Reviewer #2 (Public Review):

Summary:<br /> In this work, Boor and colleagues explored the role of microbial food cues in the regulation of neuroendocrine-controlled foraging behavior. Consistent with previous reports, the authors find that C. elegans foraging behavior is regulated by the neuroendocrine TGFβ ligand encoded by daf-7. In addition to its known role in the neuroendocrine/sensory ASI neurons, Boot and colleagues show that daf-7 expression is dynamically regulated in the ASJ sensory neurons by microbial food cues - and that this regulation is important for exploration/exploitation balance during foraging. They identify at least two independent pathways by which microbial cues regulate daf-7 expression in ASJ: a likely gustatory pathway that promotes daf-7 expression and an opposing interoceptive pathway, also likely chemosensory in nature but which requires microbial ingestion to inhibit daf-7 expression. Two neuroendocrine pathways known to regulate foraging (serotonin and PDF-1) appear to act at least in part via daf-7 induction. They further identify a novel role for the C. elegans ALK orthologue encoded by scd-2, which acts in interneurons to regulate daf-7 expression and foraging behavior. These results together imply that distinct cues from microbial food are used to regulate the balance between exploration and exploitation via conserved signaling pathways.

Strengths:<br /> The findings that gustatory and interoceptive inputs into foraging behavior are separable and opposing are novel and interesting, which they have shown clearly in Figure 1. It is also clear from their results that removal of the interoceptive cue (via transfer to non-digestible food) results in rapid induction of daf-7::gfp in ASJ, and that ASJ plays an important role in the regulation of foraging behavior.

The role of the hen-1/scd-2 pathway in mediating the effects of ingested food is also compelling and well-interpreted. The use of precise gain-of-function alleles further supports their conclusions. This implies that important elements of this food-sensing pathway may be conserved in mammals.

Weaknesses:<br /> What is less clear to me from the work at this stage is how the gustatory input fits into this picture and to what extent can it be strongly concluded that the daf-7-regulating pathways that they have identified (del-3/7, 5-HT, PDFR-1, scd-2) act via the interoceptive pathway as opposed to the gustatory pathway. It follows from the work of the Flavell lab that del-3/7 likely acts via the interoceptive pathway in this context as well but this isn't shown directly - e.g. comparing the effects of aztreonam-treated bacteria and complete food removal to controls. The roles of 5-HT and PDFR-1 are even a bit less clear. Are the authors proposing that these are entirely parallel pathways? This could be explained in better detail.

It would also be helpful to elaborate more on why the identified transcriptional positive feedback loop is predicted to extend roaming state duration - as opposed to some other mechanism of increasing roaming such as increased probability of roaming state initiation. This doesn't seem self-evident to me. Related to this point is the somewhat confusing conclusion that the effects of tph-1 and pdfr-1 mutations on daf-7 expression are due to changes in ingestion during roaming/dwelling. From my understanding (e.g. Cermak et al., 2020), pharyngeal pumping rate does not reliably decrease during roaming - so is it clear that there are in fact lower rates of ingestion during roaming in their experiments? If so, why does increased roaming (via tph-1 mutation) result in further increases in daf-7 expression in animals fed aztreonam-treated food (Fig 3B)? Alternatively, there could be a direct signaling connection between the 5-HT/PDFR-1 pathways and daf-7 expression which could be acknowledged or explained.

Reviewer #2 (Public Review):

Clarkson et al investigated the impact of in vivo ESR1 gene disruption selectively in preoptic area GABA neurons on the estrogen regulation of LH secretion. The hypothalamic pathways by which estradiol controls the secretion of gonadotrophins are incompletely understood and relevant to a better understanding of the mechanisms driving fertility and reproduction. Using CRISPR-Cas9 methodology, the authors were able to effectively reduce the expression of estrogen receptor (ER)-alpha in GABA neurons located in the preoptic area of adult female mice. The results obtained were rather variable except in the animals with concomitant suppression of kisspeptin in the rostral periventricular region of the third ventricle (RP3V), which displayed interruption of ovarian cyclicity and an altered estradiol-induced LH surge. The experimental approach used allowed for a cell-selective, temporally-controlled suppression of ER-alpha expression, providing further evidence of the critical role of RP3V kisspeptin neurons in the estrogen positive-feedback effect. Nevertheless, the assessment of the estradiol-induced LH surge was limited to only one terminal blood collection. The preovulatory LH surge is a variable phenomenon and would require serial blood sampling for a conclusive evaluation of the surge occurrence or alteration, such as in shape, amplitude, or timing. The animals were not assessed for ovulation either, which might be a functional readout for the effectiveness of the LH surge. Thus, the actual effect on the preovulatory LH surge was not fully characterized. Finally, the study leaves unanswered the role of GABA itself. As there was no evident phenotype for the ESR1 knockdown in GABA neurons that do not coexpress kisspeptin, this suggests that GABA neurotransmission in the preoptic area is not involved in the estrogen regulation of LH secretion.

Reviewer #2 (Public Review):

Summary:

In this work, the authors explore how Notch activity acts together with Bsh homeodomain transcription factors to establish L4 and L5 fates in the lamina of the visual system of Drosophila. They propose a model in which differential Notch activity generates different chromatin landscapes in presumptive L4 and L5, allowing the differential binding of the primary homeodomain TF Bsh (as described in the co-submitted paper), which in turn activates downstream genes specific to either neuronal type. The requirement of Notch for L4 vs. L5 fate is well supported, and complete transformation from one cell type into the other is observed when altering Notch activity. However, the role of Notch in creating differential chromatin landscapes is not directly demonstrated. It is only based on correlation, but it remains a plausible and intriguing hypothesis.

Strengths:

The authors are successful in characterizing the role of Notch to distinguish between L4 and L5 cell fates. They show that the Notch pathway is active in L4 but not in L5. They identify L1, the neuron adjacent to L4 as expressing the Delta ligand, therefore being the potential source for Notch activation in L4. Moreover, the manuscript shows molecular and morphological/connectivity transformations from one cell type into the other when Notch activity is manipulated.

Using DamID, the authors characterize the chromatin landscape of L4 and L5 neurons. They show that Bsh occupies distinct loci in each cell type. This supports their model that Bsh acts as a primary selector gene in L4/L5 that activates different target genes in L4 vs L5 based on the differential availability of open chromatin loci.

Overall, the manuscript presents an interesting example of how Notch activity cooperates with TF expression to generate diverging cell fates. Together with the accompanying paper, it helps thoroughly describe how lamina cell types L4 and L5 are specified and provides an interesting hypothesis for the role of Notch and Bsh in increasing neuronal diversity in the lamina during evolution.

Weaknesses:

Differential Notch activity in L4 and L5:<br /> ● The manuscript focuses its attention on describing Notch activity in L4 vs L5 neurons. However, from the data presented, it is very likely that the pool of progenitors (LPCs) is already subdivided into at least two types of progenitors that will rise to L4 and L5, respectively. Evidence to support this is the activity of E(spl)-mɣ-GFP and the Dl puncta observed in the LPC region. Discussion should naturally follow that Notch-induced differences in L4/L5 might preexist L1-expressed Dl that affect newborn L4/L5. Therefore, the differences between L4 and L5 fates might be established earlier than discussed in the paper. The authors should acknowledge this possibility and discuss it in their model.<br /> ● The authors claim that Notch activation is caused by L1-expressed Delta. However, they use an LPC driver to knock down Dl. Dl-KD should be performed exclusively in L1, and the fate of L4 should be assessed.<br /> ● To test whether L4 neurons are derived from NotchON LPCs, I suggest performing MARCM clones in early pupa with an E(spl)-mɣ-GFP reporter.<br /> ● The expression of different Notch targets in LPCs and L4 neurons may be further explored. I suggest using different Notch-activity reporters (i.e., E(spl)-GFP reporters) to further characterize these differences. What cause the switch in Notch target expression from LPCs to L4 neurons should be a topic of discussion.

Notch role in establishing L4 vs L5 fates:<br /> ● The authors describe that 27G05-Gal4 causes a partial Notch Gain of Function caused by its genomic location between Notch target genes. However, this is not further elaborated. The use of this driver is especially problematic when performing Notch KD, as many of the resulting neurons express Ap, and therefore have some features of L4 neurons. Therefore, Pdm3+/Ap+ cells should always be counted as intermediate L4/L5 fate (i.e., Fig3 E-J, Fig3-Sup2), irrespective of what the mechanistic explanation for Ap activation might be. It's not accurate to assume their L5 identity. In Fig4 intermediate-fate cells are correctly counted as such.<br /> ● Lines 170-173: The temporal requirement for Notch activity in L5-to-L4 transformation is not clearly delineated. In Fig4-figure supplement 1D-E, it is not stated if the shift to 29{degree sign}C is performed as in Fig4-figure supplement 1A-C.<br /> ● Additionally, using the same approach, it would be interesting to explore the window of competence for Notch-induced L5-to-L4 transformation: at which point in L5 maturation can fate no longer be changed by Notch GoF?

