knowledge of the neuroanatomy and the associating network of the octopus vertical lobe (learning and memory centre) remains largely based on the pioneering neuroanatomical studies in the '70s, this work indeed provides a rich and new dataset using modern-day imaging technology and reveals numerous previously-unknown neuron types and the resulting further complex network than we thought before. This new dataset reveals hundreds of cell processes from seven types of neurons located in one gyrus of the vertical lobe and can be useful for planning further approaches for advanced microscopy and other approaches including electrophysiological and molecular studies.<br /> Another strength of this study is to apply the current fashion of the deep learning technique to accelerate the imaging process on this octopus complex neural network. This could trigger some inventions to develop new algorithms for further applications on those non-model animals.
Weakness/limitations:<br /> In an effort to match the key claims of the first connectome of the octopus vertical lobe, mapping up an entire vertical lobe is essential. However, also understandably, given challenges in imaging a large-sized brain region, this study managed to image a very small proportion of the anterior part of the lateral gyrus. Along with the current limited dataset, a partially reconstructed neural network of one gyrus, it is unclear whether the wiring pattern found in this study would appear as a similar arrangement throughout an entire lateral gyrus. Furthermore, it is also unknown if another 4 gyri might keep a similar pattern of neural network as it found in the lateral gyrus. Considering some recent immunochemistry evidence that showed distinct different signals in different gyri in terms of heterogeneity of neuron types amongst gryi, to assume this newly-discovered network can represent the wiring pattern across an entire 5-gyrus vertical lobe is inadequate. As this study is the first big step to reveal the complex network in the octopus vertical lobe system, the title may be changed to "Toward connectomics of the Octopus vulgaris vertical lobe - new insights of memory acquisition network".
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The chemosensory systems of vertebrates and insects share a lot of structural and functional similarities. However, looking deeper into their molecular components reveals that these similarities likely represent remarkable examples of convergent evolution. For instance, receptor molecules that detect odors are unrelated between vertebrates and insects - vertebrates use G-protein coupled receptors while insects use ligand-gated ion channels. The latter was long regarded as specific to insects, but later studies identified putative homologs in other animals, (but not in vertebrates), some unicellular eukaryotes, and plants, raising the possibility that it is an ancient family. Still, the evolution of this protein family is notoriously difficult to analyze due to a high degree of sequence divergence between the genes despite the shared structural features of the proteins they encode. Here, the authors make use of the recent explosion of high-quality structural predictions produced by AlphaFold to conduct a deep search for previously undiscovered homologs of insect odorant and gustatory receptors.
The study describes two major findings:<br /> 1. In contrast to the previous idea that vertebrates lack any homologs of the insect receptors, two proteins in vertebrates turn out to display a similar structure (Fig. 2B).<br /> 2. The authors describe a previously uncharacterized family of Drosophila "gustatory receptor-like" proteins with a putative function in chemoreception as suggested by expression data (Fig 3A, G).
All analyses are extremely thorough, the logic of the narrative is very clear, and I find all conclusions well supported by data. The authors clearly favor a hypothesis that the family that includes insect odorant and gustatory receptors has a very deep evolutionary origin, and the homologous genes in other animals and non-animals have strongly diverged at the level of the sequence but retained detectable structural homology. However, they also acknowledge the limitations of some of their arguments and they discuss an alternative whereby the observed structural similarity is the result of convergence (which would be equally interesting). Overall, this study represents a major advance in our understanding of protein evolution and opens several avenues of research into the question of how functional demands steer the preservation of structural features of proteins while allowing their amino acid sequences to diverge.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this foundational article, the authors conduct an ancient DNA characterization of maize unearthed in archaeological contexts from Paredones and Huaca Prieta in the Chicama river valley of Peru. These maize specimens were recovered by painstakingly controlled excavation. Their context would appear to be beyond reproach though the individual radiocarbon determinations should be subject to further scrutiny.
Radiocarbon determination for at least one of the maize cobs analyzed for aDNA is not a direct date, but dates associated material. The authors should provide a table of the direct dates on the specimens that were analyzed for ancient DNA. They should also specify the type and quantity of material sent and whether the cob, glumes, pith, or husks were submitted for dates. Include δ13C determinations for each cob with laboratory analysis numbers because there is justifiable concern that at least one of these cob dates has a δ13C value suggesting the material dated is not maize. Generally, the δ13C for maize ranges from -14 to -7. One or more of the specimens subjected to ancient DNA analysis in this paper have δ13C values far outside of this confidence interval.
From the perspective of future scientists being able to repeat the analyses performed here, I would hope that all details of specimen treatment, extraction methods, read length and quality would need to be assiduously described. Routine analytical results should be reported so that comparisons with earlier and future results are facilitated, and not made difficult to decipher or search for.
The aDNA analysis may or may not be affected by the anomalous δ13C values but one would anticipate that standard aDNA extraction and analysis protocols would provide a means by which the specimen's preservation of the specimens could be ascertained, for example, perhaps deamination and fragmentation rates could be compared or average read length evaluated with modern-contemporary materials so that preservation of the Paredones samples relative to that of maize in the CIMMYT germplasm bank and the San Marcos specimens investigated by the same researchers can be evaluated.
The size and shape of the cobs depicted are similar to specimens occurring much later in Mesoamerican assemblages. For example, the approximate rachis diameter of the San Marcos specimens depicted by Valle-Bueno et al. (2016: Fig.1) averages less than 0.5cm while the specimens depicted in Valle-Bueno et al. (this manuscript) average 1.0 cm. The former - San Marcos - specimens are dated at 5300-4970 BP cal while the larger - Paredones - specimens date roughly 6777 - 5324 BP cal. The considerable disparity among the smaller more recent specimens compared to the very much larger putatively older specimens suggests the Paredones specimen's radiocarbon determinations are equivocal. The authors point this out but repeatedly state these cobs are the most ancient; a conundrum that should be resolved.
I would suggest the authors consider redating these three specimens and if they do, hope that they will prepare the laboratory personnel with depositional environment information. MacNeish was skeptical about late dates on maize at Tehuacan, at first. Adovasio was initially certain about maize's associated dates from Meadowcroft. One would prefer to be reasonably certain the foundation this article creates is solid; the author's repeated reference to these cobs as the most ancient in the Americas should be reaffirmed so retraction will not be necessary.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This study reports a novel role of thalamic activity in the late components of a cortical event-related potential (ERP). To show this association, the authors used high-density EEG together with multiple deep electrophysiological recordings combined with electrical stimulation of superficial and deep cortical layers. Stimulation of deep layers elicits a late ERP component that is closely related to bursts of thalamic activity during quiet wakefulness. This relationship is quite noticeable when deep layers of the cortex are stimulated, and it does depend on the arousal state, being maximal during quiet wakefulness, diminished during active wakefulness, and absent during anesthesia.
The study is very well performed, with a high number of subjects and appropriate methodology. Performing simultaneous recording of EEG and several neuropixels probes together with cortical microstimulation is no small feat considering the size of the mouse head and the fact that mice are freely behaving in many of the experiments. It is also noticeable how the authors use a seemingly outdated technique (electrical microstimulation) to produce compelling and significant research. The conclusions regarding the thalamic contributions to the ERP components are strongly supported by the data.
The spatiotemporal complexity is almost a side point compared to what seems to be the most important point of the paper: showing the contribution of thalamic activity to some components of the cortical ERP. Scalp ERPs have long been regarded as purely cortical phenomena, just like most EEGs, and this study shows convincing evidence to the contrary.
The data presented seemingly contradicts the results presented by Histed et al. (2009), who assert that cortical microstimulation only affects passing fibers near the tip of the electrodes, and results in distant, sparse, and somewhat random neural activation. In this study, it is clear that the maximum effect happens near the electrodes, decays with distance, and is not sparse at all, suggesting that not only passing fibers are activated but that also neuronal elements might be activated by antidromic propagation from the axonal hillock. This appears to offer proof that microstimulation might be much more effective than it was thought after the publication of Histed 2009, as the uber-successful use of DBS to treat Parkinson's disease has also shown.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This paper set out to investigate disparities in how authors of scientific papers are quoted in the context of science journalism. Quotations, the authors argue, reveal who a science journalist approaches as a source and thus who is considered an expert. At the same time, quotation in the news legitimizes experts and signals the importance of their perspective and opinions. It is therefore important to identify disparities in a quotation, both as a matter of justice and to ensure the representation of diverse viewpoints in journalism.
Here, the authors investigate disparities in quotation based on the gender and national origin of experts. They focus on science journalism in non-research articles published in the journal Nature. Articles are scraped from the Nature website and using established NLP tools the article content is parsed for quotations and the names of scientists being quoted. The gender and national origin of scientists are inferred based on their names and gendered pronouns used in the text. The rates of quotation based on gender/national origin are then compared to the demographics of authors (also inferred) of research articles published in Nature; this establishes a baseline to compare who is quoted vs. who is actually doing research. Based on these data, a variety of analyses are presented showing various aspects of bias and disparity in who is quoted in science journalism.
From their analysis, the authors make the following claims:
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Authors inferred as men were over-represented in quotations in journalistic Nature articles relative to their share of first and last authors in Nature.
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A quotation is sharply trending towards gender parity, with variation by the type of article.
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Authors with names inferred as originating from Celtic/English regions were over-represented, whereas authors with names inferred as originating from East Asia were heavily under-represented in quotations.
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The representation of authors with inferred East Asian names has increased faster among the last authors of research articles in Nature than it has in a journalistic quotation.
Claims 2-4 are solidly supported by the evidence presented in the manuscript. Claim 1 is supported by the evidence, but with some caveats. Support for Claim 1 depends on whether Nature's first or last authors are the most appropriate comparison set; if the last authors are the most appropriate, then Claim 1 only holds for 2005 through 2010. I expand on this point below.
I praise the manuscript and the authors for their commitment to reproducibility. Supplied with the paper is all the data (where possible) and code necessary to reproduce the results, as well as a Docker image that ensures that it can be re-executed far into the future.
The analyses conducted are methodologically rigorous. The authors provide bootstrapped confidence intervals for all analyzed values, choose appropriate baselines, and validate their name inference approach. In addition, I found their analysis comprehensive. By this I mean that they sufficiently explored their data to support their claims; nearly every caveat or limitation I could think of while reading was appropriately addressed either in the main or in a supplemental figure or table.
While a good paper, it is not without weaknesses. The paper is generally well-written, and the visualizations do a good job of communicating results. There is, of course, room to improve on both. In some cases, the manuscript lacks consistency in terminology, and uses word choice that is strange (e.g., "enrichment" and "depletion" when discussion representation). While this paper is methodologically rigorous and professional in its presentation, I feel that the authors could have done a better job of interpreting and contextualizing their findings. Specifically, readers should be aware of the caveats regarding Claim 1 (listed above), the limits of generalizing these findings to other areas of science journalism, and a somewhat shallow discussion section that I believe detracts from the study's significance. I outline these points in more detail below.
Despite these quibbles, the authors find solid support for their claims and achieve their goals. This paper, I believe will be of general interest to scientists and science communicators, to those interested in science communication as a field, to meta-scientists, and to those aiming to improve diversity and equity in the scientific process.
Caveats to Claim Claim 1:
One of the claims made by the authors (Claim 1) is that quotations in the dataset skew towards men. I find this true, but with two related caveats: that it depends on the choice of comparator set, and that it changes over time.
The authors assess the representation of quotation by comparison to either Nature's first authors, or last authors. However, the authors do not discuss whether one is more appropriate, and what is implied if, say, quotations match the last author but not the first authors. In most scientific fields, the last author corresponds to the conceptual lead of a paper and is often the corresponding author who is most likely to be contacted to discuss the paper's significance. First authors, in contrast, will often represent the "driver" of the project-basically the person doing most of the actual work and is usually a student or more junior researcher. This distinction is important because cases could be made for either being a more appropriate comparator - last authors due to their seniority, first authors due to their closeness to the study, and (typically) greater diversity.
The choice of comparator set becomes an issue because, as per Claim 2, the representation of women is increasing over time. Claim 1 only holds for the last authors from 2005 through 2010, and after 2018 women have higher representation given the demographics of the last authors. For the first authors, Claim 1 holds through 2017, after which they are representative or slightly over-representative of women authors.
So while Claim 1 holds, it does not hold for all comparator sets and for all years. I don't think this is critical of the paper-the authors do discuss the trend in Claim 2-but interpretation of this claim should take care of these caveats, and readers should consider the important differences in first and last authorship.
Generalizability to other contexts of science journalism:
Journalistic articles in Nature may not be representative of all contexts of science journalism. Nature has a unique readership, consisting of scientists from many disciplines who have not only a generalist interest in science but also an interest in aspects of science as a profession. Science journalism as a whole, however, is part of the broader landscape of mainstream media, consisting of outlets such as ABC, BBC, and Scientific American. The audiences for these outlets will be more general, less interested in science as a career, and will likely have a different appetite for direct quotations and for more technical topics.
This does not make the study bad. On the contrary, the author's focus on Nature allowed for many interesting analyses-but their findings should still be understood as coming from a specific context. While the authors outline many limitations of their study, they do not grapple with the limits of its generalizability, and what aspects of their analysis might translate to other contexts of science journalism. For example, part of the trend towards gender parity in a quotation is explained by the higher representation of women in the "Career Feature" article type. However, this article type will likely not be present in more general-interest contexts, which would affect the representation of women.
Shallow discussion:
I feel that the authors missed an opportunity to use their discussion to not only properly contextualize their results, but also explore their significance. In broad terms, there is literature on science journalism, its consequences for science, and the impact on public perceptions, as well as a continuous meta-discourse on journalistic ethics and best practices. The authors pay lip service to some of these themes but do little to actually place their findings in the broader discourse. Below, I provide a few specific points that could be further discussed:
What might be the downstream impacts on the public stemming from the under-representation of scientists with East Asian names?
The authors highlight gender parity in career features, but why exactly is there gender parity in this format of Representation in quotations varies by first and last author, most certainly as a result of the academic division of labor in the life sciences. However, what does it say about the scientific quotation that it appears first authors are more often to be quoted? Does this mean that the division of labor is changing such that the first authors are the lead scientists? Or does it imply that senior authors are being skipped over, or giving away their chance to comment on a study to the first author?
Moreover, there are several findings in the study which are notable but don't seem to have been mentioned at all in the discussion.
Below I highlight a few:
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According to Figure 3d, not only are East Asian names under-represented in quotations, but they are becoming more under-represented over time as they appear as authors in a greater number of Nature publications.
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Those with European names are proportionately represented in quotations given their share of authors in Nature. Why might this be, especially seeing as Anglo names are heavily over-represented?
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Ibar and colleagues address the role of the spectrin cytoskeleton in the regulation of tissue growth and Hippo signaling in an attempt to elucidate the underlying molecular mechanism(s) and reconcile existing data. Previous reports in the field have suggested three distinct mechanisms by which the Spectrin cytoskeleton regulates Hippo signaling and this is, at least in part, due to the fact that different groups have mainly focused on different spectrins (alpha, beta, or beta-heavy) in previous reports.
The authors start their investigation by trying to reconcile their previous data on the role of Ajuba in the regulation of Hippo signaling via mechanotransduction and previous observations suggesting that Spectrins affect Hippo signaling independently of any effect on myosin levels or Ajuba localization. Contrary to previous reports, the authors reveal that, indeed, depletion of alpha- and beta-heavy-spectrin leads to an increase in myosin levels at the apical membrane. Moreover, the authors also reveal that the depletion of spectrins leads to an increase in Ajuba levels.
The authors suggest that Ajuba is required for the effect of beta-heavy spectrin. However, it is still formally possible that this could be a parallel pathway that is being masked by the strong phenotype of Ajuba RNAi flies.
One of the major points of the manuscript is the observation that alpha- and beta-heavy-spectrin are potentially working independently and not as part of a spectrin tetramer. This is mostly dependent on the observation that alpha- and beta-heavy-spectrin appear to have non-overlapping localizations at the membrane and the fact that alpha- and beta-heavy-spectrin localize at the membrane seemingly independently. It is not entirely obvious that a potential lack of colocalization and the fact that protein localization at the membrane is not affected when the other partner is absent is sufficient to argue that alpha- and beta-heavy-spectrin do not form a complex. Moreover, it is possible that the spectrin complexes are only formed in specific conditions (e.g. by modulating tissue tension).
If indeed spectrins function independently, would it not be expected to see additive effects when both spectrins are depleted?
Related to the two previous points, the fact that the authors suggest that both alpha- and beta-heavy-spectrin regulate Hippo signaling via Ajuba would be consistent with the necessity of an alpha- and beta-heavy-spectrin complex being formed. How would the authors explain that both spectrins require Ajuba function but work independently?
Another major point of the manuscript is the potential competition between beta-heavy-spectrin and myosin for F-actin binding. The authors suggest that there is a mutual antagonism between the two proteins regarding apical F-actin. However, this has not been formally assessed. Moreover, despite the arguments put forward in the discussion, it seems hard to justify a competition for F-actin when beta-heavy-spectrin seems to be unable to compete with myosin. Myosin can displace beta-heavy-spectrin from F-actin but the reciprocal effect seems unlikely given the in vitro data.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The data generated for this paper provides an important resource for the neuroscience community. The locus coeruleus (LC) is the known seed of noradrenergic cells in the brain. Due to its location and size, it remains scarcely profiled in humans. Despite the physically minute structure containing these cells, its impact is wide-reaching due to the known neuromodulatory function of norepinephrine (NE) in processes like attention and mood. As such, profiling NE cells has important implications for most neurological and neuropsychiatric disorders. This paper generates transcriptomic profiles that are not only cell-specific but which also maintain their spatial context, providing the field with a map for the cells within the region.
Strengths:
Using spatial transcriptomics in a morphologically distinct region is a very attractive way to generate a map. Overlaying macroscopic information, i.e. a region with greater pigmentation, with its corresponding molecular profile in an unbiased manner is an extremely powerful way to understand the specific cellular and molecular composition of that brain structure.
The technologies were used with an astute awareness of their limitations, as such, multiple technologies were leveraged to paint a more complete and resolved picture of the cellular composition of the region. For example, the lack of resolution in the spatial transcriptomic platform was compensated by complementary snRNA-seq and single molecule FISH.
This work has been made publicly available and accessible through a user-friendly application such that any interested researcher can investigate the level of expression of their gene of interest within this region.
Two important implications from this work are 1) the potential that the gene regulatory profiles of these cells are only partially conserved across species, humans, and rodents, and 2) that there may be other neuromodulatory cell types within the region that were otherwise not previously localized to the LC
Weaknesses:
Given that the markers used to identify cells are not as specific as they need to be to definitively qualify the desired cell type, the results may be over-interpreted. Specifically, TH is the primary marker used to qualify cells as noradrenergic, however, TH catalyzes the synthesis of L-DOPA, a precursor to dopamine, which in turn is a precursor for epinephrine and norepinephrine suggesting some of the cells in the region may be dopaminergic and not NE cells. Indeed, there are publications to support the presence of dopaminergic cells in the LC (see Kempadoo et al. 2016, Takeuchi et al., 2016, Devoto et al. 2005). This discrepancy is further highlighted by the apparent lack of overlap per given Visium spots with TH, SCL6A2, or DBH. While the single-nucleus FISH confirms that some of the cells in the region are noradrenergic, others very possibly represent a different catecholamine. As such it is suggested that the nomenclature for the cells be reconsidered.
The authors are unable to successfully implement unsupervised clustering with the spatial data, this greatly reduces the impact of the spatial technology as it implies that the transcriptomic data generated in the study did not have enough resolution to identify individual cell types.
The sample contribution to the results is highly unbalanced, which consequently, may result in ungeneralizable findings in terms of regional cellular composition, limiting the usefulness of the publicly available data.
This study aimed to deeply profile the LC in humans and provide a resource to the community. The combination of data types (snRNA-seq, SRT, smFISH) does in fact represent this resource for the community. However, due to the limitations, of which, some were described in the manuscript, we should be cautious in the use of the data for secondary analysis. For example, some of the cellular annotations may lack precision, the cellular composition also may not reflect the general population, and the presence of unexpected cell types may represent the accidental inclusion of adjacent regions, in this case, serotonergic cells from the Raphe nucleus.
Nonetheless having a well-developed app to query and visualize these data will be an enormous asset to the community especially given the lack of information regarding the region in general.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This work by Sidhaye, Trepte et al. systematically investigates the relationship between transcript and protein abundance across the genome in human neurogenesis. Through analysis of the transcriptome and proteome in brain organoids, they find that for specific gene modules, transcript and protein abundance are highly disconnected. While there are already several anecdotic examples of this phenomenon in the literature, highlighting the role of post-transcriptional gene regulation in corticogenesis, Sidhaye, Trepte et al. for the first time systematically explore the pervasiveness of this phenomenon in a genome-wide manner at different stages of human neurogenesis using a dual reporter cell line to isolate neural progenitor cells and neurons.
The authors then focus on one of the modules that is characterized by the enrichment of the 5'TOP (terminal oligopyrimidine) motif in the 5'UTR of transcripts and enriched in ribosomal proteins and translation initiation factors. The authors show that partial inhibition of the translation of ribosomal genes in neural progenitor cells inhibits the translation of differentiation genes, a process that involves mTOR-mediated regulation.
Strength:
The integration of transcriptome and proteome data enables an unbiased systemic analysis revealing gene modules that follow similar trajectories, and as such may share common regulatory principles. For one of the modules, the authors dissect the posttranscriptional regulatory cascade using an elegant combination of fluorescent reporter human pluripotent stem cell lines in combination with gene knockouts.
Overall, the data presented in this work is of a very high standard and supports the conclusions put forward by the authors. The processed omics data sets are made available via a Shiny app web interface for easy access and therefore promote exploration by the scientific community.
Limitations:
This study uses a large range of specific reporter and knockout hPSC lines generated in the context of this work, however, very limited information is provided on these lines. For example, do the lines remain karyotypically normal throughout the targeting procedure? Does reporter gene expression faithfully recapitulate the activity of the promoters controlling their expression? Specifically, it appears that a significant GFP signal is detected within the neuronal layer (Figure 1B) and that there is a much larger double reporter-positive population than expected (Figure S2A).
The authors propose that stress-associated translational regulation takes place in early neural progenitors, involving the sequestration of transcripts in stress granule-like structures. However, given that at least some human brain organoid protocols have been reported to lead to ectopic activation of cellular stress pathways (Bhaduri et al., Nature 2019), it would be desirable to see this aspect of the study confirmed in primary tissue (mouse or human).
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- Jan 2023
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors set out to understand how a room-temperature X-Ray crystallography-based chemical-fragment screen against a drug target may differ from a cryo screen. They carried out two room-temperature screens and compared the results with that of a cryo screen they previously performed. With a substantial set of crystallographic evidence they showed that the modes of protein-fragment binding are affected by temperature. The conclusion of the work is compelling. It suggests that temperature provides another dimension in X-ray crystallography-based fragment screening. In a practical sense, it suggests that room-temperature fragment screen is a promising new avenue for hit identification in drug discovery and for obtaining insights into the fragment binding. Room-temperature screening carries unique advantage over cryo screening. This work is confirmative to the notion, which seems not yet universally considered, that very weak protein-small molecule binding may be inherently fluid structurally, and that crystal structures of such weak binding, especially cryo structures, cannot be taken for granted without cross validation.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this study, the authors developed a mouse model to specifically investigate whether GC B cells that present nuclear protein (NucPr) could be specifically suppressed by Tfr cells. Most current mouse models that have been used in investigating Tfr functions are based on the overall readout of autoantibody production in the scenario of loss-of-function of Tfr cells. The proposed model of gain-of-function of Tfr cells is novel and valuable.
The authors mainly compared two boosting immunizations by Strepatividin (SA) alone or SA-conjugated with nuclear proteins (SA-NucPr) and demonstrated SA-NucPr boosting immunization was able to expand Tfr cells, suppress overall and SA-specific GC/memory/plasma cell responses. The results are mostly convincing.
One major concern is the conditions and controls used in the study. The control group (SA boosting immunization) would have enhanced T and B cell responses by this boosting. Unfortunately, there was no non-boosting control group so the level was unclear. It is therefore to strictly match such boosting condition in the SA-NucPr group. Notably, both SA and SA-NucPr were used at 10ug for boosting immunization. Considering NucPr were comparable or much larger (Nucleosome, about 200KDa) than SA (about 60KDa), the dose of SA in the SA-NucPr group was far less than that in the SA group. Due to this cavity, it is difficult to judge the difference between two groups was due to less SA boosting immunization or NucPr-induced Tfr function. This was a fundamental issue weakens the conclusion.
The single cell analyses clearly demonstrated the expansion of Tfr clones. It remains unclear why other Treg populations other than Tfr cells were not expanded? The Treg cells in the CXCR5intPD-1int population were recently activated and should be able to respond to the boosting immunization. On an alternative explanation, the changes in Tfr cells could be indirectly driven by the changes in Tfh cells. For example, Tfh can produce IL-21 and restrict Tfr expansion (Jandl C, et al.2017). This could be the case of the reduction in Tfr cells in the SA-OVA group as compared to the SA group.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
In this proof-of-concept study, Richardson et al explore lifecourse effects of adiposity on leptin levels using life course Mendelian randomization and perform a tissue-partitioned MR to study the effects of tissue-specific BMI genetic instruments on leptin levels. The methods are solid and they have been nicely applied in the context of the present study. The results are important, revealing differences in the impact of adiposity on leptin levels in childhood vs adulthood, and highlighting the importance of the adipose-brain pathway in leptin homeostasis.
Additional MR analyses are suggested to explore bidirectional associations between leptin levels and adiposity, due to the interrelation of these two markers. Also, the fact that the MR instruments for childhood adiposity are based on self-reported body size, while the MR instruments for adult adiposity are based on measured adult BMI should be highlighted in the manuscript, and the possible impact of this in the findings should be discussed.
In summary, this important study is a proof of concept of life course and tissue-partitioned MR, while providing interesting insights into the regulation of leptin homeostasis by adiposity in different life stages.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors are aiming to characterize the developmental process and functional heterogeneity of liver ILC1s. The role of liver ILC1's in human health is still unknown. ILC1's are abundant in fetal liver and decline throughout development into adults.
The authors have gone to great lengths to establish the relationship between IL-7R expression and ILC1 ontogeny.
The study provides insight into the complex ILC1 ontogeny by revealing relationships among heterogenous ILC1 subsets.
The data suggests intrinsic cytotoxic programs of 7R− ILC1s differ to NK cells, proposing them as critical steady-state sentinels against infection prevention and tumor surveillance.
The big unresolved question is why ILC1 dominate fetal innate lymphocytes versus NK cells in adult life.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Scagliotti et al address how organ size is regulated by imprinted genes. Using a series of mouse models to modulate the dosage of the paternally expressed gene, Dlk1, the authors demonstrate that DLK1 is important for the maintenance of the stem cell compartment leading to the growth of the pituitary gland and the expansion of growth hormone-producing cells. The authors show that overexpression of Dlk1 leads to pituitary hyperplasia while deletion of the paternal allele leads to reduced pituitary size. Reduced pituitary size is accompanied by reduced cell proliferation in the cleft at e13.5 and an increase in the number of POU1F1+ cells, suggesting that loss of Dlk1 alters the balance between the number of cells remaining in the replicating stem cell pool and those differentiating into the POU1F1 lineage. An elegant caveat of this paper is the rescue of Dlk1 expression in the population of cells expressing Pou1f1 but not in SOX2+ stem cells. Expression of Dlk1 only in POU1F1+ cells is not sufficient to rescue pituitary size. The authors suggest that this is because DLK1 must be present in stem cells which then activate paracrine WNT signaling to promote cell proliferation in POU1F1+ cells.
Strengths:
This is an important study that provides a mechanistic understanding of how the imprinted gene, Dlk1, regulates organ size. The study employs an elegant experimental design to address the dosage requirement for Dlk1 in regulating pituitary gland size. Rescuing Dlk1 in the POU1F1+ cells, but not the marginal zone SOX2+ cells provides intriguing results about a possible role for DLK1 in paracrine signaling between these different pituitary cell types. The study uses publicly available scRNAseq and ChIPseq data to further support their findings and identify Dlk1 as a likely target of POU1F1.
Weaknesses:
The study only analyzes females for the adult time point. For embryonic and postnatal time points sexes are pooled. Gender differences in pituitary gene expression embryonically or postnatally could potentially affect experimental outcomes.
The authors employ a mouse model that rescues Dlk1 expression starting at e15.5 in POU1F1+ parenchymal cells but not in marginal zone stem cells. Rescuing Dlk1 expression in a specific population of cells is one of the strengths of this study. Based on this information and the fact that overexpression of Dlk1 leads to increased pituitary size, the authors suggest that DLK1+ marginal zone stem cells and DLK+ parenchymal cells may interact to promote postnatal proliferation. However, the ability to more carefully parse out the complex spatial and temporal contributions of DLK1 to pituitary size would be enhanced by the addition of a mouse model that rescues Dlk1 expression only in SOX2+ cells and a model that rescues expression in both stem cells and POU1F1+ cells.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this manuscript, Rahsepar et al. test the hypothesis that the precise timing of engram cell activation in relation to the phase of hippocampal theta oscillations plays a causal role in recall. This hypothesis is derived from theories (e.g. the SPEAR model) positing that the hippocampus segregates information for memory encoding and retrieval in time and that separation is organized across the many neurons and subregions of the hippocampus by theta oscillations. They test this hypothesis using stimulation of dentate gyrus neurons active during the encoding of fear memory. Using closed-loop stimulation that they developed, the authors stimulate these dentate engram cells at different phases of theta to measure freezing behavior to determine if the fear memory is recalled. They compare this stimulation to stimulation at the same average frequency regardless of theta phase, or at a constant 20Hz, in line with prior research, as control conditions. The authors use an elegant within animal design. They find that stimulating at the theta phase when CA3 inputs most strongly influence CA1 leads to significant increases in freezing (relative to baseline), while none of the other stimulation conditions have significant effects on freezing. They then show that this stimulation also causes increases in gamma modulation by theta, which is correlated with learning in prior work. However, the gamma that is theta-modulated appears to be medium gamma which is not associated with CA3 inputs to CA1. Overall, the study is well-designed and well-controlled. The stimulation effects at the "best" theta phase are modest but do appear different than the other conditions. It is unclear why the authors chose to stimulate in dentate and not CA3 as the SPEAR hypothesis centers around CA3 and EC inputs to CA1. Furthermore, I wonder if the freezing behavior itself confounds the detection of the theta phase. Finally, some of the statistical analyses require controlling for multiple comparisons.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Prasad et al investigate mechanisms of interface contractility that occur at borders between cells of different specification states. Cells of different specification states typically sort out, minimizing interface contact, in association with increased junctional contractility that can be visualized by phalloidin labeling. Here, Prasad et al show, for multiple different examples of specification and/or signaling states, that bilateral activation of JnK flanks these interfaces, which are associated with elevated rates of Jnk-dependent apoptosis. Blocking Jnk activity does not seem to affect phalloidin labeling, however, placing interphase contractility upstream or parallel to Jnk activity and apoptosis. Interestingly, activated Ras[V12] is an exceptional case where interphase contractility and bilateral Jnk activation occur without elevated apoptosis. Indeed, RasV12 can suppress apoptosis associates with interfaces between other distinct cell types. Prasad et al suggest that this property of Ras[V12] activated cells may underlie their oncogenic potential in mammals. These are potentially interesting observations that address what happens when cell of disparate signaling and/or specification states are opposed. In principle, they could be of interest both to developmental biologists, from the perspective of correction of developmental errors, and to cancer biologists, from the perspective of eliminating precancerous cells.
It is not clear how much advance is represented over the prior description of 'morphogenetic apoptosis', in which bilateral Jnk activity was also an integral part (Adachi-Yamada and O'Connor, Devl Biol vol251 pp74-90 2002). There is little new mechanistic insight provided here. As such, the observations seem preliminary and to represent only a limited advance.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Enteroendocrine cells (EEC) line the gut and prior evidence suggest that they are primary sensors of gut contents. In turn, these cells release transmitters that regulate gut function, including gut motility, enzyme secretion, and gut permeability. More recent studies have also found synaptic connections between EEC and neural sensory fibers that connect the gut to the brain, implicating this pathway in taste learning. Thus, EEC signals can be integrated with sensory signals originating in more distal areas of the alimentary canal.
EECs express a variety of receptors and transmitters that are hypothesized to contribute to the diversity of sensing and motor functions. In this report, Hayashi et al develop a novel transgenic mouse that permits manipulation of EEC subtypes via intersectional methods. Using this approach, they identify differential roles for EEC subtypes in controlling gut motility and taste learning.
Strengths
• The authors supplement existing single-cell RNA sequencing of the proximal intestine.<br /> • A Vil1-2a-Flp mouse was generated, which exhibits highly selective expression in the gut epithelium. This mouse line can be used to manipulate EEC subtypes when bred with other Cre driver lines and double conditional (Flp/Cre) mice.<br /> • Using the above tool, different EEC subtypes were histologically characterized along the alimentary canal. Additionally, other tissues were examined, including the brain, pancreas, and lungs to demonstrate the gut specificity of their approach. The intersectional approach yield sparse recombination in the pancreas, therefore the authors included controls in their gut motility and feeding studies to account for this.<br /> • In probing the function of distinct EECs, it was found that Cck(cholecystokinin) and Gcg (GLP-1) expressing EECs slow down gut motility, whereas Tac1 (substance P) and Pet1(serotonin) expressing cells increase motility.<br /> • Food intake studies revealed several subpopulations that decrease feeding (Pet1, Npy1r, Cck, Gcg).<br /> • A conditioned flavor preference assay suggests that some of the above EEC subtypes (Pet1, Tac1, Npy1r, Gcg) decrease feeding in part through conditioned flavor avoidance.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In the manuscript by Porter et al., the authors describe a putative role for the STAG proteins (SA1 and SA2), not as part of the cohesin complex, but in isolation and in particular at R-loops where they contribute to R-loop regulation, linking chromatin structure and cohesin loading.
My major concern is rather general: " the role of SA1 and SA2 proteins (or cohesion subunits) its only highlighted upon acute depletion of RAD21 (cohesin subunit that holds together the complex)". I am not sure that this context is recapitulated in living cells. I.e is there a particular phase of the cell cycle where RAD21 is acutely depleted or targeted for specific degradation? How do we know that we are not looking at remnants of a complex (cohesin) that has been partially targeted by IIA mediated degradation? Is the RNA binding of SA1 an SA2 CTCF-independent (as CTCF encompasses an RNA binding domain?).
Is there any proof that in untreated cells (ie before depletion) SA1 AND SA2 are chromatin bound independently of Rad21 (and /or SMC1-3)? Overall, it is a nice manuscript, but I am not sure whether the IAA-dependent degradation of a single subunit of pentameric complex is the right tool to assess whether other subunits of the same complex work independently.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The study of Koropouli is a tour the force investigation of the Semaphorins receptor, Neuropilin-2, modification by Palmitoylation. The work consists of biochemical, cellular and in vivo experiments and overall underscore an interesting layer of regulation of axonal guidance receptors membrane localization and function by lipid modification.
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www.youtube.com www.youtube.com
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https://www.youtube.com/watch?v=ifDi2SsQjQM
Comparing the various e-note/e-reader devices, Kit Betts-Masters ranks them overall as follows: - Boox Note Air 2 - Supernote A5X - Remarkable 2 - Bigme Inknote - Kobo Elipsa - Boyue P10
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Gold and his colleagues first ectopically expressed aACTN2 constructs with various deletions and determine the spatial proximity to CaMKII by PLA. Chemical LTP induced by brief glycine application in hippocampal cultures strongly augmented the PLA puncta density in spines (postsynaptic sites). This interaction specifically depended on the 4 EF hands near the C-terminus of aACTN. At the same time expression of the 4 EF hands (plus the C-terminal PDZ ligand) impaired the formation of larger mushroom spines under unstimulated conditions and the increase in mushroom spines seen after chemLTP when compared to non-transfected conditions or transection of the EF hands with a point mutation (L854R) that disrupted binding to CaMKII.
To further define the interaction between aACTN and CaMKII the authors then solved a crystal structure formed by the aACTN EF3/4 and regulatory segment of CaMKII. This structure confirmed the role of L854 in the interaction. It also explained earlier results that phosphorylation of threonine in position 306 but not of threonine 305 of the CaMKII regulatory domain impaired aACTN binding as T306 but not T305 is engaged in critical interactions. This contrasts with Ca/CaM binding to CaMKII, which engages both threonines and is blocked by the phosphorylation of either residue. Consistently, earlier structures of Ca/CaM with the CaMKII regulatory domains showed respective differences to the new aACTN-CaMKII structure.
Additional analysis of these data indicated that the association of the regulatory domain with the kinase domain occludes access to aACTN EF3/4. This is an important finding because it implies that only active CaMKII like T286 autophosphorylated CaMKII or bound to GluN2B would be able to effectively interact with aACTN in intact cells.
Finally, and remarkably, binding was augmented by a protein fragment of the GluN2B C-terminus that contains the binding site for CaMKII even when Ca/CaM was still present. This result suggests that with GluN2B present aACTN can bind to CaMKII even though in the absence of GluN2B Ca/CaM occludes this binding. This finding opens up new research directions.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this paper, Xiao et al. suggest that PASK is a driver for stem cell differentiation by translocating from the cytosol to the nucleus. This phenomenon is dependent on the acetylation of PASK mediated by CBP/EP300, which is driven by glutamine metabolism. Furthermore, this study showed that PASK interferes/weakens the Wdr5-APC/C interaction, where PASK interacts with Wdr5, resulting in repression of Pax7, leading to stem cell differentiation.
There exist huge interest in maintaining adult stem cells and ES cells in their pluripotent form and the work painstakingly perform several experiments to present that PASK is a good target to achieve that goal.
However, the work on the paper relies mostly on data from C2C12 cells as adult muscle stem cell models, in vivo experimental data, and primary myoblasts from mice. Using these models makes the story contextual in muscle stem cells. Authors have not tried to extrapolate similar claims in other adult stem cell models. This severely restricts the claim to muscle stem cells even though PASK is required for the onset of embryonic and adult stem cell differentiation in general. Their work could be much strengthened if it is also tried on mesenchymal stem cells as these cells are also as metabolically active as muscle cells.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this work, Verstegen and colleagues try to delineate human B cell differentiation trajectories by using in vitro differentiation culture of human naive B cells. The authors adopted a protocol of B cell stimulation with CD40L-expressing fibroblasts and IL-4/IL-21, and cultured B cells were analyzed by single-cell transcriptome analysis. Five distinct clusters were identified with features of memory B cells, germinal center-like B cells, ASCs, pre-ASCs, or post-GC B cells. This work provides a precise description of gene expression profiles of activated B cell populations and some insight into the pathways of effector B cell differentiation. This work will be a solid basis for human B cell study using in vitro culture of target B cell populations, providing an excellent experimental protocol.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
My main concern is in regards to the interpretation of these results has to do with the sparseness of data available to fit with the models. The authors pit two linear models against a nonlinear (normalization) model. The predictions for weighted average and summed models are both linear models doomed to poorly match the fMRI data, particularly in contrast to the nonlinear model. So, while I appreciate the verification that responses to multiple stimuli don't add up or average each other, the model comparisons seem less interesting in this light. This is particularly salient of an issue because the model testing endeavor seems rather unconstrained. A 'true' test of the model would likely need a whole range of contrasts tested for one (or both) of the stimuli, Otherwise, as it stands we simply have a parameter (sigma) that instantly gives more wiggle room than the other models. It would be fairer to pit this normalization model against other nonlinear models. Indeed, this has been already been done in previous work by Kendrick Kay, Jon Winawer and Serge Dumoulin's groups. So far, may concern above has only been in regards to the "unattended" data. But the same issue of course extends to the attended conditions. I think the authors need to either acknowledge the limits of this approach to testing the model or introduce some other frameworks.
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Reviewer #2 (Public Review):
This study generated a valuable preclinical model of patients with Mfn2-related lipodistrophy (R707W). Such a mouse model enables the understanding the pathogenic mechanism causing this lipodistrophy and testing specific therapeutic approaches for these patients.
The strengths are the thorough phenotypic characterization of the mice and the clear decrease in circulating leptin and adiponectin levels in the absence of changes in fat mass observed in Mfn2 R707W/R707W mice. This partially recapitulates one of the key phenotypes of human patients with these mutations.
The major weakness is the conclusion that the integrated stress response is activated in white adipose tissue is not supported by the data and the phenotype. The ISR caused by primary insults to mitochondria was defined as a response that decreases the translation of mitochondrial proteins, thus decreasing mitochondrial respiratory function via ATF4 without engaging ATF5 (Quiros et al., JCB 2016). In addition, the increase in ATF4 caused by phosphorylation of eif2alpha is in ATF4 translation and translocation to the nucleus, not in ATF4 transcription. It is a possibility that it is a selective increase in ER stress that is responsible for defective leptin secretion, as Mfn2 R707W/R707W adipose tissue shows no mitigation of mitochondrial function as expected from ATF4-ISR activation.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Barthé et al. present a manuscript examining membrane-domain specific signaling by βAR stimulation in cardiomyocytes. Specifically, the authors seek to use a size exclusion approach using PEGylated-isoproterenol to allow only surface sarcolemmal βAR receptor stimulation without T-tubule βAR stimulation. This innovative approach was advanced using confocal microscopy to determine the accessibility of the PEGylated substrates to the T-tubule network. The authors show comparable responses of L-type Ca channels, Ca transients, and contraction using equipotent doses of PEG-Iso and Iso, but differences in nuclear and cytoplasmic cAMP responses based on FRET reporters.
Strengths<br /> 1. The size exclusion strategy using PEGylation technology is well rationalized and well supported by the physicochemical characterization of PEGylated Iso. This represents a novel strategy to decipher cardiomyocyte cell surface signaling from T-tubule network signaling resulting from the stimulation of β-adrenergic receptors. This approach can be used to study the compartmentalization of various signaling pathways in cardiomyocytes as well as in other cell types that exhibit complex cytoarchitecture. The authors use multiple cAMP FRET sensors as well as assay a number of relevant physiological cellular responses to assess the effect of Iso vs. PEGylated Iso which are informative.
Weaknesses<br /> 1. The authors' evidence that PEG-FITC does not penetrate the TT network is not convincing as presented in Figure 1. A single confocal image from one cell showing a lack of fluorescence (Figure 1A) could be due to an outlier cell or lack of penetration to more central regions of the cell where images are taken from. More convincing would be a confocal Z-scan series comparing PEG-FITC and FITC in ARVM. Some form of quantification of T-tubule network density from multiple cells would provide even more robust evidence, similar to the many studies that have done this characterization in models of dilated cardiomyopathy showing a loss of TT network. This exclusion of PEG-FITC provides the critical foundation for the paper and it is somewhat unanticipated given the large dimensions of the t-tubules relative PEG-Iso, so strong data here are particularly important.
2. The conclusion on line 160 that 'the maximal efficacy of PEG-Iso was significantly lower by 30% than that of Iso,' may be overstated. What approach was used to conclude significantly differently as this implies a statistical comparison? Were the concentration-response curves fit to determine maximal responses? In the examples given, the responses are continuing to increase at the highest concentrations tested, so it is difficult to simply compare the responses to the highest doses tested.
3. For experiments using adenovirus delivery of FRET-based sensor, the culture of ARVM is required which may impact the biology. Such culture is known to result in changes in cell structure and physiology with loss of the TT network over time. It is essential for the authors to demonstrate that under the conditions of their FRET experiments, the cells continue to exhibit a robust TT network.
4. As pointed out by the authors, the interpretation of OSM/TTM adrenergic receptor functions in this study is limited by the fact that the relative contributions of β-adrenergic receptor subtypes had not been assessed. This particularly complicates the interpretation of their results in that the authors demonstrate in Figure 2 that PEGylation increases the Ki for Iso for β1 receptors by 700-fold whereas the increase for β2 receptors is about 200-fold. Thus, the relative contribution of β1 and β2 receptors to a 'comparable' dose of Iso and PEGylated Iso will potentially be different. Could that difference in relative β1/β2 receptors be the cause of the different 'efficacy of nuclear and cytoplasmic' cAMP changes between the two tested ligands in Figure 8 and supplemental Figure 3? This would fundamentally alter the conclusions of the paper.