L4-to-L3 conversion in the absence of Bsh<br /> ● Although interesting, the L4-to-L3 conversion in the absence of Bsh is never shown to be dependent on Notch activity. Importantly, L3 NotchON status is assumed based on their position next to Dl-expressing L1, but it is not empirically tested. Perhaps screening Notch target reporter expression in the lamina, as suggested above, could inform this issue.<br /> ● Otherwise, the analysis of Bsh Loss of Function in L4 might be better suited to be included in the accompanying manuscript that specifically deals with the role of Bsh as a selector gene for L4 and L5.

Different chromatin landscape in L4 and L5 neurons<br /> ● A major concern is that, although L4 and L5 neurons are shown to present different chromatin landscapes (as expected for different neuronal types), it is not demonstrated that this is caused by Notch activity. The paper proves unambiguously that Notch activity, in concert with Bsh, causes the fate choice between L4 and L5. However, that this is caused by Notch creating a differential chromatin landscape is based only in correlation (NotchON cells having a different profile than NotchOFF). Although the authors are careful not to claim that differential chromatin opening is caused directly by Notch, this is heavily suggested throughout the text and must be toned down.<br /> e.g.: Line 294: "With Notch signaling, L4 neurons generate distinct open chromatin landscape" and Line 298: "Our findings propose a model that the unique combination of HDTF and open chromatin landscape (e.g. by Notch signaling)" . These claims are not supported well enough, and alternative hypotheses should be provided in the discussion. An alternative hypothesis could be that LPCs are already specified towards L4 and L5 fates. In this context, different early Bsh targets in each cell type could play a pioneer role generating a differential chromatin landscape.

● The correlation between open chromatin and Bsh loci with Differentially Expressed genes is much higher for L4 than L5. It is not clear why this is the case, and should be discussed further by the authors.

Reviewer #2 (Public Review):

Summary:<br /> In this paper, the authors explore the role of the Homeodomain Transcription Factor Bsh in the specification of Lamina neuronal types in the optic lobe of Drosophila. Using the framework of terminal selector genes and compelling data, they investigate whether the same factor that establishes early cell identity is responsible for the acquisition of terminal features of the neuron (i.e., cell connectivity and synaptogenesis).

The authors convincingly describe the sequential expression and activity of Bsh, termed here as 'primary HDTF', and of Ap in L4 or Pdm3 in L5 as 'secondary HDTFs' during the specification of these two neurons. The study demonstrates the requirement of Bsh to activate either Ap and Pdm3, and therefore to generate the L4 and L5 fates. Moreover, the authors show that in the absence of Bsh, L4 and L5 fates are transformed into a L1 or L3-like fates.

Finally, the authors used DamID and Bsh:DamID to profile the open chromatin signature and the Bsh binding sites in L4 neurons at the synaptogenesis stage. This allows the identification of putative Bsh target genes in L4, many of which were also found to be upregulated in L4 in a previous single-cell transcriptomic analysis. Among these genes, the paper focuses on Dip-β, a known regulator of L4 connectivity. They demonstrate that both Bsh and Ap are required for Dip-β, forming a feed-forward loop. Indeed, the loss of Bsh causes abnormal L4 synaptogenesis and therefore defects in several visual behaviors.

The authors also propose the intriguing hypothesis that the expression of Bsh expanded the diversity of Lamina neurons from a 3 cell-type state to the current 5 cell-type state in the optic lobe.

Strengths:

Overall, this work presents a beautiful practical example of the framework of terminal selectors: Bsh acts hierarchically with Ap or Pdm3 to establish the L4 or L5 cell fates and, at least in L4, participates in the expression of terminal features of the neuron (i.e., synaptogenesis through Dip-β regulation).

The hierarchical interactions among Bsh and the activation of Ap and Pdm3 expression in L4 and L5, respectively, are well established experimentally. Using different genetic drivers, the authors show a window of competence during L4 neuron specification during which Bsh activates Ap expression. Later, as the neuron matures, Ap becomes independent of Bsh. This allows the authors to propose a coherent and well-supported model in which Bsh acts as a 'primary' selector that activates the expression of L4-specific (Ap) and L5-specific (Pdm3) 'secondary' selector genes, that together establish neuronal fate.

Importantly, the authors describe a striking cell fate change when Bsh is knocked down from L4/L5 progenitor cells. In such cases, L1 and L3 neurons are generated at the expense of L4 and L5. The paper demonstrates that Bsh in L4/L5 represses Zfh1, which in turn acts as the primary selector for L1/L3 fates. These results point to a model where the acquisition of Bsh during evolution might have provided the grounds for the generation of new cell types, L4 and L5, expanding lamina neuronal diversity for a more refined visual behaviors in flies. This is an intriguing and novel hypothesis that should be tested from an evo-devo standpoint, for instance by identifying a species when L4 and L5 do not exist and/or Bsh is not expressed in L neurons.

To gain insight into how Bsh regulates neuronal fate and terminal features, the authors have profiled the open chromatin landscape and Bsh binding sites in L4 neurons at mid-pupation using the DamID technique. The paper describes a number of genes that have Bsh binding peaks in their regulatory regions and that are differentially expressed in L4 neurons, based on available scRNAseq data. Although the manuscript does not explore this candidate list in depth, many of these genes belong to classes that might explain terminal features of L4 neurons, such as neurotransmitter identity, neuropeptides or cytoskeletal regulators. Interestingly, one of these upregulated genes with a Bsh peak is Dip-β, an immunoglobulin superfamily protein that has been described by previous work from the author's lab to be relevant to establish L4 proper connectivity. This work proves that Bsh and Ap work in a feed-forward loop to regulate Dip-β expression, and therefore to establish normal L4 synapses. Furthermore, Bsh loss of function in L4 causes impairs visual behaviors.

Weaknesses:

● The last paragraph of the introduction is written using rhetorical questions and does not read well. I suggest rewriting it in a more conventional direct style to improve readability.

● A significant concern is the way in which information is conveyed in the Figures. Throughout the paper, understanding of the experimental results is hindered by the lack of information in the Figure headers. Specifically, the genetic driver used for each panel should be adequately noted, together with the age of the brain and the experimental condition. For example, R27G05-Gal4 drives early expression in LPCs and L4/L5, while the 31C06-AD, 34G07-DBD Split-Gal4 combination drives expression in older L4 neurons, and the use of one or the other to drive Bsh-KD has dramatic differences in Ap expression. The indication of the driver used in each panel will facilitate the reader's grasp of the experimental results.

● Bsh role in L4/L5 cell fate:<br /> o It is not clear whether Tll+/Bsh+ LPCs are the precursors of L4/L5. Morphologically, these cells sit very close to L5, but are much more distant from L4.<br /> o Somatic CRISPR knockout of Bsh seems to have a weaker phenotype than the knockdown using RNAi. However, in several experiments down the line, the authors use CRISPR-KO rather than RNAi to knock down Bsh activity: it should be explained why the authors made this decision. Alternatively, a null mutant could be used to consolidate the loss of function phenotype, although this is not strictly necessary given that the RNAi is highly efficient and almost completely abolishes Bsh protein.<br /> o Line 102: Rephrase "R27G05-Gal4 is expressed in all LPCs and turned off in lamina neurons" to "is turned off as lamina neurons mature", as it is kept on for a significant amount of time after the neurons have already been specified.<br /> o Line 121: "(a) that all known lamina neuron markers become independent of Bsh regulation in neurons" is not an accurate statement, as the markers tested were not shown to be dependent on Bsh in the first place.<br /> o Lines 129-134: Make explicit that the LPC-Gal4 was used in this experiment. This is especially important here, as these results are opposite to the Bsh Loss of Function in L4 neurons described in the previous section. This will help clarify the window of competence in which Bsh establishes L4/L5 neuronal identities through ap/pdm3 expression.

● DamID and Bsh binding profile:<br /> ○ Figure 5 - figure supplement 1C-E: The genotype of the Control in (C) has to be described within the panel. As it is, it can be confused with a wild type brain, when it is in fact a Bsh-KO mutant.<br /> ○ It Is not clear how L4-specific Differentially Expressed Genes were found. Are these genes DEG between Lamina neurons types, or are they upregulated genes with respect to all neuronal clusters? If the latter is the case, it could explain the discrepancy between scRNAseq DEGs and Bsh peaks in L4 neurons.

● Dip-β regulation:<br /> ○ Line 234: It is not clear why CRISPR KO is used in this case, when Bsh-RNAi presents a stronger phenotype.<br /> ○ Figure 6N-R shows results using LPC-Gal4. It is not clear why this driver was used, as it makes a less accurate comparison with the other panels in the figure, which use L4-Split-Gal4. This discrepancy should be acknowledged and explained, or the experiment repeated with L4-Split-Gal4>Ap-RNAi.<br /> ○ Line 271: It is also possible that L4 activity is dispensable for motion detection and only L5 is required.

● Discussion: It is necessary to de-emphasize the relevance of HDTFs, or at least acknowledge that other, non-homeodomain TFs, can act as selector genes to determine neuronal identity. By restricting the discussion to HDTFs, it is not mentioned that other classes of TFs could follow the same Primary-Secondary selector activation logic.