5. The equipotent doses of Iso and PEG-Iso were initially defined based on their ability to elevate global [cAMP]i. The authors then further demonstrated that such equipotent doses of Iso and PEG-Iso also had equal effects on ICa,L amplitude, Ca2+ transient parameters, and cellular contractility (shortening), presumably because they raised global [cAMP]i to the same levels. These findings seem to defy the importance of nanodomain organization and local [cAMP]i in the regulation of LTCCs, Ca2+ cycling proteins, and contractile machinery. The authors argued that "Since OSM contributes to ~60% of total cell membrane in ARVMs, either β-ARs and ACs are more concentrated in OSM than TTM, or they are in large excess over what is needed to activate PKA phosphorylation of proteins involved in EC coupling. Also, cAMP produced at OSM must diffuse rapidly in the cytosol in order to activate PKA phosphorylation of substrates located deep inside the cell, such as LTCCs in TTM" (lines 336-341). Although this argument may be valid at high concentrations of Iso and PEG-Iso when PKA activation is saturated, it also implies that discrepancy could be detectable at lower (non-saturating) doses of Iso and PEG-Iso. Thus, additional experiments using lower Iso and PEG-Iso doses are required to support this notion.
6. The size excluded compartment for PEG-Iso proposed by the authors is the TT network, but this ignores other forms of sarcolemmal nanodomains such as caveolae, which include β2 receptors and AC, and may exhibit similar if not great sensitivity to the size exclusion approaches pioneered by the authors.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The study systematically looks at dynamic differences across variants longitudinally and the authors appropriately only limit their analyses to peptides that are conserved across the different variants.
There are some concerns listed below, particularly related to the ensemble heterogeneity that is reported and need considerable revision.
1) The authors explain that cold-temperature treatment of the S trimer ectodomain constructs has been shown to lead to instability and heterogeneity. They also show this with a comparison of untreated vs. 3-hour 37 C treated samples. I'm confused as to why "During automated HDXMS experiments protein samples were stored at 0 degrees". Will this not cause issues in protein heterogeneity, where the longer the protein sits at 0 C the more potential heterogeneity there will be, and thus greatly confound the analysis?
2) The authors presume that the bimodal spectra that are observed reflect EX1 kinetics, however, there can be multiple reasons for an apparent bimodal distribution in the spectra. I agree that some of the spectra indicate that more than a single species is present, but what the two populations represent is murky. In Figure 2D, the apparent size of the highly deuterated population gets larger going from the 60 sec to the 600-sec spectra, as expected for an EX1 transition. However, in Figure 3D the WT highly deuterated population gets smaller going from the 60-sec to the 600-sec spectra. Were bimodal examples observed beyond those shown in Figure 2?
3) How were the spectra that appeared broadened analyzed? There is no description of this in the methods, and the only data shown for this is in table 1. The left/right percentages are reported without any description of how they were obtained. Are these solely from a single spectrum? The most alarming issue is that Table 1B reports 9.4% for the right population of the 988-998 peptide, but the corresponding spectra in Figure 3D doesn't seem to have any highly deuterated population at all.
4) The authors state on page 12: "Replicate analysis of stabilized S trimers with incubation at 4C prior to deuterium exchange (see methods) showed a time-dependent reversal of stabilization as reported previously (Costello et al., 2022), most evident at the same peptides." Is this data shown anywhere? If not then it should be included somewhere, possibly in table 1 as I would expect the cold treatment to offset the left/right population sizes.
5) The authors state that peptide 899-913 'exhibits a slow conformational interconversion (time scale ~ 15-30 min)'. Where did this estimated rate come from? From the data shown and the limited number of time points, I don't think there is sufficient sampling of this conformational transition to really narrow down the exact timescale, especially since the ratio of left/right populations is so dependent on the pre-treatment of the sample prior to deuterium exchange. (See 1st comment)
6) The woods plots presented in the Supporting information: (Figures 2-S4, 2-S5, 3-S4, 4-S2, 5-S2, 6-S2) are not conventional Woods plots. Normally the plots would indicate a global threshold for what is deemed to be significant based on the overall error in the dataset. From what I gather the authors used error within an individual peptide to establish significance for each specific peptide, which would be okay, but the authors don't describe the number of replicates or how the p-value was calculated. I would strongly recommend that the authors instead rely on a hybrid significance testing approach, as described recently: (PMID 31099554). What's really alarming with the current approach is that several of the Woods plots shown have data points found to be significantly different that are right at zero on the y-axis.
7) Table 1: The summary of the peptides with observed bimodal behavior should include data from the replicates, particularly for assessment of how consistent the left/right population sizes are across replicates. Instead of just a percentage, the table should report an average and the standard deviation from the replicate measurements. Furthermore, the table should also include peptides that are overlapping with those presented. Based on Figure 2-figure supplement 1, there are at least two other peptides that cover the 899-913 region. These additional peptides should show a similar trend with bimodal profiles and will be important for showing how reproducible the apparent EX1 kinetics are in the dataset.<br /> All available replicates and overlapping peptides should be analyzed to ensure that these percentages reported are consistent across the data. It is also odd that the authors choose to use the 3+ charge state of the WT, but the 2+ for the D614G mutant. If both charge states were present, then both of them should be analyzed to ensure the population distributions are consistent within different charge states.
8) The method for calculating p-values used to assess the significance of a difference in observed deuterium uptake is not described. The manuscript mentions technical replicates, but no specific information as to how many replicates were collected for each time point. These details should be included as they are also part of the summary table that is recommended for the publication of HDX data.
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Reviewer #2 (Public Review):
This beautiful study identifies a genetic mechanism controlling colony morphology differences in Burkholderia thailandensis. There is a large region of the genome which can be duplicated or triplicated in a RecA-dependent recombination process, leading to phenotypic changes. In addition to colony morphology differences in cells with one, two, or three copies of the region, other phenotypes like biofilm formation are impacted. This appears to be an unstable genetic change since some of the colony types can interconvert to others after restreaking. The authors are commended for the development of elegant genetic approaches to study and carefully prove the existence of the copy number variation of this genomic region. These approaches will be of great use to the field in studying copy number variation in bacteria far beyond Burkholderia or colony morphology/biofilm formation. Bacteriology has for decades focused on average measurements of a culture, and this study helps usher the field to a new future where we appreciate and measure the behaviors of individual populations of cells within the same culture.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Zhang et al. addressed an intriguing question - whether the presence of mesenchymal stem cells (MSCs) could influence the efficacy of CAR-T therapy. After observing that CAR-T cytotoxicity was strongly inhibited by MSCs by modulating certain correlated immune response pathways, the authors sought to uncover the underlying mechanisms by examining the interaction between MSCs and macrophage, immune escaping mechanisms, and oxidative stress. Notably, the authors discovered that a single gene, STC1, played a major role in reversing the suppression when it was knocked down/out. Although more research is necessary to clarify the signaling pathways, the data presented by the authors were generally well-supported and convincing.
Major points:
1. STC-1 is expressed and secreted by many human cancer cells. This should be discussed in the introduction or discussion with more inter-related background info on both its regulation in cancer cells and secretion pattern into TME. It is important because you state that the STC-1 secreted by MSC has such strong functions, then how about those produced and secreted by cancer cells? Are those also stimulated by macrophages or other components in TME? Do they have possible functions in helping cancer cell to escape the immune surveillance mechanisms?
2. In Figure 4B, using a single marker of IL-1β to show the immune suppressive capability of MSC in vivo is not sufficient, staining for CD4+ and CD8+ should also be included to demonstrate whether MSC could modulate T cell compositions, which can give more direct evidence about MSC's impacts on CAR-T cell.
3. One of the major risks associated with CAR-T therapy is an excessive immune response that causes cytokine release syndrome. MSCs have been used in clinics as a way to suppress immune response including post-CAR-T. What does the author think about using MSC with STC-1 knockout? Can it still help reduce toxicity while maintaining CAR-T efficacy? This might be a potential application.
4. There was a recent study published in Cancer Cell (Lin et al. Stanniocalcin 1 is a phagocytosis checkpoint driving tumor immune resistance. 2021), and they also reported that STC1 negatively correlates with immunotherapy efficacy and patient survival. It should be cited, and in fact, it provided support to the authors' present study with completely different experimental settings.
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Reviewer #2 (Public Review):
Kang et. al., model the cortical dynamics, specifically distributions of beta burst durations and proportion of different kind of spatial waves using a firing rate model with local E-I connections and long range and distance dependent excitatory connections. The model also predicts that the observed cortical activity may be a result of non stationary external input (correlated at short time scales) and a combination of two sources of input, global and local.
Overall, the manuscript is very clear, concise and well written. The modeling work is comprehensive and makes interesting and testable predictions about the mechanism of beta bursts and waves in the cortical activity. There are just a few minor typos and curiosities if they can be addressed by the model. Notwithstanding, the study is a valuable contribution towards developing data driven firing rate.
1) The model beautifully reproduces the proportion of different kind of waves that can be seen in the data (Fig 3), however the manuscript does not comment on when would a planar/random wave appear for a given set of parameters (eg. fixed v_ext, tau_ext, c) from the mechanistic point of view. If these spatio-temporal activities are functional in nature, their occurrence is unlikely to be just stochastic and a strong computational model like this one would be a perfect substrate to ask this question. Is it possible to characterize what aspects of the global/local input fluctuations or interaction of input fluctuations with the network lead to a specific kind of spatio-temporal activity, even if just empirically ? Do different waves appear in the same trial simulation or does the same wave type persist over the whole trial? If former, are the transition probabilities between the different wave types uniform, i.e probability of a planar wave to transit into a synchronized wave equal to the probability of a random wave into synchronized wave?
2) Denker et al 2018, also reports a strong relationship between the spatial wave category, beta burst amplitude, the beta burst duration and the velocity (Fig 6E - Denker et. al), eg synchronized waves are fastest with the highest beta amplitude and duration. Was this also observed in the model ?
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Reviewer #2 (Public Review):
Luckey et al. investigated the mechanisms by which non-invasive transcutaneous electrical stimulation of the greater occipital nerve (NITESGON) enhances long-term memory. They find that NITESGON applied during or after a word-association task enhances memory recall at a retrieval test 7 days later but not at an immediate test, suggesting NITESGON's memory-enhancing effect involves the consolidation process. They show that NITESGON applied during a second spatial memory task not only enhances later recall for that task, but also for an initial word-association memory task unpaired with stimulation administered before the second task. This highlights NITESGON's ability to retroactively strengthen memories and provides further evidence for behavioral tagging. Furthermore, the authors perform a series of in-depth experiments to examine the mechanisms by which NITESGON enhances memory consolidation. They show that NITESGON increases salivary a-amylase levels, a marker of endogenous noradrenergic activity, and spontaneous eye blink levels, a proxy for dopamine levels, both in support of locus coeruleus involvement. Resting-state fMRI results further suggest NITESGON induces increased communication between the locus coeruleus and hippocampus, suggesting a circuit-based mechanism by which NITESGON enhances memory consolidation. Interestingly, the data also indicate that NITESGON's memory-enhancing effect is not sleep-dependent but is dopamine-receptor-dependent.
The conclusions of this paper are mostly well supported by the data, however, some of the key mechanistic findings lack the appropriate controls required for the authors' claims.
Strengths<br /> 1) The manuscript is written in an easy-to-read manner with clarity for each of the individual experiments conducted.<br /> 2) The authors provide convincing evidence that NITESGON targets the memory consolidation process and enhances long-term but not short-term memory. This provides a unique non-invasive method for enhancing memory and has an important potential impact on neurocognitive disorders.<br /> 3) The manuscript provides convincing evidence that NITESGON increases LC-hippocampus connectivity as well as MTL gamma power, providing a circuit-based mechanism by which stimulation enhances memory.
Weaknesses (major)<br /> 1) Adding control groups (sham stimulation) to Experiment 5 and Experiment 8 would be needed to increase confidence that NITESGON's memory-enhancing effects do not depend on sleep but do depend on dopamine receptor activity.<br /> 2) Task order in the interference study in Experiment 4 was randomized during the first visit for task training as well as during the memory test, however, the word-association and spatial navigation tasks used in Experiments 3 and 4 were not counterbalanced during training or memory testing. Thus, the authors cannot rule out the possibility of order effects.<br /> 3) It is unclear how Experiment 3 and Experiment 4 differ. Percent of words recalled is the measure of memory performance, however, there is not a clear measure of interference in Experiment 4 (i.e. words recalled during Memory task II that were from Memory task I).<br /> 4) In Experiment 5 the learning and test phases for the two sleep groups were conducted at different times of day (sleep group: training at 8pm and testing the next morning at 8am, sleep deprivation group: training at 8am and testing at 8pm) which introduces the possibility of circadian effects between the two groups. Additionally, the memory test occurred at the 12h point for this experiment instead of the 7-day point. Therefore, the authors' conclusions are not addressed by this experiment, and it remains unclear whether the 7-day long-term memory effects of NITESGON are sleep-dependent.
Weaknesses (minor)<br /> 1) Salivary amylase is being used as a proxy of noradrenergic activity, however, salivary amylase levels increase with stress as well, which impacts memory performance. It would be helpful if the authors addressed this and whether they measured other physiological indicators of stress/sympathetic nervous system activation.<br /> 2) Insufficient details of how the blinding experiment was conducted make it difficult to determine whether participants had awareness or subjective responses during the NITESGON stimulation. Adding physiological indicators of heart rate, skin conductance, and respiration would provide a better indicator of a sympathetic nervous system response. Additionally, a series of randomized stimulation and sham trials delivered to the participant would provide a more objective measure of the detectability of the stimulation.<br /> 3) It would be appreciated if the authors could speak to the possible role of the amygdala in the memory-enhancing effects of NITESGON, as this region is a well-known modulator of many types of memory consolidation and is implicated in noradrenergic-related memory enhancement.
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Reviewer #2 (Public Review):
The authors have demonstrated a covalent strategy to target the oncogenic K-Ras(G13C) mutation, which is found in about 3,000 cancer patients in the US each year. G13C is a major contributor to G13 mutations, the next hotspot mutation after codon 12. Moreover, there is no approved therapy for G13 mutations and no published inhibitors of any KRAS G13 mutant proteins, making this a particularly important contribution to the rapidly expanding repertoire of RAS inhibitors. A striking difference in comparison to G12 mutations, mutations occurring at Codon 13 exhibit impaired pM-nucleotide binding affinity of K-Ras. This weaker nucleotide affinity offered the authors the opportunity to develop a nucleotide based inhibitor of a RAS protein. With the high nucleophilicity of cysteine mutation, G13C the authors set out to target this mutant oncogene.
The authors developed several covalent molecules derived from GDP/GTP, the natural substrate of K-Ras's nucleotide binding pocket, interestingly, not through the oligophosphate chain (explored by Gray and co-workers in an earlier report) but the 2,3-diol of the ribose. This turned out to be a judicious choice for targeting G13C because of the closer proximity to the 2',3' rather than the phosphates. Previous work by Gray et. al. used the phosphate attachment point for the electrophile but this compromised binding affinity overall-whereas the relatively tolerant modifications at 2',3' led to higher affinity electrophilic ligands. This change led to much tighter binders and effective covalent modifiers through C13. With two co-crystal structures resolved, the authors unambiguously showed the covalent cross-linking between artificial G-nucleotides and K-Ras(G13C).
It is not surprising that one of the major limitations of these GDP-based competitive ligands suffer from permeability issues. GDP or GTP analogs made in this study were not permeable through plasma membrane. The authors nicely worked around these limitations by delivering the fully modified proteins to the cells and measured cell signaling effects. Through electroporation the authors demonstrated the covalent adduct to be able to inhibit downstream signaling by compare introduction of K-Ras WT or K-Ras(G13C) or K-Ras(G13C) covalent adduct.
A number of very intriguing aspects of the covalent adduct were noted which should guide others in the field, including that the adduct with eda-GTP could get hydrolysed to eda-GDP after the covalent modification of the protein--furthermore GAP stimulation of this adduct still occurred. By use of a non-hydrolyzable form of GTP (CP) this could be prevented and could be a very useful method for preventing hydrolysis after introduction in cells--an application Goody and coworkers applied to a previous covalent base adduct.
Overall, the manuscript addresses an important problem relating to whether covalent small molecules can engage K-Ras(G13C) and provided two timely co-crystal structures for future research and development.
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Reviewer #2 (Public Review):
The manuscript by Aggad et al., describes an interesting folded structure that links the epidermis to the cuticle in C. elegans. They analyzed the structure by TEM and tomography and found groups of parallel folds in both L4 and adult animals. They show VHA-5 localizes to this structure and have used VHA-5::GFP transgenic reporter to investigate differently cuticle furrow-related genes by RNAi. It is an important step to describe the character of this structure, which the authors named "meisosomes". However, the structure has been reported and well defined as "apical membrane stacks" in previous studies and reviewed by a few articles (Liegeois et al., 2006, Hyenne et al., 2015, Chisholm and Xu, 2012, Cohen and Sundaram 2020). It is very confusing that the authors want to change the name of this structure.
The major problem of this paper is that there is not much new information. It is already known that these stacks exist, VHA-5 localizes to the stacks, cuticle damage induces AMPs, "furrowless" dpy mutants result in complete disorganization of the epidermis, defective cuticle structure causes abnormalities via gene expression, etc. The function of these stacks remains unknown. Another issue is the transgenic reporter of VHA-5::GFP, which is not endogenously expressed, and its puncta intensity only reflects the protein distribution but not the stack structure.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Wu Yang et al. investigated how exophers (large vesicles released from neuronal somas) are degraded. They find that the hypodermal skin cells surrounding the neuron break up the exophers into smaller vesicles that are eventually phagocytosed. The neuronal exophers accumulate early phagosomal markers such as F-actin and PIP2, and blocking actin assembly suppressed the formation of smaller vesicles and the clearance of neuronal exophers. They show the smaller vesicles are labeled with various markers for maturing phagosomes, and inhibiting phagosome maturation blocked the breakdown of exophers in to smaller vesicles. Interestingly, they discover that GTPase ARF-6, effector SEC-10/Exocyst, and the phagocytic receptor CED-1 in the hypodermis are required for efficient production of exophers by neurons.
Strength<br /> The study clearly demonstrates that exophers are eliminated via hypodermal cell-mediated phagocytosis. Exophers are broken down into smaller vesicles that accumulate phagocytic markers, and inhibiting this process shows that exophers are not resolved. The paper does a thorough examination of various markers and mutants to demonstrate this process.
The hypodermal cells not only engulf these small vesicles, but they also play a role in the formation of exophers. Exopher production is reduced when ARF-6, SEC-10, or CED-1 are knocked down in the hypodermis. This is intriguing because phagocytosis is a critical step in the final elimination of cells, but in this unique situation, it appears that the neuron fails to extrude the exopher without phagocytes.
Weakness
Non-professional phagocytes engulfing cell corpses and many other types of cellular debris (e.g. degenerating axons) have been shown in multiple systems and the observations here are not surprising. Many of the markers used in the study are well-established phagocytic markers and do not bring forward a new technological advance.
What's interesting is that the breakdown of exophers into smaller vesicles and eventual clearance follows a different sequence of events than macrophages. Exophers appear to undergo phagosomal fission before interacting with lysosomes. This would be difficult to appreciate by a general reader.
While the paper has strengths, it appears that the message is not clear. The title suggests that the reader will learn about how ARF-6 and CED-1 control exopher extrusion. Although this observation is intriguing and maybe the main point of the paper, there does not appear to be a substantial amount of data to support this claim. The only data to back this up is in the final figure and the majority of the paper is focused on how hypodermal cells phagocytose exophers.
To show exopher secretion is dependent on the hypodermal cells-
1. Could authors induce exopher production through other means? And test any involvement of CED-1? For example, authors note exopher production increases under stress conditions including expression of mutant Huntingtin protein. It would be intriguing if loss of CED-1 would be sufficient to block or reduce exopher production in that context and would highlight an exciting role for phagocytic cell types.<br /> 2. It is not clear if the CED-1 localization to the exopher is due to CED-1 expression during phagocytosis or is it involved in the extrusion. Perhaps the basal level of CED-1 is important for the extrusion but the strong expression is important for recognition of the exopher.<br /> 3. While the data with ttr-52 and anoh-1 alleles is compelling, do we know that exophers actually expose PS? Especially since at a certain point, the exopher is still attached to the neuronal soma. Is PS still exposed by exopher in CED-1 background?<br /> 4. What is the fate of a neuron that is unable to produce exophers? Could one look at lifespan of ALMR neuron in CED-1, ARF-6 or Sec-10 allele (potentially with specificity to hypodermis)?
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this manuscript titled "S-adenosylmethionine synthases specify distinct H3K4me3 populations and gene expression patterns during heat stress", the authors Godbole et al investigated how C. elegans SAM synthases, SAMS-1 and SAMS-4, affected gene expression, H3K4 trimethylation (H3K4me3), and the survival under heat stress. They found in this study that SAMS-4 was required for survival during heat shock. They reasoned that SAM supplied by SAMS-4 but not SAMS-1 might be responsible for generating H3K4me3 under heat shock and claimed that the two SAM synthases differentially affected histone methylation and thus gene expression in the heat shock response. This study suggested a stress-responsive mechanism by which the specific isozyme of SAM synthetase provided a specific pool of cellular SAM for H3K4me3. Overall, this study is interesting but descriptive. Lacking necessary controls and mechanistic details weakened the significance of this work.
Strengths: Very interesting survival phenotypes in the loss of different SAM synthetases; technical success in CUT&tag in C. elegans.
Weaknesses: No clear conclusion can be drawn about whether and how SAM synthetases affect H3K4me3.
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Reviewer #2 (Public Review):
The authors use a series of subsampling methods based on phylogenetic placement and geographic setting, informed by human movement data to control for differences in sampling of SARS-CoV-2 genomes across countries. Of note, the authors show that 2 variants likely arose in Mexico and spread via multiple introductions globally, while other variant waves were driven by repeat introductions into Mexico from elsewhere. Finally, they use human mobility data to assess the impact of movement on transmission within Mexico.
Overall, the study is well done and provides nice data on an under-studied country. The authors take a thoughtful approach to subsampling and provide a very thorough analysis. Because of the care given to subsampling and the great challenge that proper subsampling represents for the field of phylodynamics, the paper would benefit from a more thorough exploration of how their migration-informed subsampling procedure impacts their results. This would not only help strengthen the findings of the paper but would likely provide a useful reference for others doing similar studies. Additionally, I would suggest the authors provide a bit more discussion of this subsampling approach and how it may be useful to others in the discussion section of the paper.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In "Complex plumages spur rapid color diversification in island kingfishers (Aves: Alcedinidae)", Eliason et al. link intraspecific plumage complexity with interspecific rates of plumage evolution. They demonstrate a correlation here and link this with the distinction between island and mainland taxa to create a compelling manuscript of general interest on drivers of phenotypic divergence and convergence in different settings.
This will be a fantastic contribution to the literature on the evolution of plumage color and pattern and to our understanding of phenotypic divergence between mainland and island taxa. A few key revisions can help it get there. This paper needs to get, fairly quickly, up to a point where the difference between plumage complexity and color divergence is defined carefully. That should include hammering home that one is an intraspecific measure, while one is an interspecific measure. It took me three reads of the paper to be able to say this with confidence. Leading with that point will greatly improve the paper if that point gets forgotten then the premise of the paper feels very circular.
Also importantly, somewhere early on a hypothesized causal pathway by which insularity, plumage complexity, and color divergence interact needs to be laid out. The analyses that currently follow are good ones, and not wrong, but it's challenging to assess whether they are the right ones to run because I'm not following the authors' reasoning very well here. I think it's possible a more holistic analysis could be done here, but I'll refrain from any such suggestions until I better get what the authors are trying to link.
We also need something near the top that tells us a bit more about the biogeography of kingfishers. Are kingfisher species always allopatric? I know the answer is no, but not all readers will. What I know less well though is whether your insular species are usually allopatric. I suspect the answer is yes, but I don't actually know.
In short, how do the authors think allopatry/sympatry/opportunity for competition link to mainland vs. island link to plumage complexity? And rates of color evolution? Make this clear upfront.
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Reviewer #2 (Public Review):
Huang and colleagues present data from experiments assessing the role of cognitive inflexibility in the vulnerability to weight loss in the activity-based anorexia paradigm in rats. The experiments employ a novel in-home cage touchscreen system. The home cage touch screen system allows reduced testing time and increased throughput compared with the more widely used systems resulting in the ability to assess ABA following testing cognitive flexibility in relatively young female rats. The data demonstrate that, contrary to expectations, cognitive inflexibility does not predispose to greater ABA weight loss, but instead, rats that performed better in the reversal learning task lost more weight in the ABA paradigm. Prior ABA exposure resulted in poorer learning of the task and reversal. An additional experiment demonstrated that rats that had been trained in reversal learning resisted weight loss in the ABA paradigm. The findings are important and are clearly presented. They have implications for anorexia nervosa both in terms of potentially identifying those at risk also in understanding the high rates of relapse.
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Reviewer #2 (Public Review):
The manuscript describes a novel transparent electrode array and demonstrates its combination with two-photon calcium imaging in mouse neocortex. Using a computational model, the authors propose that surface multi-unit activity mainly reflects L1 axonal activity and they find a small population of L2/3 neurons that correlates with this activity. While the multi-modal approach with the innovative device in our view is interesting and potentially useful, we have several technical and scientific concerns that should be addressed by the authors.
Strengths:<br /> We find the general scope of this manuscript, to establish a hybrid electrophysiological and optical approach for studying neocortical activity, very interesting and relevant. The authors provide a compelling use case for combined ECoG and two-photon imaging. While extracellular action potentials have been recorded from the cortical surface, the underlying source is unknown and the device and techniques introduced by the authors are appropriate to address this question. The introduced device can be implanted chronically and has good long-term stability, providing longitudinal optical and electrical recordings from the cortex. The authors perform recordings in awake, head-fixed animals which provides the opportunity to relate ECoG and single-cell data to the animal's behavioral state. The combination of empirical data and biophysical modelling is a powerful means by which to answer such questions.
Weaknesses:<br /> The central claim of the paper relies heavily on the computational model and the physiological data could be more completely analyzed. Based on a sample of 136 L2/3 neurons the authors find a small proportion (13%) that correlates with the ECoG MUA (eMUA). Based on this, they use a model to show that ECoG MUA likely reflects axonal spikes. They then posit that these layer 2/3 neurons are tightly correlated to the layer 1 input. The presentation of their data and the specifics of their model makes it difficult to assess the validity of this claim. They do not sufficiently discuss possible confounds in the data, caveats of their model, or alternative explanations of the observed low proportion of L2/3 neurons that correlate with the ECoG MUA.
Most relevantly, the authors do not measure single units with their ECoG. The eMUA is a complex mixture of many neuronal sources, and interpretation is therefore difficult. They relate the calcium transients of small populations of single L2/3 neurons with the aggregate measure of population activity reflected in eMUA. It is possible that the eMUA reflects population activity in the local circuit and might therefore have a low correlation with individual single units. Critically, there is no information on the sensitivity of calcium recordings. Do the imaging data detect single action potentials, or are they biased to bursts of more than 1 AP?
The analysis pipeline and values used for computing the correlation coefficients are counterintuitive. The fluorescence data are first interpolated from 15 Hz to 4 kHz and then both eMUA and imaging data are effectively down-sampled to 2 Hz. A single correlation coefficient is then estimated for each neuron, regardless of behavioral state, even though the authors themselves show that the activity of single neurons and the ECoG signal depend on the state of the animal.
There is also insufficient information on the weight of the implant and its effect on mouse behavior. How does the movement of implanted and non-implanted mice differ? Must mice be singly housed? Finally, the modeling parameters are highly specific, using independently driving spikes, while the activity of neurons can be highly correlated. Likewise, the contribution of tangentially oriented axons that could relate to long-range connections conveying information related to the animal's motion or level of arousal is not considered. The manuscript would benefit from further analysis of the physiological data, consideration of alternative explanations and forthright discussion of limitations and caveats of their device and approach.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Mitochondrial dysfunction is now widely recognized as an underlying cause of many human diseases. In many cases, however, very little is known about the molecular etiology of mitochondrial disorders. In this comprehensive study Coyne et al. describe a mechanism by which dominant pathogenic variants of adenine nucleotide translocase Aac2p/ANT1 impair mitochondrial protein import pathway leading to cytotoxicity and mitochondrial dysfunction. By elucidating the fate of this protein in yeast, human cell culture, and murine models, the authors showed that mutant Aac2p variants accumulate the outer membrane translocase TOM complex jamming up mitochondrial protein import and affecting TIM22-mediated carrier import pathway, thus causing proteostatic stress. Furthermore, they showed that the i-AAA protease Yme1p and not the ubiquitin-proteasome system is responsible for proteolytic removal of the mutant Aac2p variants. Finally, the demonstrated that mitochondrial protein import clogging caused by the ANT1 A114P, A123D variant causes severe dominant neurodegenerative phenotype in mice, which resembles neuromuscular disease manifestations in humans. The authors propose this as a candidate pathological mechanism in ANT1-linked human disorders and by extension, to other diseases arising from defects in mitochondrial protein import.
Overall, this is a well-designed and thoroughly executed study that reports on a novel aspect of ANT1 associated dysfunction and provides mechanistic insights into the pathological mechanisms at play.
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Reviewer #2 (Public Review):
The authors' goal is to uncover the most likely method used by mammals to make choices based on a time-limited stream of noisy incoming sensory data. To achieve this, they analyze with great rigor several large datasets obtained from tightly controlled two-alternative forced choice behavioral experiments. The tight control of fluctuating incoming sensory input over a large number of trials allows the authors to extract the influence of different components of that input on the behavioral choice. The conditional analysis, showing the impact of early information on the importance of later information, or vice versa, is an excellent new technique.
They compare three models and find one based on a form of weighted integration of evidence across time is very strongly favored compared to models in which only short segments of the sensory input are used, or the most extreme fluctuations of the sensory input generate a response. Overall, the results clearly do indicate that the integration-like family of models outperforms the other families. The authors succeed well in giving a fair comparison of the different families of models, allowing multiple parameters to be optimized to test different versions of each model.
It should be said that the integration model is a strange type of integration, as the weight of incoming evidence depends on the time at which it arrives-by a factor of 4 in one animal (Fig. 2)-and with an over-weighting of evidence in the middle of the sequence in one case, while the more expected effects of primacy and recency (over-weighting of early or late evidence) in another. It would be nice to see more discussion of how these differences might arise across animals, what it may say about the neural circuit performing such unbalanced integration, and how suboptimal such differential weighting of evidence is. This is important, as in some discussions integration is contrasted with state transitions, which are akin to integration over a barrier, and not necessarily ruled out by the models compared here.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The work presented by Jordan and Keller aims at understanding the role of noradrenergic neuromodulation in the cortex of mice exploring a visual virtual environment. The authors hypothesized that norepinephrine released by Locus Coeruleus (LC) neurons in cortical circuits gates the plasticity of internal models following visuomotor prediction errors. To test this hypothesis, they devised clever experiments that allowed them to manipulate visual flow with respect to locomotion to create prediction errors in visuomotor coupling and measure the related signals in LC axons innervating the cortex using two-photon calcium imaging. They observed calcium responses proportional to absolute prediction errors that were non-specifically broadcast across the dorsal cortex. To understand how these signals contribute to computations performed by V1 neurons in layers 2/3, the authors activated LC noradrenergic inputs using optogenetic stimulations while imaging calcium responses in cortical neurons. Although LC activation had little impact on evoked activity related to visuomotor prediction errors, the authors observed changes in the effect of locomotion on visually evoked activity after repeated LC axons activation that were absent in control mice. Using a clever paradigm where the locomotion modulation index was measured in the same neurons before and after optogenetic manipulations, they confirmed that this plasticity depended on the density of LC axons activated, the visual flow associated with running, and the concurrent visuomotor coupling during LC activation. Based on similar locomotion modulation index dependency on speed observed in mice that develop only with visuomotor experience in the virtual environment, the authors concluded that changes in locomotion modulation index are the result of experience-dependent plasticity occurring at a much faster rate during LC axons optogenetic stimulations.
The study provides very compelling data on a timely and fascinating topic in neuroscience. The authors carefully designed experiments and corresponding controls to exclude any confounding factors in the interpretation of neuronal activity in LC axons and cortical neurons. The quality of the data and the rigor of the analysis are important strengths of the study. I believe this study will have an important contribution to the field of system neuroscience by shedding new light on the role of a key neuromodulator. The results provide strong support for the claims of the study. However, I also believe that some results could have been strengthened by providing additional analyses and experimental controls. These points are discussed below.
Calcium signals in LC axons tend to respond with pupil dilation, air puffs, and locomotion as the authors reported. A more quantitative analysis such as a GLM model could help understand the relative contribution (and temporal relationship) of these variables in explaining calcium signals. This could also help compare signals obtained in the sensory and motor cortical domains. Indeed, the comparison in Figure 2 seems a bit incomplete since only "posterior versus anterior" comparisons have been performed and not within-group comparisons. I believe it is hard to properly assess differences or similarities between calcium signal amplitude measured in different mice and cranial windows as they are subject to important variability (caused by different levels of viral expression for instance). The authors should at the very least provide a full statistical comparison between/within groups through a GLM model that would provide a more systematic quantification.
Previous studies using stimulations of the locus coeruleus or local iontophoresis of norepinephrine in sensory cortices have shown robust responses modulations (see McBurney-Lin et al., 2019, https://doi.org/10.1016/j.neubiorev.2019.06.009 for a review). The weak modulations observed in this study seem at odds with these reports. Given that the density of ChrimsonR-expressing axons varies across mice and that there are no direct measurements of their activation (besides pupil dilation), it is difficult to appreciate how they impact the local network. How does the density of ChrimsonR-expressing axons compare to the actual density of LC axons in V1? The authors could further discuss this point.
In the analysis performed in Figure 3, it seems that red light stimulations used to drive ChrimsonR also have an indirect impact on V1 neurons through the retina. Indeed, figure 3D shows a similar response profile for ChrimsonR and control with calcium signals increasing at laser onset (ON response) and offset (OFF response). With that in mind, it is hard to interpret the results shown in Figure 3E-F without seeing the average calcium time course for Control mice. Are the responses following visual flow caused by LC activation or additional visual inputs? The authors should provide additional information to clarify this result.
Some aspects of the described plasticity process remained unanswered. It is not clear over which time scale the locomotion modulation index changes and how many optogenetic stimulations are necessary or sufficient to saturate this index. Some of these questions could be addressed with the dataset of Figure 3 by measuring this index over different epochs of the imaging session (from early to late) to estimate the dynamics of the ongoing plasticity process (in comparison to control mice). Also, is there any behavioural consequence of plasticity/update of functional representation in V1? If plasticity gated by repeated LC activations reproduced visuomotor responses observed in mice that were exposed to visual stimulation only in the virtual environment, then I would expect to see a change in the locomotion behaviour (such as a change in speed distribution) as a result of the repeated LC stimulation. This would provide more compelling evidence for changes in internal models for visuomotor coupling in relation to its behavioural relevance. An experiment that could confirm the existence of the LC-gated learning process would be to change the gain of the visuomotor coupling and see if mice adapt faster with LC optogenetic activation compared to control mice with no ChrimsonR expression. Authors should discuss how they imagine the behavioural manifestation of this artificially-induced learning process in V1.
Finally, control mice used as a comparison to mice expressing ChrimsonR in Figure 3 were not injected with a control viral vector expressing a fluorescent protein alone. Although it is unlikely that the procedure of injection could cause the results observed, it would have been a better control for the interpretation of the results.
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Reviewer #2 (Public Review):
Liu, Chen and Szolnoki investigated the coupled dynamics of individual cooperation level and collective risk (i.e. the probability of future loss of all endowment). Their model encapsulates the assumption that not only does risk affect individual decision-making, but that there is also feedback between individual strategies, i.e. the level of individual contributions, and the level of risk. The authors investigate two main forms of this feedback, considering strategies linearly affecting the evolution of risk as well as non-linear (exponential) feedback. They mathematically analyze both these dynamical systems, identifying the fixed points, parametrized by the enhancement rate of defection u and the cost/benefit ratio of cooperation, and analyzing the stability of these points. The results of this systematic analysis show that, while the undesirable equilibrium state of full defection and high risk is always stable independent of the form of the feedback, the coevolutionary dynamics can exhibit a wide range of behaviors. In particular, depending on the initial conditions (frequency of cooperators), sustainable cooperation levels can be reached. This can happen by convergence to a stable fixed point with positive cooperation rates; additionally, the authors also prove that a Hopf bifurcation can take place in the system, such that a stable limit cycle with persistent oscillations in strategy and risk state can appear. Interestingly, the evolutionary outcomes do not depend significantly on the character of the feedback between strategy and risk. These theoretical results are supplemented by representative numerical examples, visualizing the phase plane and temporal dynamics of cooperation and risk for particular initial conditions and parameters.
The main conclusions of the paper are fully supported by the results, as they are directly derived from the comprehensive mathematical analysis of the coevolutionary dynamics and do not rely on external data. Additionally, the stability analysis is clean and the comprehensive numerical examples deepen the reader's understanding. Another strength of the paper is the fact that the considered model is complex enough to be able to still represent somewhat realistic settings while being simple enough to rigorously analyze. One particularly interesting finding is the fact that the exact form of the risk feedback function or its speed does not play a very significant role in the outcome of the dynamics.
The paper hence adds to the literature on the coevolution of environment and strategies in a productive way and will be of interest to various research communities in mathematical biology/ecology and decision-making.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Fever is an ancient and conserve response to infection from invertebrates to humans. However, the functional benefits of engaging fever responses are not clear, especially when it comes to moderate fever responses where pathogen growth Is not impaired by temperature. This study aims to develop a natural in vivo fever model in fish that overcomes many of the technical challenges to investigate fever in mammals. In ectotherms, fever is manifested as a behavioral response by which animals move to warmer temperatures. By using this new developed in vivo behavioral ring, the present study reveals new functional roles for fever in vertebrates. Additionally, upon infection, sickness behavior did not only consist of fever, but two novel lethargic behaviors not previously described in fish. The experimental evidence is compelling and supports the authors' conclusions. The data presented strongly indicates that moderate fever levels are critical for fine tuning immune responses to pathogens. By triggering earlier but weaker antimicrobial defenses, moderate fever in teleosts results in controlled inflammation and improved wound healing. These exciting results reveal novel roles of fever as a way to minimize the collateral damage that inflammatory responses often cause to the host. This work advances our conceptual view of the evolutionary advantages that fever brings to host-pathogen interactions. The technological development of the annular temperature preference tank can now become the gold standard platform to investigate the consequences of fever during teleost infection.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The manuscript "A human tubular aggregate myopathy mutation unmasks STIM1-independent rapid inactivation of Orai1 channels" describes the effects of a disease-related gating checkpoint at the TM1-TM2 interface. The authors suggest that the mutation of one of the two oppositely located positions T92 - L138 into a large amino acid leads to constitutive activity due to steric clash. Notably, the mutants also exhibit robust Ca2+ dependent inactivation (CDI) suggesting that this feature is intrinsic to the Orai1 channel, and not as previously thought a key process that is triggered by STIM1. Nevertheless, STIM1 is able to fine-tune Ca2+ selectivity and CDI.
This study provides an extensive electrophysiological characterization of the tubular aggregate myopathy (TAM)-disease-related Orai1 L138F mutation and based on mutational studies provides compelling evidence that constitutive activity is caused by a steric clash between TM1/TM2 Orai helices. Additionally, yet unexpectedly, the constitutive Orai1 mutants exhibit CDI behavior which is thoroughly characterized by experiments using various intracellular Ca2+-buffering reagents. By this, it is proposed that the Orai1 T92W mutant shows increased sensitivity to intracellular Ca2+. This is further revealed in a sophisticated tow step protocol, which would profit from additional control experiments. The unusual behavior of the T92W Orai1 mutant is "corrected" to that of the Orai1 wild-type form by the presence of STIM1.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Here the authors questioned the regulation and functional roles of anti-sense transcripts at the 3'end of an important flowering-time regulator FLC.
The authors present compelling genetic, molecular biology, transgene, and biochemical data on the molecular details of how COOLAIR is induced by cold temperatures. They report that cold-induction of COOLAIR is mediated by C-repeat/dehydration-responsive elements (CRT/DREs) at the 3'-end of the FLC and relatively small deletions of the CRT/DREs prevent cold-induction of COOLAIR. They also report that long-term cold results in an increase in the expression of CRT/DRE BINDING FACTORs (CBFs) that bind to the CRT/DREs and result in the activation of genes containing CRT/DREs.
Interestingly, in lines in which COOLAIR is not induced the vernalization proceeds normally with respect to flowering behavior and cold-mediated FLC chromatin changes, a result that is at odds with some publications but consistent with other reports.
The major strength of this research is the comprehensive battery of relevant assays used to address their aim. Using ChIP they demonstrate CBF3 directly binds to the 3'end of FLC in vivo, and of less interest, but still very relevant, CBF3 binds to a CRT/DRE motif containing oligo-nucleotides in vitro using an EMSA. Using CRISPR-mediated genetic deletion of these sequences in vivo, they demonstrated that the downstream antisense transcripts are no longer transcribed. Interestingly, in these CRISPR mutants or genetic mutants of higher-order CBF mutants, the vernalisation response (chromatin modifications) is not impaired. They also show that CBF mRNA transcription occurs in at least two waves, an early peak, and over a prolonged cold period.
While the CRISPR genetic motif mutants are relatively small, a few hundred base pairs, ideally they would have been smaller if only encompassing the CRT/DRE motif.
The authors clearly achieved their aims and the presented results strongly support their conclusions. The compelling data clearly questions a widely held view in the vernalisation field. The presented methods can be widely transferable to a broader research community.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Recent work in the neurosciences has suggested that decision making in most domains consists of computations at multiple stages. In value-based choices, initial evidence is perceived, categorized, and evaluated, then accumulated over time in a process that essentially compares the relative value of two options, until the accumulated evidence passes a threshold for choice. Although previous work has shown that this basic structure also applies to decisions in the domain of prosocial choice, it has remained unclear at what stage of this decision process variation in prosocial choices arises. The authors aimed to resolve this issue by using a combination of computational modeling and EEG, applied to a choice paradigm that evokes variation in altruistic behavior through two distinct routes: exogenous variation in the inequality context of a choice (i.e., advantageous vs. disadvantageous inequality), and endogenous variation as a function of individual differences in prosocial preferences.
One of the strengths of this approach (particularly the use of EEG) over previous studies is that the authors can use the timing and nature of the EEG signals to disentangle both HOW preferences evolve, and WHEN differences evoked by context or individual preference emerge. This work very clearly shows that late-stage choice comparison processes, locked to the time of response (i.e., the evidence accumulation phase of a choice) are likely NOT where variations in altruistic choice arise. Instead, the evidence points to a set of distinct signals that occur time-locked to the onset of an option that enables participants to make a choice, which implies that the computations driving choice behavior likely occur at the perceptual and/or valuation stage. This is not wholly surprising, but is interesting and important to verify.