Reviewer #2 (Public Review):

Summary:<br /> Desiderio and colleagues investigated the role of the TALE (three amino acid loop extension) homeodomain transcription factor Meis2 during maturation and target innervation of mechanoreceptors and their sensation to touch. They start with a series of careful in situ hybridizations to examine Meis2 transcript expression in mouse and chick DRGs of different embryonic stages. By this approach, they identify Meis2+ neurons as slowly- and rapidly adapting A-beta LTMRs, respectively. Retrograde tracing experiments in newborn mice confirmed that Meis2-expressing sensory neurons project to the skin, while unilateral limb bud ablations in chick embryos in Ovo showed that these neurons require target-derived signals for survival. The authors further generated a conditional knock-out (cKO) mouse model in which Meis2 is selectively lost in Islet1-expressing, postmitotic neurons in the DRG (IsletCre/+::Meis2flox/flox, abbreviated below as cKO). WT and Islet1Cre/+ littermates served as controls. cKO mice did not exhibit any obvious alteration in volume or cellular composition of the DRGs but showed significantly reduced sensitivity to touch stimuli and various innervation defects to different end-organ targets. RNA-sequencing experiments of E18.5 DRGs taken from WT, Islet1Cre/+, and cKO mice reveal extensive gene expression differences between cKO cells and the two controls, including synaptic proteins and components of the GABAergic signaling system. Gene expression also differed considerably between WT and heterozygous Islet1Cre/+ mice while several of the other parameters tested did not. These findings suggest that Islet1 heterozygosity affects gene expression in sensory neurons but not sensory neuron functionality. However, only some of the parameters tested were assessed for all three genotypes. Histological analysis and electrophysiological recordings shed light on the physiological defects resulting from the loss of Meis2. By immunohistochemical approaches, the authors describe distinct innervation defects in glabrous and hairy skin (reduced innervation of Merkel cells by SA1-LTMRs in glabrous but not hairy skin, reduced complexity of A-beta RA1-LTMs innervating Meissner's corpuscles in glabrous skin, reduced branching and innervation of A-betA RA1-LTMRs in hairy skin). Electrophysiological recordings from ex vivo skin nerve preparations found that several, but not all of these histological defects are matched by altered responses to external stimuli, indicating that compensation may play a considerable role in this system.

Strengths:<br /> This is a well-conducted study that combines different experimental approaches to convincingly show that the transcription factor Meis2 plays an important role in the perception of light touch. The authors describe a new mouse model for compromised touch sensation and identify a number of genes whose expression depends on Meis2 in mouse DRGs. Given that dysbalanced MEIS2 expression in humans has been linked to autism and that autism seems to involve an inappropriate response to light touch, the present study makes a novel and important link between this gene and ASD.

Weaknesses:<br /> The authors make use of different experimental approaches to investigate the role of Meis2 in touch sensation, but the results obtained by these techniques could be connected better. For instance, the authors identify several genes involved in synapse formation, synaptic transmission, neuronal projections, or axon and dendrite maturation that are up- or downregulated upon targeted Meis2 deletion, but it is unresolved whether these chances can in any way explain the histological, electrophysiological, or behavioral deficits observed in cKO animals. The use of two different controls (WT and Islet1Cre/+) is unsatisfactory and it is not clear why some parameters were studied in all three genotypes (WT, Islet1Cre/+ and cKO) and others only in WT and cKO. In addition, Meis2 mutant mice apparently are less responsive to touch, whereas in humans, mutation or genomic deletion involving the MEIS2 gene locus is associated with ASD, a condition that, if anything, is associated with an elevated sensitivity to touch. It would be interesting to know how the authors reconcile these two findings. A minor weakness, the first manuscript suffers from some ambiguities and errors, but these can be easily corrected.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by David et al. describes a novel image segmentation method, implementing Local Moran's method, which determines whether the value of a datapoint or a pixel is randomly distributed among all values, in differentiating pixel clusters from the background noise. The study includes several proof-of-concept analyses to validate the power of the new approach, revealing that implementation of Local Moran's method in image segmentation is superior to threshold-based segmentation methods commonly used in analyzing confocal images in neuroanatomical studies.

Strengths:<br /> Several proof-of-concept experiments are performed to confirm the sensitivity and validity of the proposed method. Using composed images with varying levels of background noise and analyzing them in parallel with the Local Moran's or a Threshold-Based Method (TBM), the study is able to compare these approaches directly and reveal their relative power in isolating clustered pixels.

Similarly, dual immuno-electron microscopy was used to test the biological relevance of a colocalization that was revealed by Local Moran's segmentation approach on dual-fluorescent labeled tissue using immuno-markers of the axon terminal and a membrane-protein (Figure 5). The EM revealed that the two markers were present in terminals and their post-synaptic partners, respectively. This is a strong approach to verify the validity of the new approach for determining object-based colocalization in fluorescent microscopy.

The methods section is clear in explaining the rationale and the steps of the new method (however, see the weaknesses section). Figures are appropriate and effective in illustrating the methods and the results of the study. The writing is clear; the references are appropriate and useful.

Weaknesses:<br /> While the steps of the mathematical calculations to implement Local Moran's principles for analyzing high-resolution images are clearly written, the manuscript currently does not provide a computation tool that could facilitate easy implementation of the method by other researchers. Without a user-friendly tool, such as an ImageJ plugin or a code, the use of the method developed by David et al by other investigators may remain limited.

Reviewer #2 (Public Review):

This manuscript by Muñoz-Reyes et al. presents studies on the molecular mechanisms by which NCS-1 regulates Ric-8A and its interaction with Ga. They have investigated how calcium ions and phosphorylation of Ric-8A affect these interactions. They found that NCS-1 induces a conformational change in Ric-8A that prevents its phosphorylation and subsequent interaction with Ga, and this can be reversed by increasing calcium ion concentration. Using structural biology methods, they determined the interaction surfaces between NCS-1 and Ric-8A. These mechanistic analyses are needed in the field and beneficial to helping us understand specificity in the regulation of G protein signaling.

Overall, this manuscript presents an abundance of data that supports the authors' conclusions. The introduction is thorough and well-written. The structure figures are beautiful and clear - well done. Most of the biochemical and biophysical experiments are convincing. In some cases, further elaborations and explanations of data interpretation are needed. The crystallographic data is solid. However, I have major concerns with the cryo-EM data presented due to its low quality and the conclusions drawn from it.

Reviewer #2 (Public Review):

Summary:<br /> The authors set out to determine which lipid transfer proteins impact the lipids of Golgi apparatus, and they identified a reasonable number of "hits" where the lack of one lipid transfer protein affected a particular Golgi lipid or class of lipids. They then carried out something close to a "proof of concept" for one lipid (sphingomyelin) and two closely related lipid transfer proteins (ORP9/ORP11). They looked into that example in great detail and found a previously unknown relationship between the level of phosphatidylserine in the Golgi (presumably trans-Golgi, trans-Golgi Network) and the function of the sphingomyelin synthase enzyme. This was all convincingly done - results support their conclusions - showing that the authors achieved their aims.

Impact:<br /> There are likely to be 2 types of impact:<br /> (I) cell biology: sphoingomyelin synthase, ORP9/11 will be studied in the future in more informed ways to understand (a) the role of different Golgi lipids - this work opens that out and produces more questions than answers (b) the role of different ORPs: what distinguishes ORP11 from its paralogy ORP10?<br /> (ii) molecular biochemistry: combining knockdown miniscreen with organelle lipidomics must be time-consuming, but here it is shown to be quite a powerful way to discover new aspects of lipid-based regulation of protein function. This will be useful to others as an example, and if this kind of workflow could be automated, then the possible power of the method could be widely applied.

Strengths:<br /> Nicely controlled data;<br /> Wide-ranging lipidomics dataset with repeats and SDs - all data easily viewed.<br /> Simple take-home message that PS traffic to the TGN by ORP9/11 is required for some aspect of SMS1 function.

Weaknesses:<br /> Model and Discussion:<br /> No idea about the aspect of SMS1 function that is being affected. Even if no further experiments were carried out, the authors could discuss possibilities. One might speculate what the PS is being used for. For example, is it a co-factor for integral membrane proteins, such as flippases? Is it a co-factor for peripheral membrane proteins, such as yet more LTPs? The model could include the work of Peretti et al (2008), which linked Nir2 activity exchanging PI:PA (Yadav et al, 2015) to the eventual function of CERT. Could the PS have a role in removing/reducing DAG produced by CERT?

Reviewer #2 (Public Review):

Summary: The study demonstrates that deletion of a small cytoplasmic membrane protein, Tmem263, caused severe impairment of longitudinal bone growth and that the impaired bone growth was caused by suppression of expression and/or protein levels of growth hormone receptors in the liver.

Strengths: The experimental design of the study is sound and the results are in general supportive of the conclusions.

Weaknesses: The study lacks mechanistic investigation into how the deletion of a gene corresponding to a small cytoplasmic membrane protein would lead to a substantial reduction in the gene expression of growth hormone receptor, which takes place in the nuclei. Accordingly, the manuscript is of a largely descriptive nature.