A second potential strength of this approach is that the methodology allows the authors to determine whether the observed signals more strongly resemble encoding of the overall magnitude of outcomes to self and others, or instead are more related to signals sensitive to distributional values (i.e., inequality/fairness). The evidence here paints a quite intriguing, but somewhat mixed picture, in my view, and I think needs to come with more caveats than the authors currently acknowledge. The authors claim that their evidence supports the idea that people are making choices by considering inequality, rather than by computing outcomes for self or other directly. The lack of a consistently-signed association between EEG signals and either self or other outcome magnitude across contexts is not consistent with the idea that values are encoded in terms of self and other, which has sometimes been argued from fMRI data. However, I also do not think they are fully consistent with the authors' claims that they are observing signals related directly to fairness considerations either. Fairness/inequality, as typically defined by economic models of social preferences, involves computing the differences between self and other payoffs. The authors find ERP signals scaling with payoff changes for self but not other. Those signals do move in opposite directions in the two inequality contexts, which is why the authors interpret this as meaning that these ERP signals represent some calculation related to fairness. But there is no sensitivity of these signals to payoff change for the other, suggesting that these signals are not precisely driven by fairness as it is canonically conceived. Instead, it seems that these signals might reflect something about how people orient to self outcomes differently in the two contexts. This actually is an intriguing finding, but is somewhat difficult to interpret, since it is not wholly clear what these ERP signals represent (i.e., are they related to perception, valuation, attention, etc.?). Moreover, as the authors acknowledge in their discussion, the design of the study, with its presentation of a first option that determines the inequality context and a second option that determines the relative values of the options, means that it is difficult to know when and how one would expect to see raw self and other values as opposed to comparative value signals related to differences in self and other. Finally, the sensitivity (or lack thereof) of EEG to more subcortical signals means that it is not clear one is getting a whole picture of the computations driving choice. Thus, I think the conclusion that behavior is related to inequality processing rather than to a focus on self- and other-payoffs directly, while intriguing, needs to be tempered a bit.
What also seems somewhat puzzling is that the behavioral and neural signals do not always seem fully consistent with one another, or with prior research. For example, behaviorally people seem to put more weight on others' payoff changes in the advantageous inequality context. And in other work (Morishima et al., 2012), it is behavioral variation in the advantageous context that correlates with neural (anatomical) variation. Yet here, there are no EEG signals that encode changes in other outcomes as a main effect in the advantageous context, and it is individual variation in encoding of others' payoffs in the DISADVANTAGEOUS context that relate to individual differences in equality-seeking in that context. Thus, it is actually in the context where one would expect people to be paying *less* attention to other outcomes (based on the modeling parameters) that neural signals seem to be *more* sensitive to those outcomes. This doesn't mean that these signals aren't interesting, but it does point to a need to more fully understand what they represent before coming to firm conclusions about what they actually mean, computationally and psychologically.
Thus, I think this paper will likely have an impact on the field largely for the intriguing questions it raises about how people make altruistic choices rather than for providing definitive answers. This is an important contribution and researchers will, I expect, find this paper thought-provoking.
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Reviewer #2 (Public Review):
The authors provide here a very careful and thorough analysis of the effects of tomosyn elimination in neurons, in relation to dense-core vesicles. They find strong effects on vesicle generation (size, protein composition), but not on vesicle exocytosis, in spite of tomosyn's known interaction with the exocytosis SNAREs.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this manuscript, Polyák et al. report detailed and systematic functional, electrocardiographic, electrophysiologic (both in vivo and in vitro experiments) and histological analysis in a large animal (canine) model of exercise to assess risk of ventricular arrhythmia susceptibility. They find that exercise-trained dogs have a slower heart rate (not accounted by heightened vagal tone alone and consistent with recent work from Denmark), an increased ventricular mass and fibrosis, APD lengthening due to repolarisation abnormality, enhanced HCN4 expression and decreased outward potassium channel density together with increased ventricular ectopic beats and ventricular fibrillation susceptibility (open-chest burst pacing). The authors suggest these changes as underlying the risk of VA in athletes, and appropriately caution against consigning the beneficial effects of exercise. In general, this study is well done, reasonably well-written, with reasonable conclusions, supported by the data presented and is much needed. There are some methodological, however, given the paucity of experimental data in this area, I think it would still be additive to the literature.
Strengths<br /> 1. This is an area with very limited experimental data- this is an area of need.<br /> 2. The study, in general seems to be well-conducted with two clear groups<br /> 3. The use of a large animal model is appropriate<br /> 4. The study findings, in general, support the authors conclusions<br /> 5. The authors have shown some restraint in their conclusions and the limitations section is detailed and well written.
Weaknesses<br /> 1. There are some methodological issues:<br /> a. Authors should explain what the conditioning protocol was and why it was necessary.<br /> b. The rationale for the exercise parameters chosen needs to be presented.<br /> c. Open chest VF induction was a limitation, and it was unnecessary.<br /> d. A more refined VT/VF induction protocol was required. This is a major limitation to this work.<br /> e. The concept of RV dysfunction has not been considered in the study and its analysis.<br /> f. The lack of a quantitative measure for fibrosis is a limitation.<br /> 2. Statistical analysis requires further detail (checking of normality of the data/appropriate statistical test).<br /> 3. The use of Volders et al. study as a corollary in the discussion does not seem justified given that this study used AV block induced changes as an acquired TdP model.
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Reviewer #2 (Public Review):
The authors study M1 cortical recordings in two non-human primates performing straight delayed center-out reaches to one of 8 peripheral targets. They build a model for the data with the goal of investigating the interplay of inferred external inputs and recurrent synaptic connectivity and their contributions to the encoding of preferred movement direction during movement preparation and execution epochs. The model assumes neurons encode movement direction via a cosine tuning that can be different during preparation and execution epochs. As a result, each type of neuron in the model is described with four main properties: their preferred direction in the cosine tuning during preparation (denoted by θ_A) and execution (denoted by θ_B) epochs, and the strength of their encoding of the movement direction during the preparation (denoted by η_A) and execution (denoted by η_B) epochs. The authors assume that a recurrent network that can have different inputs during the preparation and execution epochs has generated the activity in the neurons. In the model, these inputs can both be internal to the network or external. The authors fit the model to real data by optimizing a loss that combines, via a hyperparameter α, the reconstruction of the cosine tunings with a cost to discourage/encourage the use of external inputs to explain the data. They study the solutions that would be obtained for various values of α. The authors conclude that during the preparatory epoch, external inputs seem to be more important for reproducing the neuron's cosine tunings to movement directions, whereas during movement execution external inputs seem to be untuned to movement direction, with the movement direction rather being encoded in the direction-specific recurrent connections in the network.
Major:
1) Fundamentally, without actually simultaneously recording the activity of upstream regions, it should not be possible to rule out that the seemingly recurrent connections in the M1 activity are actually due to external inputs to M1. I think it should be acknowledged in the discussion that inferred external inputs here are dependent on assumptions of the model and provide hypotheses to be validated in future experiments that actually record from upstream regions. To convey with an example why I think it is critical to simultaneously record from upstream regions to confirm these conclusions, consider two alternative scenarios: I) The recorded neurons in M1 have some recurrent connections that generate a pattern of activity that is based on the modeling seems to be recurrent. II) The exact same activity has been recorded from the same M1 neurons, but these neurons have absolutely no recurrent connections themselves, and are rather activated via purely feed-forward connections from some upstream region; that upstream region has recurrent connections and is generating the recurrent-like activity that is later echoed in M1. These two scenarios can produce the exact same M1 data, so they should not be distinguishable purely based on the M1 data. To distinguish them, one would need to simultaneously record from upstream regions to see if the same recurrent-like patterns that are seen in M1 were already generated in an upstream region or not. I think acknowledging this major limitation and discussing the need to eventually confirm the conclusions of this modeling study with actual simultaneous recordings from upstream regions is critical.
2) The ring network model used in this work implicitly relies on the assumption that cosine tuning models are good representations of the recorded M1 neuronal activity. However, this assumption is not quantitatively validated in the data. Given that all conclusions depend on this, it would be important to provide some goodness of fit measure for the cosine tuning models to quantify how well the neurons' directional preferences are explained by cosine tunings. For example, reporting a histogram of the cosine tuning fit error over all neurons in Fig 2 would be helpful (currently example fits are shown only for a few neurons in Fig. 2 (a), (b), and Figure S6(b)). This would help quantitatively justify the modeling choice.
3) The authors explain that the two-cylinder model that they use has "distinct but correlated" maps A and B during the preparation and movement. This is hard to see in the formulation. It would be helpful if the authors could expand in the Results on what they mean by "correlation" between the maps and which part of the model enforces the correlation.
4) The authors note that a key innovation in the model formulation here is the addition of participation strengths parameters (η_A, η_B) to prior two-cylinder models to represent the degree of neuron's participation in the encoding of the circular variable in either map. The authors state that this is critical for explaining the cosine tunings well: "We have discussed how the presence of this dimension is key to having tuning curves whose shape resembles the one computed from data, and decreases the level of orthogonality between the subspaces dedicated to the preparatory and movement-related activity". However, I am not sure where this is discussed. To me, it seems like to show that an additional parameter is necessary to explain the data well, one would need to compare fit to data between the model with that parameter and a model without that parameter. I don't think such a comparison was provided in the paper. It is important to show such a comparison to quantitatively show the benefit of the novel element of the model.
5) The model parameters are fitted by minimizing a total cost that is a weighted average of two costs as E_tot = α E_rec + E_ext, with the hyperparameter α determining how the two costs are combined. The selection of α is key in determining how much the model relies on external inputs to explain the cosine tunings in the data. As such, the conclusions of the paper rely on a clear justification of the selection of α and a clear discussion of its effect. Otherwise, all conclusions can be arbitrary confounds of this selection and thus unreliable. Most importantly, I think there should be a quantitative fit to data measure that is reported for different scenarios to allow comparison between them (also see comment 2). For example, when arguing that α should be "chosen so that the two terms have equal magnitude after minimization", this would be convincing if somehow that selection results in a better fit to the neural data compared with other values of α. If all such selections of α have a similar fit to neural data, then how can the authors argue that some are more appropriate than others? This is critical since small changes in alpha can lead to completely different conclusions (Fig. 6, see my next two comments).
6) The authors seem to select alpha based on the following: "The hyperparameter α was chosen so that the two terms have equal magnitude after minimization (see Fig. S4 for details)". Why is this the appropriate choice? The authors explain that this will lead to the behavior of the model being close to the "bifurcation surface". But why is that the appropriate choice? Does it result in a better fit to neural data compared with other choices of α? It is critical to clarify and justify as again all conclusions hinge on this choice.
7) Fig 6 shows example solutions for 2 close values of α, and how even slight changes in the selection of α can change the conclusions. In Fig. 6 (d-e-f), α is chosen as the default approach such that the two terms E_rec and E_ext have equal magnitude. Here, as the authors note, during movement execution tuned external inputs are zero. In contrast, in Fig. 6 (g-h-i), α is chosen so that the E_rec term has a "slightly larger weight" than the E_ext term so that there is less penalty for using large external inputs. This leads to a different conclusion whereby "a small input tuned to θ_B is present during movement execution". Is one value of α a better fit to neural data? Otherwise, how do the authors justify key conclusions such as the following, which seems to be based on the first choice of α shown in Fig. 6 (d-e-f): "...observed patterns of covariance are shaped by external inputs that are tuned to neurons' preferred directions during movement preparation, and they are dominated by strong direction-specific recurrent connectivity during movement execution".
8) It would be informative to see the extreme case of very large and very small α. For example, if α is very large such that external inputs are practically not penalized, would the model rely purely on external inputs (rather than recurrent inputs) to explain the tuning curves? This would be an example of the hypothetical scenario mentioned in my first comment. Would this result in a worse fit to neural data?
9) The authors argue in the discussion that "the addition of an external input strength minimization constraint breaks the degeneracy of the space of solutions, leading to a solution where synaptic couplings depend on the tuning properties of the pre- and post-synaptic neurons, in such a way that in the absence of a tuned input, neural activity is localized in map B". In other words, the use of the E_ext term, apparently reduces "degeneracy" of the solution. This was not clear to me and I'm not sure where it is explained. This is also related to α because if alpha goes toward very large values, it would be like the E_ext term is removed, so it seems like the authors are saying that the solution becomes degenerate if alpha grows very large. This should be clarified.
10) How do the authors justify setting Φ_A = Φ_B in equation (5)? In other words, how is the last assumption in the following sentence justified: "To model the data, we assumed that the neurons are responding both to recurrent inputs and to fluctuating external inputs that can be either homogeneous or tuned to θ_A; θ_B, with a peak at constant location Φ_A = Φ_B ≡ Φ". Does this mean that the preferred direction for a given neuron is the same during preparation and movement epochs? If so, how is this consistent with the not-so-high correlation between the preferred directions of the two epochs shown in Fig. 2 c, which is reported to have a circular correlation coefficient of 0.4?
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Reviewer #2 (Public Review):
This work profiles naturally acquired antibodies against Plasmodium falciparum proteins in two Ugandan cohorts, at incredibly high resolution, using a comprehensive library of overlapping peptides. These findings highlight the ubiquity and importance of intra- and inter-protein repeat elements in the humoral immune response to malaria. The authors discuss evidence that repeat elements reside in more seroreactive proteins, and that the breadth of immunity to repeat-containing antigens is associated with transmission intensity in children.
A key strength and value added to publicly available data are the breadth of proteome coverage and unprecedented resolution from using tiling peptides. The authors point out that a known limitation of PhIP-seq is that conformational and discontinuous-linear epitopes cannot be detected with short linear peptides. In addition, disulfide linkages and post-translational modifications would be absent in the T7 representations.
Several significant conclusions drawn from the results in this study are based on the humoral response to repeat elements that are present in multiple locations, including different genes. If antibodies to these regions are cross-reactive as described, it is not clear how the assay can differentiate antibodies that were developed against one or many of these loci. This potential confounding could change the conclusions about inter-protein motifs.
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Reviewer #2 (Public Review):
The authors apply their previously developed concept that osteoclasts exist in at least two flavors, tolerogenic and inflammatory osteoclasts towards the treatment of osteoporosis. They suggest that selectively targeting inflammatory osteoclasts attenuates ovariectomy-induced bone loss by agonists of pattern recognition receptors (PRR) that are higher expressed on inflammatory osteoclasts. The vision would be that the tolerogenic osteoclasts are still functioning, allowing bone remodeling with high bone quality, while the strong resorbing inflammatory osteoclasts are resorbed. By expression profiling, they detected PPR differentially expressed and confirmed these by flow cytometry and RT-QPCR. The activation of the Tlr2, Dectin-1, and Mincle reduced inflammatory osteoclast generation in vitro and affected their resorptive activity. Dendritic syk cell-specific deletion abrogated the differentiation of this osteoclast subset as well. The application of yeast Saccharomyces boulardii (Sbb) into mice attenuated trabecular bone loss (but not cortical) and seemed to inhibit in vitro the generation of inflammatory osteoclasts.
Strength:<br /> - The expression profiling between very defined in vitro generated osteoclasts, which are somehow extreme phenotypes, provides a good tool to discern gene signatures on the osteoclast level.<br /> - The candidate of PPR were evaluated in their expression at the protein level by flow cytometry and their function was evaluated by loss of function studies.<br /> - The effect of S.b. treatment is striking and exploiting such probiotic fungi could be an elegant way to treat osteoporosis.
Weakness:<br /> - The osteoclasts are generated in vitro in the presence of M-CSF to induce tolerogenic osteoclasts or GM-CSF / Il-4 to generate inflammatory osteoclasts. The demonstration of these cell populations in the S.b. treated mice in vivo is not present, despite the challenge to do this. The author tried to tackle this, by analyzing the differentiation potential of bone marrow progenitor cells of S.b. treated animals, which provides some information.<br /> - The effect on tolerogenic osteoclasts could have been further evaluated, whether they are not affected at all, or whether there are also effects.
The authors strikingly show that agonists for PPR are affecting strongly GM-CSF/IL-4 progenitor-derived osteoclasts. They show that t-Ocl and i-Ocl differ in their gene signature and convincingly show the differential expression of the PPR, with exception of mincle which is clearly acknowledged. The molecular mechanism of how Sb treatment acts via the receptors remains obscure since it might act via changes in the gut permeability or by components directly released by the fungus. The kinase syk could play a role, at least some data in vitro suggest this.
Conceptionally the authors tried to utilize the previously generated knowledge by the group published 2016 and 2020 into an approach. If the use of a probiotic fungus would be beneficial indeed this could be a suitable drug with few side effects much superior to current treatments of osteoporosis.<br /> For me, an intriguing question arises from this study, in case these i-Ocl express these receptors and are thus so "vulnerable" to the agonists to decrease their activity, evt. a negative feedback to prevent overshooting reactions?
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Reviewer #2 (Public Review):
This manuscript details the analytic methods and results of one arm of the PLATCOV study, an adaptive platform designed to evaluate low-cost COVID-19 therapeutics through enrollment of a comparatively smaller number of persons with acute COVID-19, with the goal of evaluating the rate of decrease in SARS-CoV-2 clearance compared to no treatment through frequent swabbing of the oropharynx and a Bayesian linear regression model, rather than clinical outcomes or the more routinely evaluated blunt virologic outcomes employed in larger trials. Presented here, is the in vivo virologic analysis of ivermectin, with a very small sample of participants who received the casirivimab/imdevimab, a drug shown to be highly effective at preventing COVID-19 progression and improving viral clearance (during circulation of variants to which it had activity) included for comparison for model evaluation.
The manuscript is well-written and clear. It could benefit however from adding a few clarifications on methods and results to further strengthen the discussion of the model and accurately report the results, as detailed below.
Strengths of this study design and its report include:<br /> 1. Selection of participants with presumptive high viral loads or viral burden by antigen test, as prior studies have shown difficulty in detecting effect in those with a lower viral burden.<br /> 2. Adaptive sample size based on modeling- something that fell short in other studies based on changing actuals compared to assumptions, depending on circulating variant and "risk" of patients (comorbidities, vaccine state, etc) over time. There have been many other negative studies because the a priori outcomes assumptions were different from the study design to the time of enrollment (or during the enrollment period). This highlight of the trial should be emphasized more fully in the discussion.<br /> 3. Higher dose and longer course of ivermectin than TOGETHER trial and many other global trials: 600ug/kg/day vs 400mcg/kg/day.<br /> 4. Admission of trial participants for frequent oropharyngeal swabbing vs infrequent sampling and blunter analysis methods used in most reported clinical trials<br /> 5. Linear mixed modeling allows for heterogeneity in participants and study sites, especially taking the number of vaccine doses, variant, age, and serostatus into account- all important variables that are not considered in more basic analyses.<br /> 6. The novel outcome being the change in the rate of viral clearance, rather than time to the undetectable or unquantifiable virus, which is sensitive, despite a smaller sample size<br /> 7. Discussion highlights the importance of frequent oral sampling and use of this modeled outcome for the design of both future COVID-19 studies and other respiratory viral studies, acknowledging that there are no accepted standards for measuring virologic or symptom outcomes, and many studies have failed to demonstrate such effects despite succeeding at preventing progression to severe clinical outcomes such as hospitalization or death. This study design and analyses are highly important for the design of future studies of respiratory viral infections or possibly early-phase hepatitis virus infections.
Weaknesses or room for improvement:
1. The methods do not clearly describe allocation to either ivermectin or casirivimab/imdevimab or both or neither. Yes, the full protocol is included, but the platform randomization could be briefly described more clearly in the methods section.<br /> 2. The handling of unquantifiable or undetectable viruses in the models is not clear in either the manuscript or supplemental statistical analysis information. Are these values imputed, or is data censored once below the limits of quantification or detection? How does the model handle censored data, if applicable?<br /> 3. Did the study need to be unblinded prior to the first interim analysis? Could the adaptive design with the first analysis have been done with only one or a subset of statisticians unblinded prior to the decision to stop enrolling in the ivermectin arm?<br /> 4. Can the authors comment on why the interim analysis occurred prior to the enrollment of 50 persons in each of the ivermectin and comparison arms? Even though the sample sizes were close (41 and 45 persons), the trigger for interim analysis was pre-specified.<br /> 5. The reporting of percent change for the intervention arms is overstated. All credible intervals cross zero: the clearance for ivermectin is stated to be 9% slower, but the CI includes + and - %, so it should be reported as "not different." Similarly, and more importantly for casirivimab/imdevimab, it was reported to be 52% faster, although the CI is -7.0 to +115%. This is likely a real difference, but with ten participants underpowered- and this is good to discuss. Instead, please report that the estimate was faster, but that it was not statistically significant. Similarly, the clearance half-life for ivermectin is not different, rather than "slower" as reported (CI was -2 to +6.6 hours). This result was however statistically significant for casirivimab/imdevimab.<br /> 6. While the use of oropharyngeal swabs is relatively novel for a clinical trial, and they have been validated for diagnostic purposes, the results of this study should discuss external validity, especially with respect to results from other studies that mainly use nasopharyngeal or nasal swab results. For example, oropharyngeal viral loads have been variably shown to be more sensitive for the detection of infection, or conversely to have 1-log lower viral loads compared to NP swabs. Because these models look for longitudinal change within a single sampling technique, they do not impact internal validity but may impact comparisons to other studies or future study designs.<br /> 7. Caution should be used around the term "clinically significant" for viral clearance. There is not an agreed-upon rate of clinically significant clearance, nor is there a log10 threshold that is agreed to be non-transmissible despite moderately strong correlations with the ability to culture virus or with antigen results at particular thresholds.<br /> 8. Additional discussion could also clarify that certain drugs, such as remdesivir, have shown in vivo activity in the lungs of animal models and improvement in clinical outcomes in people, but without change in viral endpoints in nasopharyngeal samples (PINETREE study, Gottlieb, NEJM 2022). Therefore, this model must be interpreted as no evidence of antiviral activity in the pharyngeal compartment, rather than a complete lack of in vivo activity of agents given the limitations of accessible and feasible sampling. That said, strongly agree with the authors about the conclusion that ivermectin is also likely to lack activity in humans based on the results of this study and many other clinical studies combined.
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Reviewer #2 (Public Review):
Zhao, Shen et al. ran molecular dynamics simulations, followed by the application of Markov State Model analysis and deep machine learning dimensional reduction, to study the dynamical behavior of two loops close to the catalytic site of L1 Metallo-β-lactamase (MBL).
The simulations are carefully executed and of sufficient length to build a representative kinetic model. Using a dimensional reduction of the loop conformational sampling based on backbone dihedral features followed by tICA embedding, the authors obtain a Markov state model that identifies the main conformational states of the loops in the absence of bound ligands and provides estimates of the timescales for the transitions between them. Next, the authors employ an alternative way to cluster the conformations of the loops, using unsupervised dimensional reduction, implemented as a convolutional VAE applied to residue distances followed by tSNE embedding. This second step gives results that are not consistent with the clustering used for the kinetic modeling (for instance, supplement 2 of figure 4 shows that the 7 macrostates obtained by the MSM analysis don't always correspond to different areas in the CVAE+tSNE embedding).
Moreover, an inspection of the results from both analysis techniques just confirms the role of interactions that are readily observed in the available crystal structure stabilising the most populated, closed conformation of the loops. The sophisticated computational analysis does not elucidate much of the role of the loop dynamics beyond the intuitive conclusion that disruption of the key interactions keeping the loops in the closed state would affect the function. For instance, it does not clarify what is the role of the other observed metastable states.
Finally, the authors propose and test mutations that would likely disrupt the stability of the closed state and find that they have variable effects on the ability of the enzyme to contrast the antibiotic effect of a panel of substrates. These experimental results look useful and can potentially be used to elucidate the role of the loops in the recognition and activity of the enzyme, and for the design of inhibitors. However, no additional attempt is made to clarify the experimental results based on the mechanistic model of loop dynamics: why do different mutations have different effects? why do some mutations affect all substrates, other mutations only some substrates, and for others, no substrate is affected? What is the role of the tetrameric arrangement?
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Reviewer #2 (Public Review):
The data presented are of high quality. Through complementary experiments involving the isolation of masseter muscle spindles, the authors perform RNA-seq and proteomic analysis, and identify genes and proteins that are differentially expressed in the muscle spindle versus the adjacent muscle fiber, and proteins that accumulate specifically in capsule cells and nerve endings. These data, while essentially descriptive, provide important information about the developmental framework of the sensory apparatus present in each muscle that accounts for its tension/contraction state. The data presented thus allow for a better characterization of muscle spindles and provide the community with a set of new markers for better identification of these structures. Analysis of the expression pattern of the Tomato reporter in transgenic animals under the control of Piezo2-CRE, Gli1-CRE and Thy1-YFP reporter reinforces the findings and the specificity of the expression pattern of the specific genes and proteins identified by the multi-omics approach and further validated by immunohistochemistry.
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Reviewer #2 (Public Review):
Hu et al. developed a new reagent to enhance single mRNA imaging in live cells and animal tissues. They combined an MS2-based RNA imaging technique and a Suntag system to further amplify the signal of single mRNA molecules. They used 8xMS2 stem-loops instead of the widely-used 24xMS2 stem-loops and then amplified the signal by fusing a 24xSuntag array to an MS2 coat protein (MCP). While a typical 24xMS2 approach can label a single mRNA with 48 GFPs, this technique can label a single mRNA with 384 GFPs, providing an 8-fold higher signal. Such high amplification allowed the authors to image endogenous mRNA in the epidermis of live C. elegans. While a similar approach combining PP7 and Suntag or Moontag has been published, this paper demonstrated imaging endogenous mRNA in live animals. Data mostly support the main conclusions of this paper, but some aspects of data analysis and interpretation need to be clarified and extended.
Strengths:<br /> Because the authors further amplified the signal of single mRNA, this technique can be beneficial for mRNA imaging in live animal tissues where light scattering and absorption significantly reduce the signal. In addition, the size of an MS2 repeat cassette can be reduced to 8, which will make it easier to insert into an endogenous gene. Also, the MCP-24xSuntag and scFv-sfGFP constructs can be expressed in previously developed 24xMS2 knock-in animal models to image single mRNAs in live tissues more easily.
The authors performed control experiments by omitting each one of the four elements of the system: MS2, MCP, 24xSuntag, and scFV. These control data confirm that the observed GFP foci are the labeled mRNAs rather than any artifacts or GFP aggregates. And the constructs were tested in two model systems: HeLa cells and the epidermis of C. elegans. These data demonstrate that the technique may be used across different species.
Weaknesses:<br /> Although the paper has strength in providing potentially useful reagents, there are some weaknesses in their approach.
Each MCP-24xSunTag is labeled with 24 GFPs, providing enough signal to be visualized as a single spot. Although the authors showed an image of a control experiment without MS2 in Figure 1B, the authors should at least mention this potential problem and discuss how to distinguish mRNA from MCP tagged with many GFPs. MCP-24xSunTag labeled with 24 GFPs may diffuse more rapidly than the labeled mRNA. Depending on the exposure time, they may appear as single particles or smeared background, but it will certainly increase the background noise. Such trade-offs should be discussed along with the advantage of this method.
Also, more quantitative image analysis would be helpful to improve the manuscript. For instance, the authors can measure the intensity of each GFP foci, show an intensity histogram, and provide some criteria to determine whether it is an MCP-24xSuntag, a single mRNA, or a transcription site. For example, it is unclear if the GFP spots in Figure 2D are transcription sites or mRNA granules.
Another concern is that the heavier labeling with 24xSuntag may alter the dynamics of single mRNA. Therefore, it would be desirable to perform a control experiment to compare the diffusion coefficient of mRNAs when they are labeled with MCP-GFP vs MCP-24xSuntag+scFv-sfGFP.
The authors could briefly explain about the genes c42d4.3 and mai-1. Why were these specific genes chosen to study gene expression upon wound healing? Did the authors find any difference in the dynamics of gene expression between these two genes?
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Reviewer #2 (Public Review):
In this manuscript, Zhang et al., address the role of Polo-like kinase signaling in restricting the activity of Chk2 kinase and coordinating synapsis among homologous chromosomes with the progression of meiotic prophase in C. elegans. While individual activities of PLK-2 and CHK-2 have been demonstrated to promote chromosome pairing, and double-strand break formation necessary for homologous recombination, in this manuscript the authors attempt to link the function of these two essential kinases to assess the requirement of CHK-2 activity in controlling crossover assurance and thus chromosome segregation. The study reveals that CHK-2 acts at distinct regions of the C. elegans germline in a Polo-like kinase-dependent and independent manner.
Strengths:<br /> The study reveals distinct mechanisms through which CHK-2 functions in different spatial regions of meiosis. For example, it appears that CHK-2 activity is not inhibited by PLK's (1 and 2) in the leptotene/zygotene meiotic nuclei where pairing occurs. This suggests that either CHK-2 is not phosphorylated by PLK-2 in the distal nuclei or that it has a kinase-independent function in this spatial region of the germline. These are interesting observations that further our understanding of how the processes of meiosis are orchestrated spatially for coordinated regulation of the temporal process.
Weaknesses:<br /> While the possibilities stated above are interesting, they lack direct support from the data. A key missing element in the study is the actual role of PLK-2 signaling in controlling CHK-2 activity and thus function. I expand on this below.
Throughout the manuscript, the authors test the role of each of the kinases (CHK-2 or PLK-1, or 2) using auxin-induced degradation, which would eliminate both phosphorylated and unphosphorylated pools of proteins. This experiment thus does not test the role of PLK-2 signaling in controlling CHK-2 function or the role of CHK-2 activation. To test the role of signaling from PLK-2 or CHK-2, the authors need to generate appropriate alleles such as phospho-mutants or kinase-dead mutants. The authors do generate unphosphorylatable and phosphomimetic versions of CHK-2, however, they find that the protein level for both these alleles is lower than wild-type CHK-2 (which the authors state is already low). The authors conclude that the lower level of protein in the CHK-2 phospho-mutants is because the mutations cause destabilization of the protein. I am sympathetic with the authors since clearly these results make interpretations of actual signaling activity more challenging. But there needs to be some evidence of this activity, for example through the generation of a phosphor-specific antibody to phosphorylated CHK-2. While not functional, at least the phosphorylation status of CHK-2 would provide more information on its spatial pattern of activation and inactivation. In addition, it would still be of interest to the readership to present the data on these phosphor-mutant alleles with crossover designation and COSA-1::GFP. Is the phenotype of the WT knockin, and each of the phosphomutant knock-ins similar to auxin-induced degradation of CHK-2?
Given that the CHK-2 phosphomutants did not pan out for assessing the signaling regulation of PLK-2 on CHK-2, to directly assess whether PLK-2 activity restricts CHK-2 function in mid-pachytene but not leptotene/zygotene, the authors should generate PLK-2 kinase dead alleles. These alleles will help decouple the signaling function of PLK-2 from a structural function.
Similarly, to assess the potentially distinct roles of CHK-2 in leptotene/zygotene and mid-pachytene it would be important to assess CHK-2 kinase-dead mutant alleles. At this time, all of the analysis is based on removing both active CHK-2 and inactive CHK-2 (i.e. phosphorylated and unphosphorylated pool) using auxin-induced degradation. The kinase-dead alleles will help infer the role of the kinase more directly. The authors can then superimpose the auxin-induced degradation and assess the impact of complete removal of the protein vs only loss of its kinase function. These experiments may help clarify the role of signaling outcomes of these proteins, vs their complete loss. For example, what does kinase dead PLK-2 recruitment to the synapsed chromosomes appear like? Are their distinct activities for active and inactive PLK-2 that are spatially regulated? The same can be tested for CHK-2.
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Reviewer #2 (Public Review):
This is an interesting manuscript establishing a role for Ecdysone signaling in the control of sleep. The authors show that the Ecdysone receptor EcR is required primarily in cortex glia for the control of sleep and that its target E75 is also involved in sleep regulation. This is a novel function for both cortex glia and steroid signaling in Drosophila. The authors also present evidence that Ecdysone signaling would be important for response to starvation, and that lipid droplet mobilization would mediate the effect of ecdysone on sleep. This work is certainly innovative. However, the main conclusions need to be strengthened. In particular: variability in sleep amounts in certain strains could complicate interpretation, the idea that ecdysone modulates sleep response to starvation is not sufficiently well supported, and genetic evidence for mobilization of lipid droplets being the mechanism linking steroid signaling to sleep is currently quite weak.
Major concerns:
1) I have concerns with the variability observed with the GS drivers (whether nSyb or repo). This is particularly striking in figure S3 when comparing experiments conducted with EcR-c and the Ecl RNAi. Daytime is most affected, but even nighttime looks significantly different. Definitely, nighttime quantification should be shown in addition to total sleep in figure S3. However, I feel that confirming the key results of this study with an additional driver would be reassuring. Could repo-GAL4 combined with GAL80ts be used to drive EcR RNAi, instead of repo-GS? The same combination could help determine whether glia is responsible for the 20E-mediated increase in sleep after starvation (figure S4A).<br /> 2) The idea that ecdysone might suppress the response to starvation is interesting, but the results are not convincing. First, there is an important control missing. It is important to test the effect of Ecdysone on fed flies, to ensure that Ecdysone does not simply make flies sleepy. Second, it is not clear that EcR RNAi has a specific effect on starved flies. Starvation reduces sleep, but is this reduction really exaggerated in flies expressing EcR RNAi than in control flies? It seems to me that starvation reduces sleep by the same amount when comparing results in panels 3D and E. The effect of EcRNAi and starvation might be simply additive, which would suggest that 20E impacts sleep independently of starvation.<br /> 3) The material and method section needs to be improved. In particular, it is not clear to me how the starvation/ecdysone feeding assay was done. There are some additional explanations in the figure legend, but the approach is still not clear to me. Indicate clearly when the flies were starved, and when they were exposed to Ecdysone.<br /> 4) I am not convinced that the Lsd2 results necessarily support the idea that this gene is required for the effect of 20E on sleep. Sleep is dramatically reduced during the day in the Lsd2 mutant. This is actually an interesting observation, but this strong effect on baseline sleep might be masking the ability of 20E to modulate sleep.
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Reviewer #2 (Public Review):
The manuscript reports on the complex variability of expression, trafficking, assembly/stability, and peptide loading among different MHC I haplotypes. In particular by analyzing two distinct MHC I molecules as representative members of groups of allotypes, that favor canonical or non-canonical assembly modes, the PI reports on preferential cytosolic or endo-lysosomal MHC I loading. Overall, the data shed light on the intersection between MHC I conformation and subcellular sites of peptide loading and help explain MHC I immunosurveillance at a different subcellular location.
In the first series of experiments the authors report an uneven surface expression of HLA-B vs HLA-A, and C on circulating monocytes, with HLA-B being expressed 4 times higher, also they report that as compared to the TAP-dependent allotype B*08:01 the TAP-independent allotype B*35:01 has a lower surface half-life and if often present as an empty molecule. These data set the basis for the author's hypothesis that B*35:01 could traffic in Rab11+ compartment and be involved in cross-presentation, which indeed is demonstrated in a series of pulse-chase peptide experiments and using cathepsin inhibitors.
Overall, the experiments could be improved by performing subcellular fractionation and organelle purification to conclusively demonstrate the differential trafficking of B*08:01 vs B*35:01, as well as quantitative mass spectrometry to determine cytosolic vs endosomal processing for one selected epitope presented by the different haplotypes.
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Reviewer #2 (Public Review):
Yeatman and colleagues used MEG in pre-literate children following a literacy intervention program to investigate changes in cortical responses to visual images of words, faces, and objects. Children who participated in a literacy intervention program showed improvements in letter knowledge and increased neural responses to words relative to an object category. The authors interpret these findings in the framework of the neuronal recycling hypothesis proposed by Dehaene and colleagues. This is important work. The opportunity to use a causal manipulation to study neural and behavioral development in humans is rare. The finding of neural changes from just 2 weeks of intervention is striking. The scope of the work extends beyond understanding brain development and has potential relevance for social and educational policies. The study appears well-designed and includes an important control group. Overall, I am enthusiastic about this work. However, it is unclear whether the results are specific to the area of interest - the visual word form area. The increased response to words from the intervention appears quite widespread cortically (Figure 5). These issues are central to the idea of neuronal recycling and the authors' proposal that training leads to increased modularization. Thus, the results currently only provide modest support for the conclusions. Additionally, aspects of the analysis need clearer motivation/justification.
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Reviewer #2 (Public Review):
The molecular characteristics of OCNs in normal or ototoxic conditions are poorly understood before. The strength of this study is that it provides the first single-cell RNA-seq database of OCNs as well as surrounding facial branchial motor neurons. By thoroughly analyzing the database, they found high heterogeneities within OCN populations and identified distinct markers that are enriched in different OCN subtypes. Furthermore, a few previously unknown neuropeptides are revealed, including Npy which is more enriched in the LOC-2 located on the medial side. They also found that neuropeptide expression levels and distributions are subjected to hearing experience and noise exposure. On the other hand, the weakness of the study is that the numbers of single-cell RNA-seq are not sufficient, and may underscore the MOC heterogeneity (Figure 3A). Moreover, the physiological functions of the LOC-2 are not revealed in this study, and no specific markers in one OCN subtype are identified that can predict the morphological or projecting axon features. Those might be addressed in the following studies.
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Reviewer #2 (Public Review):
This study reports interesting findings on the influence of a conserved phosphatase on mitochondrial biogenesis and function. In the absence of it, many nucleus-encoded mitochondrial proteins among which those involved in ATP generation are expressed much better than in normal cells. In addition to a better understanding of th mechanisms that regulate mitochondrial function, this work may help developing therapeutic strategies to diseases caused by mitochondrial dysfunction. However there are a number of issues that need clarification.
1) The rationale of the screening assay to identify genes required for the gene expression modifications observed in mct1 mutant is not clear. Indeed, after crossing with the gene deletion libray, the cells become heterozygote for the mct1 deletion and should no longer be deficient in mtFAS. Thank you for clarifying this and if needed adjust the figure S1D to indicate that the mated cells are heterozygous for the mct1 and xxx mutations.
2) The tests shown in Fig. S1E should be repeated on individual subclones (at least 100) obtained after plating for single colonies a glucose culture of mct1 mutant, to determine the proportion of cells with functional (rho+) mtDNA in the mct1 glucose and raffinose cultures. With for instance a 50% proportion of rho- cells, this could substantially influence the results of the analyses made with these cells (including those aiming to evaluate the MMP).
3) The mitochondria area in mct1 cells (Fig.S1G) does not seem to be consistent with the tests in Fig. 1C. that indicate a diminished mitochondrial content in mct1 cells vs wild-type yeast. A better estimate (by WB for instance) of the mitochondrial content in the analyzed strains would enable to better evaluate MMP changes monitored with Mitotracker since the amount of mitochondria in cells correlate with the intensity of the fluorescence signal.
4) Page 12: "These data demonstrate that loss of SIT4 results in a mitochondrial phenotype suggestive of an enhanced energetic state: higher membrane potential, hyper-tubulated morphology and more effective protein import." Furthermore, the sit4 mutant shows higher levels of OXPHOS complexes compared to WT yeast.
Despite these beneficial effects on mitochondria, the sit4 deletion strain fails to grow on respiratory substrates. It would be good to know whether the authors have some explanation for this apparent contradiction.
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Reviewer #2 (Public Review):
Shah and colleagues tackle a significant impediment to exploiting tissue culture systems that enable prospective ex vivo experimentation in real-time. Namely, the ability to identify and track dynamic and coordinated activities of multiple composite cell types in response to experimental perturbations. They develop a clever label-free approach that collects biologically-encoded autofluorescence of epithelial cells by 2-photon imaging of mouse tracheal explant culture over 2 days. They report the ability to distinguish 7 cell types simultaneously, including rare ones, by developing a machine-learning approach using a combination of fluorescence and cytologic features. Their algorithm demonstrates high accuracy by Mathew's Correlation Coefficient when applied to a test set. Lastly, they show the ability of their approach to visualize the dynamic uptake and expulsion of fluorescently-tagged dextran by individual secretory cells. Overall, the results are intriguing and may be very useful for specific applications.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
The manuscript of Penha et al performs genetic correlation, Mendelian randomization (MR), and colocalization studies to determine the role of genetically determined leukocyte telomere length (LTL) and susceptibility to lung cancer. They develop an instrument from the most recent published association of LTL (Codd et al), which here is based on n=144 genetic variants, and the largest association study of lung cancer (including ~29K cases and ~56K controls). They observed no significant genetic correlation between LTL and lung cancer, in MR they observed a strong association that persisted after accounting for smoking status. They performed colocalization to identify a subset of loci where LTL and lung cancer risk coincided, mainly around TERT but also other loci. They also utilized RNA-Seq data from TCGA lung cancer adenocarcinoma, noting that a particular gene expression profile (identified by a PC analysis) seemed to correlate with LTL. This expression component was associated with some additional patient characteristics, genome stability, and telomerase activity.
In general, most of the MR analysis was performed reasonably (with some suggestions and comments below), it seems that most of this has been performed, and the major observations were made in previous work. That said, the instrument is better powered and some sub-analyses are performed, so adds further robustness to this observation. While perhaps beyond the scope here, the mechanism of why longer LTL is associated with (lung) cancer seems like one of the key observations and mechanistically interesting but nothing is added to the discussion on this point to clarify or refute previous speculations listed in the discussion mentioned here (or in other work they cite).
Some broad comments:
1. The observations that lung adenocarcinoma carries the lion's share of risk from LTL (relative to other cancer subtypes) could be interesting but is not particularly highlighted. This could potentially be explored or discussed in more detail. Are there specific aspects of the biology of the substrata that could explain this (or lead to testable hypotheses?)
2. Given that LTL is genetically correlated (and MR evidence suggests also possibly causal evidence in some cases) across a range of traits (e.g., adiposity) that may also associate with lung cancer, a larger genetic correlation analysis might be in order, followed by a larger set of multivariable MR (MVMR) beyond smoking as a risk factor. Basically, can the observed relationship be explained by another trait (beyond smoking)? For example, there is previous MR literature on adiposity measures, for example (BMI, WHR, or WHRadjBMI) and telomere length, plus literature on adiposity with lung cancer; furthermore, smoking with BMI. A bit more comprehensive set of MVMR analyses within this space would elevate the significance and interpretation compared to previous literature.
3. In the initial LTL paper, the authors constructed an IV for MR analyses, which appears different than what the authors selected here. For example, Codd et al. proposed an n=130 SNP instrument from their n=193 sentinel variants, after filtering for LD (n=193 >>> n=147) and then for multi-trait association (n=147 >> n=130). I don't think this will fundamentally change the author's result, but the authors may want to confirm robustness to slightly different instrument selection procedures or explain why they favor their approach over the previous one.
4. Colocalization analysis suggests that a /subset/ of LTL signals map onto lung cancer signals. Does this mean that the MR relationships are driven entirely by this small subset, or is there evidence (polygenic) from other loci? Rather than do a "leave one out" the authors could stratify their instrument into "coloc +ve / coloc -ve" and redo the MR analyses.
Mainly here, the goal is to interpret if the subset of signals at the top (looks like n=14, the bump of non-trivial PP4 > 0.6, say) which map predominantly to TERT, TERC, and OBFC1 explain the observed effect here. I.e., it is biology around these specific mechanisms or generally LTL (polygenicity) but exemplified by extreme examples (TERT, etc.). I appreciate that statistical power is a consideration to keep in mind with interpretation.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The study is a careful investigation of the physical properties of hagfish slime and the underlying cellular framework that enables this extraordinary evolutionary innovation. I appreciate the careful and detailed measurements and images that the authors provide. The results presented here will surely be extremely important for researchers working on this particular organism and those interested in understanding the evolution, biomedical relevance, and biochemistry of mucus. However, I had difficulty contextualizing the findings in broader biological questions (e.g., the evolution of functional novelty, the adaptive processes, and the links between genetic and phenotypic evolution). I also think that the conclusions on the evolutionary origins and underlying genetics of hagfish slime based on comparative transcriptomic data may be premature.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Chinnaiya et al. integrated recent scRNA transcriptomics with high-resolution multiplexing in situ hybridization, fate mapping and tissue explants to unravel the spatiotemporal development of early chick tuberal hypothalamus. They show that a wave of BMP signaling passes through anterior and posterior regions sequentially. Interestingly, they showed that neuroepithelial-intrinsic BMPs drive and maintain tuberal hypothalamus late development. Using bioinformatical and in situ profiling, the authors indicated the potential of the tuberal progenitors transferring into radial glia-like cells.
This is a remarkable piece of work and I commend the authors for their bold endeavor to decipher the complex developmental of the tuberal hypothalamus.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This manuscript shows that two doses of the live attenuated Coronavac vaccine induce neutralising antibodies in the majority of individuals, though neutralisation is modest for Omicron BA.1 even after 1 month post-dose two, and substantial waning at 12 months is noted. Boosting achieves higher neutralisation than for prior doses.