Reviewer #2 (Public Review):

Summary:

The authors provide strong evidence that bacteria, such as E. coli, compete with tumor cells for iron resources and consequently reduce tumor growth. When sequestration between LCN2 and bacterobactin is blocked by upregulating CDG(DGC-E. coli) or salmochelin(IroA-E.coli), E. coli increase iron uptake from the tumor microenvironment (TME) and restrict iron availability for tumor cells. Long-term remission in IroA-E.coli treated mice is associated with enhanced CD8+ T cell activity. Additionally, systemic delivery of IroA-E.coli shows a synergistic effect with chemotherapy reagent oxaliplatin to reduce tumor growth.

Strengths:

It is important to identify the iron-related crosstalk between E. coli and TME. Blocking lcn2-bacterobactin sequestration by different strategies consistently reduces tumor growth.

Weaknesses:

As engineered E.coli upregulate their function to uptake iron, they may increase the likelihood of escaping from nutritional immunity (LCN2 becomes insensitive to sequester iron from the bacteria). Would this raise the chance of developing sepsis? Do authors think that it is safe to administrate these engineered bacteria in mice or humans?

Reviewer #2 (Public Review):

Summary:<br /> The authors embarked on a journey to understand the mechanisms and intensity-dependency of ultrasound (US)-induced extracellular vesicle (EV) release from myotubes and the potential anti-inflammatory effects of these EVs on macrophages. This study builds on their prior work from 2021 that initially reported US-induced EV secretion.

Strengths:<br /> 1. The finding that US-treated myotube EVs can suppress macrophage inflammatory responses is particularly intriguing, hinting at potential therapeutic avenues in inflammation modulation.

Weaknesses:<br /> 1. The exploration of output parameters for US induction appears limited, with only three different output powers (intensities) tested, thus narrowing the scope of their findings.<br /> 2. Their claim of elucidating mechanisms seems to be only partially met, with a predominant focus on the correlation between calcium responses and EV release.<br /> 3. While the intracellular calcium response is a dynamic activity, the method used to measure it could risk a loss of kinetic information.<br /> 4. The inclusion of miRNA sequencing is commendable; however, the interpretation of this data fails to draw clear conclusions, diminishing the impact of this segment.

While the authors have shown the anti-inflammatory effects of US-induced EVs on macrophages, there are gaps in the comprehensive understanding of the mechanisms underlying US-induced EV release. Certain aspects, like the calcium response and the utility of miRNA sequencing, were not fully explored to their potential. Therefore, while the study establishes some findings, it leaves other aspects only partially substantiated.

Reviewer #2 (Public Review):

The manuscript of Akter et al is an important study that investigates the role of astrocytic Gi signaling in the anterior cingulate cortex in the modulation of extracellular L-lactate level and consequently impairment in flavor-place associates (PA) learning. However, whereas some of the behavioral observations and signaling mechanism data are compelling, the conclusions about the effect on memory are inadequate as they rely on an experimental design that does not allow to differentiate acute or learning effect from the effect outlasting pharmacological treatments, i.e. effect on memory retention. With the addition of a few experiments, this paper would be of interest to the larger group of researchers interested in neuron-glia interactions during complex behavior.<br /> • Largely, I agree with the authors' conclusion that activating Gi signaling in astrocytes impairs PA learning, however, the effect on memory retrieval is not that obvious. All behavioral and molecular signaling effects described in this study are obtained with the continuous presence of CNO, therefore it is not possible to exclude the acute effect of Gi pathway activation in astrocytes. What will happen with memory on retrieval test when CNO is omitted selectively during early, middle, or late session blocks of PA learning?<br /> • I found it truly exciting that the administration of exogenous L-lactate is capable to rescue CNO-induced PA learning impairment, when co-applied. Would it be possible that this treatment has a sensitivity to a particular stage of learning (acquisition, consolidation, or memory retrieval) when L-lactate administration would be the most efficacious?<br /> • The hypothesis that observed learning impairments could be associated with diminished mitochondrial biogenesis caused by decreased l-lactate in the result of astrocytic Gi-DREADDS stimulation is very appealing, but a few key pieces of evidence are missing. So far, the hypothesis is supported by experiments demonstrating reduced expression of several components of mitochondrial membrane ATP synthase and a decrease in relative mtDNA copy numbers in ACC of rats injected with Gi-DREADDs. L-lactate injections into ACC restored and even further increased the expression of the above-mentioned markers. Co-administration of NMDAR antagonist D-APV or MCT-2 (mostly neuronal) blocker 4-CIN with L-lactate, prevented L-lactate-induced increase in relative mtDNA copy. I am wondering how the interference with mitochondrial biogenesis is affecting neuronal physiology and if it would result in impaired PA learning or schema memory.

Reviewer #2 (Public Review):

Summary:

The manuscript by Wohlwend et al. investigates the implications of inhibiting ceramide synthase Cers1 on skeletal muscle function during aging. The authors propose a role for Cers1 in muscle myogenesis and aging sarcopenia. Both pharmacological and AAV-driven genetic inhibition of Cers1 in 18-month-old mice lead to reduced C18 ceramides in skeletal muscle, exacerbating age-dependent features such as muscle atrophy, fibrosis, and center-nucleated fibers. Similarly, inhibition of the Cers1 orthologue in C. elegans reduces motility and causes alterations in muscle morphology.

Strengths:

The study is well-designed, carefully executed, and provides highly informative and novel findings that are relevant to the field.

Weaknesses:

The following points should be addressed to support the conclusions of the manuscript.

1) It would be essential to investigate whether P053 treatment of young mice induces age-dependent features besides muscle loss, such as muscle fibrosis or regeneration. This would help determine whether the exacerbation of age-dependent features solely depends on Cers1 inhibition or is associated with other factors related to age-dependent decline in cell function. Additionally, considering the reported role of Cers1 in whole-body adiposity, it is necessary to present data on mice body weight and fat mass in P053-treated aged-mice.

2) As grip and exercise performance tests evaluate muscle function across several muscles, it is not evident how intramuscular AAV-mediated Cers1 inhibition solely in the gastrocnemius muscle can have a systemic effect or impact different muscles. This point requires clarification.

3) To further substantiate the role of Cers1 in myogenesis, it would be crucial to investigate the consequences of Cers1 inhibition under conditions of muscle damage, such as cardiotoxin treatment or eccentric exercise.

4) It would be informative to determine whether the muscle defects are primarily dependent on the reduction of C18-ceramides or the compensatory increase of C24-ceramides or C24-dihydroceramides.

5) Previous studies from the research group (PMID 37118545) have shown that inhibiting the de novo sphingolipid pathway by blocking SPLC1-3 with myriocin counteracts muscle loss and that C18-ceramides increase during aging. In light of the current findings, certain issues need clarification and discussion. For instance, how would myriocin treatment, which reduces Cers1 activity because of the upstream inhibition of the pathway, have a positive effect on muscle? Additionally, it is essential to explain the association between the reduction of Cers1 gene expression with aging (Fig. 1B) and the age-dependent increase in C18-ceramides (PMID 37118545).

Addressing these points will strengthen the manuscript's conclusions and provide a more comprehensive understanding of the role of Cers1 in skeletal muscle function during aging.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, Nie et al investigate the effect of PARG KO and PARG inhibition (PARGi) on pADPR, DNA damage, cell viability, and synthetic lethal interactions in HEK293A and Hela cells. Surprisingly, the authors report that PARG KO cells are sensitive to PARGi and show higher pADPR levels than PARG KO cells, which are abrogated upon deletion or inhibition of PARP1/PARP2. The authors explain the sensitivity of PARG KO to PARGi through incomplete PARG depletion and demonstrate complete loss of PARG activity when incomplete PARG KO cells are transfected with additional gRNAs in the presence of PARPi. Furthermore, the authors show that the sensitivity of PARG KO cells to PARGi is not caused by NAD depletion but by S-phase accumulation of pADPR on chromatin coming from unligated Okazaki fragments, which are recognized and bound by PARP1. Consistently, PARG KO or PARG inhibition shows synthetic lethality with Pol beta, which is required for Okazaki fragment maturation. PARG expression levels in ovarian cancer cell lines correlate negatively with their sensitivity to PARGi.

Strengths:<br /> The authors show that PARG is essential for removing ADP-ribosylation in S-phase.

Weaknesses:<br /> 1) This begs the question as to the relevant substrates of PARG in S-phase, which could be addressed, for example, by analysing PARylated proteins associated with replication forks in PARG-depleted cells (EdU pulldown and Af1521 enrichment followed by mass spectrometry).<br /> 2) The results showing the generation of a full PARG KO should be moved to the beginning of the Results section, right after the first Results chapter (PARG depletion leads to drastic sensitivity to PARGi), otherwise, the reader is left to wonder how PARG KO cells can be sensitive to PARGi when there should be presumably no PARG present.<br /> 3) Please indicate in the first figure which isoforms were targeted with gRNAs, given that there are 5 PARG isoforms. You should also highlight that the PARG antibody only recognizes the largest isoform, which is clearly absent in your PARG KO, but other isoforms may still be produced, depending on where the cleavage sites were located.<br /> 4) FACS data need to be quantified. Scatter plots can be moved to Supplementary while quantification histograms with statistical analysis should be placed in the main figures.<br /> 5) All colony formation assays should be quantified and sensitivity plots should be shown next to example plates.<br /> 6) Please indicate how many times each experiment was performed independently and include statistical analysis.

Reviewer #2 (Public Review):

This paper explores how minimal active matter simulations can model tissue rheology, with applications to the in vivo situation of zebrafish morphogenesis. The authors explore the idea of active noise, particle softness and size heterogeneity cooperating to give rise to surprising features of experimental tissue rheologies (in particular an increase and then a plateau in viscosity with fluid fraction). In general, the paper is interesting from a theoretical standpoint, by providing a bridge between concepts from jamming of particulate systems and experiments in developmental biology. The idea of exploring a free space picture in this context is also interesting. However, I'm still unsure right now though of how much it can be applied to the specific system that the authors refer to - which could be fixed either by doing theoretical checks or considering other experimental systems/models reported in the recent literature.

Reviewer #2 (Public Review):

The authors investigate the origin of asexual reproduction through hybridization between species. In loaches, diploid, polyploid, and asexual forms have been described in natural populations. The authors experimentally cross multiple species of loaches and conduct an impressively detailed characterization of gametogenesis using molecular cytogenetics to show that although meiosis arrests early in male hybrids, a subset of cells in females undergo endoreplication before meiosis, producing diploid eggs. This only occurred in hybrids of parental species that were of intermediate divergence. This work supports an expanding view of speciation where asexuality could emerge during a narrow evolutionary window where genomic divergence between species is not too high to cause hybrid inviability, but high enough to disrupt normal meiotic processes.

I enjoyed reading this study and I was impressed by the rigorous experiments. The authors provide strong evidence that premeiotic genome endoreplication is the mechanism behind asexually-reproducing females. In addition, I found the evidence convincing that this phenomenon is a consequence of combining two divergent genomes in an F1 hybrid female. The authors did not observe a single incidence of genome duplication in any of the parental species among a large number of surveyed oocytes.

Reviewer #2 (Public Review):

Summary:<br /> The authors study through theory and simulations the diffusion of microscopic particles and aim to account for the effects of inhomogeneous viscosity and diffusion - in particular regarding the intracellular environment. They propose a mechanism, termed "Diffusive lensing", by which particles are attracted towards high-viscosity regions where they remain trapped. To obtain these results, the authors rely on agent-based simulations using custom rules performed with the Ito stochastic calculus convention, without spurious drift. They acknowledge the fact that this convention does not describe equilibrium systems, and that their results would not hold at equilibrium - and discard these facts by invoking the fact that cells are out-of-equilibrium. Finally, they show some applications of their findings, in particular enhanced clustering in the high-viscosity regions. The authors conclude that as inhomogeneous diffusion is ubiquitous in life, so must their mechanism be, and hence it must be important.

Strengths:<br /> The article is well-written, and clearly intelligible, its hypotheses are stated relatively clearly and the models and mathematical derivations are compatible with these hypotheses.

Weaknesses:<br /> The main problem of the paper is these hypotheses. Indeed, it all relies on the Ito interpretation of the stochastic integrals. Stochastic conventions are a notoriously tricky business, but they are both mathematically and physically well-understood and do not result in any "dilemma" [some citations in the article, such as (Lau and Lubensky) and (Volpe and Wehr), make an unambiguous resolution of these]. Conventions are not an intrinsic, fixed property of a system, but a choice of writing; however, whenever going from one to another, one must include a "spurious drift" that compensates for the effect of this change - a mathematical subtlety that is entirely omitted in the article: if the drift is zero in one convention, it will thus be non-zero in another in the presence of diffusive gradients. It is well established that for equilibrium systems obeying fluctuation-dissipation, the spurious drift vanishes in the anti-Ito stochastic convention (which is not "anticipatory", contrarily to claims in the article, are the "steps" are local and infinitesimal). This ensures that the diffusion gradients do not induce currents and probability gradients, and thus that the steady-state PDF is the Gibbs measure. This equilibrium case should be seen as the default: a thermal system NOT obeying this law should warrant a strong justification (for instance in the Volpe and Wehr review this can occur through memory effects in robotic dynamics, or through strong fluctuation-dissipation breakdown). In near-equilibrium thermal systems such as the intracellular medium (where, although out-of-equilibrium, temperature remains a relevant and mostly homogeneous quantity), deviations from this behavior must be physically justified and go to zero when going towards equilibrium.

Here, drifts are arbitrarily set to zero in the Ito convention (the exact opposite of the equilibrium anti-Ito), which is the equilibrium equivalent to adding a force (with drift $- grad D$) exactly compensating the spurious drift. If we were to interpret this as a breakdown of detailed balance with inhomogeneous temperature, the "hot" region would be effectively at 4x higher temperature than the cold region (i.e. 1200K) in Fig 1A.

It is the effects of this arbitrary force (exactly compensating the Ito spurious drift) that are studied in the article. The fact that it results in probability gradients is trivial once formulated this way (and in no way is this new - many of the references, for instance, Volpe and Wehr, mention this). Enhanced clustering is also a trivial effect of this probability gradient (the local concentration is increased by this force field, so phase separation can occur). As a side note the "neighbor sensing" scheme to describe interactions is very peculiar and not physically motivated - it violates stochastic thermodynamics laws too, as the detailed balance is apparently not respected. Finally, the "anomalous diffusion" discussion is at odds with what the literature on this subject considers anomalous (the exponent does not appear anomalous).

The authors make no further justification of their choice of convention than the fact that cells are out-of-equilibrium, leaving the feeling that this is a detail. They make mentions of systems (eg glycogen, prebiotic environment) for which (near-)equilibrium physics should mostly prevail, and of fluctuation-dissipation ("Diffusivity varies inversely with viscosity", in the introduction). Yet the "phenomenon" they discuss is entirely reliant on an undiscussed mechanism by which these assumptions would be completely violated (the citations they make for this - Gnesotto '18 and Phillips '12 - are simply discussions of the fact that cells are out-of-equilibrium, not on any consequences on the convention).

Finally, while inhomogeneous diffusion is ubiquitous, the strength of this effect in realistic conditions is not discussed (this would be a significant problem if the effect were real, which it isn't). Gravitational attraction is also an ubiquitous effect, but it is not important for intracellular compartmentalization.

To conclude, the "diffusive lensing" effect presented here is not a deep physical discovery, but a well-known effect of sticking to the wrong stochastic convention.

Reviewer #2 (Public Review):

Summary:<br /> In the manuscript by Luo et al, the authors investigated the nature and function of TRAIL-HS binding for the regulation of TRAIL-mediated apoptosis in cancer cells. The authors discovered that TRAIL binds to 12mer HS and identified the amino acid residues critical for the binding. The authors further nicely showed that 12mer HS binds to TRAIL homotrimer and larger HS can further promote the formation of larger TRAIL oligomers. Structural analyses were conducted to characterize the binding of TRAIL/HS complexes. At functional level, the authors demonstrated that HS promotes the cell surface binding of TRAIL to enhance TRAIL-mediated apoptosis in a variety of cancer cells. Moreover, the ability of TRAIL to induce apoptosis is correlated with cell surface HS level. Lastly, the authors showed that HS forms complex with TRAIL and its receptor DR5 and promotes DR5 internalization.

Strengths:<br /> Overall, this is a nicely executed study providing both mechanistic and functional insight for TRAIL-mediated apoptosis. It conducted detailed characterization on the direct binding between HS and TRAIL and provided solid evidence supporting the role of such interaction for the regulation of TRAIL-induced apoptosis. The experiments were well-designed with proper controls included. The data interpretation is accurate. The manuscript was clearly written and easy to follow by general readers.

Weaknesses:<br /> There is no major weakness identified from this study. However, the role of HS for the formation of TRAIL homotrimer needs to be further clarified. In addition, the current relationship between cell surface HS level and sensitivity to TRAIL-mediated apoptosis is still correlative, as the authors indicated. Additional evidence to support the regulatory function of HS would further strengthen the significance of the study.

Reviewer #2 (Public Review):

Summary:<br /> In the manuscript by Chiu et al., "Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts," the authors address the effect of cholesterol on array formation by AQP0. Using a combination of electron crystallography and molecular dynamics simulations, the authors show binding of a "deep" cholesterol molecule between AQP0 tetramers. Each AQP0 tetramers binds four deep cholesterols to form a crystallographic array of AQP0.

Strengths:<br /> The combined approaches of electron crystallography and MD simulations under different lipid conditions (different sphingomyelin and cholesterol concentrations) are a strength of the study. The authors provide a thorough and convincing assessment of cholesterol binding, protein-protein interactions, and array formation by AQP0. The MD simulations allow the authors to consider the propensity of cholesterol to occupy the observed binding sites in the absence of crystal contacts. The combined methods and the breadth of analyses set a high standard in the field of membrane protein structural biology.

The findings of the authors fit nicely into a growing body of literature on cholesterol binding sites that mediate membrane protein-protein interactions. Cholesterol interacts with a variety of membrane proteins via its smooth alpha face of rough beta face. AQP0 is somewhat unique in that it binds the rough face of cholesterol in a "deep" binding site that places cholesterol in the middle of the membrane bilayer. So-called "deep" cholesterol binding sites have been described for GPCRs and docking studies suggest they may exist on other ion channels and transporters. In the case of AQP0, the deep cholesterol acts as a glue that holds two tetramers together. Since each tetramer has four binding sites for deep cholesterol, the assembly and mechanical stability of an extended two-dimensional array of AQP0 tetramers is a natural consequence in lens membranes.