Strengths of the work are the significant sample size in the cross-sectional part and a smaller prospective part which adds value to the study as a whole.
The assays used are appropriate, with PV bearing Wu-hu-1, Delta, and Omicron spike proteins.
Weakness includes the fact that the cross-sectional aspect recruits at different sites at different time points, introducing the fact that observed differences in vaccine response may be related to the underlying population differences.
In addition, the data on third-dose boosting do not appear to include VOC. This is important because data from other vaccines suggest broadening of neutralisation with the third dose.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
To advance the understanding of the initial events in recognition of HIV-1 genome by the viral structural protein Gag, in this study, the authors examined the involvement of the CA domain in the specific interaction between Gag and the viral genomic RNA. Previous studies including a study from the same group (Kutluay et al 2010) showed that the CA C-terminal domain plays a role in Gag binding to viral genomic RNA. In the current study, they analyzed a panel of CA mutants using a modified PAR-CLIP RNA sequencing, which allows identification of Gag binding sites in the viral genome, and a chemical crosslinking approach, which allows assessment of the multimerization status of Gag in cells. They found that substitutions of CA residues at the CA dimer, trimer, or hexamer interfaces, which reduce Gag multimerization as expected, also reduce the Ψ sequence-specific viral RNA binding, whereas substitutions elsewhere in CA have no impact. They further found that substitutions of the Lys residues important for IP6 binding, which disrupt Gag lattice formation, reduce the Ψ-specific RNA binding, whereas a second-site mutation that restores virus assembly in these Lys substitution mutants restores the RNA binding. These results strongly support the authors' conclusion that Gag lattice formation driven by CA plays an important role in NC-mediated recognition of the Ψ sequence.
The strengths of the work include the application of the modified PAR-CLIP method to the analysis of a large panel of CANC constructs. This provided the detailed information on the specific molecular features in CA required for interactions between Gag and the Ψ sequence, which was not obtainable in the previous studies. The absence of the MA domain in these constructs allowed the authors to focus on the cytoplasmic interactions. The data obtained with oligomer-forming NC constructs and CANC constructs that differ in the IP6 dependence also add support to the authors conclusion that CA-mediated lattice formation of CANC and not just NC oligomerization plays a key role in Gag-vRNA binding. Overall, the data support the conclusion that the ability to form the CANC lattice is essential for the initial NC-vRNA interaction.
The only notable weakness is that previous work by this group and others have already shown that CA and/or its interaction interfaces plays an important role in the Gag-vRNA interaction. Therefore, the current work can be regarded as a refinement of the previously presented concept rather than a conceptual breakthrough. Nonetheless, these mechanistic details are likely to help the retrovirology community gain a clearer grasp of the early steps of infectious particle formation.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This interesting manuscript uses a collection of whole genome sequences of TB isolates to associate specific sequence polymorphisms with MDR/XDR strains, and having found certain mutations in DNA repair pathways, does a detailed analysis of several mutations. The evaluation of the MutY polymorphism reveals it is loss of function and TB strains carrying this mutation have a higher mutation frequency and enhanced survival in serial passage in macrophages. The strengths of the manuscript are the leveraging of a large sequence dataset to derive interesting candidate mutations in DNA repair pathway and the demonstration that at least one of these mutations has a detectable effect on mutagenicity and pathogenesis. The weaknesses of the manuscript are a lack of experimental exploration of the mechanism by which loss of a DNA repair pathway would enhance survival in vivo. The model presented is that these phenotypes are due to hypermutagenicity and thereby evolution of enhanced pathogenesis, but this is not actually directly tested or investigated. There are also some technical concerns for some of the experimental data which can be strengthened.
This paper presents the following data:
- Analyzed whole-genome sequences 2773 clinical strains: 160 000 SNPs identified<br /> - 1815 drug-susceptible/422 MDR/XDR strains: 188 mutations correlated with Drug resistance.<br /> - Novel mutations associated with the drug resistance have been found in base excision repair (BER), nucleotide excision repair (NER), and homologous recombination (HR) pathway genes (mutY, uvrA, uvrB, and recF).<br /> - Specific mutations mutY-R262Q and uvrB-A524V were studied.<br /> - mutY-R262Q and uvrB-A524V mutations behave as loss of function alleles in vivo, as measured by non-complementation of the increased mutation frequency measured by resistance to Rif and INH.<br /> - The mutY deletion and the mutY-R262Q mutation increase Mtb survival over WT in macrophages when Mtb has not been submitted to previous rounds of macrophage infection.<br /> - This advantage is exacerbated in presence of antibiotic (Rif and Cipro but not INH).<br /> - The MutY deletion and the MutY-R262Q mutation result in an enhanced survival of Mtb during guinea pig infection.
Major issues:
The finding that mutations in MutY confers an advantage during macrophage infection is convincing based on the macrophage experiments, but it is premature to conclude that the mechanism of this effect is due to hypermutagenesis and selection of fitter bacterial clones. It is described in E. coli (Foti et al., 2012) and recently in mycobacteria (Dupuy et al., 2020) that the MutY/MutM excision pathways can increase the lethality of antibiotic treatment because of double-strand breaks caused by Adenine/oxoG excisions. The higher survival of the mutY mutant during antibiotic treatment could more be due to lower Adenine/oxoG excision in the mutant rather than acquisition of advantageous mutations, or some other mechanism. The same hypothesis cannot be excluded for the Guinea pig experiments (no antibiotics, but oxidative stress mediated by host defenses could also increase oxoG) and should at least be discussed. Experiments that would support the idea that the in vivo advantage is due to hypermutagenesis would be whole genome sequencing of the output vs input populations to directly document increased mutagenesis. Similarly, is the ΔmutY survival advantage after rounds of macrophage infections dependent on macrophage environment? What happens if the ΔmutY strain is cultivated in vitro in 7H9 (same number of generations) before infecting macrophages?
- It would be useful to present more data about the strain relatedness and genome characteristics of the DNA repair mutant strains in the GWAS. For example, the model would suggest that strains carrying DNA repair mutations should have higher SNP load than control strains. Additionally, it would be helpful to know whether the identified DNA repair pathway mutations are from epidemiologically linked strains in the collection to deduce whether these events are arising repeatedly or are a founder effect of a single mutant since for each mutation, the number of strains is small.
- Some of the mutation frequency, survival and competition data could be strengthened by more experimental replicates. Data Lines 370-372 (mutation frequency), lines 387-388 (Survival of strains ex vivo), line 394 (competition experiment) : "Two biologically independent experiments were performed. Each experiment was performed in technical triplicates. Data represent one of the two biological experiments." Two biological replicates is insufficient for the phenotypes presented and all replicates should be included in the analysis. In addition, the definition of "technical triplicates" should be given, does this mean the same culture sampled in triplicate?
- MutY phenotypes. One caveat to the conclusion that the MutY R262Q mutant is nonfunctional is the lack of examination of the expression of the complementing protein. I would be informative to comment on the location of this mutation in relation to the known structures of MutY proteins. Similarly, for the UvrB polymorphism, this null strain has a clear UV sensitivity phenotype in the literature, so a fuller interrogation for UV killing would be informative re: the A524V mutation.
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socialsci.libretexts.org socialsci.libretexts.org
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Public speaking was practiced long before the Greeks.Systemic the-art of public speaking, which they called "rhetoric".
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Reviewer #2 (Public Review):
Wang and colleagues previously characterized the protein interactome for GABA subunits and identified HSP47 chaperone as a top interacting protein. Here, they follow up to assess the function of this HSP47-GABA interaction. Using primarily HEK293 cells, they provide evidence that the ER-resident HSP47 chaperone promotes the folding of GABA receptor subunits and the assembly of GABA subunits into multimeric ion channels. Interestingly, they demonstrate HSP47 can rescue the folding and function of a missense mutant A332D epilepsy-associated GABA subunit. They also demonstrate similar enhanced folding/function for acetylcholine receptor assembly. Overall, the experimental data are well-presented and provide insight into new ion channel clients whose folding and assembly are dependent on the HSP47 chaperone. The study also identifies HSP47 expression as a potential strategy to target and enhance the function of misfolded ion channels, and this may have broader biomedical therapeutic significance beyond GABA channels.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Overall, the manuscript is clearly written and remarkably comprehensive, presenting a very large amount of data. Experimental methods are well-documented and rigorous, and I have no significant technical concerns about any of the work presented. There are some points where the presentation might be improved by modifications to the text or figures, particularly with the goal of making this important work accessible to a broad audience.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This mechanistic PK/PD model simultaneous characterized several important factors, including formation of immunological synapses synapse variants, target/tumor cell densities, target CD3/tumor antigen expression levels, tumor antigen escape and the associated cancer relapse, in a unified model structure.
This model has the potential to be used in optimization dosage of T cell redirecting bispecific treatment towards best clinical outcome.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This study by Yang & al. explores the mechanism of X dosage compensation in the nematode species C. briggsae; which is a close relative of C. elegans. The mechanism is well described in C. elegans, and the authors have asked whether the same condensin-like complex (DCC) is responsible for the silencing of the X and which motifs on the X are responsible for this binding specificity in C. briggsae. They discovered that although the general principle of X inactivation is conserved between these 2 species, and ortholog proteins of the pathway (xol-1, sdc-2, and the genes encoding the DCC complex) are conserved, the sequences on the X that are recognized by the DCC complex have evolved very rapidly. The motifs of C. briggsae are not recognized by the C. elegans proteins and vice versa. The authors have accumulated very solid data, both in vitro and in vivo, to support this conclusion.
Overall, the results are very convincing and extremely interesting, for the chromatin field but also from an evolutionary perspective. This finding is comparable to the discovery that centromeric sequences and centromere proteins, despite their essential function in cells, evolve extremely rapidly. The reason is that they are involved in genetic conflicts, are a perfect target to generate hybrid incompatibilities during crosses, and therefore, under such selective pressure, evolve super fast. Most examples of hybrid incompatibilities rely on chromatin conflicts, and with this study, it appears that the dosage compensation system could be one other way to generate hybrid breakdown.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Briševac et al. investigate the genetic architecture of an exceptional ecological system where Clunio marinus populations have diverged in their timing of reproduction, controlled by a circalunar clock. These loci may be important in sympatric speciation and/or rapid evolution of reproductive isolation but there are some issues that need to be resolved. I outline these below:
1) The QTL mapping relies on a modest number of individuals and there are important details missing. The manuscript is missing information on heritability of the trait which is important for interpretation. While the variance explained by the QTL is hight, for the estimates of QTL effect sizes from such small samples, there is a common issue known as the Beavis effect that can inflate the effect size of individual QTL.
2) My major concern with the paper is the interpretation of divergence within the inversion as linked causally to the genes underlying ecological divergence. As the authors observe, divergence will vary within an inverted region. This can be traced to myriad factors, including variation in mutation rate, variation in constraint, patterns of ancestral polymorphism within this region, and variation in gene conversion within the inversion. Given this, I do not think it is valid to interpret the regions of high differentiation as the causal drivers of the ecological differentiation.
3) The authors imply in the discussion based on historical results that the ecotype evolved in situ in the last ~60 years. This seems substantially less likely to me than a number of alternative hypotheses including missing the phenotype in previous samples, plasticity in the phenotype causing it to be missed or migration from populations where the phenotype already existed.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
This study aims to describe the distribution and functional status of monocytes and dendritic cells in the blood and nasopharyngeal aspirate (NPA) after respiratory viral infection in more than 50 patients affected by influenza A, B, RSV and SARS-CoV2. The authors use flow cytometry to define HLA-DR+ lineage negative cells, and within this gate, classical, intermediate and non-classical monocytes and CD1c+, CD141+, and CD123+ dendritic cells (DC). They show a large increase in classical monocytes in NPA and an increase in intermediate monocytes in blood and NPA, with more subtle changes in non-classical monocytes. Changes in intermediate monocytes were age-dependent and resolution was seen with convalescence. While blood monocytes tended to increase in blood and NPA, DC frequency was reduced in blood but also increased in NPA. There were signs of maturation in monocytes and DC in NPA compared with blood as judged by expression of HLA-DR and CD86. Cytokine levels in NPA were increased in infection in association with enrichment of cytokine-producing cells. Various patterns were observed in different viral infections suggesting some specificity of pathogen response. The work did not fully document the diversity of human myeloid cells that have arisen from single-cell transcriptomics over the last 5 years, notably the classification of monocytes which shows only two distinct subsets (intermediate cannot be distinguished from classical), distinct populations of DC1, DC2 and DC3 (DC2 and 3 both having CD1c, but different levels of monocyte antigens), and the lack of distinction provided by CD123 which also includes a precursor population of AXL+SIGLEC6+ myeloid cells in addition to plasmacytoid DC. Furthermore, some greater precision of the gating could have been achieved for the subsets presented. Specifically, CD34+ cells were not excluded from the HLA-DR+ lineage- gate, and the threshold of CD11c may have excluded some DC1 owing to the low expression of this antigen. Overall, the work shows that interesting results can be obtained by comparing myeloid populations of blood and NPA during viral infection and that lineage, viral and age-specific patterns are observed. However, the mechanistic insights for host defense provided by these observations remain relatively modest.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The paper describes a fairly complete set of experiments describing a mechanism by which 4-hour treatment with 25HC can provide reductions in plasma membrane cholesterol for up to 22 hours. The basic finding is that 25HC depletes the ER of cholesterol by stimulating esterification and that SREBP activation is also inhibited. This effect is associated with the slow loss of 25HC from the cells.
The paper describes detailed studies of the long-lasting effects of a 4-hour exposure to 25HC on the loss of plasma membrane cholesterol. The paper characterizes the effects on SREBP processing to account for this. The possible long-lasting effects of ACAT stimulation were not investigated but may play an equal role.
The paper presents data that the effects on plasma membrane cholesterol can account for the inhibitory effects on some bacterial toxins and viruses.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
In this article, a multi-modal strategy for live birth prediction is proposed using blastocyst images and clinical features. The CNN architecture is used for the imaging dataset, while an MLP is built for the clinical features, and the final model is developed by concatenating CNN and MLP features. 17,580 samples are used for training and testing the model. The proposed model performed significantly better than the previous ones, with an AUC of 0.77.
By creating activation maps in both scenarios: I) when imaging and clinical features were used, and II) when only imaging data was used, authors highlight the parts of images that are crucial for predictions. Their results confirm the benefits of utilizing multi-modal datasets.
However, the manuscript is currently lacking crucial methodological information that is necessary to judge the validity of various claims.<br /> Furthermore, it lacks discussion of the potential applications of the proposed model in clinical settings.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
There are fundamental differences in resting state with eyes open or eyes closed regardless of visual stimulation. Without visual stimulation, these differences are attributed to the switching of involuntary attention from internal (eyes closed) to external (eyes open). The authors employ a monocular deprivation paradigm by patching one eye (with it either open or closed) to induce differences in alpha amplitude that are similar to differences measured with both eyes open or closed. They then examine how these differences from monocular deprivation impact after-effects in contrast sensitivity and binocular balance.
The authors pose an interesting and well-supported hypothesis based on prior knowledge that internal oscillations (i.e. alpha waves) can be modulated with eyes open vs eyes closed. The presented experiments build well upon one another and the authors clearly describe how relevant findings from experiment 1 contribute to the design of the following monocular deprivation experiments. The authors also combine several metrics including EEG, SSVEP and contrast sensitivity to assess both neural activity and perception in tandem.
Despite these strengths, the reported data in the first experiments only shows a modest difference between conditions. In experiment one, the authors make the assumption that differences in alpha measured with binocular eyes open vs closed translates to differences in alpha noted with a patched eye open or closed. Although changes in alpha amplitude appear comparable under monocular and binocular viewing, the differences in perceptual contrast sensitivity between the patched eye open and closed condition are quite modest. The authors do not report differences in contrast sensitivity in the binocular condition, so it is difficult to assess if these are comparable (contrast sensitivity changes in binocular (both eyes open vs closed) and monocular (patched eye open vs closed). The authors also employ their results to make claims about neuroplasticity, however this may be too general a claim. It seems as though the authors are specifically using an adaptation paradigm to elicit short-term changes (within 30 minutes from deprivation). While technically, the visual system is changing, it may be slightly misleading to refer to these neuroplastic changes given there are no measured long-term effects. The authors also fail to explain differences in binocular paradigm, noting recovery of binocularity in their phase combination paradigm, but persistent changes in their rivalry assessment. The authors also may overstate the implications of this in the discussion, as they provide no direct evidence that their reported changes after monocular deprivation are attributed to GABA interactions in primary visual cortex.
This work is important to our understanding of not only endogenous modulators of visual perception, but may have implications in how this knowledge is applied in clinical practice, specifically the treatment of amblyopia with patching.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The manuscript compares the chondrogenic potential of iPSCs derived from human chondrocytes isolated from healthy and osteoarthritic AC tissue. Both iPSCs derived from healthy and osteoarthritic AC tissue exhibit markers of pluripotency and were able to give rise to mesenchymal progenitors, although they had distinct differences in metabolic and chromatin modifier genes, as found by RNA seq analysis. The impact of these transcriptome signatures was functionally reflected in a lower chondrogenic potential of the MSCs derived from OA iPSCs compared to healthy donor (AC) iPSCs. This was assessed based on the reduced expression of hyaline cartilage markers and the reduced deposition of the glycoprotein-rich ECM matrix upon chondrogenic differentiation of day 21 micromass cultures from OA patients compared to healthy donors. The distinct gene expression profiles of OA chondrocytes were also found to be consistent with publicly available RNA-seq data performed on healthy and OA cartilage tissues further confirming that the newly identified differences in epigenetic and metabolic signatures are imprint from healthy and OA-chondrocytes.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Tools that enable labeling and genetic manipulations of synaptic partners are important to reveal the structure and function of neural circuits. In a previous study, Barnea and colleagues developed an anterograde tracing method in Drosophila, trans-TANGO, which targets a synthetic ligand to presynaptic terminals to activate a postsynaptic receptor and trigger nuclear translocation of a transcription factor. This allows the labeling and genetic manipulation of cells postsynaptic to the ligand-expressing starter cells. Here, the same group modified trans-TANGO by targeting the ligand to the dendrites of starter cells to genetically access pre-synaptic partners of the starter cells; they call this method retro-TANGO. The authors applied retro-TANGO to various neural circuits, including those involved in escape response, navigation, and sensory circuits for sex peptides and odorants. They also compared their retro-TANGO data with synaptic connectivity derived from connectivity obtained from serial electron microscopy (EM) reconstruction and concluded that retro-TANGO can allow trans-synaptic labeling of presynaptic neurons that make ~ 17 synapses or more with the starter cells.
Overall, this study has generated and characterized a valuable retrograde transsynaptic tracing tool in Drosophila. It's simpler to use than the recently described BAcTrace (Cachero et al., 2020) and can also be adapted to other species. However, the manuscript can be substantially strengthened by providing more quantitative data and more evidence supporting retrograde specificity.
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Reviewer #2 (Public Review):
The cycling of "co-substrates" in metabolic reactions is possibly a very important but often overlooked determinant of metabolic fluxes. To better understand how the turnover dynamics of co-substrates affect metabolic fluxes the authors dissect a few metabolic reaction motifs. While these motifs are necessarily much simpler than real metabolic networks with dozens or hundreds of reactions, they still include important characteristics of the full network but allow for a deeper mathematical analysis. I found this mathematical approach of the manuscript convincing and an important contribution to the field as it provides more intuitive insights how co-substrate cycling could affect metabolic fluxes. In the manuscript, the authors stress particularly how the pool sizes of co-substrates and the enzymes involved in the cycling of those can constrain metabolic fluxes but the presented results also go substantially beyond this statement as the authors further illustrate how turnover characteristics of substrates in branches/coupled reactions can affect the ratio of produced substrates.
The authors further present an analysis of previously published experimental data (around Figure 3). This is a very nice idea as it can in principle add more direct proof that the cycling of co-substrates is indeed an important constraint shaping fluxes in real metabolic networks and (instead of being merely a theoretical phenomena which occurs only in unphysiological parameter regimes). However, the way currently presented, it remained unclear to which extent the data analysis is adding convincing support that co-cycling substantially constrains metabolic fluxes. Particularly, it remains unclear for which organisms and conditions the used experimental dataset holds, how it has been generated, and with what uncertainty different measured values come. For example, the comparison requires an estimation of v_max. How can these values determined in-vivo? Are (expected) uncertainties sufficiently low to allow for the statement that fluxes are higher than what enzyme kinetics predict? Furthermore, I am wondering to which extent the correlations between co-substrate pool levels and flux is supporting the idea that co-substrate cyling is important. The positive relation between ATP/AMP/ADP levels for example, is a nice observation. However, it remains a correlation which might occur due to many other factors beyond the limitations of co-substrate cycling and which might change with provided conditions.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
The authors are building on previous work by Dahlén et al testing for phenome-wide associations between ABO/RhD blood groups. This is important for identifying potential disease mechanisms related to the blood groups, and for identifying blood groups that may be at higher risk of certain diseases. As we begin to create predictive models across diseases for precision medicine approaches in clinical care, this type of information informs the inclusion of blood groups as predictors in these models.
Notably, this study looks at each subset of A, B, AB, and O versus the remaining groups as compared to other studies which focus on comparing O and non-O blood groups. This paper successfully estimates the incidence rate ratios for 1,312 phecodes for A, AB, B, O, and RhD blood groups. The authors also tested for associations between the age of diagnosis and blood groups. The study's conclusions largely summarize these associations, which are important for the community to browse and interpret. However, the conclusion that ABO/RhD groups are the result of selective pressure driven partially by robustness to disease is not well founded simply from the significant association statistics within the paper.
As in all studies, there are inherent limitations in the data. The Danish National Patient Registry (DNPR) is a population-level cohort, so findings may be generalizable to Denmark or European countries. However, ascertainment biases may exist from what subset of the DNPR also had blood group determination (patients who may need blood transfusions during their hospital stay) and from the use of diagnoses from a hospital setting (most severe diseases) rather than the primary care setting.
The statistical model used to identify these associations is sound, although additional sensitivity analyses and rationale descriptions would add clarity to the appropriateness of this model and variable selection. The authors carefully note that, based on the study design, any associations here are not to be causally interpreted. The study is well powered with nearly 500,000 patients and a median follow-up time of 40.8 years. Multiple testing burden is accounted for using FDR-adjusted p-values. The established method of phecode mapping is used for this phenome-wide approach.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The HIV inflammasome sensor CARD8 senses intracellular HIV-1 protease activity through direct cleavage by HIV-1 protease between the F59 and F60 positions in the human CARD8 protein. The authors show that the F60 position is variable across non-human primate species that show varying levels of cleavage efficacy. They also posit that inflammasome induction may be dependent upon Toll-like receptor signaling.
Strengths: The authors are able to show that both HIV-1 and HIV-2 cleave and activate the human CARD8 inflammasome. The authors also demonstrate that changes to the 60th position of CARD8 cause a decrease in cleavage efficacy in vitro by HIV-1.
Weaknesses: The study is limited to the introduction of a few mutations in human CARD8 and their cleavage and activation by HIV. The physiological relevance remains unclear without direct investigation of different versions of simian CARD8 protein and SIVs in T cells and macrophages.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
By now, the public is aware of the peculiarities underlying the omicron variants emergence and dissemination globally. This study investigates the mutational biography underlying how mutation effects and epistasis manifest in binding to therapeutic receptors.
The study highlights how epistasis and other mutation effect measurements manifest in phenotypes associated with antibody binding with respect to spike protein in the omicron variant. It rigorously tests a large suite of mutations in the omicron receptor binding domain, highlighting differences in how mutation effects affect binding to certain therapeutic antibodies.
Interestingly, mutations of large effect drive escape from binding to certain antibodies, but not others (S309). The difference in the mutational signature is the most interesting finding, and in particular, the signature of how higher-order epistasis manifests in the partial escape in S309, but less so in the full escape of other antibodies.
The results are timely, the scope enormous, and the analyses responsible.
My only main criticisms walk the stylistic/scientific line: many of the others have pioneered discussions and methods relating to the measurement of epistasis in proteins and other biomolecules. While I recognize that the purpose of this study is focused on the public health implications, I would have appreciated more of a dive into the peculiarity of the finding with respect to epistasis. I think the authors could achieve this by doing the following:
a) Reconciling discussions around the mutation effects in light of contemporary discussions of global epistasis "vs" idiosyncratic epistasis, etc. Several of the authors of the manuscript have written other leading manuscripts of the topic. I would appreciate it if the authors couched the findings within other studies in this arena.
B)While the methods used to detect epistasis in the manuscript make sense, the authors surely realize that methods used to measure is a contentious dimension of the field. I'd appreciate an appeal/explanation as to why their methods were used relative to others. For example, the Lasso correction makes sense, but there are other such methods. Citations and some explanation would be great.
Lastly (somewhat relatedly), I found myself wanting the discussion to be bolder and more ambitious. The summary, as I read it, is on the nose and very direct (which is appropriate), but I want more: What do the findings say for greater discussions surrounding evolution in sequence space? For discussions of epistasis in proteins of a certain kind? In, my view, this data set offers fodder for fundamental discussion in evolutionary biology and evolutionary medicine. I recognize, however, the constraints: such topics may not be within the scope of a single paper, and such discussions may distract from the biomedical applications, which are more relevant for human health.
But I might say something similar about the biomedical implications: the authors do a good job outlining exactly what happened, but what does this say about patterns (the role of mutations of large effect vs. higher-order epistasis) in some traits vs others? Why might we expect certain patterns of epistasis with respect to antibody binding relative to other pathogenic virus phenotypes?
In summary: rigorous and important work, and I congratulate the authors.
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Reviewer #2 (Public Review):
In the submitted manuscript under the title "NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice", Zhang et al. applied human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. They reported that NSC-derived exosomes can ease the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in mouse brain. Using the NSC together with their exosomes can ameliorate the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. Finally, they speculated that the miRNA(s) in the exosomes is the key factor to improve the treatment of the NSC transplantation for the stroke. This is an interesting study that contributes important findings which will be of interest to the researcher in the field of the NSC transplantation. However, there are some key points should be further explained.
Major points:<br /> 1). This study does not provide any evidence about the cell death of the transplanted cells. The immunostaining of the Caspase-3 or TUNEL staining should be used to address this issue.
2). The authors showed that the neurological functions (evaluated by balance beam, ladder lung, rotarod test and Modified Neurological Severity Score (mNSS) up to 8 weeks after treatment (Figure 1C)) were significantly improved in the NES+Exo group compared to their control groups. However, these cells (transplanted cells) are progenitors (Nestin+) or undifferentiated cells (Tuj1+) at this stage (Figure 3). Thus, I was curious about that how can the immature neurons play neurological functions? This point should be explained.
3). The authors used the Golgi staining to show the NES+Exo can improve dendritic density and length. How do you know these neurons are transplanted cells?
4). The cell morphology of tdTomato+ cells is fuzzy and it is difficult to distinguish the cell body. It looks like that these cells out of whack.
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Reviewer #2 (Public Review):
To understand the origins of life, it is often necessary to establish synthetic molecular systems that model how primitive cells might have operated. Adopting this approach, here Le Vay et al. tackle one of the mysteries of early cells: how could primitive biomolecules have controlled the behavior of the compartments they inhabited? By forming coacervate droplets from polylysine peptides and ribozymes (catalytic RNAs), they observe changes in droplet properties driven by ribozyme activity and propose a route to form an integrated protocellular system that allows the evolution of biomolecules based on compartment behavior, modeling potential early life processes.
Polymers of opposite charge can phase-separate into coacervate droplets in equilibrium with surrounding aqueous phases. Such condensates are thought to act as subcellular compartments mediating some cellular functions. Coacervates, though, are also of interest as model compartments for biomolecules at the origins of life. A number of studies have shown how the properties and behavior of coacervates can be modulated based on external biological or physicochemical changes. There remains a key question: for coacervates to serve as a vessel for biology at the origin of life, can coacervate behavior be controlled from within? Previously this has been shown possible in some systems of membranous vesicles, an alternative model of primordial compartments.
Proteinaceous enzymes have been deployed to transform precursor compounds into potential coacervate components and induce the formation of condensed-phase microdroplets, but such enzymes are not thought to have been available at the origins of life. Instead, ribozymes are thought to have catalysed key reactions in early biology. Here, by using a ribozyme ligase to concatenate RNA molecules when together in a polylysine coacervate, the authors clearly demonstrate that coacervate properties change, showing a more rounded droplet shape and reduced fusion tendencies. Interestingly, the authors find that this distinctive behavior emerges when the reaction occurs in the coacervate phase, instead of before coacervate formation.
This influence of sequence-encoded phenotype on compartment properties has few precedents and has long been a target of origin of life research. The authors propose that it could serve as the basis for the establishment of coacervate droplets as units of selection and evolution. For this, a trio of critical challenges must be overcome and the authors begin to shed light on these.
First, the droplets must support ribozyme activity, without overly inhibiting it (or the droplet becomes an unfavorable habitat for these catalysts). Other ribozymes have often suffered inhibition due to conformation effects or substrate availability when mixed in a coacervate. The authors show here that the ligase ribozyme maintains activity (and may even be accelerated) in the coacervate. However, it appears to operate under single-turnover conditions and it is not yet clear whether multiple-turnover catalysis is possible in the coacervate.
Second, the droplet properties must be responsive to the activity of the biomolecules inside. The authors' observations of changes in coacervate behavior are robust, and they make some suggestions as to how such changes might be leveraged to establish selection pressure to drive the evolution of content molecules. In this study, though, the ribozyme comprises a substantial fraction (~1/2) of the coacervate negatively charged components, and in an evolutionary situation (with fewer molecules of RNA catalyst per compartment) it is not known whether the resulting droplet phenotype will change impactfully.
Third, the droplet must hold together its contents and avoid mixing with the contents of other droplets, to hold a molecular species together and defend against molecular parasites. Though there may still be some exchange of smaller molecules, the authors demonstrate that the lengthening of RNAs by ribozyme ligases in a coacervate can prevent fusion with other similar droplets (which otherwise occurs in the absence of RNA ligation) and preserve droplet identity. To use the coacervate as an evolutionary unit, droplets with active ribozyme will also need to be resistant to fusion with inactive droplets.
Putting such a system together based on the phenomenon observed by the authors would be a breakthrough in modeling primordial biology. A range of compartments have been proposed to act as habitats for early molecular biology, including porous rocks, mineral surfaces, ice phases, aerosols as well as membranous vesicles, and a key challenge is demonstrating how internal biological activities can influence compartment behavior. Establishing coacervates as genetically-controllable habitats for biomolecules will add to experimental models of such "life but not as we know it" and provide a new view of early biology.
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Reviewer #2 (Public Review):
Gyrencephaly has been linked to the split of the subventricular zone (SVZ) and the formation of an outer subventricular zone (OSVZ) during neurogenesis. This paper proposes a convincing multizone computational model of neurogenesis allowing exploration of the role of this OSVZ in the folding dynamics. This model is a bridge between knowledge of cell proliferation and migration and the physics of growth.
Strengths<br /> • The computational model described in this paper is probably the most ambitious to date. It succeeds in translating the complexity of microscopic biological phenomena that describe cell proliferation and migration into physical phenomena from continuum mechanics. It is truly a tour de force.<br /> • The description of neurogenesis is particularly clear, within the reach of a naive reader despite its complexity. The figure illustrating the chronology of the phenomena at work is a success.<br /> • The paper builds on impressive efforts to estimate from real human brain sections some of the complex parameters of the model such as the density of cells at different stages of migration.<br /> • The physical model is able to show ripples in the deep zones of proliferation that seem induced by the folding of the cortex. This observation is consistent with feedback from folding on the organization of the migration, as these ripples are not part of the model. I do not know to what extent these ripples have been demonstrated in reality.<br /> • The model shows that significant proliferation in the OSVZ leads to a doubling of the frequency of folding, a phenomenon observed in reality in large brains, which gives rise to allometric laws between folding and brain size (see Toro et al., Germanaud et al.)<br /> • The paper includes an experiment based on heterogeneous proliferation in the OSVZ, which is difficult to model in more classical models such as Tallinen's one. This is a particularly interesting possibility for modelling spatial heterogeneity in the expression of genes that modulate neurogenesis (see Llinares-Benadero et al.).
Weaknesses<br /> • To account for the complexity of biological phenomena, the model relies on a large number of ad hoc choices whose consequences are difficult to predict.<br /> • The physical model description is highly technical and out of reach for a non-specialist.<br /> • The description of neurogenesis shows three zones of cell proliferation, each inhabited by a specific cell type. Despite its realism, the proposed model does not take into account the ISVZ where the intermediate progenitors operate.<br /> • The experiment of comparing several regimes derived from the relative importance of proliferation in the VZ and OSVZ is not very clear. It leads to the observation of the evolution of cell density maxima over time, which seems insufficient to conclude the importance of the OSVZ for folding. One wonders whether the key parameter that leads to folding is the rate of OSVZ proliferation or simply the total quantity of neurons generated by the two or even the three zones.<br /> • The experiment on the heterogeneity of proliferation in the OSVZ is a bit frustrating. I would like to see a set-up corresponding to the mosaics found in ferrets and closely associated with folding patterns.<br /> • It would be interesting to elaborate a little on the possibility of extending the model in 3D, which seems imperative to evaluate the nature of the folding pattern generated. Comparing them to reality is an essential step in gauging the credibility of the model. For instance, it would be interesting to test to which extent the model can father the type of variability observed in the general population (Mangin et al.). It will also be particularly interesting to work on the inverse model between the real folding patterns and the heterogeneous proliferation maps that can generate them.
Conclusion
The computational model of neurogenesis described in this paper is the most sophisticated model proposed to date. It is a convincing step towards a model that could one day simulate perturbations of neurogenesis that may give rise to the gyration abnormalities observed in certain developmental pathologies. A better understanding of the genesis of these anomalies could contribute to their use as a signature of hidden deleterious events occuring during neurogenesis.
References
Toro, R., Perron, M., Pike, B., Richer, L., Veillette, S., Pausova, Z., & Paus, T. (2008). Brain size and folding of the human cerebral cortex. Cerebral cortex, 18(10), 2352-2357.<br /> Germanaud, D., Lefèvre, J., Toro, R., Fischer, C., Dubois, J., Hertz-Pannier, L., & Mangin, J. F. (2012). Larger is twistier: spectral analysis of gyrification (SPANGY) applied to adult brain size polymorphism. NeuroImage, 63(3), 1257-1272.<br /> Tallinen, T., Chung, J. Y., Rousseau, F., Girard, N., Lefèvre, J., & Mahadevan, L. (2016). On the growth and form of cortical convolutions. Nature Physics, 12(6), 588-593.<br /> Llinares-Benadero, C., & Borrell, V. (2019). Deconstructing cortical folding: genetic, cellular and mechanical determinants. Nature Reviews Neuroscience, 20(3), 161-176.<br /> Mangin, J. F., Le Guen, Y., Labra, N., Grigis, A., Frouin, V., Guevara, M., ... & Sun, Z. Y. (2019). "Plis de passage" deserve a role in models of the cortical folding process. Brain topography, 32(6), 1035-1048.
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Reviewer #2 (Public Review):
The authors of this paper identify a knowledge gap in our understanding of the generalizability of ecological associations of gut bacteria across hosts. Theoretically, it is possible that ecological associations between bacteria are consistent within a host organism but differ between hosts, or that they are universal across hosts and their environmental gradients. The authors utilize longitudinal data with a unique temporal resolution, on Amboseli baboons, 56 individuals who were sampled for gut microbiome hundreds of times over a decade. This data allows disentangling ecological dynamics within and across individuals in a way that as far as I know has never been done before. The authors show that ecological relationships among baboon gut bacteria, measure through a correlation based on covariation, are largely universal (similar within and across host individuals) and that the most universally covarying taxa are almost always positively associated with each other. They also compare these results with two sets of human data, finding similar patterns in one human data set but not in the other.
The main aim of this paper is to establish whether gut microbial ecologies are universal across hosts, and this the authors generally show to be true in a thorough and convincing way. However, some re-assessment or re-assurance on the solidity of their chosen method of estimating co-variation would be needed to fully assess the robustness of subsequent results. Specifically, the authors measure the correlation between microbial taxa from data on their abundance co-variation across samples. While necessary steps have been taken to validate the estimates across spurious correlations due to the compositional nature and autocorrelation structures present in the data, I worry that the sparsity of the data might influence the estimation of positive and negative correlations in a slightly different manner. There exist more microbial taxa than samples in the data and some taxa are present in as few as 20% of the samples, meaning that the covariation data will have a large amount of 0-0 pairs. I worry that the abundance of 0-0 pairs in the data might inflate the measures of positive co-variation, making taxa seem highly positively correlated in abundance when they in fact are missing from many samples. Of course, mutual absence is also a form of biologically meaningful covariation but taking the larger number of taxa than samples and the inability of sequencing technology to detect all low-abundance taxa in a sample, I am currently not convinced that all of the 0-0 pairs are modeled as a realistic and balanced way as a continuum of the other non-zero co-variation between taxa in the data. This may become problematic when positive and negative relationships are compared: The authors state that even though most associations between taxa were negative, the most universally correlated taxa pairs (taxa pairs with strongest correlations in abundance both within and between hosts) were enriched in positive associations. It may be possible that this is influenced by the fact that zero inflation in the data lends more weight to positive links than negative links. Whether these universal positive correlations are driven by positive non-zero abundance covariation or just 0-0 links in the data is currently unclear.<br /> Another additional result that would benefit from a more clear context is the result that taxa correlation patterns were more similar between phylogenetically close taxa and between genetically close host individuals. The former notion is to be expected if taxa abundances are driven by environmental (or host physiology-related) selective forces that favor bacteria with similar phenotypes. This yields more support to the idea that covariation is environmentally driven rather than driven by the ecological network of the bacteria themselves, and this could be more clearly emphasized. The latter notion of covariation being more similar in genetically related hosts is currently impossible to disentangle from the notion that covariation patterns were more similar with individuals harboring a more similar baseline microbiome composition since microbiome composition and genetic relatedness were apparently correlated. To understand if something about relatedness was actually influential over correlation pattern similarity, one would need to model that effect on top of the baseline similarity effect. Currently, it is not clear if this was done or not.
The authors also slightly overemphasize the generalizability of their results to humans, taking that only one of the human data sets they compare their results to, shows similar patterns. While they mention that the other human data set (that was not similar in patterns to theirs) was different in some key aspects (sampling frequency was much higher), the other human data set was also dissimilar to the other two (it only contained infants, not adults). Furthermore, to back up the statement that higher sampling frequency would be the reason this data set had dissimilar covariation between taxa, one would need to show that the temporal variation in this data set was different from the baboon one and show that these covariation patterns were sensitive to timescale by subsampling either data to create mock data sets with different sampling frequency and see how this would change the inference of ecological associations.
To the extent that the results are robust, particularly regarding to the main result of the universality of gut microbial ecological associations, the impact of this paper is not small. This question has never been so thoroughly and convincingly addressed, and the results as they stand have the power to strongly influence the expectations of gut microbial ecology across many different systems. Moreover, as the authors point out, evidence for universal gut microbial ecology is important for the future development of probiotics. An important point here, under-emphasized by the authors, is that universal gut microbe ecologies will allow specific interventions that use gut microbe ecology to manipulate emergent community properties of microbiomes to be more beneficial for the host, rather than just designing compositional cocktails that should fit all. In addition to the main finding of this study, the unique data set and the methods developed as part of this study (e.g. the universality score, the enrichment measures, the model of log-ratio dynamics, the assessment of covariation from time-ordered abundance trajectories) will doubtlessly be translatable to many other studies in the future.
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Reviewer #2 (Public Review):
The synaptonemal complex (SC) is a ladder-like structure that is assembled between homologous chromosomes during meiotic prophase I. This structure is critical for accurate chromosome segregation as it is required for both crossover formation and regulating crossover frequency. In this study, the composition of the SC throughout meiotic prophase, SC dynamics, and its contribution to crossover formation is compared between male meiosis and female meiosis using C. elegans. Although the SC is found in both sexes, many aspects of meiosis, including recombination initiation and formation, differ between sexes. Whether sex-specific differences extend to the SC and how this influences recombination events has not been investigated. The authors use fluorescently-tagged SC central region proteins (SYP-2 and SYP-3) to quantify the amount of SC protein accumulation per nucleus. The data indicate that the composition of the SC is dynamic throughout the meiotic prophase with sexually dimorphic properties. In addition, by examining and quantifying the number of proteins that mark different recombination intermediates, the authors found that not only does the SC regulate different aspects of recombination, but the regulation is sex-specific. Overall, the assays and quantification in this manuscript are of high quality.
Overall, the manuscript is largely descriptive and doesn't test possible mechanisms behind the observed sex-specific differences. However, this study is of high interest as these sexually dimorphic phenotypes have not been previously studied. The data presented in this paper set a nice foundation for future work. The manuscript is mostly well-written and the data is presented well but lacks explanations for some of the observed phenotypes. Some minor textual revisions would provide insights into some of the male-specific phenotypes that were noted without explanation (e.g. Why might SYP-3 be more dynamic in early pachytene in spermatocytes?). In addition, the introduction could be revised to provide a more coherent flow and to highlight the significance of sexual dimorphic aspects of meiosis.
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Reviewer #2 (Public Review):
The study by Rossi et al. is focused on the role of the SASP factor BAFF as a key regulator of senescent cell biology. Using both in vivo and in vitro studies, the authors show that BAFF, particularly in the monocytic cell line THP-1, is a type I interferon-induced gene. The authors further showed, using both proteomics, transcriptomics, and genetic studies that while BAFF does not play a role in the cell viability or cell cycle arrest of senescent cells, BAFF does regulate other aspects of senescent cell Biology. This includes SA-B-GAL activity and inflammatory gene expression of multiple SASP genes. Lastly, the authors demonstrate that via potential autocrine/paracrine signaling mechanisms BAFF can likely bind to multiple BAFF receptors upregulated in senescent cells, and affect both the p53 and NF-kB pathways to control inflammatory gene expression.
In summary, we find the manuscript to be both well written and organized, and a nice study on the role of BAFF as a key regulator of senescent cell biology. We believe this finding will be of significant interest to both the senescent cell field and the aging field in general.
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Reviewer #2 (Public Review):
In this work, the authors present a high-resolution cryo-EM structure of mitochondrial complex I, which was isolated from the model protostomian Drosophila melanogaster. Although multiple structures of related complexes have been published earlier, this system is particularly interesting as it seems not to adopt a so-called off-pathway "deactive" (D) state in contrast to the complex from Deuterostomia (including mammals) and therefore may provide novel mechanistic insights into complex I. The work is interesting, as it provides a novel contribution to the current discussion about the assignment of structural conformations to states in the catalytic cycle and/or in the active/deactive state transition of the complex.
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Reviewer #2 (Public Review):
In this study, Labuz and collaborators characterize the impact of burn injury on the T cell populations of the human skin. The authors use multiparametric flow cytometry and single-cell transcriptomics to analyze the numbers and the transcriptional profile of conventional and unconventional T cell populations in samples collected from patients with acute burn injury, late burn injury, and without burn injury. Their results show that burn injury disturbs the balance of T cell subtypes by increasing the percentage of CD4 T cells and decreasing the percentage of CD8 T cells. Both CD4 and CD8 T cells in the burn tissue presented lower expression of CD69 and higher expression of CD38, IFN-gamma, and TNF-alpha. The percentage of gamma delta T cells and MAIT cells positive for TNF-alpha and IFN-gamma also increased in the burn tissue. The authors then use single-cell RNA sequencing to gain further insights into how burn injury impacts the overall functions of skin T cells. This unbiased transcriptional profiling confirmed their previous observations that both conventional and unconventional T cells in the skin are replaced by new clusters that express lower levels of "tissue-resident" signature genes such as CD69 and higher levels of homing markers such as SELL and S1PR1. CD8 T cells of the burn skin samples show a clear reduction in the expression of cytotoxic molecules such as GZMK, GZMH, and GNLY, and this contrasts with the upregulation of cytotoxic molecules that are observed in the populations of unconventional T cell populations.