Weaknesses:<br /> The authors report that the findings generally apply to raft formation in membranes. However, this point is less clear as the lens membrane in which AQP0 resides is rather unique in lipid and protein content and density. Nonetheless, the authors achieve the overall goal of evaluating cholesterol binding to AQP0, and there are many valuable and informative figures in the main manuscript and supplement that provide convincing results and interpretations.

Reviewer #2 (Public Review):

Summary:<br /> Pulfer A. et al. developed a deep learning-based apoptosis detection system named ADeS, which outperforms the currently available computational tools for in vitro automatic detection. Furthermore, ADeS can automatically identify apoptotic cells in vivo in intravital microscopy time-lapses, preventing manual labeling with potential biases. The authors trained and successfully evaluated ADeS in packed epithelial monolayers and T cells distributed in 3D collagen hydrogels. Moreover, in vivo, training and evaluation were performed on polymorphonucleated leukocytes in lymph nodes and spleen.

Strengths:<br /> Pulfer A. et colleagues convincingly presented their results, thoroughly evaluated ADeS for potential toxicity assay, and compared its performance with available state-of-the-art tools.

Weaknesses:<br /> The use of ADeS is still restricted to samples where cells are fluorescently labeled either in the cytoplasm or in the nucleus, which limits its use for in vitro toxicity assays that are performed on primary cells or organoids (e.g., iPSCs-derived systems) that are normally harder to transfect. In conclusion, ADeS will be a useful tool to improve output quality and accelerate the evaluation of assays in several research areas with basic and applied aims.

Reviewer #2 (Public Review):

Summary:<br /> The objective of authors using metabolomics analysis of primary angle closure glaucoma (PACG) is to demonstrate that serum androstenedione is a novel biomarker that can be used to diagnose PACG and predict visual field progression.

Strengths:<br /> Use of widely targeted and untargeted metabolite detection conditions. Use of liquid chromatography-tandem mass spectrometry and a chemiluminescence method for confirmation of androstenedione.

Weaknesses:<br /> The "predict" part is on much less solid ground. The visual field progression and association with serum androstenedione within the current experimental design eludes to a correlation. It truly cannot be stated as predictive. To predict one needs to put the substance when nothing is there and demonstrate that the desired endpoint is reached. Conversely, the substance (androstenedione) can be removed, and show that the condition regresses. None of these are possible without model system experiments, which have not been done. The authors could put some additional details in the methods, such as: 1) how much sample was collected, 2) whether equal serum volume for analysis had equal serum proteins (or cells). They have used a LC-MS/MS and a Chemiluminescence method, but another independent method such as GC-MS/MS or NMR to detect androstenedione for a subset of patients with different stages of visual field defect would be desirable.

Reviewer #2 (Public Review):

Summary:<br /> Zhao et al. aimed to explore an important question - how to overcome the resistance of hepatocellular carcinoma cells to radiotherapy? Given that the immune-suppressive microenvironment is a major mechanism underlying resistance to radiotherapy, they reasoned that a drug that blocks the PD-1/PD-L1 pathway could improve the efficacy of radiation therapy and chose to investigate the effect of Nifuroxazide, an inhibitor of stat3 activation, on radiotherapy efficacy in treating hepatocellular carcinoma cells. From in vitro experiments, they find combination treatment (Nifuroxazide+ radiotherapy) increases apoptosis and reduces proliferation and migration, in comparison to radiotherapy alone. From in vivo experiments, they demonstrate that combined treatment reduces the size and weight of tumors in vivo and enhances mice survival. These data indicate a better efficacy of combination therapy compared to radiotherapy alone. Moreover, they also determined the effect of combination therapy on tumor microenvironment as well as peripheral immune response. They find that combination therapy increases infiltration of CD4+ and CD8+ cells as well as M1 macrophages in the tumor microenvironment. Interestingly, they find that the ratio of Treg cells in spleen is increased by radiotherapy but decreased by Nifuroxazide. Considering the immune-suppressive role of Treg cells, this finding is consistent with reduced tumor growth by combination therapy. However, it is unclear whether the combined therapy affects the ratio of Treg cells in the tumors or not. The most intriguing part of the study is the determination of the effect of Nifuroxazide on PD-L1 expression in the context of radiotherapy. Considering Nifuroxazide is a stat3 activation inhibitor and stat3 inhibition leads to reduced expression of PD-L1, one would expect Nifuroxazide decreases PD-L1 expression through stat3. However, they found that the effect of Nifuroxazide on PD-L1 is dependent on GSK3 mediated Proteasome pathways and independent of stat3, in the given experimental context. To determine the relevance to human hepatocellular carcinoma, they also measured the PD-L1 expression in human tumor tissues of HCC patients pre- and post-radiotherapy. The increased PD-L1 expression level in HCC after radiotherapy is impressive. However, it is unclear whether the patients being selected in the study had resistant disease to radiotherapy or not.

Overall, the data are convincing and supportive to the conclusions.

Strengths:<br /> 1) Novel finding: Identified novel mechanism underlying the effect of Nifuroxazide on PD-L1 expression in hepatocellular carcinoma cells in the context of radiotherapy.<br /> 2) Comprehensive experimental approaches: using different approaches to prove the same finding. For example, in Fig 4, both IHC and WB were used. In Fig 5, both IF and WB were used.<br /> 3) Human disease relevance: Compared observations in mice with human tumor samples.

Weaknesses:<br /> 1. It is hard to tell whether the observed phenotype and mechanism are generic or specific to the limited cell lines used in the study. The in vitro experiments were performed in one human cell line and the in vivo experiments were performed in one mouse cell line.<br /> 2. The study did not distinguish the effect of increased radiosensitivity by nifuroxazide from combined anti-tumor effects by two different treatments.

Reviewer #2 (Public Review):

Summary:<br /> The authors have taken their previous finding that arpin is important for epithelial junctions and extended this to endothelial cells. They find that the positive effects of arpin on endothelial junctions are not dependent on Arp2/3 activity but instead on suppression of actinomyosin contractility.

Strengths:<br /> The study uses standard approaches to test each of the components in the model. The quality of the experimental work is good and the amount of experimental evidence is sufficient to support this straightforward story.

Weaknesses:<br /> The major weakness is that the story is a simple extension of the previous work on arpin and junctions in epithelial cells. The additional information is that the effects are not via Arp2/3 directly, but instead through an increase in actinomyosin contractility. However, the connection between arpin and increased ROCK activity is not revealed.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by Hadebe and colleagues describes a striking reduction in airway hyperresponsiveness in Igm-deficient mice in response to HDM, OVA and papain across the B6 and BALB-c backgrounds. The authors suggest that the deficit is not due to improper type 2 immune responses, nor an aberrant B cell response, despite a lack of class switching in these mice. Through RNA-Seq approaches, the authors identify few differences between the lungs of WT and Igm-deficient mice, but see that two genes involved in actin regulation are greatly reduced in IgM-deficient mice. The authors target these genes by CRISPR-Cas9 in in vitro assays of smooth muscle cells to show that these may regulate cell contraction. While the study is conceptually interesting, there are a number of limitations, which stop us from drawing meaningful conclusions.

Strengths:<br /> Fig. 1. The authors clearly show that IgMKO mice have striking reduced AHR in the HDM model, despite the presence of a good cellular B cell response.

Weaknesses:<br /> Fig. 2.<br /> The authors characterize the cd4 t cell response to HDM in IGMKO mice.<br /> They have restimulated medLN cells with antiCD3 for 5 days to look for IL-4 and IL-13, and find no discernible difference between WT and KO mice. The absence of PBS-treated WT and KO mice in this analysis means it is unclear if HDM-challenged mice are showing IL-4 or IL-13 levels above that seen at baseline in this assay. The choice of 5 days is strange, given that the response the authors want to see is in already primed cells. A 1-2 day assay would have been better. It is concerning that the authors state that HDM restimulation did not induce cytokine production from medLN cells, since countless studies have shown that restimulation of medLN would induce IL-13, IL-5 and IL-10 production from medLN. This indicates that the sensitization and challenge model used by the authors is not working as it should. The IL-13 staining shown in panel c is also not definitive. One should be able to optimize their assays to achieve a better level of staining, to my mind.

In d-f, the authors perform a serum transfer, but they only do this once. The half life of IgM is quite short. The authors should perform multiple naïve serum transfers to see if this is enough to induce FULL AHR.

The presence of negative values of total IgE in panel F would indicate some errors in calculation of serum IgE concentrations.

Overall, it is hard to be convinced that IgM-deficiency does not lead to a reduction in Th2 inflammation, since the assays appear suboptimal.

Fig. 3. Gene expression differences between WT and KO mice in PBS and HDM challenged settings are shown. PCA analysis does not show clear differences between all four groups, but genes are certainly up and downregulated, in particular when comparing PBS to HDM challenged mice. In both PBS and HDM challenged settings, three genes stand out as being upregulated in WT v KO mice. these are Baiap2l1, erdr1 and Chil1.

Fig. 4. The authors attempt to quantify BAIAP2L1 in mouse lungs. It is difficult to know if the antibody used really detects the correct protein. A BAIAP2L1-KO is not used as a control for staining, and I am not sure if competitive assays for BAIAP2L1 can be set up. The flow data is not convincing. The immunohistochemistry shows BAIAP2L1 (in red) in many, many cells, essentially throughout the section. There is also no discernible difference between WT and KO mice, which one might have expected based on the RNA-Seq data. So, from my perspective, it is hard to say if/where this protein is located, and whether there truly exists a difference in expression between wt and ko mice.

Fig. 5 and 6. The authors use a single cell contractility assay to measure whether BAIAP2L1 and ERDR1 impact on bronchial smooth muscle cell contractility. I am not familiar with the assay, but it looks like an interesting way of analysing contractility at the single cell level.<br /> The authors state that targeting these two genes with Cas9gRNA reduces smooth muscle cell contractility, and the data presented for contractility supports this observation. However, the efficiency of Cas9-mediated deletion is very unclear. The authors present a PCR in supp fig 9c as evidence of gene deletion, but it is entirely unclear with what efficiency the gene has been deleted. One should use sequencing to confirm deletion. Moreover, if the antibody was truly working, one should be able to use the antibody used in Fig 4 to detect BAIAP2L1 levels in these cells. The authors do not appear to have tried this.

Other impressions:<br /> The paper is lacking a link between the deficiency of IgM and the effects on smooth muscle cell contraction.<br /> The levels of IL-13 and TNF in lavage of WT and IGMKO mice could be analysed.

Moreover, what is the impact of IgM itself on smooth muscle cells? In the Fig. 7 schematic, are the authors proposing a direct role for IgM on smooth muscle cells? Does IgM in cell culture media induce contraction of SMC? This could be tested and would be interesting, to my mind.

Reviewer #2 (Public Review):

In this study by Jing, Fooksman, and colleagues, a Blimp1-CreERT2-based genetic tracing study is employed to label plasma cells. Over the course of several months post-tamoxifen treatment, the only remaining labeled cells are long-lived plasma cells. This system provides a way to sort live long-lived plasma cells and compare them to unlabeled plasma cells, which contain a range of short-to-long-lived cells. From this analysis, several observations are made: 1) the turnover rate of plasma cells is greater in the spleen than in the bone marrow; 2) the turnover rate is highest early in life; 3) subtle transcriptional and cell surface marker differences distinguish long- from shorter-lived plasma cells; 4) long-lived plasma cells in the bone marrow are sessile and localize in clusters with each other; 5) CXCR4 is required for plasma cell retention in these clusters and in the bone marrow; 6) Repertoire analysis hints that the selection of long-lived plasma cells is not random for any cell that lands in the bone marrow.

Strengths:

1) The genetic timestamping approach is a clever and functional way to separate plasma cells of differing longevities.

2) This approach led to the identification of several markers that could help prospective separation of long-lived plasma cells from others.

3) Functional labeling of long-lived plasma cells allowed for a higher resolution analysis of transcriptomes and motility than was previously possible.

4) The genetic system allowed for a revisitation of the importance of CXCR4 in plasma cell retention and survival.

Weaknesses:

1) Most of the labeling studies, likely for practical reasons, were done on polyclonal rather than antigen-specific plasma cells. The triggers of these responses could vary based on age at the time of exposure, anatomical sites, etc. How these differences might influence markers and transcriptomes, independently of longevity, is not completely known.

2) The fraction of long-lived plasma cells in the unlabeled fraction varies with age, potentially diluting differences between long- and short-lived plasma cells.

3) The authors suggest their data favors a model by which plasma cells compete for niche space. Yet there is no evidence presented here that these niches are limiting.

4) The functional importance of the observed transcriptome differences between long- and shorter-lived plasma cells is unknown. An assessment as to whether these differences are conserved in human long- and short-lived bone marrow plasma cells might provide circumstantial supporting evidence that these changes are important for longevity.

Reviewer #2 (Public Review):

This study investigates T-cell repertoire responses in a mouse model with a transgenic beta chain, such that all T-cells in all mice share a fixed beta chain, and repertoire diversity is determined solely by alpha chain rearrangements. Each mouse is exposed to one of a few distinct immune challenges, sacrificed, and T-cells are sampled from multiple tissues. FACS is used to sort CD4 and Treg cell populations from each sample, and TCR repertoire sequencing from UMI-tagged cDNA is done.

Various analyses using repertoire diversity, overlap, and clustering are presented to support several principal findings: 1) TCR repertoires in this fixed beta system have highly distinct clonal compositions for each immune challenge and each cell type, 2) these are highly consistent across mice, so that mice with shared challenges have shared clones, and 3) induction of CD4-to-Treg cell type transitions is challenge-specific.

The beta chain used for this mouse model was previously isolated based on specificity for Ovalbumin. Because the beta chain is essential for determining TCR antigen specificity, and is highly diverse in wildtype mice, I found it surprising that these mice are reported to have robust and consistently focused clonal responses to very diverse immune challenges, for which a fixed OVA-specific beta chain is unlikely to be useful. The authors don't comment on this aspect of their findings, but I would think it is not expected *a priori* that this would work. If this does work as reported, it is a valuable model system: due to massively reduced diversity, the TCR repertoire response is much more stereotyped across individual samples, and it is much easier to detect challenge-specific TCRs via the statistics of convergent responses.

While the data and analyses present interesting signals, they are flawed in several ways that undermine the reported findings. I summarize below what I think are the most substantive data and analysis issues.

1. There may be systematic inconsistencies in repertoire sampling depth that are not described in the manuscript. Looking at the supplementary tables (and making some plots), I found that the control samples (mice with mock challenge) have consistently much shallower sampling-in terms of both read count and UMI count-compared with the other challenge samples. There is also a strong pattern of lower counts for Treg vs CD4 cell samples within each challenge.

2. FACS data are not reported. Although the graphical abstract shows a schematic FACS plot, there are no such plots in the manuscript. Related to the issue above, it would be important to know the FACS cell counts for each sample.

3. For diversity estimation, UMI-wise downsampling was performed to normalize samples to 1000 random UMIs, but this procedure is not validated (the optimal normalization would require downsampling cells). What is the influence of possible sampling depth discrepancies mentioned above on diversity estimation? All of the Treg control samples have fewer than 1000 total UMIs-doesn't that pose a problem for sampling 1000 random UMIs? Indeed, I simulated this procedure and found systematic effects on diversity estimates when taking samples of different numbers of cells (each with a simulated UMI count) from the same underlying repertoire, even after normalizing to 1000 random UMIs. I don't think UMI downsampling corrects for cell sampling depth differences in diversity estimation, so it's not clear that the trends in Fig 1A are not artifactual-they would seem to show higher diversity for control samples, but these are the very same samples with an apparent systematic sampling depth bias.

4. The Figures may be inconsistent with the data. I downloaded the Supplementary Table corresponding to Fig 1 and made my own version of panels A-C. This looked quite different from the diversity estimations depicted in the manuscript. The data does not match the scale or trends shown in the manuscript figure.

5. For the overlap analysis, a different kind of normalization was performed, but also not validated. Instead of sampling 1000 UMIs, the repertoires were reduced to their top 1000 most frequent clones. It is not made clear why a different normalization would be needed here. There are several samples (including all Treg control samples) with only a couple hundred clones. It's also likely that the noted systematic sampling depth differences may drive the separation seen in MDS1 between Treg and CD4 cell types. I also simulated this alternative downsampling procedure and found strong effects on MDS clustering due to sampling effects alone.

It is not made clear how the overlap scores were converted to distances for MDS. It's hard to interpret this without seeing the overlap matrix.

6. The cluster analysis is superficial, and appears to have been cherry-picked. The clusters reported in the main text have illegibly small logo plots, and no information about V/J gene enrichments. More importantly, as the caption states they were chosen from the columns of a large (and messier-looking) cluster matrix in the supplementary figure based on association with each specific challenge. There's no detail about how this association was calculated, or how it controlled for multiple tests. I don't think it is legitimate to simply display a set of clusters that visually correlate; in a sufficiently wide random matrix you will find columns that seem to correlate with any given pattern across rows.

7. The findings on differential plasticity and CD4 to Treg conversion are not supported. If CD4 cells are converting to Tregs, we expect more nucleotide-level overlap of clones. This intuition makes sense. But it seems that this section affirms the consequent: variation in nucleotide-level clone overlap is a readout of variation in CD4 to Treg conversion. It is claimed, based on elevated nucleotide-level overlap, that the LLC and PYMT challenges induce conversion more readily than the other challenges. It is not noted in the textual interpretations, but Fig 4 also shows that the control samples had a substantially elevated nucleotide-level overlap. There is no mention of a null hypothesis for what we'd expect if there was no induced conversion going on at all. This is a reduced-diversity mouse model, so convergent recombination is more likely than usual, and the challenges could be expected to differ in the parts of TCR sequence space they induce focus on. They use the top 100 clones for normalization in this case, but don't say why (this is the 3rd distinct normalization procedure).

Although interpretations of the reported findings are limited due to the issues above, this is an interesting model system in which to explore convergent responses. Follow-up experimental work could validate some of the reported signals, and the data set may also be useful for other specific questions.