This is a relatively simple and descriptive work that will likely be an important resource for future studies investigating the role of T cell responses in skin wound healing and the maintenance of skin barrier function against pathogens following burn injury. A broader and more unbiased analysis of scRNA-seq data is necessary to better understand the biological processes and cellular responses that are being affected by the transcriptional changes observed in each T cell population as well as the possible implications of their findings.
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Reviewer #2 (Public Review):
With warming, fishes are generally expected to grow faster to smaller adult body sizes, as described by the temperature-size rule and other similar theories. However, the generality of this shrinking and the patterns among age classes within a species remain major research questions made all the more urgent by the rapid warming faced by many aquatic ecosystems. In this manuscript, the authors take advantage of an artificially heated ecosystem to investigate the impacts of warming on an unharvested population of fish and investigate patterns of growth, size structure, and mortality in an unexploited fish population. Surprisingly, while faster growth rates in juveniles are demonstrated, as would be expected, adult size remains higher in the heated habitat compared to a nearby non-heated habitat. This unexpected result will be of broad interest.
Strengths
The semi-natural experiment provided by the artificial warming from the power plant is a very nice design. While it is not the only place this type of study could be conducted, this system seems to have an unusually high degree of heating, that fact and the unexpected results make for a very interesting study that should be of broad interest. The study is also presented in a clear and concise manuscript and the conclusions are well-supported.
Weaknesses
In certain sections, it seems like the paper would benefit from a more thorough consideration of alternative explanations for the higher body size in the warmed population, like the release from density dependence or altered prey availability, and how those alternative explanations do or do not fit with the result that mortality was higher for the heated population. The consideration of mortality is a strength of the paper, but this result and how it fits with the result that heated adults did not shrink could be discussed in greater depth. It is unfortunate that factors other than the heat that might influence mortality, like predation rates, remain unknown in this system, but then they are rarely well understood in real-world settings like whole ecosystems.
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Reviewer #2 (Public Review):
This is an interesting study. In this study, the authors have linked single-cell RNA sequencing, spatial transcriptomic, and multiplex fluorescence in situ hybridization to characterize human oral mucosa in health and oral chronic inflammatory disease. They defined highly specialized epithelial and stromal compartments and spatially mapped a rare pathogenic fibroblast population likely responsible for lymphocyte recruitment and angiogenesis. They highlighted that the most dramatic variation in transcriptional/cellular spatial variability corresponds to oral mucosal tissue depth. The comparison of the list of genes with altered expression in gingival inflammation with the ones highlighted from the GWAS analysis related to patients with periodontitis is very interesting and will help to generate new hypotheses for future studies. Together with the recent publication from Williams et al., 2021, these studies are of particular interest and a valuable resource for researchers who study oral mucosa, especially gingiva in healthy conditions and periodontal diseases.
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Reviewer #2 (Public Review):
In the paper, the authors aimed to repurpose a previously developed Variational Autoencoder (VAE) trained on adult rsfMRI data to characterise the in vivo foetal-neonatal brain development. Although the attempts to understand both healthy and aberrant early functional development are becoming increasingly popular, the processing and interpretation of the foetal-neonatal rsfMRI remain challenging due to methodological difficulties and the extremely fast and complex nature of the early brain development itself. For this reason, the non-linear computational models, such as the proposed VAE, have the potential to represent the rsfMRI data and capture the early neurodevelopmental trajectories with higher accuracy compared to more prevalent linear methods such as ICA.
In this vein, the authors successfully apply the adult-trained VAE to compress the spatial representation of foetal-neonate rsfMRI cortical patterns into 256 latent features. Due to the non-linear nature of the VAE, this latent representation has the potential to yield more informative brain representations of rsfMRI data compared to other available methods making it a strength of the article.
Nevertheless, one important limitation is that the direct application of the model trained on adult data to early functional connectome and more importantly, the interpretation of the reconstructed latent space-based maps rests on a strong assumption that the adult connectome features are stable and recognisable in the very early period. Moreover, such a model trained on the adult data would also be incapable to reveal possible network structures that would be present in the developing but not in the adult brain.
The attempt to validate the method and assess its generalisability on two independent, fairly large datasets that include foetuses, and preterm- and term-born infants is commendable. However, the interpretation of the results in light of the subject, image acquisition, and processing (which is widely recognised to be very difficult, especially in foetuses) heterogeneity requires caution. For example, the VAE reconstruction error is positively correlated with the age at scan in dHCP, and DBI full-terms, but the relationship is very strong in the reverse direction in DBI foetuses. This suggests differences between the subgroups of subjects which might be driven by factors other than age. Thus, we cannot exclude the possibility that the high age-predictive power of the models based on the latent features is partly driven by those differences in addition to the age-dependant features of the infant functional connectome.
The approach for the extraction and mapping of the group-level brain resting state networks is interesting and has the potential to uncover new insights into the early connectome. However, some of the current results are rather surprising and put into question their biological plausibility. For example, the authors suggest observing the precursor of the default-mode network in the DBI but not the dHCP dataset. This is rather strange given the DBI subjects (including foetuses) were on average scanned earlier than the dHCP subjects. Also, the pattern similarity of the best matched extracted independent component ('brain network') in the full-term dHCP vs full-term DBI comparison is 0.6 which is rather low if expecting the same networks to be extracted in the age-matched comparison. Additionally, the network visualisations show large heterogeneity of the distribution of activation/deactivations within extracted independent components between the datasets (even after ordering them for pattern similarity) which contradicts the expectation that the extracted networks (if real) should be stable, if not along the whole development, then at least between the narrower age ranges within the datasets.
Overall, the interpretation of the current work is somewhat limited, and careful analysis of the latent representations derived from foetal-neonate data might be required to dissociate the effects of potential confounders from biological/developmental mechanisms. This might be difficult in the context of the highly complex and mostly black-box strategy such as VAE (this applies not only to the current method but to all novel methods proposed to study rsfMRI). Despite these limitations, the proposed approach could be very interesting methodologically with a potential impact on the future analysis of rsfMRI data. Overall, the authors achieved their aim of applying a novel VAE method to foetal-neonatal functional data and demonstrated that the extracted latent variables are predictive of brain age. However, careful evaluation of the latent representations and differences in predictive results and the mapped networks between the two datasets might be necessary to support the conclusion that the VAE-derived representations of foetal-neonatal rsfMRI carry informative neural signatures.
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Reviewer #2 (Public Review):
This study combines molecular analysis of human melanoma cells with in vivo functional experiments in zebrafish. ChIP-seq analysis of A375 melanoma cells stimulated with TGFB revealed a TGFB enhancer. The human enhancer was a clone and a zebrafish transgenic line driving GFP by this enhancer (TIE:EGFP) revealed that TIE:EGFP was only expressed in late melanomas. TIE:EGFP+ cells showed downregulated IFN response but upregulation of novel chronic GHB target genes. AP-1 transcription factor is required for the activation of this enhancer. Expression of the chromatin remodeller SATB2 promoted activation of TIE:EGFP in early melanomas. Finally, in vivo imaging, flow cytometry and scRNA seq showed that macrophages preferentially phagocytosed TIE:EGFP+ melanoma cells.
The identification of this novel TGFB enhancer is important since most studies focused on acute TGFB effects in melanoma. However, the present study identified a set of chronic TGFB target genes that may be relevant in melonoma and probably other tumors. Therefore, this study paves the way for future studies aiming at revealing the importance of this enhancer in different tumor histotypes and the novel identified chronic TGFB target genes.
Most conclusions are supported by the data, with the exception of the ones related to macrophages that are not fully convincing.
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Reviewer #2 (Public Review):
There is currently much discussion about the function of several viral proteins hypothesized to be "viroporins", especially specific proteins within SARS-CoV-1 and CoV-2, such as Orf3a. While some prior studies suggest that Orf3a exhibits ion channel activity, others disagree on this important topic. In the present study, compelling evidence is presented that Orf3a does not function as an ion channel, and suggestions are made as to its actual function. The study combines imaging to delineate Orf3a location in the cell, extensive functional analyses that demonstrate a lack of ion channel activity beyond endogenous currents, and compelling structural evidence that Orf3a does not take the form of an ion channel - lacking a clear conduction pathway and also having a basic aqueous vestibule that would not be predicted to support cation channel activity. Finally, co-assembly with trafficking proteins suggest, instead, functioning of Orf3a as a host cell trafficking disruptor that could contribute to immune cell evasion or even viral exit.
The authors present exhaustive, high-quality data to support their conclusions that Orf3a proteins from SARS-CoV-1 and SARS-CoV-2 do not exhibit ion channel activity. They clearly show Orf3a at the cell membrane and fail to detect ion channel activity using multiple modalities. I believe this work closes the book on the question of Orf3a as a viroporin. It is difficult to find any deficiencies in the experimental work. The parts about a role disrupting trafficking are a little more speculative but nevertheless appropriate and serve as a guidepost for future studies to fully elucidate the true role of Orf3a.
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Reviewer #2 (Public Review):
The manuscript presents a very simple and clear result. It demonstrates that neither place-cell nor time-cell presence is a constant in the rat hippocampus, but that both of these modes of activity are engaged flexibly depending on task demands. This result fits into a growing body of published work showing similar examples of flexibility in hippocampal representations; the authors do a fair job in relating their results to these studies. The innovative aspect of their manuscript is that it specifically addresses place cells and time cells, which have been different, and sometimes confusing, ways of thinking about hippocampal activity. By showing that the hippocampus shifts between distance and time encoding, the authors fit place cells and time cells into a more general framework of flexible representations.
The manuscript uses somewhat unusual and not very well-motivated criteria for classifying cells as distance or time cells. To detect the timing of neural activity on each trial, the authors look at the earliest onset of firing prior to the peak. It seems that this method would be highly susceptive to noise, and it is unclear why it would be better than the more standard methods like detecting the actual peak of firing or fitting a stretchable template to the entire firing pattern on each trial. This is a minor weakness of the manuscript, since the main conclusion shouldn't depend on the exact method used to classify cells. The difference between fixed-time and fixed-distance trials reported by the manuscript appears to be large and statistically robust.
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Reviewer #2 (Public Review):
In their manuscript "Growth cone advance requires EB1 as revealed by genomic replacement with a light-sensitive variant", Dema et al. showcase a CRISPR-based strategy to introduce a photo activatable EB1 variant into cultured cells in a single genome engineering step. Upon photoactivation this EB1 variant, which they term π-EB1, dissociates, thus severing the connection between the microtubule tip and +TIP proteins. They demonstrate this technique in human induced pluripotent stem cells, verifying that this genetic engineering procedure neither influences the cells beyond the EB1 gene nor hinders their ability to differentiate into neurons. Subsequently, they nicely verify that dissociation of π-EB1 leads to hindered microtubule growth, which subsequently leads to growth cone retraction. Accordingly, π-EB1 expressing axons cannot grow into an area illuminated with blue light, demonstrating the system's usefulness in circuit engineering. Finally, the authors try to specifically redirect growth cones by illuminating defined sections of the growth cone. This however leads mainly to growth cone retraction, in 70% of axons as the authors note, but succeeds in the remaining axons. Sadly, the authors do not further investigate the mechanism at the bottom of the observed axon retraction. Nevertheless, this study adds a valuable tool to the optogenetic toolbox of neurobiologists in the axon growth as well as circuit engineering fields.
Besides a few small writing and figure-editing faux pas, the study is well-written and robustly designed. The conclusions drawn by the authors are well supported by the data, which itself is technically well-prepared and controlled.
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Reviewer #2 (Public Review):
Previous studies have shown that the transcription factor Emx2 controls mirror-image PCP along the line of polarity reversal (LPR) by regulating the trafficking of an orphan receptor GPR156. However, the underlying mechanism is unknown. Here, the authors provide evidence that Emx2 represses transcription of Stk32a, which, in turn, negatively regulates GPR156 surface expression, thereby coupling cell-intrinsic and tissue-level PCP in the vestibular sensory epithelia.
Overall, the data are clearly presented and largely convincing. Using RNA-seq and ISH and both loss- and gain-of-Emx2 in vivo, the authors show that Stk32a is expressed in a complementary domain to Emx2 via Emx2-mediated repression. Gain- and loss-of-Stk32a experiments demonstrate that Stk32a is required for hair cell PCP in the Emx2-negative regions and is sufficient to reorient PCP in the Emx2-positive region. Moreover, Stk32a negatively regulates GPR156 localization to apical junctions without affecting core PCP proteins or Emx2 expression. However, there are several notable weaknesses, including a) because transcripts of the Stk32a mutant allele were still present, the nature of the Stk32a mutation is unclear; b) Mechanisms by which Emx2 represses Stk32a transcription were not addressed or discussed; c) Mechanisms by which Stk32a regulates GPR156 surface expression were not addressed. Addressing these issues at least partially would provide stronger support for the proposed model and improve the paper's impact.
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Reviewer #2 (Public Review):
This study combines data from different experiments to provide a detailed and conclusive mechanism of how transition metal ions are transported by a prokaryotic member of the SLC11 family. Although insight into this process was already provided in previous investigations, the novelty here concerns the presentation of X-ray structures at high resolution which, in combination with previously determined structures of the same protein, show three relevant conformations on the transport cycle in the presence and absence of substrate. For the interpretation of mechanisms, the conclusions derived from these structures are supported by complementary functional experiments from isothermal titration calorimetry and transport assays. Finally, a series of molecular dynamics simulations illustrate the stability of the investigated conformations and the interaction network that was proposed to be relevant for conformational transitions.
The strength of the manuscript lies in the thoughtful experimental design of the study and the high quality of the data. The X-ray structures are as good as they probably can get for a delicate membrane protein and the interaction with ions was confirmed by anomalous scattering experiments. Although the structure of the outward-facing conformation has relied on a mutation that stabilizes this state, the conformation is similar to known outward-facing conformations of other family members. The presented complementary ITC experiments are of high quality and the experimental design is intriguing.
A comparably smaller weakness concerns a shortage in the critical assessment of the data and their relation to previous findings in the field. This is in no way meant to question major conclusions drawn from this study, but it might help the reader to better understand the limits of the results and their interpretation. This weakness can be addressed by better documentation of the data and some revision of the text.
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Reviewer #2 (Public Review):
As described in the manuscript, gaze following is a dynamic process that should be investigated with similarly dynamic stimuli (wherever possible). In this case, the authors used videos, rich with visual information, that could be deemed an appropriate example of such stimuli. By constructing scenarios where actors gazed toward 1) a target person, 2) distractor or 3) nothing, the authors were able to easily study observers' eye movements. First, they were able to determine a baseline for how observers follow gaze in each of the three aforementioned conditions which is an important reference for future studies of this nature. Further, they suggest that eye movements are affected by how gaze following interacts with peripheral information (i.e., processing gaze-related information from the actor is combined with peripheral information about the presence/absence of a target person). Second, the authors also determined that eye movement behavior is affected by gaze information (i.e., changes in the gaze of the principal actor), in an anticipatory manner. This was verified using a DNN approach (using only the gazer's head direction) and then, confirmed through human observers' ratings. Lastly, the authors noted the presence of subsequent, reverse saccades (in the direction of the gazer and then, toward the target), which were shown to play a role in correcting an initial inference based on a slow head velocity of the gazer (confirmed with an SVM approach). While these are important first inquiries related to understanding eye movement behavior elicited in response to gaze following, a few items remain to be further elucidated, including what additional, peripheral information (besides target/distractor absence and presence) drives eye movements during gaze following. Overall, the dynamic videos used by the authors, in combination with their investigations, provide an important first step toward studying gaze following in more realistic conditions.
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Reviewer #2 (Public Review):
In mammalian genomes (with some exceptions), the location of recombination hotspots is driven by the PRDM9 zinc-finger protein that recognizes some specific DNA motifs and recruits the machinery inducing double-strand breaks (DSBs) initiating recombination. As DSBs are repaired with the homologous chromosome, "hot motifs" can be rapidly eroded through gene conversion occurring during the repair. This led to the "hotspot paradox" question and to the development of red queen models of hotspot evolution where the lack of enough DSB motifs can select for new PRDM9 alleles recognizing new sets of motifs, which in turn are eroded. However, this model fails to explain some observations, in particular, that the number of DSB seems not limited by PRDM9 sites. Recent findings also showed that PRDM9 played a central role in the symmetrical binding of homologous chromosomes.
In this study, the author incorporated this new finding (and more realistic assumptions compared to previous models) in a model of hotspot evolution. Their main result is that it affects the evolution dynamics and in particular the causes of selection on new PRDM9 alleles. Instead of selection pressure to increase the number of DSB targets, they showed that selection likely occurred instead to limit the number of hotspots to the hottest and symmetrical ones. These results are important as they changed our view and understanding of the evolution of mammalian hotspots and should have general implications for the study of recombination. The article focuses on complex mechanisms and can appear rather specific and technical. However, it nicely exemplifies the importance of taking molecular mechanisms into account to model genome evolution.
Overall, the model is sound with no apparent flaw and should be an important contribution to the field. The model is rather complex but the authors focused on a few key parameters while fixing others based on empirical knowledge. This allows for highlighting the novelty of the results without being lost within too many scenarios and hypotheses. However, two main issues should be addressed but they mostly concern the way the model and the results are presented and do not. First, partly due to the complexity of the mechanisms, the core of the manuscript is rather difficult to follow and would deserve a more careful and explicit presentation to guide the reader, as detailed below. Second, the implications of the model and the practical and testable predictions it makes could be developed more, in particular, to compare with previous models. The main comments are listed below.
1) The introduction reads very well and clearly explains complex mechanisms. It is a bit long and could be reduced a bit.<br /> 2) It is quite helpful to analyze the model step by step. However, the objective of each step is not clearly explained, and it is left to the reader to understand where the authors want to go. At first read, it is not clear whether the authors present an analysis of the model or simulation results and why they do that. So, the results part deserves rewriting and re-organization to guide the reader.<br /> - In the two first parts (Fitness with one heat and two heats) it should be stated more explicitly that it corresponds to an analysis of the fitness landscapes generated by the molecular mechanisms than results on the evolutionary dynamics<br /> - The part "Dynamics of the two-heat model" corresponds to simulations and it is only at this point that mutation on PRDM9 is introduced.<br /> - In the present form, the presentation of the results describes many mechanisms (which is fine). However, as the model is complex, stressing the main conclusion for each part could be useful as then making a clear link between the different steps of the reasoning.<br /> 3) The choice of key parameters is well justified with a detailed review of the literature and it is well justified to fix most of them to focus on the key unknown (or not well-known) ones. However, in a few cases, additional simulations or at least better justification would be welcome, in particular on the mutation dynamics of PRDM9.<br /> 4) The model clearly gives new insights into the evolution of recombination hotspots and appears better to explain some results. However, it is not clear what are the predictions of the model that could be properly tested with data, in particular against previous models. Some predictions are proposed but remain mainly qualitative. For example, can one quantify that this model predicts a skewer distribution of hotspots compared to previous red-queen models? How good is the model at predicting the number of PRDM9 alleles in human and mouse for example? Only the diversity at PRDM9 is given, it may be interesting to also give the number of alleles to compare to observations. The discussion on this remains a bit vague. Finally, are there additional predictions of the model that could be used to test it?<br /> 5) The Penrose stair metaphor is appealing but it seems to be dependent on the definition of hotspot, so not to represent a real biological process. Related to metaphors, it is also not very clear whether the authors suggest abandoning the red-queen metaphor for the benefit of the Penrose stair one. Actually, we can still consider that it is a red-queen dynamics but with a different underlying driver.
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Reviewer #2 (Public Review):
This paper studies how relative values are encoded in a learning task, and how they are subsequently used to make a decision. This is a topic that integrates multiple disciplines (psych, neuro, economics) and has generated significant interest. The experimental setting is based on previous work from this research team that has advanced the field's understanding of value coding in learning tasks. These experiments are well-designed to distinguish some predictions of different accounts for value encoding. However there is an additional treatment that would provide an additional (strong) test of these theories: RN would make an equivalent set of predictions if the range were equivalently adjusted downward instead (for example by adding a "68" option to "50" and "86", and then comparing to WB and WT). The predictions of DN would differ however because adding a low-value alternative to the normalization would not change it much. Would the behaviour of subjects be symmetric for equivalent ranges, as RN predicts? If so this would be a compelling result, because symmetry is a very strong theoretical assumption in this setting.
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Reviewer #2 (Public Review):
The manuscript by Torcal Garcia et al. shows that the mutation of a single arginine residue in a transcription factor, C/EBPα is able to accelerate the kinetics of B-cell to macrophage transdifferentiation without impacting the characteristics of the fully reprogrammed cell state. The authors delve into the mechanism underlying this phenotype and demonstrate that R35A mutation increases the affinity of C/EBPα for another transcription factor PU.1, and accelerates chromatin accessibility changes that accompany the transition from B-cell to macrophage program. The authors subsequently demonstrate that R35 is a methylation site for the arginine methyltransferase Carm1. Through Carm1 gain- and loss-of-function experiments, authors recapitulate R35me2/R35A effects on transdifferentiation. Overall, this is an interesting and well-executed study that provides one of the most striking examples of transcription factor regulation by methylation and documents the profound impact it can have on the kinetics of cell fate transition. Data are of high quality, experiments are rigorous, and deeply probe into the mechanism. Overall, the study sheds light on an under-appreciated level of transcription factor regulation.
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Reviewer #2 (Public Review):
This manuscript describes several general findings that are relevant to multiple fields. First, using bioinformatic sequence analysis the authors show that RNA Recognition Motif (RRM)-containing proteins often contain a domain with a specific amino acid repeat sequence (Arg-Ser, or RS) that is enriched in proteins that form condensates. With this understanding, the authors sought to use high concentrations of Arg in buffers in an attempt to solubilize an RRM-containing protein that has a C-terminal "RS" repeat region (SRSF1) for NMR structural studies. The high salt content of these samples is not ideal for NMR studies; however, the authors found that small peptides that mimic the RS sequence within SRSF1 can enhance the solubility of SRSF1 with more favorable conditions for NMR. Using paramagnetic relaxation enhancement (PRE) NMR, the authors show that an 8 amino acid RS peptide (RS8) interacts with one of the RRM domains in SRSF1, and the addition of RS8 does not abolish inter- and intra-molecular SRSF1 interactions. PRE NMR-based structure calculations provide a visual assessment of the potential interactions between RS8 and SRSF1. Finally, the authors performed bioinformatic and structural analysis of RRM domains, which was facilitated by AlphaFold-calculated structures, and found that surface-exposed aromatic sequence features appear to be conserved among phase-separating RRM domains.
Strengths of the work include the rigorous approach and the impact that solubilizing repeat peptides could have across many different biological fields where structural data on phase-separating proteins is difficult to obtain. The finding that the RS8 peptide can increase SRSF1 solubility and enable high-resolution NMR analysis should inspire other NMR experimentalists to seek out similar peptide-stabilizing co-solutes for their systems. The bioinformatic analysis that indicates surface-exposed aromatic residues are enriched in RRM domains involved in phase separation provides reasonable hypotheses, which are not directly tested using experimental approaches here but lay the foundation for studies that could be tested in future work and should be generally informative to other researchers interested in RNA-binding proteins.
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Reviewer #2 (Public Review):
In this study, the authors were seeking to determine the major antigens presented by the MHC-1 complex during the infection of human macrophages with virulent M. tuberculosis. Major strengths include rigorous and well-controlled experiments. The careful identification of mycobacterial peptides in the context of host peptides was impressive and well done. The results generally support the conclusions drawn in the study. Overall, the study is well-presented and rigorous and adds new knowledge to the field. This study provides new information regarding the mycobacterial peptides that are presented to the immune system via the MHC pathway, and the role of alternate secretion systems and known peptide processing pathways during M. tuberculosis infection of human macrophages. Importantly, adapting a protocol to identify MHC antigens in the BSL-3 pathogen will be of use to several fields. However, the study could be further strengthened by improving the discussion of prior work in the ESX and MHC fields to strengthen the context of this work and clarify its contribution to the field, as well as considering potential weaknesses of the study.
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Reviewer #2 (Public Review):
In this work Lemerle et al. provide long-awaited insight into how transverse tubules develop in skeletal muscle. Together with the sarcoplasmic reticulum transverse tubules form the triad, a specialized structure required for excitation-contraction coupling in skeletal muscle. Defects in transverse tubules or the triad can lead to problems such as muscular dystrophy. Whilst the involvement of specialist membrane structures (caveolae) and the membrane-bending protein Bin1 have long been recognized the precise mechanism of how caveolae and Bin1 cause transverse tubules to form and extend has remained unknown. This work provides compelling evidence, correlating antibody labelling with electron microscopy, to support the concept that caveolae rings form underneath the cell membrane which is surrounded by the endo/sarcoplasmic reticulum. These rings contain caveolin-3 and Bin1 and the authors show Bin1 enriched tubes extend from multiple points on these rings. Their data suggest that Bin1 assembles to initially form these scaffolds that then recruit the caveolae to form the ring. In addition, tubules appear continuous with the extracellular environment which is necessary for their function of facilitating calcium release during excitation-contraction coupling. In patients with mutations in caveolin-3 the caveolin ring formation as well as Bin1 tubulation were defective which may play a role in the pathology. The elegant experiments including time-lapse work clearly support the conclusions of the authors.
The ability of the authors to combine labelling studies with advanced microscopy to show the underlying structures provides very strong evidence for the proposed mechanisms. The authors suggest that the muscle-specific isoforms of BIN1 are key to tubule extension from caveolae rings but it would be interesting for them to discuss how this fits with studies suggesting that constitutive Bin1 isoforms can also form transverse tubules. It would also be interesting to understand the authors' views on whether caveolae rings are involved in the turnover of transverse tubules in adult myotubes as well as the initial formation and, additionally, if the caveolae rings are restricted to the region just under the surface membrane.
Insight into how transverse tubules are formed sets the groundwork for future therapies. This is clearly important for skeletal muscle myopathies but should also be considered in the heart. Cardiac transverse tubule loss and disorder play an important role in dysfunction in heart failure and atrial fibrillation and as such lessons learned in skeletal muscle may be successfully applied to the heart.
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Reviewer #2 (Public Review):
During Influenza virus infection, newly synthesized viral ribonucleoproteins (vRNPs) form cytosolic condensates, postulated as viral genome assembly sites and having liquid properties. vRNP accumulation in liquid viral inclusions requires its association with the cellular protein Rab11a directly via the viral polymerase subunit PB2. Etibor et al. investigate and compare the contributions of entropy, concentration, and valency/strength/type of interactions, on the properties of the vRNP condensates. For this, they subjected infected cells to the following perturbations: temperature variation (4, 37, and 42{degree sign}C), the concentration of viral inclusion drivers (vRNPs and Rab11a), and the number or strength of interactions between vRNPs using nucleozin a well-characterized vRNP sticker. Lowering the temperature (i.e. decreasing the entropic contribution) leads to a mild growth of condensates that does not significantly impact their stability. Altering the concentration of drivers of IAV inclusions impact their size but not their material properties. The most spectacular effect on condensates was observed using nucleozin. The drug dramatically stabilizes vRNP inclusions acting as a condensate hardener. Using a mouse model of influenza infection, the authors provide evidence that the activity of nucleozin is retained in vivo. Finally, using a mass spectrometry approach, they show that the drug affects vRNP solubility in a Rab11a-dependent manner without altering the host proteome profile.
The data are compelling and support the idea that drugs that affect the material properties of viral condensates could constitute a new family of antiviral molecules as already described for the respiratory syncytial virus (Risso Ballester et al. Nature. 2021).
Nevertheless, there are some limitations in the study. Several of them are mentioned in a dedicated paragraph at the end of a discussion. This includes the heterogeneity of the system (vRNP of different sizes, interactions between viral and cellular partners far from being understood), which is far from equilibrium, and the absence of minimal in vitro systems that would be useful to further characterize the thermodynamic and the material properties of the condensates.
There are other ones.<br /> 1) The concentrations are mostly evaluated using antibodies. This may be correct for Cdilute. However, measurement of Cdense should be viewed with caution as the antibodies may have some difficulty accessing the inner of the condensates (as already shown in other systems), and this access may depend on some condensate properties (which may evolve along the infection). This might induce artifactual trends in some graphs (as seen in panel 2c), which could, in turn, affect the calculation of some thermodynamic parameters.<br /> 2) Although the authors have demonstrated that vRNP condensates exhibit several key characteristics of liquid condensates (they fuse and divide, they dissolve upon hypotonic shock or upon incubation with 1,6-hexanediol, FRAP experiments are consistent with a liquid nature), their aspect ratio (with a median above 1.4) is much higher than the aspect ratio observed for other cellular or viral liquid compartments. This is intriguing and might be discussed.<br /> 3) Similarly, the fusion event presented at the bottom of figure 3I is dubious. It might as well be an aggregation of condensates without fusion.<br /> 4) The authors could have more systematically performed FRAP/FLAPh experiments on cells expressing fluorescent versions of both NP and Rab11a to investigate the influence of condensate size, time after infection, or global concentrations of Rab11a in the cell (using the total fluorescence of overexpressed GFP-Rab11a as a proxy) on condensate properties.
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Reviewer #2 (Public Review):
This interesting study looks into the evolution of putative spider venom toxins, specifically disulfide-rich peptides (DRPs). The authors use published sequence data to gain new insights into the evolution of DRPs, which are the major component of most spider venoms. Through a series of sequence comparisons and phylogenetic analyses they identify a substantial number of new spider toxin superfamilies with distinct cysteine scaffolds, and they trace these back to a primitive scaffold that must have been present in the last common ancestor of mygalomorph and araneomorph spiders. Looking at the taxonomic distribution of these putative venom DRPs, they conclude that mygalomorph and araneomorph DRPs have evolved in different ways, with the former being recruited into venom at the level of genera, and the latter at the level of families. In addition, they perform selection analyses on the DRP superfamilies to uncover the surprising result that mygalomorph and araneomorph DRPs have evolved under different selective regimes, with the evolution of the former being characterised by positive selection, and the latter by purifying (negative) selection.
However, I don't think that in the current state of the manuscript these conclusions are robustly supported for several reasons. First, it seems that not all previously published data were included in the phylogenetic analyses that were used to identify new superfamilies of DRPs. Second, much of the data were obtained from whole-body transcriptome data, which leaves a degree of uncertainty that these data indeed derive from the venom glands that produce the toxins. Third, the taxonomic representation of mygalomorph and araneomorph diversity in this study is so sparse that it becomes impossible to distinguish whether toxin recruitments have happened at the level of genera, families, or even higher-level taxa. Fourth, only a selection of DRP superfamilies was used for natural selection analyses, without the authors explaining how this selection was made. Yet, they attempted to draw general conclusions about toxin evolution in mygalomorphs and araneomorphs, even though most of the striking differences they found were restricted to just two mygalomorph genera, and one family of araneomorphs.
If these concerns are addressed this study can shed important new light on venom toxin evolution in one of the most diverse venomous taxa on Earth.
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Reviewer #2 (Public Review):
The manuscript nicely describes the use of a humanized NSG mice HIV model that mimics HIV infection in humans. Using this model, the Authors were able to clearly illustrate substantial evidence of inflammasome activation in HIV infection. This was done via analysis of mRNA transcripts of proteins pivotal of NLRP3, IFI16, and AIM 2 inflammasome pathway activation, and also measurement of plasma level of various inflammatory cytokines via multiplex U-PLEX Biomarker assay kit. Furthermore, they elaborated clearly on the negative correlation between inflammasome activation and some inflammatory cytokines with the percentage of CD4 T cells. From this study, the increase in inflammasome activation contributed remarkably to CD4 T cell depletion, beginning from three days post infection and reaching the climax by day 28. Interestingly, the authors were able to elucidate a decrease in inflammasome activation and CD4 T cell depletion with the use of anti-caspase 1 inhibitor VX-765.
The kinetics of viremia and CD4 T cell depletion, as well as levels of HIV RNA expression in different compartments (Figure Suppl 1 and 2) was a clever illustration of HIV dissemination in early infection. Furthermore, the evaluation of gene expression in the different compartments (lung, bone marrow, lymph node, and spleen) using qPCR at different time points of the study was supportive at the molecular level of inflammasome activation in early HIV infection (Figure 1, Figure Suppl 3) gave more credibility to the study. it was interesting to see good illustrations of different effector molecules(cytokines) of inflammasome activation at different time points of the study. The choice of using an anti-caspase 1 inhibitor VX-765 in HIV infection was a smart idea to limit the inflammatory changes and CD4 T cell death in HIV infection. The graphs supported their claim as we could see a decrease IL1B, and IL18 (Figure 4) which are key effector molecules during inflammasome activation. They also showed a decrease in CD4 T cell depletion with VX-765 compared to the negative control (Figure 5).
Despite the novelty and strengths of the study, there were some weaknesses on the design of the study. The Authors explained well in the introduction the elimination of HIV reservoirs as a key factor for HIV cure. Also, the Authors reported anti-caspase 1 inhibitor VX-765 reduces HIV reservoirs. However, in the study the Authors did not quantify the different HIV reservoirs (For example Central memory and effector memory CD4 T cells) and the effect of VX-765 on the population of these HIV reservoirs Furthermore the expression of genes associated with inflammasome activation in HIV infection was well presented. However, there was no gene expression profiling after administration of the anti-caspase 1 inhibitor VX-765, which would have been a better method to evaluate the effect of the drug on inflammasome activation
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Reviewer #2 (Public Review):
This study by Liu et al. investigates the mechanism that enables the Neurospora circadian clock to maintain robust molecular and physiological rhythms under conditions of nutrient stress. The authors showed that the nutrient-sensing GCN2 signaling pathway is required to maintain robust circadian clock function and output rhythms under amino acid starvation in the filamentous fungus Neurospora. Specifically, they observed that under amino acid starvation conditions, knocking out GCN2 pathway components GCN4 (CPC-1) and GCN2 (CPC-3) severely disrupts rhythmic transcription of core clock gene frequency (frq) and clock-regulated conidiation rhythm. They provided data to indicate that the observed disruptions are due to reduced binding of the White Collar (WC) complex to the frq promoter stemming from lower histone H3 acetylation levels. This prompted the authors to propose a model in which GCN2 (CPC-3) and GCN4 (CPC-1) are activated upon sensing amino acid starvation, recruit GCN-5 containing SAGA acetyltransferase complex to maintain robust histone acetylation rhythm at the frq promoter. They then performed a battery of assays to show that both GCN-5 and ADA-2 are necessary for maintaining robust H3ac, frq mRNA, and conidiation rhythms under normal conditions. To support that low H3ac level at the frq promoter is the cause for impaired WC binding and frq transcription, they demonstrated they can partially rescue the observed rhythm defects of the knockout mutants under amino acid starvation using an HDAC inhibitor. Finally, the authors used RNA-seq to identify genes and pathways that are differentially activated by GCN4 (CPC-1) under amino acid starvation conditions. Many of these genes are involved in amino acid metabolism and they showed that 3 of them exhibit rhythmic expression in WT but low and non-rhythmic expression in the CPC-1 KO strain.
Strength: The 24-hour period length of the circadian clock is known to be stable over a range of environmental and metabolic conditions because of circadian compensation mechanisms. Whereas temperature compensation (maintenance of circadian period length over a physiological range of temperature) has been studied extensively in multiple model organisms, the phenomenon of nutritional compensation and its underlying mechanisms are poorly understood. This study provides new insights into this important yet understudied area of research in chronobiology. In addition to advancing our understanding of fundamental mechanisms governing clock compensation mechanisms, this study also adds to our understanding of metabolic regulation of rhythmic biology and the relationship between nutrition and healthy biological rhythms. Given that the GCN2 nutrient-sensing pathway is broadly conserved beyond Neurospora, findings from this study will likely be relevant to other eukaryotic systems.
The authors provided strong evidence supporting their claims that the GCN2 signaling pathway is important for maintaining the robustness of the Neurospora clock under conditions of amino acid starvation. The authors performed parallel experiments in normal (no 3-AT) vs amino acid-starved conditions (+3-AT). Their observations of relatively minor disruptions of molecular and conidiation rhythms in cpc-3 and cpc-1 KO strains in normal nutrient conditions compared to starvation conditions support their model that sensing of amino acid starvation by GCN2 pathway-induced changes at the chromatin and transcriptional level that are necessary to maintain a robust frq oscillator. Without the comparison between normal vs amino acid starved conditions, this part of their model will not be as strong.
Previously Karki et al. (2020) showed that rhythmic activation of GCN2 kinase is regulated by the clock, resulting in clock-control rhythmic translation initiation. This study uncovers an additional mechanism through which GCN2 pathway modulates circadian rhythms by regulating histone acetylation of rhythmic genes. RNA-seq as described in Figure 7 provides some potential targets.
Weakness:<br /> (1) The authors propose a model (Figure 8) in which the GCN2 pathway is activated by amino acid starvation and recruits the SAGA complex to promote histone acetylation level at the frq promoter. There is however no data in this study showing that the GCN2 pathway is activated in amino acid-starved conditions, only that it is required to maintain robust frq and conidiation rhythms. The authors should clarify how they are defining "activation of the GCN2 pathway" in this study. For example, is it recruitment of GCN-5 and SAGA complex to frq promoter?
(2) The experiments to examine the involvement of GCN-5 and ADA-2 were performed in normal conditions (no amino acid starvation). Unlike cpc-1 and cpc-3 KO strains, gcn-5 and ada-2 KO strains showed severely disrupted frq rhythms in normal nutrient conditions, suggesting they are normally required for robust circadian rhythms. If GCN-5 and the SAGA complex are normally involved in regulating H3ac rhythms in the frq loci, how does GCN2 pathway modulates the activity of GCN-5 and SAGA complex in conditions of amino acid starvation? Are the interactions between GCN2/4 with GCN-5 and SAGA complex different in normal vs amino acid starved conditions? The authors should clarify their model.
(3) Given that the GCN2 pathway is important for nutrient sensing, the authors should not disregard the alternative hypothesis that the GCN2 pathway may be important for nutrient compensation and plays a role in maintaining the robustness of rhythms in a range of nutrient conditions.
(4) The authors should use circadian statistics to compute the phase and amplitude of the mRNA, DNA binding of the WC complex, and H3Ac rhythms. This will allow them to compare between rhythms and provide statistical significance values, rather than just providing qualitative descriptions. This will be valuable when comparing rhythms between strains and between nutrient conditions.
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Reviewer #2 (Public Review):
This article aims to extend human disease-related studies of PLA2G6 from fly models to iPS-neurons, mouse models, to look for drugs that suppress phenotypes and test them, and to attempt AAV whole body rescue. Generally, each of these questions/aims/experiments is excellent, but as presented, it's a bit of an underdeveloped hodgepodge of results, with each experiment somewhat underdeveloped or analyzed for the respective phenotype, in my opinion. I think the general thrust of the experiments is excellent. But the data are relatively cursory in many instances. Further development and characterization of the phenotypes would require quite a bit of work but vastly improve the paper.
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Reviewer #2 (Public Review):
This study utilizes extensive molecular dynamics simulations to probe the binding of a widely-used myosin II inhibitor to several closely-related myosin isoforms. The authors focused on so called 'cryptic' drug binding site, which is not apparent in isolated 'apo' states of the proteins, but are unveiled in simulations. The probability of unveiling these sites was implicated as the factor that distinguished myosins that bind blebbistatin from those that do not. Importantly, they focus on targetting an allosteric site, which can circumvent issues with targeting the binding site of the cognate ligand that can lead to nonselective binding in other targets. These simulations were accompanied by markov state model decompositions of those trajectories to isolate states conducive to drug binding, which were assessed using molecular docking to yield aggregated drug binding free energies. To demonstrate the reliability of their model, they performed a blinded prediction for an as-of-then uncharacterized myosin variant and found strong agreement with experimentally measured affinity (micromolar). Another finding of note includes identifying the ADP/Pi-bound myosin state as the preferred conformation for blebbistatin, which is line with the drug's inhibition of myosin ATPase activity.
Strengths:<br /> This study is impactful for several reasons. Firstly, the authors provide a molecular basis for the allosteric inhibition of myosin II by blebbistatin, through extensive GROMACS molecular dynamics simulations. They implicate a cryptic binding site that is obscured in apo state structures of the enzyme, for differences in the ligand's affinity measured for several myosin proteins. Their simulations indicate that the binding site spontaneously opens for apo state myosin isoforms that are inhibited by blebbistatin, but remains closed for other myosins. Moreover, they discovered that the drug's apparent affinity is proportional to the probability of forming the open conformation of the cryptic binding site in the apo state structure. This knowledge is important for guiding selective drug development, because there is generally lesser conservation in allosteric binding sites, e.g. off-target binding is less likely, relative to the primary site for endogenous ligands that are shared for homologous proteins. In addition, they used Markov State Models (MSMs) to identify protein conformational states that are conducive to ligand binding, to which they docked blebbistatin using Autodock Vina. The predicted drug affinities for each state in the MSM ensemble were weighted according to the state's probability, which yielded an aggregate estimate of drug affinity that strongly agreed with experimental data. To further establish the approach's validity, the modeler co-authors predicted the affinity for blebbistatin binding to a myosin protein that had not yet been characterized. The predicted affinity was also found to be in very good agreement with the affinity ultimately reported by the experimentalist co-authors. Overall, this is a strong computational approach applied to a drug/target interaction that is invaluable to the research and clinical community. The researchers' claims are well-supported by the provided data.
Weaknesses<br /> A prominent limitation in the study is that the contributions of entropy in their `multi-state' ligand binding model is not apparent - at the very least I would anticipate an entropic contribution from the states identified from the MSM characterization of the apo myosin simulations. Relatedly, the docking scores likely account for changes in ligand entropy upon binding, but it is unlikely that the 3 structures selected from each MSM state would be sufficient to describe the protein disorder within the state. This limitation does not impact the novelty of the study, but is rather an opportunity to discuss extension of the method in future applications. Additionally, by design the myosins used for the study shared 90% or greater sequence identity. On one hand, this is a great set for testing the limits of predicting selectivity. On the other hand, it would be helpful to know how the approach might work for myosins with lower homology but very similar tertiary structures. Would there still be a cryptic site amenable to drugging, and if so, would its open probability necessarily scale with ligand binding affinity? On a related note, would this approach perform best for well-buried ligand binding domains, or could it also be expected to perform well for more surface exposed sites or those with extensive loops?
It is expected that this work will be impactful to the scientific community on two fronts. The first of which is establishing a molecular mechanism of selective myosin inhibition, which will be invaluable for drug design efforts targeting the myosin II cardiac isoform in particular. The abundance of ATPases and ATP-responsive proteins in cardiac tissues renders difficult the task of designing molecular species that competitively bind to the ATP pocket - targeting an allosteric site with lesser homology across isoforms is a compelling alternative. The use of markov state models with standard docking techniques to improve binding free energy estimates among closely related proteins has the potential to be broadly used by the computer aided drug design community. The potential for widespread adoption is tempered by the authors' use of a specialized resource, folding at home, to achieve millisecond-length simulations. Enhanced sampling techniques, however, may yield similar results with smaller simulation requirements.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this manuscript the authors explain in greater detail a recent testis snRNAseq dataset that many of these authors published earlier this year as part of the Fly Cell Atlas (FCA) Li et al. Science 2022. As part of the current effort additional collaborators were recruited and about 6,000 whole cell scRNAseq cells were added to the previous 42,000 nuclei dataset. The authors now describe 65 snRNseq clusters, each representing potential cell types or cell states, including 43 germline clusters and 22 somatic clusters. The authors state that this analysis confirms and extends previously knowledge of the testis in several important areas.
However, in areas where testis biology is well studied, such as the development of germ cells from GSC to the onset of spermatocyte differentiation, the resolution seems less than current knowledge by considerable margins. No clusters correspond to GSCs, or specific mitotic spermatogonia, and even the major stages of meiotic prophase are not resolved. Instead, the transitions between one state and the next are broad and almost continuous, which could be an intrinsic characteristic of the testis compared to other tissues, of snRNAseq compared to scRNAseq, or of the particular experimental and software analysis choices that were used in this study.
A goal of the study was to identify new rare cell types, and the hub, a small apical somatic cell region, was mentioned as a target region, since it regulates both stem cell populations, GSCs and CySCs, is capable of regeneration, and other fascinating properties. However the analysis of the hub cluster revealed more problems of specificity. 41 or 120 cells in the cluster were discordant with the remaining 79 which did express markers consistent with previous studies. Why these cells co-clustered was not explained and one can only presume that similar problems may be found in other clusters. Indeed, many other indications of specificity issues were described, including contamination of fat body with spermatocytes, the expression of germline genes such as Vasa in many somatic cell clusters like muscle, hemocytes, and male gonad epithelium, and the promiscuous expression of many genes, including 25% of somatic-specific transcription factors, in mid to late spermatocytes. The expression of only one such genes, Hml, was documented in tissue, and the authors for reasons not explained did not attempt to decisively address whether this phenomenon is biologically meaningful.
A truly interesting question mentioned by the authors is why the testis consistently ranks near the top of all tissues in the complexity of its gene expression. In the Li et al. (2022) paper it was suggested that this is due an inherently greater biological complexity of spermiogenesis than other tissues. It seems difficult to independently and rationally determine "biological complexity," but if a conserved characteristic of testis was to promiscuously express a wide range of (random?) genes, something not out of the question, this would be highly relevant and important.
Unfortunately, the most likely problems are simply technical. Drosophila cells are small and difficult to separate as intact cells. The use of nuclei was meant to overcome this inherent problem, but the effectiveness of this new approach is not yet well-documented. Support for the view that the problems are mostly technical, rather than a reflection of testis biology, comes from studies of scRNAseq in the mouse, where it has been possible to resolve a stem cell cluster, and germ cell pathways that follow known germ cell differentiation trajectories with much more discrete steps than were reported here (for example, Cao et al. 2021 cited by the authors).
The conclusions that were made by the authors seem to either be facts that are already well known, such as the problem that transcriptional changes in spermatocytes will be obscured by the large stored mRNA pool, or promises of future utility. For example, "mining the snRNA-seq data for changes in gene expression as one cluster advances to the next should identify new sub-stage-specific markers." If worthwhile new markers could be identified from these data, surely this could have been accomplished and presented in a supplemental Table. As it currently stands, the manuscript presents the dataset including a fair description of its current limitations, but very little else of novel biological interest is to be found.
In sum, this project represents an extremely worthwhile undertaking that will eventually pay off. However, some currently unappreciated technical issues, in cell/nuclear isolation, and certainly in the bioinformatic programs and procedures used that mis-clustered many different cells, has created the current difficulties. Most scRNAseq software is written to meet the needs of mammalian researchers working with cultured cells, cellular giants compared to Drosophila and of generally similar size. Such software may not be idea for much smaller cells, but which also include the much wider variation in cell size, properties and biological mechanisms that exist in the world of tissues.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Summary:
This manuscript will be of interest for investigators in the field of development and the biology of pregnancy. The major strengths of the data are the detailed description of a hypoxia-induced mouse model of fetal growth restriction, where phenotypes, tissue histology, MRI images and metabolic analysis combine to characterize the experimental system. The data seem descriptive and preliminary, and the comparison to human pregnancy is neither supportive nor rigorous.
Strengths:
• The mouse pregnancy has been used by the authors and by others as a model for placental insufficiency. The manuscript provides incremental data to characterize hypoxia-induced fetal growth restriction<br /> • The 15.2T MR imaging technology is high quality and informative, even if the results did not reveal marked changes.<br /> • The detailed characterization of BPGM expression in the apical mouse placental surfaces is valuable.<br /> • The provided model may be useful for future studies by the authors.
Weaknesses<br /> • The metabolic analysis was restricted to one enzyme and metabolite. Placental analysis of 2,3-BPG and BPGM were already published (ref 29-30). At best, if the 2,3 BPG is related to the phenotype, it night be interpreted as a part of the injury in human cases, and adaptive response in the mouse models (as the authors suggested lines 286-288 and 332-336.). However, these assumptions are not tested.<br /> • The human cases are not very informative. The causes of FGR were not known, but clearly (Table 1) not analogous to that of the mouse model. Systemic hypoxia in humans might have been more informative. In its absence, the value of cross-species comparison is low.<br /> • While the provided experiments are of good quality, the approach is very descriptive and not advancing mechanistic understanding of FGR-related placental insufficiency.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
In this manuscript, a drug discovery pipeline was developed using a human iPSC derived organoid-based high-throughput screening platform to be used to identify drug candidates for maintaining photoreceptor survival in LCA10 retinopathies. Reserpine proved effective in patient organoids and in mutant mouse retina in vivo to improve photoreceptor survival and outer segment structure. Protein homeostasis was restored after reserpine treatment by increasing p62 levels, decreasing the 20S proteasome, and increasing proteasome activity. The manuscript is clearly written, contains a large amount of valuable and high-quality data and demonstrates that rebalancing proteostasis can stabilize photoreceptor overall homeostasis in the presence of a mutation that causes retinal degeneration.
The manuscript may lack functional in vivo data on the treatment by reserpine in RD16 mice such as ERG measurements or other functional tests (the authors also refer to it as future direction). Nevertheless, in my view, the study provides a solid and convincing set of data and substantially advances our understanding on the neuroprotective effects of reserpine beyond the scope of the retina and therefore can be expected to have widespread influence on a readership interested in the principles of neuroprotection rebalancing proteostasis.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
This manuscript describes the first human subject with a demonstrated recessive pathogenic variant of MCAT. Analysis of cells from this subject in general showed similar abnormalities as previously demonstrated for MCAT deficiency in the mouse. This includes combined oxidative phosphorylation deficiency. The hypothesis that MCAT deficiency causes lowering of co-factor lipoate was tested, as PDH and other enzymes require this for function. However, no evidence for this concept was observed.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this study, the authors follow up on their previous work demonstrating that NLRC4-deficient mice are susceptible to shigellosis and therefore can be used as a model to dissect immune control of infection in a tractable animal host (Mitchell & Roncaioli et al. 2020). This is therefore the first direct, mechanistic study on other immune pathways that contribute to protection of the host from Shigella in vivo. Importantly, the authors report that epithelial cell death is a critical protective mechanism against Shigella infection, and differences in the ability of the bacteria to antagonize host cell death explains in part why humans are susceptible while mice are resistant to infection.
Strengths
The authors use elegant genetic approaches to investigate the roles of distinct cell death pathways in anti-Shigella defense. The evidence presented convincingly shows that caspase-1, caspase-11, and caspase-8 mediate a hierarchy of protection against Shigella infection. The authors additionally show that the Shigella effector OspC3 drives colonization and infection by blocking caspase-11 function, which is, to this reviewer's knowledge the first demonstration that OspC3 facilitates infection in vivo. Overall, this is an important study and the work will have a large impact on the field by building a foundational understanding of the in vivo immune response against Shigella.
Weaknesses
A major limitation of the current study is absence of direct evidence that cell death within the intestinal epithelium is responsible for the loss of bacterial control. TNF is a pleiotropic cytokine that regulates cell death as well as inflammatory/antimicrobial gene expression. Similarly, caspase-8 has been found to also regulate inflammatory gene expression independent of its cell death functions. The authors propose that caspase-11 and caspase-8 contribute to protection from infection by driving epithelial cell death and extrusion. While this interpretation is supported by studies implicating cell death in eliminating the Shigella replicative niche, a formal demonstration that caspase-11 and TNF⍺/caspase-8 contribute to epithelial cell death in response to Shigella infection in vivo would strengthen the conclusions of the paper.
Furthermore, the claim that TNF⍺/caspase-8 signaling mediates protection against Shigella by driving cell death and not by NF-kB activation may be overstated, based on the evidence presented. While the work demonstrates that there is no difference in inflammatory cytokines in the Casp1/11/8/Ripk3 mice, this interpretation is less straightforward in a setting where there is substantially more CFU. Nonetheless, the study is overall very strong, and this point could be addressed experimentally or by modification to the text that would acknowledge this possibility.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The aim of the present work was to find physiological mechanisms for the phenomenon of "latent inhibition" in honey bees. To achieve this goal, the authors have very successfully combined different population genetic, behavioral pharmacological, and electrophysiological methods. From my point of view, the experiments were mostly carried out accurately, but some aspects of the methods used should be described more fully and/or justified. With the identification of the tyramine receptor AmTYR1 as an important mediator of latent inhibition, the goal was achieved. In any case, the work should stimulate investigation of whether the orthologous receptor of the fruit fly Drosophila has comparable functions in this model organism. Thus, in the future, the more powerful genetic tools of this alternative model organism could be used. So far, only dopamine receptor pathways have been associated with latent inhibition in Drosophila. Comparisons with the mechanisms of latent inhibition in vertebrates are now also possible.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The manuscript sets out to explain how the large micro-diversity of closely-related microbial strains might be produced and maintained. It proposes a scenario of spatiotemporal chaos, in which interactions between strains drive large changes in the relative abundances; space helps strains survive by migration between islands, and evolution produces new strains. The work presents a mathematical framework and discusses its biological relevance, and then examines its outcomes through a combination of simulations and mathematical analysis.
An important main result is that, under certain conditions, the diversity (number of extant strains) can grow continually and indefinitely. It is presented through simulations and then analyzed theoretically. Much of the work goes into understanding this increase in diversity, and the conditions required for it to happen. In particular, the effects of the distribution of mutant fitnesses, and of correlations between mutant and parent are examined.
This main result represents a significant conceptual advance on a central question in ecology. It is of broad interest in the field of ecology and evolution, likely to generate significant interest and lead to future work in a number of directions.<br /> The simulations strongly support the results. The mathematical analysis provides significant insight into phenomenology. It also develops tools that are of interest in their own right.
In tackling this difficult and general question, the authors must make simplifying assumptions in the modeling.<br /> The theoretical model does not assume the existence of niches (in the form of significant differences between inter- and intra-species interactions), or fine-tuned tradeoffs except as they may emerge from the evolutionary process. That such assumptions are not made is very appealing for microbial ecology.<br /> The interactions between species are taken to be anti-symmetric or close to that, as in predator-prey interactions. The authors motivate this assumption by bacteria-phage interactions. As the authors note, in a community with many strains of both bacteria and phage, the interactions are also expected to have a block structure, with different interactions between and within each group. This additional block structure could potentially have a significant effect on phenomenology. It is not implemented in the present work and is only briefly discussed in the Discussion section, referring to unpublished work-in-progress.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The dinosaur literature from the 1970s through 1990s is rife with claims purporting to have identified sexual dimorphism in the skeletons of dinosaurs. Mallon (2017) penned a critical review of these claims and showed that nearly all of them are without statistical support. He also suggested some more appropriate methods that might be fruitfully applied to the matter. This contribution from Pintore et al. heeds Mallon's prior recommendations and, I think, fairly convincingly demonstrates the existence of sexual dimorphism in the femora of the ornithomimosaurs they investigated. Their argument is bolstered by the numerous examples they cite of similar dimorphism seen in the femora of various tetrapod groups. I believe this manuscript holds much merit.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this paper, the authors developed a new device for online decoding of position based on calcium imaging in freely moving rodents. This device could be used in the brain-computer interface to investigate neurofeedback-based therapies for neurological disorders. The technical part is properly done and gives convincing results that can be truly helpful for the scientific community using the miniscope. Nevertheless, as a methodological article, there should be more details regarding the accuracy of the decoding and of the different steps to follow if someone wants to use their methodology. Moreover, a true online real-time experiment should be performed to validate the device.
Please find below my comments:
- From what I read the authors did not perform a true real-time experiment. I think this step is crucial to ensure the quality of their device.
- There should be a validation against a classical offline Bayesian decoding.
- "To mimic these steps using the virtual sensor in our performance tests, one session of image data was collected and stored from each of the 13 rats, yielding ~7 min (8K-9K frames) of sensor and position tracking data per rat. The linear classifier was then trained on data from the first half of each session and tested on data from the second half." This sentence is not clear enough. The authors should clearly describe the exact time needed for each experimental step. What is the time needed for instance for the experimental step 2, during which the linear classifier is trained to decode behavior from the initial dataset? This is crucial information if someone wants to use this device. How the accuracy varies with the duration (or the quality) of the initial dataset? It is important that the authors provide an investigation of this to validate their device.
- For instance, what is the decrease in decoding accuracy 1) with fewer place cells? What is the approximative number of place cells to obtain reliable decoding? 2) with the duration of the initial recording session. Here it seems to be of the order of 3-4 min. What if the recording session is shorter? Is there some constraint about this recording session (in terms of speed, stops, etc...) to obtain good decoding? 3) Is there a link between the decoding accuracy and the number of place cells nearby?
- The authors specified the time delay of 2.5ms for their device. Yet, it is pointless regarding the purpose of the decoding. The important information is the precise position of the animal when the device is used to trigger a stimulation at a given location. Again, a true online experiment should be done to validate that a TTL can be triggered by the device at a precise location (with a quantification of the error made).
- There is no information on the accuracy of the decoding with respect to the location in the linear track. It is likely that the extremities of the linear track will be better identified. Figure 4C does not provide a clear description of the error made. The choice of D=2 (which seems to represent the spatial bin) is not justified. Two spatial bins seem to represent +/-40 cm which is quite large.
- The movement artefacts are not equally observed in the maze. The way they are corrected might be captured by the linear decoder. These artefacts might have a strong influence on the decoding. Please provide a quantification of the correction made during steps 1 and 2 in relation to the position of the animal on the linear track. The authors should provide a correlation between the presence of these corrections with the decoding accuracy.
- Besides the methodological part, I have some physiological questions. It is quite common in linear tracks to have bi-directional and unidirectional place cells. Is it the case here? How many? It is difficult to see this in figure C. Is there an error due to the online decoding of the position in the two directions of the linear track?
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Periodontal inflammation is a very common disease and constitutes a challenge for public health. Healing of periodontal tissue after an acute or chronic inflammation remains to be very difficult, if not possible. Although MSCs were known to be present and support periodontal physiological turnover, periodontal tissue hardly regenerates after the inflammation process. Therefore, learning the difference between periodontal MSCs under physiological or inflammation conditions is a fundamental issue. Due to the technical challenges, a comprehensive single-cell Seq analysis on periodontal tissue has never been performed. The current study made the first breakthrough on this issue.
Overall, the manuscript provides important information on the response of periodontal tissue towards acute inflammation.Additional experiments are needed to support their major conclusions.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The work presented aims at analyzing the effect of the loss of function of WFS1, the gene responsible for Wolfram syndrome, in visual physiology. They analyzed the vision of knock-out mice and deciphered the potential altered signaling pathways using transcriptomics and proteomics approaches. Interestingly, they identified monocarboxylate transport isoform 1 and its partner Basigin as downregulated proteins. In addition, they demonstrated that excessive neuroinflammation may contribute to the observed phenotype. These data add, in an interesting way, a novel pathophysiological mechanism leading to Wolfram syndrome.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This study systematically integrates multi-omics (plasma lipidomic and metabolomic, and fecal 16s microbiome) data to identify the metabolic at-risk profiles within people living with HIV on antiretroviral therapy (PLWHART). As a result, three groups of PLWHART (SNF-1 to 3) were identified, which showed distinct phenotypes. Such insights cannot be obtained by a single type of omics data or clinical data, and have implications in personalized medicine and lifestyle intervention. Connecting the findings in this study with specific medical/clinical insights is the next challenge.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The major strengths of the manuscript are 1) the widely used mouse model, 2) the extensive analysis of transition metals other than iron, 3) the molecular data providing evidence for the cellular effects of excess iron accumulation on gene expression and protein levels, and 4) the phenotypic and lifespan data in animals treated with diet manipulations.
The major weakness of the manuscript is the lack of a link between the iron status of individual animals and their behaviors. The authors attempt to correlate molecular and behavioral parameters in Figure 5C, but the strength of this analysis (sample size and resolution) is modest.
The conclusions are entirely justified by the data. Moreover, this study opens several questions that, if answered, would potentially have a major impact on mitochondrial disease research. As the authors note, whether patients with different genetic defects affecting the OxPhos complexes exhibit iron excess, and whether this is detectable in the blood or other biofluid is an important question.
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Weread, for example, of Philistine incursions into the hill country, toMichmash in Benjamin (1 Samuel 13:23), and the Rephaim Valley nearJerusalem (2 Samuel 5:17–22). It was in one of these border disputes thatthe city at Khirbet Qeiyafa was conquered and destroyed.
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kmitov.com kmitov.com
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But it does not work, because the association with authors will return empty authors for the Material as the materials are also soft deleted.
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The problem is that Globalize knows nothing about acts_as_paranoid. You can delete a Material, and it should delete the translations, but when you try to recover the Material then there is an error because of how the translations are implemented and the order in which the translations and the Material are recovered. Which record should be recovered first?
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Remember that the Material has all of its translations for the title in a table that just got soft deleted. So the correct answer is “nil”. The title of the delete material is nil.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In this manuscript by Seroussi et al, the authors describe a global analysis of Argonaute (AGO) protein biology in the model organism C. elegans. Small RNAs regulate most facets of gene expression and, therefore, play important roles in all aspects of biology, including development and health. C. elegans has been at the forefront of attempts by biologists to understand the biological roles played by AGOs and small RNAs in animals. Here, the authors make a significant contribution to this effort by epitope tagging all 21 of the elegans AGO genes. The reagents they generate allow the authors to explore at a global level the where, when, and why of C. elegans AGOs. Whenever possible the authors confirm that their tagged proteins are functional. The authors then analyze the expression patterns of elegans AGOs, sequence small RNAs that associate with these AGOs, and identify small RNA populations that change in animals lacking the AGOs.
In many cases the data presented are consistent with previously published studies, establishing that the author's approach was likely successful. In other cases, the data allow the authors to make novel observations. For instance, the authors categorize the 21 AGOs into four major categories- based on their small RNA binding profiles. They define the types of genomic loci targeted by each group of AGOs and show that these AGO groups regulate distinct classes of transposable elements, such as DNA cut-and-paste transposons, LTR retrotransposons, and Rolling transposons. This differential targeting suggests that sequence features intrinsic to each target transcript may help direct different RNAs into different silencing pathways. A metagene analysis defines differences in the 3' and 5' distribution of small RNAs across target genes for each AGO. These patterns are likely to have important implications for understanding RdRP function. The authors identify an AGO, which they name VSRA-1, which binds broadly to most classes of small RNAs. This data is likely to be an important step towards understanding how different AGOs bind different small RNAs. The authors present evidence that they have identified ten new miRNAs. The low expression levels of these miRNAs suggest that additional work is needed to ensure that these miRNAs have a biological function. The authors show that miRNAs with higher precursor duplex complementarity are preferentially loaded into the AGO RDE-1. This observation has important implications for miRNA evolution. The authors identify several hundred new candidate piRNAs as well as reclassify many mis-annotated miRNAs as piRNAs. Finally, the authors link several AGOs to interesting phenotypes, such as germ cell immortality and innate immunity.
The paper is very well written. No small accomplishment given the huge amount of data presented. As far as I can tell, experimental approaches and statistical analyses follow best practices. Alternative explanations for data are usually acknowledged. In summary, the paper provides novel insights into small RNA biology (described above), establishes high-quality reagents that will empower future studies into the myriad of ways that C. elegans use small RNAs to regulate gene expression, and demonstrate quite clearly that the C. elegans small RNA systems are intertwined and remarkably complex.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This paper examined the effects of sertraline alone and with standard TB drugs in a variety of cell culture and animal models. The main finding was a reduction in CFU counts in the models. This may be of interest to the field generally.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Nociception is an essential sense to detect threats to bodily integrity, and nociceptive behavior is essential to deal with such threats adaptively to minimize actual harm. Intuitively, these processes might be regarded as hard-wired, and so the choice of topic of the present paper, namely the way nociceptive behavior can be MODULATED, is a strength. Also, a strength is the most elegant use of a wide range of suitable methods.
Weaknesses are a lack of proper genetic controls for leaky transgene expression in some of the experiments, and what appears to be an incomplete discussion of results that, as the authors acknowledge, are unexpected or seemingly contradictory.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This paper has huge potential for influencing the way we think about bats as foragers. But, I think that it can be improved.<br /> Specifically, there is no clearly articulated hypothesis underlying the work. Second, there should be specific testable predictions arising from the hypothesis. This change, while relatively minor, will vastly improve the focus of the work, and hence its impact on the reader.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This is a highly interesting paper that provides important insights into the understanding of how HC-derived osteoblasts contribute to trabecular bone formation. Using single-cell transcriptomics, the authors found that HC descendent cells activate MMP14 and the PTH pathway as they transition to osteoblasts in neonatal and adult mice. They further demonstrate that HC lineage-specific Mmp14 null mutants (Mmp14ΔHC) produce more bone. By performing a panel of elegant in vitro studies, the authors show that MMP14 cleaves the extracellular domain of PTH1R, dampening PTH signaling. The authors provide more in vivo evidence showing that HC-derived osteogenic cells respond to PTH which is enhanced in Mmp14ΔHC. Generally, this is a very well-performed study that may contribute important novel aspects to the field.
I have the following issues for the authors to address:
1. The novel mechanism identified in this study (i.e. MMP14-induced PTH1R cleavage) is intriguing. It is unclear how specific this pathway is in the transition of HCs to osteoblasts. Are other MMPs besides MMP14 involved in the PTH1R cleavage? Is PTH1R the only substrate of MMP14?<br /> 2. Would it be possible for the authors to detect the truncated PTH1R fragment(s) from the conditioned medium prepared from either 293T or osteoblast culture?<br /> 3. The finding that HC-descendants persist and contribute to the anabolic response to PTH in aged mice is interesting. Have the authors examined the changes in MMP14 expression in bone with age and in response to PTH treatment?
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The human cerebellum likely has a significant but understudied contribution to cognition and behavior beyond the motor domain. Clarifying its functional relationship with the cerebral cortex is a critical detail necessary for understanding cerebellar functions. This paper addresses this challenge by testing three simple but intuitive models: winner-take-all, one-to-one model versus two converging input models. Results showed that the convergence model outperformed the one-to-one mapping model, indicating that cerebellar regions received multiple converging inputs from the different cortical regions. Overall the paper is well-written, and the results are clean and interesting. The methodological rigor of using cross-validation and generalization is also a strength of this paper.
The authors concluded that some cerebellar regions receive converging inputs from multiple cortical regions because the Ridge and Lasso models outperformed the WTA model. The WTA model has a fixed diagonal pattern, in contrast, Ridge/Lasso models included more weights in the connectivity matrix. Considering what's being estimated in this matrix, then perhaps the findings are not surprising because even after penalizing and regularization, the ridge regression models are still more complex than the WTA model (more elements are allowed to vary). In other words, Lasso/Ridge models allow more variables from the X side to explain variances in Y, similar to how throwing in more regressors can always improve the R square. I am unsure if cross-validation mitigates this issue. It would be more straightforward for the authors to compare model performance in a way that controls for the number of variables in the Ridge/Lasso models.
The authors did an excellent job reviewing the anatomical relationship between the cerebral cortex and the cerebellum. There are several issues that the authors should address in the introduction or discussion. First, if the anatomical relationship between the cerebellum and the cortex is closed-loop as suggested in the intro, then how convergence can arise from multiple cortical inputs given there is no physical cross-talk? Second, there are multiple synapses connecting a cerebellar region and the cortex, and therefore could integration occur at other sites but not the cerebellum? For example, the caudate, the thalamus, or even the cortex (integrating inputs before sending to the cerebellum)?
The dispersion metric quantifying the spread level in cortical inputs is interesting. Could the authors expand this finding and show anatomically what the physical spread is like in cortical space? The metric is novel but hard to interpret. A figure demonstrating the physical spread in the cortex should help readers interpret this result.
At the end of the discussion section, the authors discussed how results are more likely driven by cortical inputs to the cerebellum but not the other way around. This interpretation is likely overstated given the hemodynamic blurring and low temporal resolution of BOLD. Without a faster imaging sequence and accurate models that account for differences in hemodynamic properties, the more parsimonious interpretation is results are driven by bidirectional cortico-cerebellar interactions. The results are still very interesting without this added nuisance.
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docdrop.org docdrop.org
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hume is not in book one arguing that persons do not exist in fact in book two he's going to spend most of his time explaining what persons 01:17:41 are he when instead what he's claiming is that persons don't have selves
!- David Hume : book 1 and 2 - book 1 explains what persons are - book 2 explains that persons don't have selves
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Reviewer #2 (Public Review):
The thrombopoietin receptor (TpoR) regulates stem cell proliferation, platelet production, and megakaryocyte differentiation. Past cell biology and biophysical studies have established that ligand-induced dimerization constitutes the mechanism of activation of TpoR. Specifically, ligands bind to the extracellular domain of TpoR and generate an allosteric response that is transmitted to the transmembrane domain, activating downstream signaling. However, up to now the molecular details of how the allosteric signals are transmitted to the intramembrane domains have been elusive. In this manuscript, Constantinescu and co-workers combined NMR, in vitro, and in vivo assays to investigate the activation and oncogenicity of TpoR. The authors concluded that the unwinding of the juxtamembrane domain is the main structural event that determines TpoR activation and regulates oncogenicity. The solid-state NMR studies were carried out in lipid membranes with polypeptides spanning the juxtamembrane and transmembrane residues. The authors show a series of spectra of 13CO resonances that encompass the juxtamembrane domain that is diagnostic of a structural transition from a helical conformation to a partially disordered state. The unwinding of the helical juxtamembrane domain was confirmed by site-specific mutations in this region. The chemical shift changes clearly indicate the transition from order to disorder (and vice versa) for selected sites. These conclusions are compounded by INEPT-type experiments that detect the most dynamic region of polypeptides. To rationalize the molecular mechanism for activation, the authors also used Ala-Ala insertions at strategic positions along the transmembrane domain. These experiments showed that the specific orientation of the transmembrane residues is central for TpoR activation, and a slight rotation of the helix is critical for activation of the receptor. Transcriptional activity assays confirm the importance of the proper orientation of the transmembrane domain for receptor activation.
Overall, I believe the data are solid, and both biophysical and cell biology studies support the conclusions of the authors. These new findings represent a significant advancement in understanding cytokine receptor activation.
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Reviewer #2 (Public Review):
The acrosome is a unique sperm-specific subcellular organelle required for the fertilization process, and it is also an organelle undergoing extensive morphological and structural transformation during sperm development. The mechanism underlying the extensive acrosome morphogenesis and biogenesis remains incompletely understood. Xu et al in their manuscript entitled "The Slingshot phosphatase 2 is required for acrosome biogenesis during spermatogenesis in mice" reported that the Slingshot Phosphatase 2 is essential for acrosome biogenesis and male fertility through their characterization of spermatogenic and acrosomal defects in Ssh2 knockout mice they generated. Specifically, the authors provided molecular, genetic, and subcellular evidence supporting that Ssh2 mutation impaired the phosphorylation of an acting-binding protein, COFILIN during spermiogenesis and accordingly actin cytoskeleton remodeling, crucial for proacrosomal vesicle trafficking and acrosome biogenesis.
Strengths:<br /> Nicely written manuscript, addresses an important mechanistic question of the roles of cytoskeleton remodeling in acrosome biogenesis and provided genetic, subcellular, and molecular evidence to build up their support for their hypothesis that Ssh2 regulates actin cytoskeleton remodeling, a process essential for proacrosomal vesicle trafficking and acrosome biogenesis, through dephosphorylation actin-binding protein during spermiogenesis.
Weaknesses:<br /> For body weight, and testis weight of the mutants, the authors concluded that there is no significant difference between the mutant and wildtype (Fig 1E -1G), but they appear to use mice between 6-8 wk old, both the testis and body weight of males at 6-8 wks is still growing, with the number of mice analyzed being six, you could easily miss the significant difference of the testis size and or body weight with such a varied age and a small sample size.
Could the uniform cytoplasmic distribution of diminutive actin filaments in the wild type and disrupted actin filament remodeling be examined at the EM level on the round spermatids?
Any other defects are seen besides acrosome in the mutant testis given the important roles of actin cytoskeleton network and high expression of Ssh2 in spermatocytes, were chromatoid bodies or mitochondria affected in any way? Any other defects in the mice overall including female fertility and other organs, given the previously reported roles in the nervous system. It could be helpful information for others interested in Ssh 2 protein and actin cytoskeleton's roles in general.
Providing detailed information on the number of animals used and cells analyzed in the legend is nice, but it might be even better for the readers to include sample size and the number of cells examined in the figure/graph if possible.
Nice discussion and comparison with GOPC and GM130, how about comparison and discussion with other acrosome defective mutants like PICK1, and ATG to provide some insights into acrosome biogenesis and proacrosomal vesicle trafficking?<br /> Given the literature on Cofilin's requirement for male fertility and the increased p-Cofilin in Ssh2 mutant testis by Western and IF, the authors have a strong case for their hypothesis. But given the general role of phosphatase, it might be prudent to discuss alternative possibilities.
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Reviewer #2 (Public Review):
This is a well-written manuscript in which the authors' conclusions are supported by well-established mouse genetic conditional approaches and phenotypic analyses.
Strengths:<br /> 1. The authors utilized well-established genetic tools, Adipoq-Cre to target MALPs and Prx1-Cre to globally target limb skeletal cells, and combined these drivers with Csf1 floxed alleles. This double-angled approach helps the authors determine the importance of Csf1 secreted by different skeletal cell populations in regulating bone mass.<br /> 2. The scRNA-seq analysis and the in vivo phenotypic analyses (3DmicroCT, histology, dynamic histomorphometry, serum bone resorption and formation markers) of the Csf1 CKO models are well-conducted. The authors convincingly show that cortical bone parameters are unaffected in MALP-specific Csf1 CKO mice, while serum CTX-1 is reduced in these mice. The confidence for the reported phenotypes is high.<br /> 3. The data presented in this manuscript are of very high quality. Particularly, the authors detected no changes in osteoclasts at the chondral-osseous junction and the endosteal surface, emphasizing the uniqueness of the CKO model.
Weaknesses:<br /> 1. The relevance of the LPS-induced calvarial osteolysis model is not clear. Calvaria is mostly composed of cortical bone-like structures lacking marrow space, though small marrow space exists near the suture. Osteolysis appears to occur in areas apart from where marrow is located. The authors did not show in the manuscript which cells Adipoq-Cre marks in the calvaria.<br /> 2. Although the contrast between the two Csf1 conditional deletion models (Adipoq-Cre and Prx1-Cre) is very interesting, the relationship between these two cell populations are not well described. The authors did not clarify if MALPs are also targeted by Prx1-Cre, or these two cell types are from different cell lineages. "Other mesenchymal lineage cells" in the subtitle is not extremely helpful to place this finding in context.<br /> 3. The data supporting defective bone marrow hematopoiesis in Csf1 CKO mice are not particularly strong. They observed a reduction in bone marrow cellularity, but this was only associated with an expected reduction in macrophages and a mild reduction in overall HSPC populations. More in-depth analyses might be required to define mechanisms underlying reduced bone marrow cellularity in CKO mice.<br /> 4. Some of the phenotypic analyses are still incomplete. The authors did not report whether CHet (Adipoq-Cre Csf1(flox/+)) showed any bone phenotype. Further, the authors did not report whether Csf1 mRNA or M-Csf protein is indeed expressed by MALPs, with current evidence solely reliant on scRNAseq and qPCR data of bulk-isolated cells. More specific histological methods will be helpful to support the premise of the study.
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Reviewer #2 (Public Review):
The authors aim to test the hypothesis that dopamine mediates the evaluation of temporal costs in intertemporal choice in humans, with a specific goal of synthesizing the competing accounts and previous results regarding whether dopamine increases or decreases evaluation of delays in comparing differently delayed future rewards. To do this, they computationally dissect the impact of the drug amisulpride, a D2R antagonist, using a variant of a sequential sampling model, the drift-diffusion model (DDM), that is well established in decision-making literature as a cognitive process model of choice. This model allows the dissociation of starting bias from the rate at which decision evidence is integrated ('drift'), which the authors map to different accounts of the role of dopamine: the temporal proximity of an outcome is proposed to impact bias, while the cost of a delay to impact the drift rate of evidence evaluation/accumulation. Consistent with previous results, and perhaps integrating conflicting findings, the authors find that d2R blockade impacts both bias and drift rate in a cohort of 50 participants, demonstrating dopaminergic action at this receptor is implicated in dissociable components of intertemporal choice, with D2R block reducing the bias towards sooner, more temporally proximate rewards as well as enhancing the contrast between reward magnitudes irrespective of delay, effectively diminishing the effect of delay in the drug condition. These effects are consistent across a small subset of alternative models, confirming the multiple cognitive mechanisms through which D2R block impacts intertemporal choice is a robust feature of decisions on this task.
Overall, this study is a detailed dissection of the specific effects of amisulpride on a type of future-oriented, hypothetical intertemporal choice, and provides consistent evidence integrating conflicting accounts that implicate dopaminergic signaling on evaluation of the cognitive costs, such as a delay, on choice. However the specificity of the empirical intervention and the task design limits the interpretation of the broader dopaminergic mechanisms at play in intertemporal choice, especially given the complexity of receptor specificity of this drug, dopamine precursor availability and individual differences and the specifics of the intertemporal choice in this task. As it stands, the results contribute an interesting, synthesized account of how D2R manipulation can impact evaluation of delays in multiple ways, that will likely be useful for motivating future studies and more detailed computational assessments of the cognitive process-level components of intertemporal choice more generally.
The focus of this study is important, and delineating the role of DA in intertemporal choice is of high relevance given DA disfunction is prevalent in many psychiatric disorders and a key target of pharmacological treatment. While the hypotheses of the current study are framed with respect to "costs", the task used by the authors reduces these to evaluation of a hypothetical delay, one which the participants do not necessarily experience in the context of the task. In some respects this is reasonable, given the prevalence of this task paradigm in testing temporal aspects of choice in humans in an economic sense. However, humans are also notoriously subject to framing effects and the impact of instructions in cognitive tasks like these, which can limit the generality of the conclusions, and in particular the specific ways in which a delay can be interpreted as costly (for eg cost as loss of potential earnings, cost as effortful waiting, cost as computational/simulation cost in future evaluation). Given the hypothesis recruits the idea of cost in assessing the role of dopamine, testing for generality in the effects of amisulpride in related but differently framed tasks seems critical for making this link in a general sense, and in connecting it to the previous studies in the literature the authors point to as demonstrating conflicting effects.
Further, while the study aims to test the actions of dopamine broadly, the empirical manipulation is limited to the action of amisulpride, a D2R anatgonist. There is little to no discussion of, or control for, the relationship between dopaminergic action at D2 receptors (the site of amisulpride effects) and wider mechanisms of dopaminergic action at other sites eg D1-like receptors, and the interplay between activation at these two receptor types alongside baseline levels of dopamine concentration. This is necessary for a comprehensive account of dopamine effects on intertemporal choice as the authors aim to test, as opposed to a specific test of the role of the D2 receptor, which is what the study achieves. On a related note, in some preparations at least, amisulpride also acts at some of the 5-HT receptors, raising the possibility of a non-dopaminergic mechanism by which this drug might impact intertemporal decisions. This possibility, while it would not be expected to act without dopaminergic effects as well, is consistent with established effects of serotonin on waiting behaviors and patience. Granted, the limits of pharmacology in humans does not necessarily mean this can be controlled for, it should be kept in mind with a systemic manipulation such as this.
Overall the modeling methods are robust and appropriate for the specific test of decision impacts of D2R blockade, and include several prima facie variable alternative models for comparison. Some caution is warranted, since there are not many trials per subject, and some trials are discarded as well as outliers, which raises the question of power. Given the models are fit hierarchically, which gives both group-level and individual-level parameter estimates, the elements are there to probe more deeply into individual differences, and to test how reliably this approach can dissociate the dual effects of bias and drift rate at the individual level, and perhaps correlate it with other informative subject measures of either dopamine activity/capacity or other dopamine-dependent behaviors. Alternative DDMs might also capture some of this individual variation, with meaningful differences potentially in model comparison at the individual level. It should be noted that the scope of these models do not exhaust the ways in which proximity (here, temporal) of rewards and contrast between choice options might be incorporated into a cognitive process model account of choice; all alternatives here rest on the same implicit 2-alternative forced choice assumption of the DDM, and the assumptions of this model are not here tested against other accounts of choice, for example the linear ballistic accumulator (LBA) and its derivatives. Further, the concept of proximity as a global feature of a trial (on average, how soon are these options overall?) is never tested on my read of the alternative models.
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Reviewer #2 (Public Review):
Richardson et al. characterize through immunophenotyping and high-throughput sequencing humanized mice versus human repertoires using many different immunological/immune repertoire metrics. They find that overall, the naïve Kymouse BCR repertoire is diverse and similar to human repertoires.
Strengths
Overall the study is carefully designed and of broad interest.<br /> - Detailed and established phenotypic and repertoire metrics are used to compare mice and human models.<br /> - Rigorous statistical analysis is mostly used to establish similarity.<br /> - Detailed description of the analyses performed.
Weaknesses
- Improvements could be made in the analyses (at times not far-reaching enough), figures (not self-explanatory enough), and text (too verbose).
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
This manuscript presents a rather technical modelling analysis of the impact of local lockdowns on Covid-19 hospitalisations in the Netherlands. The major strength of the study is that the authors attempt to calibrate their model to a novel data source, a commercial database of mobility patterns between municipalities. The major weakness is that the model seems overly complicated, many parameters seem to have been 'guessed' without a formal uncertainty analysis, e.g. within a Bayesian framework, so that it is impossible to judge how robust the results and therefore the conclusions are.
Major points:
1) In some aspects the structure of the model presented seems overly complicated: It is not clear why the authors chose the 1:100 population scale and why they didn't go directly for modelling the full population. Artificially reducing the population size has important stochastic effects at the early phase of the epidemic. Also it is not clear what it means when 1:100 of one municipality mixes with 1:100 of another municipality? The authors should at least attempt to see what impact this has on output, i.e. conduct a sensitivity analysis.
2) On the other hand the model goes into (too) much detail regarding mixing behaviour and attempts to model processes during each hour of the day. This does not seem to be informed by actual data, but the data seems to be made up e.g. as in A.6. As an ex-student and a father of a teenager I can tell you that the susceptibility profile guessed in Table 3 does not seem to be very realistic. As it is stated in the appendix, the Mezuro data set only provides daily averages of travelling between communitities, so it is not clear why the hourly resolution is actually needed in the model.
3) It is not clear why the authors rely on only one short period of the Mezuro data set in March 2019 and not investigate the same data source during the actual lockdown in 2020, or even for the full year, as travelling is likely to be very season dependent. This would provide much better estimates of the effects of lockdown on travel patterns. The analysis presented and categorisation into frequent, regular and incidental also need further explanation. It is not clear how international travel is accounted for in the mobility data.
4) Beyond the technical points on the modelling, the main hypothesis of whether local lockdowns may work has also not been sufficiently discussed outside of the Dutch context. The authors fail to mention that this was the approach chosen in Northern Italy at the start of the epidemic (https://en.wikipedia.org/wiki/COVID-19_lockdowns_in_Italy) where it didn't work, as we all know. On the other hand, more recent local lockdowns in China appeared to be successful, albeit at a great societal cost in terms of restrictions to freedom (https://en.wikipedia.org/wiki/COVID-19_lockdown_in_China).
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The manuscript entitled "IL-4 and helminth infection downregulate Mincle-dependent macrophage response to mycobacteria and Th17 adjuvanticity" by Schick et al. demonstrate the inhibitory activity of IL-4 and helminth infection on mycobacteria-mediated Th17 immunity. Overall, the authors reported interesting findings with solid data that advance our understanding of CLR function in fungal-bacterial co-infection.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Previous research using GWAS and population genetics approach identified a genetic haplotype on chromosome 3 derived from Neanderthals as the major risk factor for severe COVID-19. However, the specific variants that are causative of the severe COVID-19 phenotype remain unknown. Here, Jagoda et al. aim to identify the causative variants for the severe COVID-19 by leveraging eQTL analysis followed by Massively parallel reporter assays (MPRA). Their datasets and results are unique and novel. Their research is well designed, and will serve as a model strategy for future studies of functional annotation of disease-associated variants. However, there are following critical weaknesses in this manuscript that reduce the impact of this work; (1) The quantitativity of the MPRA output is questionable because of their incomplete definition of MPRA activity, which is based on absolute barcode counts without comparing negative controls. (2) Molecular mechanisms (binding transcription factors, etc.) of causative variants that underly the regulation of CCR1/5 expression and COVID19 severity are not analyzed and validated.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The tongue muscles play a major role in many important behaviors including suckling, swallowing, and ensuring that the upper airway remains open during breathing. Hypoglossal motoneurons innervate tongue muscles and as such play a key role in homeostasis. Previous work has shown that heme-oxygenase-2 (HO-2) null mice have severe airway obstruction. HO-2 forms carbon monoxide, suggesting that CO contributes to hypoglossal motoneuron excitability. In addition to HO-2, the present study also shows that hypoglossal motoneurons express cystathionine ϒ-lyase (CSE), which produces H2S and is regulated by CO. Interestingly, the authors show that H2S reduced transmission of the breathing-related drive to hypoglossal motoneurons. Together these observations suggest that CO and H2S interact to maintain the excitability of hypoglossal motoneurons. An imbalance of these competing influences may underlie tongue muscle dysfunction in conditions such as obstructive sleep apnea and dysphagia. Thus, the novel observations reported here open new avenues that will lead to a better understanding of the highly complex tongue muscle motor system.
The team used brain stem slices containing hypoglossal motoneurons that were receiving rhythmic, breathing-related depolarizing drive from the pre-Botzinger complex, the putative respiratory central pattern generator. Extracellular population activity was recorded from the pre-Botzinger complex and the ipsilateral hypoglossal motor nucleus-and in some experiments-the hypoglossal premotor population located in the ipsilateral reticular formation. In these rhythmic slices, the fidelity between hypoglossal and pre-Botzinger bursts approached 100% and blocking HO-2 with drugs reduced fidelity by about 25%. In addition, HO-2 null mice showed an even larger reduction in pre-Botzinger-hypoglossal bursting fidelity of 40-45%. Since these interventions did not significantly impact the pre-Botzinger population activity, the data show convincingly that CO contributes to hypoglossal motoneuron excitability. While whole cell intracellular recordings of hypoglossal motoneurons showed that blocking HO-2 reduced the magnitude of inspiratory drive currents and the number of action potentials generated in response to the depolarizing drive, these effects were relatively modest, suggesting that the mechanisms that underlie these important observations are unsettled.
The other key part of these experiments was demonstrating that the H2S forming enzyme CSE is expressed in the hypoglossal nucleus, and that exogenous application of NaHS, an H2S donor, reduces the fidelity of pre-Botzinger-hypoglossal coupling. Interestingly, H2S activity was lower in HO-2 null mice, and HO-2-dependent uncoupling could be rescued by bath application of the CO donor CORM-3. Moreover, failed transmission between pre-Botzinger and hypoglossal population bursts was not observed in preparations from mice null for both HO-2 and CSE. These data support excitatory-inhibitory interactions that are triggered by the gases CO and H2S.
Mechanistic experiments showed that blockade of CSE with L552 propargylglycine could restore transmission fidelity, and this was accompanied by a substantial increase in the magnitude of inspiratory-related drive currents in hypoglossal motoneurons. The team also showed that blocking small-conductance potassium channels with apamin in slices where HO-2 was first blocked pharmacologically enhanced inspiratory drive currents, though this observation needs re-examination given that the effect was large in two neurons, but very small in the remaining four (Fig. 8 A3). Finally, similar experiments focused on the ATP-sensitive potassium channel (KATP), which was previously shown to be enhanced by H2S. Blockade of KATP with tolbutamide had no impact on hypoglossal motoneuron output. In conclusion, the experiments reveal a very important contribution of gas-mediated transmitters in setting the balance of excitation and inhibition of hypoglossal motoneuron excitability. More work will be needed to unravel the mechanisms behind these exciting observations.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors performed preclinical studies to investigate the underlying mechanism of how the combination of pyrotinib, letrozole and dalpiciclib achieved satisfactory clinical outcomes in the MUKDEN 01 clinical trial (NCT04486911). Mechanistically, using anti-HER2 drugs such as pyrotinib and trastuzumab could degrade HER2 and facilitate the nuclear transportation of ER in HER2+HR+ breast cancer, which enhanced the function of ER signaling pathway. The introduction of dalpiciclib partially abrogated the nuclear transportation of ER and exerted its canonical function as cell cycle blockers, which led to the optimal cytotoxicity effect in treating HER2+HR+ breast cancer. Furthermore, using mRNA-seq analysis and in vivo drug susceptibility test, the authors succeeded in identifying CALML5 as a novel risk factor in the treatment of HER2+HR+ breast cancer.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
The purpose of this paper is to consider the utility of the long non-coding RNA PCA3, along with the gene PCA3 in the diagnosis of human prostate cancer. The study extends earlier findings by this group that the PRUNE2 gene product may function as a prostate tumor suppressor. The study employed two separate patient cohorts: one of 107 patients from the University of New Mexico Comprehensive Cancer Center, with organ-confined prostate cancer at their original diagnosis, and one of 497 patients with organ-confined prostate cancer from The Cancer Genome Atlas (TCGA). The authors report an overall increase in PCA levels along with a general decrease in PRUNE2 gene expression. The authors conclude that PRUNE2 functions as a prostate tumor suppressor whose levels negatively correlate with PCA3 levels. They further surmise that PCA3 in turn functions as a dominant-negative oncogene. Consequently, they expect that loss of increased PCA3 levels can lead to loss of PRUNE2 and increased prostate cancer tumor formation.
One interesting observation, consistent with earlier studies, is that PCA3 levels are highest in low-grade tumors, and then decrease as the tumors progress to a higher stage and grade. This suggests that increased PCA3 may be important for early tumor formation while possibly impeding tumor progression. The decreased PCA3 levels seen in later prostate cancer may, the authors hypothesize, be related to alterations in androgen receptor (AR) function in these higher-grade cancers. Thus, while the presence of PCA3 may be an early marker of prostate cancer formation, the results indicate that its presence in early cancers is not, by itself, predictive of future patient outcomes, as tumor progression may actually depend on the later decrease in PCA3 levels.
A strength of this study is the use of two non-redundant patient cohorts to thoroughly analyze the consequence of alterations in PRUNE2 and PCA3 by directly analyzing analyte levels in human tissue samples. The study provides important data supporting the occurrence of a loss of PRUNE2 and gain of PCA3 in organ-confined prostate cancer. The principal takeaway from this report is to highlight the role of the PRUNE2/PCA3 axis in early prostate cancer and to encourage the use of PCA3 antagonists in the prevention and treatment of early prostate cancer. It is unlikely that examination of tissue samples for alterations in PRUNE2 or PCA3 levels will be useful in prostate cancer diagnosis or prognosis as the data do not suggest that these changes in early cancers are predictive of future outcomes. It may be, however, that longitudinal analysis of PCA3 levels in patient plasma or circulating tumor cells could be a useful adjunct to follow the course of tumor progression.
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- Dec 2022
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Dipeptide repeat (DPR) proteins produced from both sense GGGGCC (poly-GA, poly-GP and poly-GR) and antisense CCCCGG (poly-PR, poly-PG, poly-PA) repeat RNAs are found C9ORF72-linked ALS/FTD and contribute to neurodegeneration. The translation of the repeat RNA can initiate without the AUG start codon, a process known as repeat associated non-AUG (RAN) translation. In this manuscript, the authors used luciferase reporter construct to show that the translation of PR and PG from the CCCCGG repeats initiated from in-frame AUG in the C9 sequences before the repeats. After mutating candidate AUG codons, the translation can initiate from other AUG, so there is redundancy. But if mutating all the in-frame AUG codons, the luciferase was dramatically reduced, supporting the translation initiated at the AUG start codon. The translation initiation factor eIF2D has been shown to be important for CUG start codon-dependent poly-GA translation from GGGGCC repeats. Here it is shown that eIF2D is not required for poly-PG and poly-PR translation from CCCCGG repeats using both reporter and patient iPS-neurons. The data using luciferase reporter to study antisense repeat translation is solid, the translation initiates from AUG start codon as there are AUG in frame with PG and PR in the constructs containing the antisense sequences.
On the other hand, as the reporter construct includes the sequences containing the AUG codon, it is not surprising that AUG was used. This is canonical translation. Additionally, the AUG-initiated translation of antisense repeats has been reported previously. Therefore, the novelty is limited. How the antisense DPRs are translated endogenously, AUG-canonical translation or RAN translation, depends on whether the AUG is included in the antisense RNA in patients and where the transcription of the antisense starts, upstream or downstream of the AUG start codons. However, this is not considered in the manuscript.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Convergence of cellular/molecular phenotypes across seemingly different types and subtypes of neurodevelopmental disorder represent an exciting frontier to identify effective drug targets. In this study, authors compared early neurodevelopmental processes, namely neurite outgrowth and migration, between a form of autism caused by copy number variation mutation in 16p11.2 (16pdel), which deletes 28 genes, to idopathic autism (I-ASD), in which genetic causes are unknown. All experiments involved neurospheres or neural precursor cells (NPCs) derived from human iPSCs. Three patients with I-ASD and their unaffected siblings as well as three patients with 16pdel were included in the study. Authors then go on to show perturbed migration and neurite length phenotypes shared between I-ASD and 16p11 NPCs. Interestingly they identified two subclasses of I-ASD patients, either with high or low levels of mTOR, and show that change in mTOR level in either direction result in similar migration and neurite extension phenotypes, either at baseline or induced by pro-migratory factors. The study design is particularly strong and communication of sample structure throughout the manuscript is commendable. This study effectively points to the potential of patient-derived in vitro models to uncover novel molecular drivers of disease. I only have a few comments below:
(1) I found that interpreting how differential EF sensitivity is connected to the rest of the story difficult at times. First, it is unclear why these extracellular factors were picked. These are seemingly different in nature (a neuropeptide, a growth factor and a neuromodulator) targeting largely different pathways. This limits the interpretation of the ASD subtype-specific rescue results. One way of reframing that could help is that these are pro-migratory factors instead of EFs broadly defined that fail to promote migration in I-ASD lines due to a shared malfunctioning of the intracellular migration machinery or cell-cell interactions (possibly through tight junction signaling, Fig S2A). Yet, this doesn't explain the migration/neurite phenotypes in 16p11 lines where EF sensitivity is not altered, overall implying that divergent EF sensitivity independent of underlying mTOR state. What is the proposed model that connects all three findings (divergent EF sensitivity based on ASD subtypes, 2 mTOR classes, convergent cellular phenotypes)?
(2) A similar bidirectional migration phenotype has been described in hiSPC-derived human cortical interneurons generated from individuals with Timothy Syndrome (Birey et al 2022, Cell Stem Cell). Here, authors show that the intracellular calcium influx that is excessive in Timothy Syndrome or pharmacologically dampened in controls results in similar migration phenotypes. Authors can consider referring to this report in support of the idea that bimodal perturbations of cardinal signaling pathways can converge upon common cellular migration deficits.
(3) Given that authors have access to 8 I-ASD hiPSC lines, it'd very informative to assay the mTOR state (e.g. pS6 westerns) in NPCs derived from all 8 lines instead of the 3 presented, even without assessing any additional cellular phenotypes, which authors have shown to be robust and consistent. This can help the readers better get a sense of the proportion of high-mTOR vs low-mTOR classes in a larger cohort.
(4) Does the mTOR modulation rescue EF-specific responses to migration as well (Figure 7)?
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Reviewer #2 (Public Review):
The authors seek to determine how various species combine their effects on the growth of a species of interest when part of the same community.
To this end, the authors carry out an impressive experiment containing what I believe must be one of the largest pairwise + third-order co-culture experiments done to date, using a high-throughput co-culture system they had co-developed in previous work. The unprecedented nature of this data is a major strength of the paper. The authors also discover that species combine their effect through "dominance", i.e. the strongest effect masks the others. This is important as it calls into question the common assumption of additivity that is implicit in the choice of using Lotka-Volterra models.
A stronger claim (i.e. in the abstract) is that joint effect of multiple species on the growth of another can be derived from the effect of individual species. Unless I am misunderstanding something, this statement may have to be qualified a little, as the authors show that a model based on pairwise dominance (i.e. the strongest pairwise) does a somewhat better job (lower RMSD, though granted, not by much, 0.57 vs 0.63) than a model based on single species dominance. This is, the effect of the strongest pair predicts better the effect of a trio than the effect of the larger species.
This issue makes one wonder whether, had the authors included higher-order combinations of species (i.e. five-member consortia or higher), the strongest-effect trio would have predicted better than the strongest-effect pair, which in turn is better predictor than the strongest-effect species. This is important, as it would help one determine to what extent the strongest-effect model would work in more diverse communities, such as those one typically finds in nature. Indeed, the authors find that the predictive ability of the strongest effect species is much stronger for pairs than it is for trios (RMSD of 0.28 vs 0.63). Does the predictive ability of the single species model decline faster and faster as diversity grows beyond 4-member consortia?
While this may limit the scope of the paper somewhat, it does not subtract from its overall impressiveness. This is a very strong paper that combines state of the art methodology, of a kind that will change the field, with an important question and an intriguing finding that will surely motivate further work. Therefore, it will be of wide interest and appeal to the broad audience of microbial ecologists, and it is an important and compelling step forward in the field.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
I am not a specialist in cryo-EM, so cannot comment on the technicalities of the structure reconstruction or methods used. I thus focus on the conclusions and observations that the authors provide in the manuscript and their relevance to functional photosynthesis.
The authors attempt to resolve the structure of PSII from Dunaliella and noticed that three types of PSII could be identified: two conformational states, and a stacked configuration. There is no doubt that these structures add to our current knowledge of PSII and that they exist in abundance upon solubilisation of the sample. My main issue however is the relevance to in vivo conditions, and the efforts to exclude the possibility that pigment loss and conformational states and stacking are a reflection of ex-vivo manipulations.
I see a number of questions pertaining to this work. Starting from the two conformations of PSII, compact and stretched, the authors say that both are highly active based on oxygen measurements at a saturating light intensity. In the meantime, they report large variations in the chl content and positions of the chlorophyll molecules in these structures (also compared to other known PSIIs). This gives the impression that one can lose two chlorophylls, and freely modify the distance between others without losing efficiency, certainly a risky conclusion. Are the samples highly active also in light-limiting conditions? It is thought that even tiny movements and alterations in chl-chl distances alter their coupling and spectral properties, how come the variations in this report are so huge? In other words, the assay tests the charge separation activity of the PSII RC in the preps, but not the light-harvesting efficiency.
How does one ascertain that the lost chlorophyll molecules in CP29 are not a preparation error? Does slightly increasing the detergent concentration impact the proportion of stretched:compact forms?<br /> On a similar note, how do the authors exclude that a certain interaction with this type of grid impacts the distribution of these complexes? Is it identical to a biologically separate preparation of algae? In case of discoveries of this type, it is of high importance to exclude as many possibilities of non-native conditions or influences on the structure.
I would further like to encourage the authors to elaborate on the CP29 phosphorylation. What is the proportion of PSIIcomp that are phosphorylated? I assume it is not 100%, as in this case, the authors would propose that this is the effect that modulates between compact and stretched architectures.
In line 290, the authors highlight the structural heterogeneity within the two groups' PSII conformations. I would like to see how does the distribution look like for all the structures together: are the two (stretched and compact) specifically forming two heterogenous distributions? Or is it possible that the distribution between the two is quasi-continuous? In other words, if the structures are not perfectly defined, how do the authors decide that two- and not more or less subtypes exist?
Considering the stacked PSII, I also have a few concerns. Contrary to previous studies the authors do not assign a functional role to the stacking beyond the structural aspect. This could be better backed by a discussion about the closest chlorophyll a molecules across the stacked PSII, which given the rather large distance shown in fig. 4L seems to be too large for any EET across the stromal gap.<br /> There is a report that suggests the presence of some density between the stacked PSII - could the authors comment on the differences between it and their work? Are the angles and positions conserved between these types of stacks? https://doi.org/10.1038/s41598-017-10700-8
Line 387, the authors state that due to the transient nature of the interactions across the stromal gap, the stacks could be "under-detected" in cryo-ET data. This statement is in my opinion misformulated. For once, the transient interaction argument would apply the same (if not more due to changing conditions induced by the purification process) to the single particle analysis performed in this paper. Second, tomographic volumes detect hundreds of PSII in a suspended state. Any transient interaction that adds up to 25% of particle population in a steady state cell should be clearly visible, while the in situ data suggests not more than random cross-stromal-gap orientations. Of course, this can be a specificity of Chlamydomonas or a particular growth condition. The statement used by the authors could be indeed converted into: the PSII stacks are *over-detected in vitro*, and it is certainly a simpler explanation for their presence. It is also important to mention that PSII stacking alone is not the only reason for grana architecture - stacking with the antenna of larger complexes, absent in the authors' preparation could also contribute to grana maintenance; and auxiliary proteins such as CURT help with this issue as well. Here a recent demonstration of the importance of minor antenna should probably be also cited: https://doi.org/10.1101/2021.12.31.474624
Taking these last thoughts, I would like to finish by mentioning one more thing - almost philosophical. The authors are certainly at the forefront of the booming cryoEM revolution in biology which is profoundly changing the way we understand the living. There is absolutely zero doubt that this powerful technique is of the highest interest. But a growing number of structures of photosynthetic complexes remain puzzling, in particular with regard to their abundance in vivo (such as the PSII stacks) and functional relevance. How do we ascertain that these interactions are not due to in vitro preparation (isolation from cells, solubilisation)? Which ways can we use to try to exclude this (simple) hypothesis? I suggest that at least a small extent of biological replicas - experiments performed on separate batches, in different technical conditions, with slightly altered solubilization conditions, and so on - could shed light on the nature of these structures and their occurrence in vivo. Technical reps of the freezing+analysis pipeline could also be tried to see the variability. This would strongly reinforce this manuscript and its conclusions, and while not completely unequivocal (the stacked PSII, for example, could form upon each purification), a quantification of the effects would be of high interest.
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Reviewer #2 (Public Review):
The central nucleus of the amygdala (CEA) has been the subject of numerous studies related to the processing of both aversive and pleasurable events; however, prior to this study a comprehensive understanding of the number of molecularly distinct neurons, their location in the CEA and their axonal projections have not been available. This paper provides a rich resource that fills this gap. The results will facilitate a more refined analysis of the roles of specific CEA neurons in mediating mouse behavior and physiology. A major strength of the paper is the application of their three-dimensional spatial profiling methodology of molecularly defined neurons to the CEA and then determining the axonal projections of those neurons to five of the most prominent target brain regions. The data are clearly presented and rigorously analyzed. The are no weaknesses in this valuable contribution.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Overall this is a very interesting and important paper that demonstrates a novel synthetic interaction between nucleoporin inhibition and oncogene-driven hyperproliferation. This work is especially significant because of the paucity of effective treatments for hepatocellular carcinoma (HCC). The authors' demonstration that the Nup inhibitor Selinexor decreases larval liver size in KRAS-overexpressing zebrafish but does not cause toxicity in wild-type animals lays the groundwork for exploiting this class of drugs in HCC treatment. This paper represents an elegant demonstration of the utility of zebrafish models in cancer studies. The relevance of this work to human cancer is supported by the authors' studies using TCGA data, wherein they demonstrate that decreased NUP expression is associated with increased survival in HCC.<br /> Other major strengths of the paper include beautiful pictures demonstrating that ahctf1+/- decreases the density and volume of nuclear pores in TO(kras) larvae and increases the rate of multipolar spindle formation, misaligned chromosomes, and anaphase bridges. The experiments are very well-controlled, including detailed analysis of the effects of ahctf1 heterozygosity and Selinexor on wild-type animals. The inclusion of distinct methods for disruption nucleoporins (ranbp2 heterozygosity and drug treatment) bolsters the authors' conclusion that this represents a viable drug target in HCC.
My major concerns are as follows:
1. The authors state that "the beneficial effect of ahctf1 heterozygosity to reduce tumour burden persists in the absence of functional Tp53, due to compensatory increases in the levels of tp63 and tp73". However, tp63 and tp73 appear similarly upregulated in ahctf1 heterozygotes regardless of tp53 status. The authors do not provide enough evidence that tp63 and tp73 are compensating for tp53 loss. An alternative possibility based on the data presented is that the effects of ahctf1+/- are independent of tp53 family members, and the effects on apoptosis go through a different pathway.
2. The authors state in multiple locations that nucleoporin inhibition decreases tumor burden. In my opinion, this is not strictly correct. The TO(kras) model clearly results in HCC in adults, but it's a little unclear whether the larval liver overgrowth is truly HCC or not based on the original paper by Nguyen et al. (2012 Dis Model Mech).
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Reviewer #2 (Public Review):
The goal of this study was to understand population bottlenecks during colonization in the context of different microbial communities. Capsular polysaccharide mutants, diet, and enteric infection were also used paired to short-term monitoring of overall colonization and the levels of specific strains. The major strength of this study is the innovative approach and the significance of the overall research area.
The first major limitation is the lack of clear and novel insight into the biology of B. theta or other gut bacterial species. The title is provocative, but the experiments as is do not definitively show that the microbiota controls the relative fitness of acapsular and wild-type strains or provide any mechanistic insights into why that would be the case. The data on diet and infection seem preliminary. Furthermore, many of the experiments conflict with prior literature (i.e. lack of fitness difference between acapsular and wild-type strain and lack of impact of diet) but satisfying explanations are not provided for the lack of reproducibility.
Another major limitation is the lack of data on the various background gut microbiotas used. As such, describing what microbes are in LCM, OligoMM, or SPF groups is important. The authors seem to assume that the gut microbiota will reflect prior studies without measuring it themselves. I also did not follow the logic of concluding that any differences between SPF and the two other groups are due to microbial diversity, which is presumably just one of many differences. For example, the authors acknowledge that host immunity may be distinct. It is essential to profile the gut microbiota by 16S rRNA amplicon sequencing in all these experiments and to design experiments that more explicitly test the diversity hypotheses vs. alternatives like differences in the membership of each community or other host phenotypes.
Given the prior work on the importance of capsule for phage, I was surprised that no efforts are taken to monitor phage levels in these experiments. Could B. theta phage be present in SPF mice, explaining the results? Alternatively, is the mucus layer distinct? Both could be readily monitored using established molecular/imaging methods.
The conclusion that the acapsular strain loses out due to a difference of lag phase seems highly speculative. More work would be needed to ensure that there is no difference in the initial bottleneck; for example, by monitoring the level of this strain in the proximal gut immediately after oral gavage.
Another major limitation of this paper is the reliance on short timepoints (2-3 days post colonization). Data for B. theta levels over 2 weeks or longer is essential to put these values in context. For example, I was surprised that B. theta could invade the gut microbiota of SPF mice at all and wonder if the early time points reflect transient colonization.
Finally, the number of mice/group is very low, especially given the novelty of these types of studies and uncertainty about reproducibility. Key experiments should be replicated at least once, ideally with more than n=3/group.
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www.medrxiv.org www.medrxiv.org
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Reviewer #2 (Public Review):
In this study, the authors have successfully utilized and compared various supervised machine-learning techniques to identify the risk for the development of diabetic kidney disease. The study was further able to identify some potential novel risk factors for the development of diabetic kidney disease.
The heterogenous population and the identification of novel risk factors for diabetic kidney disease are some of the strengths of this study. Their definition of diabetic kidney disease, however, relies only on the decline in eGFR and is lacking in details of any other major significant events that may have impacted the decline in kidney function during the follow-up time period.
Overall it is an interesting study that advances the field of kidney disease, though its results need to be interpreted with caution due to significant limitations in the study design.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This study by De Virgilio and co-workers examines the role of SNF1, the AMPK ortholog in yeast, in regulating TORC1 activity and cell growth. The authors combine the use of an analog-sensitive allele of SNF1 and SILAC to characterize the yeast phospho-proteome under nutrient-complete and glucose-starved conditions. Using this approach, in addition to confirming previously identified targets of SNF1, many potential new substrates were identified. The authors follow up on two of these: PIB2, a known upstream regulator of TORC1 linked previously to glutamine signaling; and SCH9, an important downstream target that is directly phosphorylated by TORC1. The authors use a combination of mutagenesis and in vitro and in vivo assays to demonstrate that SNF1 is a bona fide kinase for PIB2 and SCH9 and that phosphorylation of these targets impacts TORC1 kinase activity. In general, the data are thorough and convincing, and these findings will be appreciated by the wide readership of this journal.
Specific points to consider:
1. Because PIB2 is a major focus of the manuscript, I was surprised that it was not discussed in the introduction. I think it would be appropriate to discuss prior evidence linking this protein to TORC1.
2. The authors introduce mutations into PIB2 at two sites determined to be phosphorylated by SNF1, at S268 and S309. Somewhat confusing results are obtained, in that the PIB2 null and phosphomimic mutants (S268E and S309E) confer a similar TORC1 phenotype, compared to the S268A S308A mutant. These results require further explanation than simply that "TORC1 inactivation defect in SNF1-compromised cells is due to a defect in PIB1 phosphorylation". This is particularly intriguing given that the opposite results are observed with the SCH9 mutants, where the null and alanine mutants confer a similar phenotype compared to the S to E mutants.
3. The authors conclude, based on the co-IP data in Figure 4H, that interactions between KOG1 and PIB2 are direct. However, it remains possible that interactions between these proteins are mediated by other components of TORC1 or within cells. This should be addressed.
4. The authors demonstrate convincingly that the PIB2 and SCH9 SNF1-specific phospho-site mutants have a detectable effect on TORC1, primarily by examining TORC1-dependent phosphorylation of SCH9. What is unclear is whether phosphorylation at these sites has a significant physiological impact on cells. It appears that the rapamycin hyper-sensitivity displayed in Figure 6E is the only data presented to address this question. It would be appropriate for the authors to comment further on the significance of SNF1-dependent phosphorylation of these two substrates.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
The authors describe observations of an innovative food caching behavior attributed to two species of flying squirrels and likened the behavior to architectural joints used by humans. The discovery of nuts stored in the crook of shrub branches, facilitated by indented rings seemingly carved by squirrels, possibly represents an interesting food handling innovation that may function to prevent spoilage in a damp tropical ecosystem.
I applaud the efforts to survey the area multiple times after the initial discovery, and the use of trail cameras to try capture evidence of animal associations. For what is in essence a natural history note, the authors did a great job of trying to gather a variety of supporting evidence. The videos capturing squirrels visiting and retrieving the cached nuts were compelling, and the shaking of the shrubs demonstrating the difficulty in dislodging the nuts helps build the case that the nuts are cached effectively.
The most glaring gap in the evidence is that there is no direct observation of the squirrels actually performing this nut carving behavior, only associating with the nuts after they have been cached. There must be more documentation provided to explicitly link the causality between squirrels and this caching innovation.
The second major weakness is more to do with writing style and could be addressed with significant revisions to phrasing and development of ideas. This is namely to do with the claim that this is somehow an evolved behavior, without providing evidence that 1) it is indeed the squirrels performing this behavior, 2) that is confers some kind of fitness benefit, and 3) hard evidence that this caching method does indeed prevent decomposition/germination in comparison to the more traditional caching methods of these species. Given the limited geographic range of the observations, I wonder how much of this is actually attributable to learning and/or innovation by these individuals. These ideas are not developed fully, and sometimes the writing wanders among learning and evolution without exploring the deep links among the two concepts.
Third, the connection to architecture is attention-grabbing, but I'd like to see this fleshed out a bit more with more text description (and a visual here would help immensely).
Ultimately this work stands to potentially contribute a fascinating piece of evidence into the growing literature on animal cognition, spatial awareness, caching behavior, innovation, and adaptation, but currently, the claims are unsupported by the evidence presented.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Fortier and Pritchard investigated the breadth and depth of trans-species polymorphism (TSP) within six primate classical (antigen-presenting) major histocompatibility complex (MHC) genes (three MHC class I and three MHC class II). The MHC is of wide interest because of its unique evolutionary patterns within the genomes of jawed vertebrates and for its extensive and consistent associations with disease phenotypes. The findings of the paper are:<br /> 1) Trans-species polymorphism (TSP) within major histocompatibility complex (MHC) genes, whereby some alleles are more similar between rather than within species, occurs between humans and non-human primates despite rapid allelic turnover.<br /> 2) Highly polymorphic/rapidly evolving sites are mostly involved in peptide binding.<br /> 3) The identified, rapidly-evolving sites are associated with disease.
However, because these general findings have been previously demonstrated to varying extents by numerous other studies, these are not the strength of this paper. The strength and importance of this paper are in its utilization of a large evolutionary range of species and genes and its methodological approach and the extent of analyses undertaken to characterize the depth and extent of the TSP among primates. The major contribution of this paper is showing that TSP in the MHC is widespread among diverse primate taxa, and, depending on the particular MHC gene, TSP can be detected between humans and non-human primates as distantly diverged from the human lineage as new world monkeys of the Americas, ~45 million years ago. The paper, overall, made good methodological choices to account for the fascinating but challenging nature of the MHC, which includes its extensive allelic polymorphism (much of which is only characterized for the peptide-binding domain, encoded by exons 2 and 3), the difficulty in assessing phylogenetic relationships (particularly due to recombination and/or interallelic gene conversion), and differentiating convergence from conservation. There is no single analysis that can perfectly account for all these factors. This paper used two methods to test for TSP, Bayesian evolutionary analysis and synonymous nucleotide distances (dS), each with their respective strengths and limitations articulated. TSP, to varying degrees, is supported by both analyses. The paper further identifies rapidly evolving positions within the MHC molecules (predominantly located in the MHC peptide-binding domain), quantitatively shows that they are more likely to be in proximity to the bound peptide within the peptide binding domain, and shows, via a literature review of HLA fine-mapping studies, that those positions are associated with both infectious and autoimmune disease.
The conclusions of the paper, therefore, are supported and appropriate with the most important caveats noted, but the paper would benefit from:<br /> 1) Addressing how copy number variation of MHC class I genes among primate species might have affected their analyses and results (only single representative genes of the class II MHC, which also exhibit copy number variation, were used for this study).<br /> 2) Considering the differences between class I and class II MHC roles in immune function and how those might relate to the observed patterns.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Guo et al. have investigated the consequences of a frameshift mutation in the rcsD gene in the Yersinia pseudotuberculosis progenitor that is conserved in modern Y. pestis strains. Interestingly, they identify a start codon with a ribosome binding site that enables production of an Hpt-domain protein from the C-terminus in Y. pestis. Targeted deletion of this Hpt-domain increased biofilm production in Y. pestis. They find that the ancestral RcsDpstb (full length) is a positive regulator of biofilm in Y. pestis while the Hpt-domain version (RcsDYP) represses biofilm in vitro. When fleas were infected with Y. pestis expressing the ancestral RcsDPSTB protein, there was no difference in bacterial survival or rate of proventricular blockage. This strain also killed mice the same rate (in a different Y. pestis strain background). However, replacing RcsDYP with RcsYPTB dramatically increases the frequency of pgm locus deletion (containing Hms ECM and yersiniabactin genes) during flea infection. The authors predict that this would reduce the invasiveness of the bacteria in mammals and/or flea blockage in subsequent flea-rodent-flea transmission cycles. They also measured global gene expression differences between RcsDPSTB compared to the wild-type strain. They argue that the frameshift of RcsD maintaining the Hpt-domain (RcsDYP) was needed to regulate biofilm while limiting loss of the pgm locus.
Loss of the pgm locus was not tested in the Y. pestis rcsD mutant strain (lacking the entire gene or just the C-terminal Hpt domain). Therefore, the claim that maintaining the Hpt-domain protein was important lacks convincing evidence. Additionally, it is possible that the population of rcsDpe::rcsDpstb after in vitro growth for 6 days would still be proficient at infecting and blocking fleas, even though many of the bacteria would have lost the pgm locus. Production of Hms polysaccharide by pgm+ could trans-complement those that are pgm-. The nature of the pgm locus loss is assumed to be due to recombination between IS elements. This is certainly the likeliest explanation but not the only one. The authors checked for pgm loss by phenotype (CR binding) and by two sets of primers, one targeting the hmsS gene and another set that is unspecified. Loss of the entire pgm (especially yersiniabactin genes) should be clarified.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
In general, the authors do a thorough exploration of Drosophila larval crawling, specifically looking at where within the crawl cycle changes in speed are manifest. They find a strong correlation between changes in speed and with contraction of transverse muscles. The authors then characterize a neuron (A31c) known to be activated during the time in the crawl cycle where speed is altered. Unlike many neurons that have a wave of activity across the segments of the body during crawling, these neurons are active synchronously in the segments along the anterior-posterior axis. Also, the A31c neurons have synaptic output onto pre-motor neurons (A26f) whose output ultimately controls transverse muscles.
Experimentally, the authors use all the tools at hand to make a compelling case for their conclusions. They look at crawling in freely crawling animals. Although the data on muscle length is obtained in restrained or semi-dissected animals, it is convincing. It would be more convincing if done in intact freely moving animals, but that is a technical reach. To look at neuron morphology they use immunofluorescence and connectomic data in an effective manner. They are able to manipulate the activity of their neurons of interest in order to show that they have control over transverse muscle length and crawling speed.
Finally, the authors claim that the neurons they examine are sufficient and required to alter crawling speed. They appear to be sufficient to alter transverse muscle length and crawling speed, but the data do not support the requirement for these neurons for these processes. One way to show this would be to inhibit or ablate the neurons and find that the larvae were unable to alter the speed.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
One of the greatest challenges to the containment of the SARS-CoV-2 pandemic is the generalist nature of this virus and its ability to infect across non-human animal species, and successfully cycle within non-human species. It is, therefore, critical to understand the potential for transmission and evolution of the virus in non-human animal species and draw generalizations from both to help predict the occurrence of new viral variants and their associated risk for secondary spillover events back into human populations. This manuscript describes cross-species transmission between humans and non-human hosts, as well as non-human host-specific SNVs that have arisen presumably due to continued successful transmission cycles in non-human species. Using publicly available SARS-CoV-2 genomic sequences from four animal host species and humans, the study revealed that the highest number of animal-to-human transmission events have occurred between farmed mink populations and humans and that white-tailed deer have the highest number of single nucleotide variants specific to a non-human species from those included in the study. The authors are careful to point out the limitations of the dataset, as there are still too few publicly available SARS-CoV-2 whole genome sequences for non-human animal taxa, making non-human species inclusion impossible in some cases and creating unbalanced datasets that reflect sequencing and sampling effort. The authors could have offered a greater justification of statistical methods employed given this hurdle, both in terms of quantitative mitigation steps or qualitative justification of the methods used, but their methods provide a pipeline for addressing cross-species transmission and the emergence of non-human species-specific SNVs as scientists work to accumulate more genomic sequences from animal taxa. Their results are also largely congruent with another recently published manuscript using SARS-CoV-2 genomic data from the same source and aimed at understanding human-to-animal transmission solely. In addition to the two main goals, cross-species transmission, and species-specific SNVs, the authors have offered an evaluation and discussion of several species-specific SNVs that will aid the scientific community in the future in drawing connections between viral evolution, host biology, and epidemiological patterns related to SARS-CoV-2 across species.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
This work provides a method for extracting morphological features of cells and their neighborhoods from EM volumes in a self-supervised manner. The authors generate these MorphoFeatures using a set of neural networks, and show the usefulness of the features for cell type classification, symmetric partner identification, and the automated clustering of cells into morphologically similar groups, tissues and organs.
The main innovation of this method compared to similar studies is the separation of the input into shape, coarse, and fine texture. A combination of an auto-encoder (for texture features) and a contrastive loss (for all features) is used to obtain features without task-specific bias. The learned features are consistent with cell type when compared to manual annotations, and genetic markers. The distinction between shape, coarse, and fine features is not used beyond the development of the method.
The authors later include a descriptor of the cell's neighborhood, with the goal of automatically discovering tissues and organs. Clustering in this MorphoContextFeature space successfully delineates the different parts of the *P. dumerilii* ganglia, and shows some advantages over both manual segmentation and clustering in gene expression space. A detailed analysis of the method on finding tissues in the *P. dumerilii* foregut is given as an additional example.
Strengths
The use of an unsupervised method means that this method can be applied on data where no cell types are known a priori, and the authors have made clear that a cell type classification can be obtained from MorphoFeatures with minimal annotation. Used as a first exploratory pass, this method can help quickly guide and narrow the scope of further analysis.
By separately obtaining features at three levels of resolution, the method has the potential to pinpoint the structural features most predictive of a cell type more precisely than a single-resolution method. Most interestingly, Figure 3 indicates that the learned features are visually meaningful: this would greatly increase the impact of such a method, as it would lead to testable hypotheses.
The training method that the authors suggest for the neural network is sound, and successfully avoids the potential pitfalls of using augmentation with a contrastive loss in a situation where shape is an important signal. Similarly, the authors appropriately choose clustering methods that can discover clusters of varying sizes.
The authors make good use of prior knowledge to confirm the hypotheses generated by clustering cells in MorphoFeature space. They include specific genetic explanations for both expected and unexpected clusters found (figures 5 and 6), and provide clear indication where the gene expression atlas does not give an explanation for a MorphoFeature cluster (Figure 6D). The examples given for clustering in the MorphoContextFeature space are similarly clear and well supported by additional data (figures 8 and 9).
Weaknesses
1. In the section on "visually interpretable" features, I would have liked a more quantitative idea of how many features the authors considered meaningful, and how those can be found. For example, are the six features shown in Figure 3 particularly meaningful, or were they chosen among many? A discussion of the feature selection protocol would be useful for replicating the method on new data. Furthermore, a supplementary figure with some of the features which are not meaningful would give the reader a better idea of the range of interpretability to expect.
2. The section on MorphoContextFeatures is missing a comparison with the MorphoFeatures. This made it unclear to me whether adding the neighborhood information is necessary for the discovery of tissues and organs. This could be remedied with a supplementary figure showing the same analysis as in figures 7 and 8 on the MorphoFeatures without the additional neighborhood information. Alternatively, since the MorphoFeatures are a subset of the MorphoContextFeatures, the authors could run a post-hoc analysis of whether the MorphoFeatures or the neighborhood features best explain the inter-class variance.
3. Finally, some extra guidance is needed to replicate this work on new data. In particular the following points could use more discussion:
3.1. How to choose the size of the MorphoFeatures vector - did the authors attempt a number other than 80 and if so, what was affected by this choice?
3.2. The protocol for when and how to define sub-clusters - were the chosen thresholds based on prior knowledge such as known tissues/organs? What do the authors suggest if this kind of information is missing?
3.3. How to link the obtained clusters back to specific, potentially meaningful, MorphoFeatures. For example, does the distinctive shape of the enteric neurons in cluster 8.3 of figure 5 correspond to an extreme of the cytoplasm shape feature described in figure 3 (lower left)?
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
Lee, Chen, Kaku, Zhuo et. al. demonstrate that a single injection of ube3a-ASO in a new mutant ube3a mouse model restores Ube3a protein expression and EEG function and sleep patterns. A key feature of these findings is the development of a new mouse model that eliminates any expression of ube3a mRNA. Moreover, they demonstrate that the impact of their treatment can last up to 6 weeks. They determine that the phenotype correction correlates with Ube3a protein level. There is an impressive amount of work that has gone into this study. It does appear, however, that much of this work is derivative of previous studies. It is less clear what is novel. While a new mouse model is introduced, it is unclear whether such a mouse model is any better defining Angelman syndrome than previous models. Several conclusions appear to be a bit too strong based on the modesty of the findings. For example, it is not clear that the current findings constitute a strong enough foundation for future drug studies.
Overall, this study describes another set of potentially interesting findings using ASO to restore Ube3a expression and phenotypic rescue. Not all phenotypes are tested, not every tested phenotype shows truly robust changes that would encourage one to move to clinical trials.
The authors did succeed in describing this new mouse line at the level of ube3a expression, EEG, sleep patterns and poly-spikes. They did so across many brain regions and multiple ages. Within these findings and approaches, there is useful information that can benefit the field. The impact of this work is that the authors may have demonstrated an approach which will have a longer lasting impact on recovery. Such an advance would be a great benefit to the population of those greatly impacted by Angelman syndrome.
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www.biorxiv.org www.biorxiv.org
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Reviewer #2 (Public Review):
It is my opinion that the principle utility of this approach lies in its ability to identify the set of 'easily learnable' stimulus-response mappings from neural data which makes strong behavioral predictions that can be easily evaluated. I envision a simple experiment in which empirically obtained kernel functions are used to rank stimulus-response mappings according to their learnability which can then be plotted against measures of performance like the observed learning rate and saturated performance. Because kernel functions are empirically obtained, there is even the potential for meaningful cross-species comparisons. If behaviorally validated, one could also use this approach to label cortical populations by the set of easily learned stimulus-response mappings for that population. This allows for the identification of task-relevant neurons or regions which can be subsequently manipulated to enhance or degrade learning rates.
Of course, any theoretical approach is only as good as the underlying assumptions and so while the primary strength is the simplicity and generality of this approach, the primary weakness is its neglect of some very real and very relevant aspects of neural data in particular and statistical learning in general. In particular, the three principle limitations of this work are tied to its reliance on the assumptions that (1) neurons are noiseless, (2) decoders are linear, and (3) learned weights are unbiased.
(1) Within this framework, a realistic stimulus-dependent noise model can be easily introduced and its effects on the kernel and set of easily learned stimulus-response mappings investigated. So while the kernel would be substantially altered via the addition of a realistic noise model, the applications of the approach outlined above would not be affected. The same cannot be said for the efficient coding application described in this manuscript. There, the authors note that rotations and constant shifts of neural activity do not affect the kernel and thus do not affect the generalization error. This kernel invariance is not present when a non-trivial (i.e. non-isotropic) noise model is added. For example, suppose that neurons are independent and Poisson so that noise scales with the mean of the neural response. In this case, adding a baseline firing rate to a population of unimodal neurons representing orientation necessarily reduces the information content of the population while rotations can affect the fidelity with which certain stimulus values are represented. It is important to note, however, that while this particular efficiency result is not compelling, I believe that it is possible to perform a similar analysis that takes into account realistic noise models and focuses on a broad set of 'biologically plausible' kernels instead of particular invariant ones. For example, one could consider noise covariance structures with differential correlations (Moreno-Bote 2014). Since the magnitude of differential correlations controls the redundancy of the population code this would enable an analysis of the role of redundancy in suppressing (or enhancing) generalization error.
(2) Similarly, the linearity assumption is somewhat restrictive. Global linear decoders of neural activity are known to be highly inefficient and completely fail when decoding orientation in the primary visual cortex in the presence of contrast fluctuations. This is because contrast modulates the amplitude of the neural response and doubling the amplitude means doubling an estimate obtained from a linear decoder even when the underlying orientation has not changed. While the contrast issue could be partially addressed by simply considering normalized neural responses, it is not yet clear how to extend this approach to account for other sources of neural variability and co-variability that cause global linear decoders to fail so badly.
(3) This analysis relies on the assumption that decoder weights learned in the presence of finite data are efficient and unbiased. This assumption is problematic particularly when it comes to inductive bias and generalization error. This is because a standard way to reduce generalization error is to introduce bias into the learned decoder weights through a penalization scheme that privileges decoder weights with small magnitudes. This kind of regularization is particularly important when neurons are noisy. Fortunately, this issue could be addressed by parameterizing changes in the kernel function by the degree and type of regularization potentially leading to a more general result.
Finally, I would like to conclude by explicitly stating that while the limitations imposed by the assumptions listed above temper my enthusiasm in regards to conclusions drawn in this work, I do not believe there is some fundamental problem with the general theoretical framework. Indeed, items 1 and 3 above can be easily addressed through straightforward extensions of the authors approach and I look forward to their implementation. Item 2 is a bit more troublesome, but my intuition tells me that an information-theoretic extension based upon Fisher information may be capable of eliminating all three of these limiting assumptions by exploiting the relationship between FI(\theta) and FI(y=f(\theta)).
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Reviewer #2 (Public Review):
In the present study, Liu and colleagues set out to assess the mechanisms of the therapeutic action of FGF21 on non-alcoholic steatohepatitis in the setting of obesity and dyslipidemia. They used a liver-targeted adeno-associated virus to overexpress FGF21 as a method for chronic pharmacological-type treatment of the mice. They found that FGF21 overexpression in their mouse model prevented weight gain in high-fat, high-cholesterol (HFC) diet-fed mice, compared to the control virus on the HFC diet. In addition, many of the features of obesity, insulin resistance, and NAFLD are prevented by hepatic FGF21 overexpression in their model. The authors have performed extensive phenotyping and the results leave little doubt of the efficacy of the treatment.
My main concern with the study is the distinction between a therapeutic paradigm and the preventative paradigm employed here. Based on the body-weight curves, one might expect that real liver pathology never occurred in the FGF21-overexpressing animals. In which case, it is difficult to comment on the possibility of reversing these aspects in a therapeutic setting. This point is highly relevant to the ongoing clinical trials of FGF21 analogs for NASH that the authors have referenced.
A second point raised by the authors is the aspect of FGF21 increasing thermogenic adipose tissue activity. Their results showing FGF21-induced expression of UCP1 are not in doubt, but the fact that this increase alone is responsible for the observed phenotype is not clear. For example, FGF21 has been shown to be anorexigenic in certain models (non-human primates: Talukdar, et al. Cell Metab 2016, mini-pigs: Christoffersen, et al. Diabetes Obesity Metabolism 2019, among others). Moreover, there is evidence that some effects of FGF21-driven metabolic improvements do not require UCP1 (Samms, et al. Cell Reports 2015). Given the differences in brown fat activity and physiology between mice and humans, it would be important for the authors to either moderate their comments on the UCP1 dependence of their phenotype or provide more data to clarify to what extent their findings are UCP1-dependent (e.g. food intake in the FGF21 overexpression model and/or evidence of increased energy expenditure).
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Reviewer #2 (Public Review):
Optogenetic proteins are important tools for circuit neuroscience. The authors characterize five proteins, GtCCR4, KnCHR2, BeGC1, bPAC, and OaPAC with respect to their ability to suppress normal cell excitability and compare the results to those for the more established GtACR1 and CrChR2[T159]. The study makes use of expression in the zebrafish heart and hindbrain, as well as in a cell line. Electrophysiology in the cell line demonstrates that GtCCR photo-activation induces similar currents as CrChR2 activation and shows less signs of desensitization. Using a transgenic vsx2:Gal4 zebrafish line, immunohistochemistry shows that the tools are expressed. When activated, they triggered the expected behavioral responses (swimming) at short latency (<4s). This was true even for the three tools that are guanylyl or adenylyl cyclases (BeGC1, bPAC, OaPAC) and thus affect cell excitability only indirectly. At the tested light intensity, the Klebsormidium nitens channelrhodopsin (KnChR) had the shortest latency (<0.5 s) and highest (100%) probabilities of inducing locomotion. When expressing the tools in the zebrafish heart, brief illumination (100 ms) induces brief (100 ms - 1500 ms) suppression of the heartbeat. Notably, also tools that evoke depolarization induce heartbeat suppression. Heartbeat movies and calcium imaging demonstrate that this is caused by prolonged cardiomyocyte contraction. The optogenetic guanylyl and adenylyl cyclases were not effective in perturbing zebrafish heartbeat (except for bPAC over longer time scales).
Given the large number of optogenetic proteins available to date and the challenge of employing them in well-controlled neuroscience experiments, this study presents an important contribution for neuroscientists performing optogenetic research in animal models. Two light-gated cation channels, GtCCR4 and KnChR, are tested for the first time in vivo. The evidence supporting the claims regarding heartbeat and induced swimming behavior is solid. Since GtCCR4 is more Na+-selective than other channelrhodopsins, it should allow better control of experimental variables and is a valuable addition to the optogenetic tool box. The created transgenic zebrafish lines will be useful for the zebrafish neuroscience community.
The expression in zebrafish was compared using immunohistochemical staining (of a single Gal4 driver line). From this experiment alone, it is difficult to judge the expression level, the in vivo visibility of the fluorescence under the microscope, and the proportion of target cells that do express the optogenetic gene of interest.
The evidence for optogenetically induced alteration of swimming behavior is compelling. However, the associated neuronal responses and their dependence on different light intensity levels remain uncharacterized. Therefore, if anyone plans to use these tools to investigate a neural circuit in the future, the needed light levels and the specificity of the manipulation would still need to be determined.
For the optogenetic guanylyl and adenylyl cyclases, which clearly were able to alter behavioral responses, the signaling and circuit mechanisms that lead to neuronal depolarization remain unknown, but possible activation pathways are discussed.
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Reviewer #2 (Public Review):
The presented study aims at deciphering the physiological function of GPCR signaling in excitable cells. To this end, the authors developed transgenic zebrafish models expressing a selection of Gq- and Gi/o-coupled bistable rhodopsins in either reticulospinal neurons or cardiomyocytes and elucidated behavioral responses (tail movements) or physiological responses (heartbeat) as well as intracellular Ca2+ dynamics following optical stimulation of rhodopsins.
One of the major strengths of the presented study is the functional comparison of five Gq- and five Gi/o-coupled rhodopsins in two major classes of excitable cells, however; the selection of rhodopsins tested remains elusive. More importantly, it is not obvious why some of the effects of rhodopsin activation were assessed in both neurons and cardiomyocytes, while others were only tested in one of the two systems without further explanation. The main chosen experimental readouts (swimming/tail bending or cardiac contractions) have limited informative value regarding GPCR signaling, as they will only report the peak of the iceberg, namely whether movements are elicited or heartbeats inhibited. No analysis on subtle changes in heart rate and contraction force was included, but such modulation of cardiac activity (e.g. positive or negative chronotropic, inotropic, dromotropic, bathmotropic, and/or lusitropic responses) would represent better the physiological modulation of the heart via GPCR and down-stream signaling events. In line, the presented data only represents behavior at one light intensity tested, whereas a light titration of observed effects could provide more meaningful insight into both rhodopsin responses and signaling mechanisms. Also, the potential promiscuity of G protein activation of selected receptors has not been addressed, neither experimentally nor in the discussion part. As a result of the above-mentioned limitations, it is difficult to follow the logic of the study and especially to interconnect the data obtained in reticulospinal neurons (where activation of jumping spider rhodopsin elicited tail bending) to myocyte data (where three Gi-coupled rhodopsins suppressed cardiac activity). Moreover, as such, the study does not provide explanations on why a certain tool might evoke an effect in one system or the other, or not, which could be the main deliverable of such a comparative analysis.
While the presented data is interesting, the graphical presentation and description of the data are insufficient. Most importantly, the current version of the text does not include a quantitative description of effects and statistical analyses (which are found in the figures and legends!). The lack of quantitative description also extends to both the introduction and discussion, which remain general without a specific dissection of observed effects.
One major concern is the selective citation of own work. While single statements in both the introduction and discussion are supported by up to ten own papers, recent studies using rhodopsins for dissecting GPCR signaling in neurons are not sufficiently discussed and new data is not compared to published results by other teams. Moreover, relevant papers on cardiomyocytes (e.g. PMID: 35579776, 35365606, 34987414, 30894542) are not cited at all, despite the use of similar rhodopsins and/or optogenetic activation of the same signaling pathways. Taking into account these published studies may help to better understand the observed responses.
Additional comment: Data were obtained from larvae zebrafish. It would be useful to include a discussion on how GPCR signaling might be different in adult fish compared to larvae, and how to test whether the observed effects are more generally applicable.
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Reviewer #2 (Public Review):
The reciprocal adaptation of host immune systems and pathogens leads to complex co-evolutionary dynamics. How this dynamical process shapes host and pathogen diversity is a fundamental question in immunology and virology. To study this question experimentally, the CRISPR-Cas system which some prokaryotes use for adaptive immunity against phages has recently emerged as an important model system. In this system both host and viral adaptation can be read out by sequencing, as CRISPR-Cas immunity is guided by genomic spacers incorporated into the host genome. In this context, the current work presents a welcome deep dive into the dynamical regimes predicted by a simple phenomenological model of the co-evolution between CRISPR loci and phages. Among the notable results are the following: First, diversity primarily depends on a single scalar parameter, and does so in a sublinear manner. Second, different types of cross-reactivity are linked to different shapes of viral phylogenies. Third, comparison of spacer turnover and average immunity between theoretical and experimental timeseries data provides hints as to the operative regime in different CRISPR systems. These results together with the extensive discussion should be greatly useful in guiding further work in this field. There are many avenues for further theoretical work generalizing to less simplifying assumptions, and importantly, many concrete suggestions for future experiments.
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Reviewer #2 (Public Review):
In this manuscript, Karsenty et al. describe postnatal development in the rat between P20 and P60 where crests of the cardiomyocyte lateral membranes mature. The authors previously described these crests in a Cardiovascular Res paper, where they highlighted how they facilitate interactions between cardiomyocytes in claudin-5 dependent manner. The authors previously also reported claudin-5 ephrin-b1 interactions on the cardiomyocyte lateral surface. Presently, the authors try to link together the following observations: a) crest height, mitochondrial number and area increase from postnatal day 20 to 60 in rats, and this correlates with increase claudin-5 expression, as well as gene expression accessed by microarray; b) changes in diastolic function occur in rats between days 20 and 60 postnatal life; c) cardiomyocyte-specific knockout of ephrin-b1 leads to diastolic dysfunction and a heart failure with preserved ejection fraction like phenotype.
The major strength of the paper is the detailed analysis of postnatal cardiomyocyte structure using electron microscopy and echocardiography. However, there are multiple major weaknesses of the methodology that should be clarified.
1. Most importantly, it is unclear how these mice are maintained. The authors explain the mice are in a mixed background. If this is the case, it is extremely important that littermate controls are used. Otherwise, it is very difficult to interpret the physiological data if the animals being compared are from two separate crosses.
2. The authors should clarify the echo and cath data in mice and rats. First with respect to the rat data, the end-diastolic pressure of the p60 rats reported in Figure 3 is around 9 mmHg. This is significant and abnormal, and also unexplained. More globally, the authors conclusion that "diastolic maturation" is occurring should be tempered by the fact that loading conditions at these two postnatal days are completely different, as highlighted by the blood pressures of the animals (~70/40 at p20 vs ~120/80 at P60). Third, the heart rates are significantly higher at p60 vs p20 in panel A, but not panel B. The authors report these studies were performed under isofluorane, so I imagine this reflects differences in anesthesia, which can significantly affect the heart rate and thus the diastolic parameters (particularly IVRT), so this should at least be commented on as a significant limitation.
With respect to data interpretation and whether the results are correctly interpreted, the following considerations should be taken into account:
1. The author conclusions in Figure 2d appear overstated. While the methodology of figure 2d is explained in the figure panel, it is generally looked over in the main text. Is there any precedent for utilizing human single-cell sequencing in this purpose - essentially the authors are superimposing the rat P20 and P60 data on the human UMAP plot. The authors walk back the statement in the text and clarify that these genes are expressed in the following cell types in adult human hearts.
2. The ephrin-b1 cardiomyocyte specific knockout mice are not a model of HFpEF. These mice show an accelerated death rate and clear evidence of progressive systolic impairment. Furthermore, it is completely unclear that the murine diastolic parameters are meaningfully different, and hence the overall evidence presented that this is a HFpEF phenotype is weak.
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Reviewer #2 (Public Review):
The authors present a compendium of diffusion MR, dynamic contrast-enhanced MR, histological, and other results in AQP4 KO vs. WT mice which suggest that AQP4 deletion results in stagnation of interstitial fluid movement, enlargement of interstitial volume, and an increase in total brain water. The authors also provide evidence that these effects do not arise due to changes in CSF production, perfusion, or vascular density, strengthening the conclusion that AQP4 is specifically involved in modulating parenchymal resistance, rather than another aspect of glymphatic function. While the study of AQP4 deletion using various MR and histological methods is not novel per se, the breadth of concurrent methodological approaches presented here is uncommonly extensive, and thus provides a strong, self-contained case for the conclusion(s) - more so than other works on such mouse models. The key strength and utility of this work lie in the extent of corroborating evidence provided for the conclusions.
Another strength of the paper is the development of what appears to be a robust CSF space segmentation approach, which may be of interest to others aiming to quantify glymphatic function using MR. The source code, however, is not provided at this time.
I have some concerns, specifically about the discussion around transmembrane water exchange - i.e., whether the exchange is truly being measured by the diffusion MR methods - and about the validity of applying an IVIM signal model across the brain. These concerns, however, do not affect the major conclusions of the paper. Indeed, the authors have included analyses using standard ADC fitting which avoids the issues with IVIM. In summary, the paper presents a compelling body of evidence describing the effects of AQP4 deletion in mice.
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Reviewer #2 (Public Review):
The manuscript by Niu and colleagues reported that ET after mastectomy did not prolong the DFS of Chinese HR+ DCIS patients, but rather increased adverse effects. For the first time, the authors analyzed the beneficial effect and safety of ET after mastectomy in Chinese patients with HR+ DCIS through the clinical case review. The conclusion of this study is of great significance to guide the choice of appropriate treatment for Chinese patients with HR+ DCIS, and it has obvious benefits to reduce the economic burden of the patient's family and improve the quality of life for patients.
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Reviewer #2 (Public Review):
Although many broadly-neutralizing antibodies were discovered against virus accumulating mutations such as HIV, Influenza, and Sars-CoV-2, the methodology to induce such antibodies or design to generate them is highly demanded. The authors take the broadly-neutralizing antibody, CH65 as a model antibody and try to recapitulate the generation of the broadly-neutralizing antibody from an unmutated common ancestor over time. By performing Tite-Seq assays, Epistasis analysis, Pathway analysis, and Affinity measurement, and structural study, the authors proposed a scenario of the evolution of CH65.
Strengths<br /> Combining the models and affinity/structure data, the authors enable us to show the possible track of gaining the breadth of the CH65 antibody from the unmutated repertoire. Using the Tite-Seq assay, the authors took a forward genetics approach which is high-throughput and non-bias and mimics the situation of the evolution of a B cell repertoire in an individual over time. The data is robust, and its outcome will provide an opportunity to build a prediction model to design the antibody in silico. Especially their identification of amino acid positions important for epistasis mode in antibody evolution is valuable. Antigen selection scenarios are decisive in this study.
Weakness<br /> The proposed scenarios cannot be tested using human CH65. The readers would have great interest in how these hypothetical scenarios are fitting to the evolution occurring in vivo situation, especially in a quantitative way. The broadly neutralizing antibodies often react with self-antigens as the authors cite previous work(ref 19). How do these environmental factors affect the evolution of the antibody? These already-known facts could be mentioned and discussed in detail.
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Reviewer #2 (Public Review):
Huang Mi, et al. investigated the role of MTIF3, the mitochondrial translation initiation factor 3, in the function of adipocytes. They first detected the expression of the obesity-related MTIF3 variants based on the G5Ex database and found two variants lead to an increase in MTIF3 expression. Then they knockout MTIF3 in differentiated hWAs adipocytes and characterized the mitochondrial function. They found loss of MTIF3 decrease mitochondrial respiration and fatty acid oxidation. They further treated cells with low glucose medium to mimic weight loss intervention and found MTIF3 knockout adipocytes lose fewer triglycerides than control adipocytes. This paper provides new information about MTIF3 in adipocytes and the potential functional role of MTIF3 in mitochondrial function.
1. The authors provided sufficient data to show those two genetic variants increase MTIF3 expression. Their CRISPR/Cas9 knockin cell line is also convincing. But they didn't show if the genetic variants affect adipogenesis. Adipogenesis is an important process for weight gain and fat deposition. In lines 103-107, the authors mentioned that the "allele-edited cells have some problem in differentiated state, e.g. triglyceride or mitochondrial content", so they used an inducible Cas9 system. However, the issue of differentiated allele-edited cells may be the functional effect of MTIF3 genetic variants, such as interrupting adipogenesis, decreasing triglyceride, or affecting mitochondrial number. The authors should provide that information.
2. In Figure 4, the author mentioned that MTIF3 knockout does not affect the expression of adipogenic differentiation markers. They need to provide more evidence to prove their point. Oil-red O staining is a clearer way to quantify adipocyte differentiation in cell culture. In addition, in Fig. 4B western blot, the author should include MTIF3 as a control to show the knockout efficiency. It is not clear the meaning of plus and minus in that panel. The author should also compare the total triglyceride levels in MTIF3 knockout cells and control cells.
3. MTIF3 is a translation initiation factor in mitochondria and is involved in the protein synthesis of mitochondrial DNA-encoding genes. The authors should check protein levels rather than the mRNA levels of mitochondrial DNA-encoding genes (Fig. 6E). It's interesting to see the increase of mRNA levels of ND1 and ND2, which might be feedback of lower translation. Since ND1 and ND2 are in OXPHOS complex I, the expression levels of complex I in MTIF3 KO cells would be worth checking. Additionally, the author should also check the mitochondria copy number.
4. MTIF3 knockout adipocytes retain more triglycerides under glucose restriction is interesting. It may link to the previous result of lower fatty acid oxidation in MTIF3 knockout adipocytes. However, the authors then showed there is no difference in lipolysis. The author should discuss those results in the manuscript. The authors could also check lipolysis in glucose restriction conditions. It's also necessary to include the triglyceride levels of KO cell lines at full medium.
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Reviewer #2 (Public Review):
The authors present a manuscript that addresses an important topic of bacterial co-existence. Specifically modeling infection-relevant scenarios to determine how two highly antibiotic-resistant pathogens will develop over time. Understanding how such organisms can persist and tolerate therapeutic interventions has important consequences for the design of future treatment strategies.
A major strength of this paper is the methodical approach taken to assess the dynamics between the two bacterial species. Using carbon sources to regulate growth to test different community structures provides a level of control to be able to directly assess the impact of one dominant pathogen over another.
The modeling aspect of this manuscript provides a basis for testing other disturbances and/or the impact of additional incoming pathogens. This could easily be applied to other infection settings where multiple microbes are observed ( for example viral/bacterial interactions in the lung).
The authors clearly show that by altering the growth rate and metabolism of various carbon sources, population structure can be modified, with one out-competing the other. Both modeling and experimental approaches support this.
The exploration of the role of virulence factors is less clear, for example how strains unable to produce virulence factors are impacted in regard to their overall growth and whether S. aureus is able to sense virulence factors without transcriptional assays here. Although the hypothesis is strong, the experimental data does not fully support this conclusion.
Spatial disturbance has a significant impact on community structure. Although using one approach to assess this, it is not clear if the spatial structure is impacted without the comparable microscopy evaluation.
Overall this paper highlights the use of modeling approaches in combination with wet lab experiments to predict microbial interactions in changing environments.
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Reviewer #2 (Public Review):
The idea that decidualization is related to or evolved from wound healing, including fibroblast activation, is old, going back all the way to Creighton 1878 who pointed to the similarity between granulation tissue and decidual tissue, and is supported by the fact that embryo implantation is a compensated form of the endometrial lesion. Nevertheless, the mechanistic connection between FB activation and decidualization is an important fact necessary for understanding decidualization, a fact that is reflected in previous work, for instance, Kim et al., 1999 (Hum Reprod 14 Suppl 2), their reference 20, and Oliver et al., 1999 (Humn Reprod 14), their reference 56 a.o.m. More specifically, a recent single-cell study of in vitro decidualization has shown that a myofibroblast-like cell state is a transient state in the process of decidualization, i.e. decidual cells themselves are not so much activated fibroblasts, but rather decidual cells differentiate after endometrial stromal fibroblasts undergo a FB activation like process, and the decidual re-programming happens from these activated FB like states (Stadtmauer et al., 2021, Biol. of Reprod. 1-18).
The above assessment of how the current study fits into the conceptual landscape of mammalian reproductive biology does not diminish the importance of the paper under consideration. The study contributes a large amount of observational and experimental facts to the understanding of how FB activation and decidualization are related. The authors suggest, in particular, that blastocyst-derived TNF activates the cLPA-producing Arachidonic acid (AA), activating PGI2 and PPARd signaling pathway (more about this later).
Other major comments:
The authors suggest that luminal epithelial cells signal through the release of arachidonic acid (AA) in response to TNF. That is interesting and supported by in vitro experiments inducing decidualization and FB activation by AA. What makes this conclusion a little problematic is that it is known that luminal epithelial cells also express COX2/PTGS2 and thus the synthesis of prostaglandins is already starting in the LE and thus LE can also signal to the stoma via PGE2, PGI2 as well as PGL2 rather than AA directly. The in vitro experiments can not exclude the possibility that the ESF is producing some prostaglandin and then having an autocrine effect.
344: here the authors report that PGE2 has no effect on FB activation marker expression, but the problem with that is, that (at least in human ESF), progesterone is causing a change in the expression of the PGE2 receptors from EP4 to EP2, and it is only the EP2 receptor that activates cAMP/PKA pathway.
The fact that the authors show an effect of PGI2 is interesting because PGI2 receptors are among the strongest expressed PTG receptors in mammalian ESF. Prostacyclin receptor is a GPCR rather than a nuclear receptor. So the question is really why the authors have not pursued the role of prostacyclin receptor and instead have focused on PPARd?
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Reviewer #2 (Public Review):
The manuscript of Xu and colleagues examines in detail the regulation of the important transcription factor IRF8 in dendritic cell (DC) subsets. They identify a long noncoding RNA arises from the +32kb enhancer of IRF8 specifically in plasmacytoid DCs (pDCs)and show clearly that this lncIRF8 marks the activity of a region of this enhancer but the RNA itself does not appear to have any function. Deletion of the promoter of the lncIRF8 ablated cDC1 and pDC differentiation using an in vitro cell differentiation model. The authors propose an innovative model that the lncIRF8 promoter sequences act to limit IRF8 expression in cDC1, but are inactive in pDCs, resulting in their characteristically very high IRF8 expression.
This is a conceptually interesting study that makes excellent use of an extensive set of genomic data for the DC subsets. There has been a lot of recent research investigating the regulation of the IRF8 gene in hematopoiesis and this study provides an important new aspect to the work. The use of an in vitro model of DC differentiation is a powerful practical approach to investigating IRF8 regulation, as is the innovative use of CRISPR technology. Perhaps the biggest limitation of this study is that the authors have not conformed to the in-cell system data by creating a mouse strain lacking the lncIRF8 element. Such approaches by others, most notably the Murphy lab, have been instrumental in pushing this field forward. Nevertheless, Xu et al. significantly add to our current knowledge of the regulation of IRF8, a critical step in forming the dendritic cell network.
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Reviewer #2 (Public Review):
Slusarczyk et al. investigate the functional impairment of red pulp macrophages (RPMs) during aging. When red blood cells (RBCs) become senescent, they are recycled by RPMs via erythrophagocytosis (EP). This leads to an increase in intracellular heme and iron both of which are cytotoxic. The authors hypothesize that the continuous processing of iron by RPMs could alter their functions in an age-dependent manner. The authors used a wide variety of models: in vivo model using female mice with standard (200ppm) and restricted (25ppm) iron diet, ex vivo model using EP with splenocytes, and in vitro model with EP using iRPMs. The authors found iron accumulation in organs but markers for serum iron deficiency. They show that during aging, RPMs have a higher labile iron pool (LIP), decreased lysosomal activity with a concomitant reduction in EP. Furthermore, aging RPMs undergo ferroptosis resulting in a non-bioavailable iron deposition as intra and extracellular aggregates. Aged mice fed with an iron restricted diet restore most of the iron-recycling capacity of RPMs even though the mild-anemia remains unchanged.
Overall, I find the manuscript to be of significant potential interest. But there are important discrepancies that need to be first resolved. The proposed model is that during aging both EP and HO-1 expression decreases in RPMs but iron and ferroportin levels are elevated. In their model, the authors show intracellular iron-rich proteinaceous aggregates. But if HO-1 levels decrease, intracellular heme levels should increase. If Fpn levels increase, intracellular iron levels should decrease. How does LIP stay high in RPMs under these conditions? I find these to be major conflicting questions in the model.
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Reviewer #2 (Public Review):
Xie et al. investigated the medial temporal lobe (MTL) circuitry contributions to pattern separation, a neurocomputational operation to distinguish neutral representations of similar information. This presumably engages both long-term memory (LTM) and working memory (WM), bridging the gap between the working memory (WM) and long-term memory (LTM) distinction. Specifically, the authors combined an established retro-cue orientation WM task with high-resolution fMRI to test the hypothesis that the entorhinal-DG/CA3 pathway retains visual WM for a simple surface feature. They found that the anterior-lateral entorhinal cortex (aLEC) and the hippocampal DG/CA3 subfield both retained item-specific WM information that is associated with fidelity of subsequent recall. These findings highlight the contribution of MTL circuitry to item-specific WM representation, against the classic memory models.
I am a long-term memory researcher with expertise in representational similarity analysis, but not in inverted encoding modeling (IEM). Therefore, I cannot verify the correctness of these models and I will leave it to the other reviewers and editors. However, after an in-depth reading of the manuscript, I could evaluate the significance of the present findings and the strength of evidence supporting these findings. The conclusions of this paper are mostly well supported by data, but some aspects of image acquisition and data analysis need to be clarified. I would like to list several strengths and weaknesses of this manuscript:
Strengths:<br /> • Methodologically, the authors addressed uncertainty in previous research resulting from several challenges. Namely, they used a high-resolution fMRI protocol to infer signals from the MTL substructures and an established retro-cue orientation WM task to minimize the task load.<br /> • The authors selected a control ROI - amygdala - irrelevant for the experimental task, and at the same time adjacent to the other MTL ROIs, thus possibly having a similar signal-to-noise ratio. The reported effects were observed in the aLEC and DG/CA3, but not in the amygdala.<br /> • Memory performance, quantified as recall errors, was at ceiling - an average recall error of 12 degrees was only marginally away from the correct grating towards the closest incorrect grating (predefined with min. 20 degrees increments). However, the authors controlled for the effects of recall fidelity on MTL representations by comparing the IEM reconstructions between precise recall trials and imprecise recall trails (resampled to an equal number of trials). The authors found that precise recall trails have yielded better IEM reconstruction quality.<br /> • The author performed a control analysis of time-varying IEM to exclude a possibility that the mid-delay period activity in the aLEC-DG/CA3 contains item-specific information that could be attributed to perceptual processing. This analysis showed that the earlier TR in the delay period contains information for both cued and uncued items, whereas the mid-delay period activity contains the most information related to the cued, compared to uncued, item.
Weaknesses:<br /> • The authors formulate their main hypothesis building on an assumption related to the experimental task. This task requires correctly selecting the cued grating orientation while resisting the interference from internal representations of the other orientation gratings. The authors hypothesize that if this post-encoding information selection function is supported by the MTL-s entorhinal-DG/CA3 pathway, the recorded delay-period activity should contain more information about the cued item that the uncued item (even if both are similarly remembered). Thus, the assumption here is that resolving the interference would be reflected by a more distinct representation in MTL for the cued item. Could it be the opposite, namely the MTL could better represent the unresolved interference, for example by the mechanism of hippocampal repulsion (Chanales et al., 2017). It could strengthen the findings if the authors comment on the contrary hypothesis as well.<br /> • It is not clear for me why the authors chose the inverted encoding modelling approach and what is its advantage over the others multivoxel pattern analysis approaches, for example representational similarity analysis also used in this study. How are these two complementary? Since the IEM is still a relatively new approach, maybe a little comment in the manuscript could help emphasizing the strength of the paper? Especially that this paper is of interest to researchers in the fields of both working memory and long-term memory, the latter being possibly not familiar with the IEM.
Overall, this work can have a substantial impact of the field due to its theoretical and conceptual novelty. Namely, the authors leveraged an established retro-cue task to demonstrate that a neurocomputational operation of pattern separation engages both working-memory and long-term memory, both mediated by the MTL circuitry, beyond the distinction in classic memory models. Moreover, on the methodological side, using the multivariate pattern analyses (especially the IEM) to study neural computations engaged in WM and LTM seems to be a novel and promising direction for the field.
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Reviewer #2 (Public Review):
This paper reports that neonatal CD43- B cells produce IL-10 upon BCR stimulation, which inhibits TNF-alpha secretion from the peritoneal macrophage. In the neonatal CD43- B cells, the BCR-mediated signal transmitted Stat5 activation and induced IL-6 production, and subsequently, the secreted IL-6 activated Stat3 finally leading to IL-10 production. The authors identified a unique signaling pathway leading to IL-10 production and revealed the different responses between CD43+ and CD43- B cells against BCR crosslinking. A weakness of this study is that the neonatal CD43- B cell subset secreting IL-10 has not been characterized and discussed as well. BCR expression levels between adult CD43- B cells and neonatal CD43- B cells have been overlooked to explain the different reactivity. Clarity on these points would substantially enhance the impact of the manuscript.
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Reviewer #2 (Public Review):
The Kaiser lab has been on the forefront in understanding the mechanism of dopamine release in central mammalian neurons. assessing dopamine neuron function has been quite difficult due to the limited experimental access to these neurons. Dopamine neurons possess a number of unique functional roles and participate in several pathophysiological conditions, making them an important target of basic research. This study here has been designed to describe the proteome of the dopamine release apparatus using proximity biotin labeling via active zone protein domains fused to BirA, to test in which ways its proteome composition is similar or different to other central nerve terminals. The control experiments demonstrating proper localization as well as specificity of biotinylation are very solid, yielding in a highly enriched and well characterized proteome data base. Several new proteins were identified and the data base will very likely be a very useful resource for future analysis of the protein composition of synapse and their function at dopamine and other synapses.
Major comment:
The authors find that loss of RIM leads to major reduction in the number of synaptically enriched proteins, while they did not see this loss of number of enriched proteins in the Syt1-KO's, arguing for undisrupted synaptome. Maybe I missed this, but which fraction of proteins and synaptic proteins are than co-detected both in the Syt1 and control conditions when comparing the Venn diagrams of Fig2 and Fig 3 Suppl. 2? This analysis may provide an estimate of the reliability of the method across experimental conditions.
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Reviewer #2 (Public Review):
This paper identifies the need for improved pre-clinical models for the study of human primordial germ cells (PGCs) and suggests the common marmoset (Callithrix jacchus) as a suitable primate model. In vitro gametogenesis offers an alternative method to generate germ cells from pluripotent stem cells for study and potential pre-clinical applications. Therefore, the authors aimed to take the first steps toward developing this technology for the marmoset. Here, iPSCs have been derived from the marmoset and differentiated to PGC like-cells (PGCLCs) in vitro that have similarities in gene expression with PGCs identified from single-cell studies of marmoset embryos, as demonstrated through immunofluorescence and RT-qPCR approaches, as well as RNA-sequencing.
The authors have successfully developed a protocol that produces PGCLCs from marmoset iPSCs. These are shown to express key germline gene markers and are further shown to correlate in gene expression with PGCs from the marmoset. This study uses a 2D culture system for further expansion of the PGCLCs. When cultured with mouse testicular cells in a xenogeneic reconstituted testis culture, evidence is provided that cjPGCLCs have the capacity to develop further, expressing marker genes for later germline differentiation. However, the efficiency of generating these prospermatogonia-like cells in culture is unclear. Nonetheless, with the importance of developing protocols across species for in vitro gametogenesis, this paper takes a key step towards generating a robust preclinical system for the study of germ cells in the marmoset.
The claims of the authors are generally justified by the data provided; however, some conclusions should be clarified. In particular, the authors have failed to show convincingly that cjPGCLCs are a distinct cell type to the iPSCs that generated them. cjiPSCs cultured in feeder conditions (OF) with IWR1 are reported to cluster closely with the derived cjPGCLCs using principal component analysis of RNA-Seq data. This contrasts with the cjiPSCs cultured in feeder-free (FF) conditions which maintain a more undifferentiated/less primed state, and are not capable of differentiating to the germline lineage. Therefore, the OF/IWR1 cjiPSCs could rather be an intermediate cell-state between iPSCs and cjPGCLCs.
The reasons behind improved germline competence of iPSCs in the different media conditions are unclear. The authors reject the idea that this is due to the presence of IWR1, since this condition has not affected FF iPSCs. However, the efficiency of differentiation was greatly increased in OF conditions when IWR1 was used, indicating inhibition of WNT does indeed have a positive effect on induction to the germline lineage. This area requires further clarification.
Another area requiring clarification is the reporting of RNA sequencing data as representative of a developmental trajectory, without defining which cell lines produced clusters, or defining the stages of this trajectory. The authors refer to the identification of four clusters representative of a developmental trajectory, however, they provide unclear information as to what this refers to. Importantly, detailed transcriptomic comparisons between in vivo-derived PGCs and in vitro PGCLCs are not provided.
Functional validation of iPSC lines generated in the study is not provided besides confirming that the cells express pluripotency markers OCT3/4, SOX2, and NANOG. It is important to confirm tri-lineage differentiation of iPSCs, e.g., through an embryoid body assay. Since FF cjiPSCs were unable to differentiate into cgPGCLCs, it is even more important to confirm cells are genuine iPSCs.
In summary, although there are issues surrounding clarity, this paper is generally justified in its conclusions. The authors present an optimised protocol for the derivation of PGCLCs from marmoset iPSC-like cells, with defined expansion conditions and evidence of further differentiation to prospermatogonia-like cells.
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Reviewer #2 (Public Review):
Many cancers, including pancreatic tumors, host microbes that have the ability to metabolize anti-cancer drugs, thus altering cancer response to these treatments. However, many anti-cancer drugs also are quite toxic to bacteria. Thus, the authors first investigate how a model bacterium that could live pancreatic tumors can become resistant to the pancreatic chemotherapy gemcitabine. Second, they investigate how bacteria that are resistant to gemcitabine impact cancer cell response to this therapy compared to bacteria that are not resistant. By answering these two questions, the authors hope to determine how bacterial evolution to chemotherapy can impact how well chemotherapy works in pancreatic cancer.
To answer the first question, the authors perform both genetic screens and laboratory evolution experiments of E. coli bacteria exposed to gemcitabine. Both the genetic screen and laboratory evolution experiments identified mutation of the bacterial protein nupC as mediating bacterial resistance to gemcitabine. NupC is the transporter protein that bacteria use to take up gemcitabine. Thus, the authors conclude that loss of ability to take up gemcitabine would likely underlay bacterial evolution to gemcitabine in pancreatic tumors.
To answer the second question, the authors take either control of nupC mutant bacteria and expose these to gemcitabine. They then take the bacterial media with its residual gemcitabine and treat mouse colorectal cancer cells with these media. They find the amount of gemcitabine is higher in nupC mutant media and media from these mutants cause correspondingly higher killing of cancer cells.
Thus, the authors conclude that bacteria become resistant to gemcitabine by not taking it up, leaving more gemcitabine around in tumors to kill the cancer cells. The findings of the first question are a major strength of the manuscript - the complementary genetic screen and laboratory evolution experiment convincingly show that loss of nupC is likely a major genetic route for bacteria to become resistant to gemcitabine. Excellent biochemical studies delineate mechanistically how the different mutations including nupC contribute to gemcitabine resistance in the bacteria.
However, a major weakness of the manuscript is the extension to how this laboratory evolved nupC resistance to gemcitabine influences tumor response to gemcitabine. The only experiments done to assess this are performed in colorectal cell culture models in vitro. Importantly, these in vitro models do not recapitulate chemotherapy resistance observed in pancreas cancer and utilize levels of bacteria and gemcitabine that are likely not relevant to tumor physiology. Thus, additional experiments assessing in vivo if nupC mutations become prevalent in the pancreatic tumor microbiome and how much mutations affect tumor gemcitabine levels and response will be necessary to fully answer the authors second question of how bacterial evolution to gemcitabine affects tumor response to this agent.
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Reviewer #2 (Public Review):
The paper provides a natural extension of 2D multiphase field models for cell monolayers to 3D, addressing cell deformations, cell-cell interaction, cell-substrate interactions and active components for the cells. As known from 2D, the cell arrangement leads to positional (hexatic) defects and if the elongation of the cells is coarse-grained to define a global nematic order also to orientational (nematic) defects. These defects are characterized, see Figure 2. However, this is done in 2D and it remains unclear if the projected basal or apical side is considered in this figure and the following statistics. The authors identify correlations between orientational defects and extrusion events. In terms of positional defects such statistics seem not to be considered and the relation between positional defects and cell extrusion events remains vague. Also in-plane and out-of-plane stresses are computed. These results confirm a mechanical origin for cell extrusions. However, these are the only 3D information provided. The final claim that the results clearly demonstrate the existence of a mechanical route related with hexatic and nematic disclinations is not clear to me. 3D vertex models for such systems e.g. showed the importance of different mechanical behavior of the apical and basal side and identified scutoids as an essential geometric 3D feature in cell monolayers. These results are not discussed at all. A comparison of the 3D multiphase field model with such results would have been nice.
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Reviewer #2 (Public Review):
Skeletal muscle is the main regulator of glycemia in mammals and a major puzzle in the field of diabetes is the mechanism by which skeletal muscle (as well as other tissues) become insensitive to insulin or decrease glucose intake. the authors had proposed in a previous publication that high intracellular calcium, by means of calpain activation, could cleave and decrease the availability of GLUT4 glucose transporters. In this manuscript, the authors identify two additional targets of calpain activation. One of them is GSK3β, a specialized kinase that when cleaved, inhibits glycogen synthase and impairs glucose utilization. The second target is junctophilin 1, a protein involved in the structure of the complex responsible for E-C coupling in skeletal muscle. The authors succeeded in showing that a fragment of junctophilin1 (JPh44) moves from the triad to other cytosolic regions including the nuclei and they show changes in gene expression under these conditions, some of them linked to glucose metabolism.
Overall, the manuscript shows a novel and audacious approach with a careful treatment of the data (that was not always easy nor obvious) that allow sensible conclusions and definitively constitutes a step forward in this field.
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Reviewer #2 (Public Review):
This paper investigates the maintenance and function of memory follicular helper T (Tfh) cell subsets using in vitro approaches, murine immunization models and vaccine-challenged humans. Murine Tfh cell subsets (Tfh1, Tfh2, Tfh17) were generated using in vitro polarization (iTfh1, iTfh2, iTfh17), and then tested for support of humoral response following adoptive transfer or adoptive transfer with resting in vivo for 35 days. iTfh17 cells were statistically better than iTfh1 and iTfh2 cells in promoting GC B cell and plasma cell maturation after resting in vivo, although all 3 populations were capable of B cell help. Tfh17 cells were comparatively enriched among blood borne Tfh central memory cells in humans, and were enriched at the memory phase of vaccination with hepatitis B and influenza vaccines, compared to effector phase, suggesting the possibility they are comparatively superior in Tfh cell memory formation, with greater persistence in aged individuals.
Significance<br /> The enrichment of Tfh17 cells in Tfh cell central memory compartment and the dominance of Tfh17 cell population and the Tfh17 transcriptional signature in circulating Tfh cells at the memory phase are nicely demonstrated, and may well be helpful for understanding the heterogeneity of memory Tfh cells and potentially providing clues for vaccine design. The in vitro differentiation system for mouse Tfh cells also provides a strategy for others to build upon in dissection of Tfh cell development and function.
Points to consider<br /> 1. Even though Tfh17 cells are more likely to persist at memory timepoints in mice and in humans, or produce more GC B cells or plasma cells following transfer, all subsets can do this. Is GC output otherwise distinguishable following transfer of the individual subsets, or is their effect (cytokine related perhaps) pre-GC with differential CSR? It is also not clear if the individual subsets populate the GC and assuming they do so, if their respective phenotypes persist when they become GC Tfh cells.
2. iTfh17 cells induce more GC B cells and antibodies after resting and antigen challenge (Figures 1, 2). However, it's not clear whether this effect is a consequence of comparatively enhanced iTfh17 survival during resting (as suggested by latter figures), or better expansion or differential skewing to Tfh differentiation during challenge (as suggested by Figure 1 J,K). The total number of remaining adoptively-transferred cells right before challenge and 7 days post challenge will be helpful to understand that.
3. The authors tried to address whether Tfh17 cells have better ability to survive till memory phase or Tfh17 cells with memory potential are generated at higher frequency at the effector phase of vaccination (Figure 5); however, the experiment is not conclusive. The cTfh population 7 days post vaccination is a mixed population with effector Tph cells and Tfh memory precursors. The increased frequency of Th17 cells at day 28 compared to day 7 could be a consequence of superior survival ability, or Tfh memory precursors with Tfh17 signature are better generated.
4. Experiments to confirm expansion ability of the human subsets or their B cell helper ability were not performed.
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Reviewer #2 (Public Review):
This study addresses the ways in which bacteriophages antagonize or coopt the DNA restriction or recombination functions of the bacterial RecBCD helicase-nuclease.
The strength of the paper lies in the marriage of biochemistry and structural biology.
A cryo-EM structure of the RecBCD•gp5.9 complex establishes that gp5.9 is a DNA-mimetic dimer composed of an acidic parallel coiled coil that occupies the dsDNA binding site on the RecB and RecC subunits. The structure of gp5.9 is different from that of the RecBCD-inhibiting DNA mimetic protein phage λ Gam.
Cryo-EM structures of Abc2 are solved in complex with RecBCD bound to a forked DNA duplex, revealing that Abc2 interacts with the RecC subunit. A companion structure is solved containing PPI that copurifies with RecBCD•Abc2.
Whereas the gp5.9 structure fully rationalizes the effect of gp5.9 on RecBCD activity, the Abc2 structure - while illuminating the docking site on RecBCD, a clear advance - does not clarify how Abc2 impacts RecBCD function.
The authors speculate that Abc2 binding prevents RecA loading on the unwound DNA 3' strand while favoring the loading of the phage recombinase Erf.
Does the structure provide impetus and clues for further experiments to elaborate on that question and, if so, how?
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Reviewer #2 (Public Review):
The molecular changes of the aged tendon are not well understood. Loiselle et al previously established a mouse model that mimics aging tendon, where they depleted Scleraxis lineage (Scxlin) cells from tendon by injecting diptheria toxin (DT) in mice expressing the DT receptor under the control of the Scx promoter (DTR mice). In this manuscript, the authors demonstrate that the tendons from DTR mice resemble tendons from aged WT mice, in that they both have decreased cellularity, altered collagen organization (via SHG imaging), and impaired biomechanical properties. Proteomic analysis of WT, DTR, and aged WT tendons show that both DTR and aged WT tendons have decreased expression of extracellular matrix proteins (ECM). Corresponding with this, single RNA seq analysis of tendons from these three groups of mice showed that while WT tendons are enriched for genes related to collagen and ECM synthesis and also inflammation, DTR tendons express genes associated with ECM organization and structure and aged tendons express genes that regulate inflammation. The authors point out that this supports designing therapies to prevent tendon cell death to prevent the changes seen in aging tendon.
These data enhances the understanding of the protein and gene changes associated with aging in the tendon and in particular characterizes the importance of Scx+ cells to tendon organization and the aging process. The conclusions are supported by the data presented.
The manuscript would be strengthened by:<br /> 1) Improved clarity of figures presented<br /> 2) More details on the methodology used for biomechanical testing<br /> 3) Clarification if the decrease in ECM protein expression is due to decreased cellularity in the tendons of the DTR and aged mice, or decreased expression per cell<br /> 4) Providing more details on genes that are downregulated in comparison between groups
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Reviewer #2 (Public Review):
These discoveries are strongly supported by a large amount of clear and convincing data. Thus, the expression of seven distinct pol III-transcribed genes covering all types of promoter is shown to increase in three cell lines when STAT3 is overexpressed and to decrease when endogenous STAT3 is depleted. The proliferation of HepG2 liver cancer cells can be increased by STAT3 overexpression and decreased by STAT3 depletion. Crucially, proliferative induction by STAT3 is dependent on increased pol III activity, as it can be blocked using a pol III-specific inhibitor at a concentration that allows normal levels of pol III activity, but prevents further elevation. Growth of HepG2 xenograft tumours in mice is also slowed significantly when STAT3 is depleted. The effects of STAT3 on pol III output are indirect, mediated by miR-106a-5p. Thus, the knockdown of miR-106a-5p reverses the drop in pol III product expression following STAT3 depletion; conversely, pol III output is stimulated by a miR-106a-5p mimic. Elevated levels of miR-106a-5p correlate with significantly worse prognosis for patients with liver cancer. A key target for miR-106a-5p is a sequence in the 3'-UTR of the mRNA encoding TP73. Complementarity to this sequence allows miR-106a-5p to deplete the expression of TP73 and this is shown to be crucial for STAT3 to regulate the proliferation of HepG2 cells. Furthermore, TP73 is revealed to be a direct repressor of pol III-mediated transcription, an activity not previously known. TP73 is shown to inhibit the assembly of TFIIIB, the factor that is responsible for recruiting pol III to all of its genetic templates. A clear and convincing causal flow can therefore be traced: STAT3 induces miR-106a-5p, which depletes TP73, thereby removing a brake that limits pol III output and cell proliferation.
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Reviewer #2 (Public Review):
Summary:<br /> Dominant mutations in the gene encoding LIS1 cause lissencephaly, a severe developmental brain disorder. LIS1 regulates the multisubunit microtubule motor, cytoplasmic dynein 1, which can exist in an autoinhibited (closed) form and an activatable (open) form. Dynein is only active when bound to another complex, dynactin, and one of several known cargo adaptors. Because dynactin and cargo adaptors only interact with the open form, the local ratio of open to closed dynein can potentially dictate the proportion of "activatable" motors. The current view is that LIS1 stimulates dynein by reducing the autoinhibited closed form, and by recruiting two dynein motors to the active complex, which is thought to increase speeds and run lengths. LIS1 is highly conserved across animal and fungal species. The budding yeast LIS1 ortholog, called Pac1, is around 43% identical to human LIS1. Both Pac1 and LIS1 regulate dynein but there have been intriguing differences in their effect on dynein processivity in assays with purified proteins. The authors of the current manuscript recently published high resolution cryo-EM studies of Pac1 bound to yeast dynein (Gilles 2022). Based on their models they tested several mutations predicted to impact Pac1 binding to dynein and showed these mutations disrupted the single dynein dependent process in budding yeast, translocation of the mitotic spindle. However, mutations in yeast dynein that impacted LIS1 binding apparently only modestly impacted human dynein, prompting the current study that compares cryo-EM studies of human LIS1 bound to human dynein with the previously published studies using yeast proteins. The work points to subtle differences in how yeast and human LIS1 interact with the stem and loop regions of yeast and human dynein heavy chains and reveal an intriguing difference in the residues predicted to be important for the interaction between the two LIS1 propeller structures in the LIS1 dimer. They also report map known disease causing mutations in LIS1 and dynein on the structures and find three that might impact residues involved in protein-protein interaction.
Methods:<br /> This group has been able to use innovative methods to increase the resolution of CryoEM images to 3-4 Å, allowing them to make more accurate predictions about residues involved in protein-protein interactions. They have substantial expertise in the analysis of the resultant data, as demonstrated by past peer review studies. These are very labor-intensive experiments that allow a level of detail not possible with standard biochemical or cell biological analyses.
Results:<br /> The studies revealed subtle, but potentially important, differences between the yeast and human proteins.
Based on their analyses, the authors predicted specific residues that are likely to be important for human LIS1-dynein interactions with the stem region of dynein (sitestem) and with dyneins AAA domain containing ring (sitering). They also predicted specific residues that are likely to be important for an interaction between the two LIS1 beta-propellers, which in the yeast protein is apparently critical for dynein regulation.
The prediction that K147 could be important in the interaction between beta-propellers is very intriguing, given evidence that a K147A mutation disrupts LIS1 binding to dynein, but not to NDEL1, another interacting protein.
Impact
The predictions set out in this manuscript, if they hold up, could inform the design of tools to study LIS1 in the context of human disease. It seems likely from the data that at least some of the indicated residues will be important for human LIS1/dynein interactions
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