Reviewer #2 (Public Review):

Summary:<br /> The authors have developed a Myoscreen platform, which is a scalable and physiologically relevant system for generating and characterizing patient-derived myotubes. The platform can be used to accurately predict the DMD disease phenotype in a disease-relevant cell type and has wide applications in the drug development process.

Strengths:<br /> The Myoscreen platform is scalable, meaning that it can be used to generate and characterize a large number of patient-derived myotubes. This is important for drug discovery, as it allows researchers to test a wider range of potential treatments. The Myoscreen platform also uses a physiologically relevant system for generating and characterizing myotubes. This means that the results obtained from the platform are more likely to be relevant to the human disease. This compared for example to using C2C12 myotubes. The Myoscreen platform has been shown to be effective in predicting the DMD disease phenotype. This means that it can be used to identify potential treatments that are likely to be effective in patients with DMD.

Weaknesses:<br /> The study has several limitations. The method and material section could be improved. The authors rely heavily on UMAP to identify differences between non-DMD and DMD donor myotubes. They do not validate their findings using pharmacological small drugs. Additionally, the biological replicates used are extremely low, which raises concerns about the reproducibility of the findings.

Reviewer #2 (Public Review):

Summary:<br /> The paper by Kuhn and colleagues follows upon a 2022 paper in which they identified residues in CD4 constrained by evolutionary purifying selection in placental mammals and then performed functional analyses of these conserved sequences. They showed that sequences distinct from the CXC "clamp" involved in recruitment of Lck have critical roles in TCR signaling, and these include a glycine-rich motif in the transmembrane (TM) domain and the cys-containing juxtamembrane (JM) motif that undergoes palmitoylation, both of which promote TCR signaling, and a cytoplasmic domain helical motif, also involved in Lck binding, that constrains signaling. Mutations in the transmembrane and juxtamembrane sequences led to reduced proximal signaling and IL-2 production in a hybridoma's response to antigen presentation, despite retention of abundant CD4 association with Lck in the detergent-soluble membrane fraction, presumably mislocalized outside of lipid rafts and distal to the TCR. A major conclusion of that study was that CD4 sequences required for Lck association, including the CXC "clasp" motif, are not as consequential for CD4 co-receptor function in TCR signaling as the conserved TM and JM motifs. However, the experiments did not determine whether the functions of the TM and JM motifs are dependent on the Lck-binding properties of CD4 - the mutations in those motifs could result in free Lck redistributing to associate with CD4 in signaling-incompetent membrane domains or could function independently of CD4-Lck association. The current study addresses this specific question.

Using the same model system as in the earlier paper (the entire methods section is a citation to the earlier paper), the authors show that truncation of the Lck-binding intracellular domain resulted in a moderate reduction in IL-2 response, as previously shown, but there was no apparent effect on proximal phosphorylation events (CD3z, Lck, ZAP70, PLCg1). They then evaluated a series of TM and JM motif mutations in the context of the truncated Lck-nonbinding molecule, and showed that these had substantially impaired co-receptor function in the IL-2 assay and reduced proximal signaling. The proximal signaling could be observed at high ligand density even with a MHC non-binding mutation in CD4, although there was still impaired IL-2 production. This result additionally illustrates that phosphorylation of the proximal signaling molecules is not sufficient to activate IL-2 expression in the context of antigen presentation.

Strengths:<br /> The strength of the paper is the further clear demonstration that the classical model of CD4 co-receptor function (MHCII-binding CD4 bringing Lck to the TCR complex, for phosphorylation of the CD3 chain ITAMs and of the ZAP70 kinase) is not sufficient to explain TCR activation. The data, combined with the earlier paper, further implicate the gly-rich TM sequence and the palmitoylation targets in the JM region as having critical roles in productive co-receptor-dependent TCR activation.

Weaknesses:<br /> The major weakness of the paper is the lack of mechanistic insight into how the TM and JM motifs function. The new results are largely incremental in light of the earlier paper from this group as well as other literature, cited by the authors, that implicates "free" Lck, not associated with co-receptors, as having the major role in TCR activation. It is clear that the two motifs are important for CD4 function at low pMHCII ligand density. The proposal that they modulate interactions of TCR complex with cholesterol or other membrane lipids is an interesting one, and it would be worth further exploring by employing approaches that alter membrane lipid composition. The JM sequence presumably dictates localization within the membrane, by way of palmitoylation, which may be critical to regulate avidity of the TCR:CD4 complex for pMHCII or TCR complex allosteric effects that influence the activation threshold. Experiments that explore the basis of the mutant phenotype could substantially enhance the impact of this study.

Reviewer #2 (Public Review):

Summary: This paper investigates the role of motor practice and sensory feedback when a motor action returns to a learned or established baseline. Adult male zebra finches perform a stereotyped, learned vocalization (song). It is possible to shift the pitch of particular syllables away from the learned baseline pitch using contingent white noise reinforcement. When the reinforcement is stopped, birds will return to their baseline over time. During the return, they often sing hundreds of renditions of the song. However, whether motor action, sensory feedback, or both during singing is necessary to return to baseline is unknown.

Previous work has shown that there is covert learning of the pitch shift. If the output of a song plasticity pathway is blocked during learning, there is no change in pitch during the training. However, as soon as the pathway is unblocked, the pitch immediately shifts to the target location, implying that there is learning of the shift even without performance. Here, they ask whether the return to baseline from such a pitch shift also involves covert or overt learning processes. They perform a series of studies to address these questions, using muting and deafening of birds at different time points. learning.

Strengths: The overall premise is interesting and the use of muting and deafening to manipulate different aspects of motor practice vs. sensory feedback is a solid approach.

Weaknesses: One of the main conclusions, which stems primarily from birds deafened after being pitch-shifted using white noise (WNd) birds in comparison to birds deafened before being pitch-shifted with light as a reinforcer (LOd), is that recent auditory experience can drive motor plasticity even when an individual is deprived of such experience. While the lack of shift back to baseline pitch in the LOd birds is convincing, the main conclusion hinges on the responses of just a few WNd individuals who are closer to baseline in the early period. Moreover, only 2 WNd individuals reached baseline in the late period, though neither of these were individuals who were closer to baseline in the early phase. Most individuals remain or return toward the reinforced pitch. These data highlight that while it may be possible for previous auditory experience during reinforcement to drive motor plasticity, the effect is very limited. Importantly, it's not clear if there are other explanations for the changes in these birds, for example, whether there are differences in the number of renditions performed or changes to other aspects of syllable structure that could influence measurements of pitch.

While there are examples where the authors perform direct comparisons between particular manipulations and the controls, many of the statistical analyses test whether each group is above or below a threshold (e.g. baseline) separately and then make qualitative comparisons between those groups. Given the variation within the manipulated groups, it seems especially important to determine not just whether these are different from the threshold, but how they compare to the controls. In particular, a full model with time (early, late), treatment (deafened, muted, etc), and individual ID (random variable) would substantially strengthen the analysis.

The muted birds seem to take longer to return to baseline than controls even after they are unmuted. Presumably, there is some time required to recover from surgery, however, it's unclear whether muting has longer-term effects on syrinx function or the ability to pass air. In particular, it's possible that the birds still haven't recovered by 4 days after unmuting as a consequence of the muting and unmuting procedure or that the lack of recovery is indicative of an additional effect that muting has on pitch recovery. For example, the methods state that muted birds perform some quiet vocalizations. However, if birds also attempt to sing, but just do so silently, perhaps the aberrant somatosensory or other input from singing while muted has additional effects on the ability to regain pitch. It would also be useful to know if there is a relationship between how long they are muted and how quickly they return to baseline.

Reviewer #2 (Public Review):

Erk2 is an essential element of the MAP kinase signaling cascade and directly controls cell proliferation, migration, and survival. Therefore, it is one of the most important drug targets for cancer therapy. The catalytic subunit of Erk2 has a bilobal architecture, with the small lobe harboring the nucleotide-binding pocket and the large lobe harboring the substrate-binding cleft. Several studies by the Ahn group revealed that the catalytic domain hops between (at least) two conformational states: active (R) and inactive (L), which exchange in the millisecond time scale based on the chemical shift mapping. The R state is a signature of the double phosphorylated Erk2 (2P-Erk2), while the L state has been associated with the unphosphorylated kinase (0P-Erk2). Interestingly, the X-ray structures reveal only minimal differences between these two states, a feature that led to the conclusion that active and inactive states are structurally similar but dynamically very different. The Ahn group also found that ATP-competitive inhibitors can steer the populations of Erk2 either toward the R or the L state, depending on their chemical nature. The latter opens up the possibility of modulating the activity of this kinase by changing the chemistry of the ATP-competitive inhibitor. To prove this point, the authors present a set of nineteen compounds with diverse chemical substituents. From their combined NMR and HDX-Mass Spec analyses, fourteen inhibitors drive the kinase toward the R state, while four compounds keep the kinase hopping between the R and L states. Based on these data, the authors rationalize the effects of these inhibitors and the importance of the nature of the substituents on the central scaffold to steer the kinase activity. While all these inhibitors target the ATP binding pocket, they display diverse structural and dynamic effects on the kinase, selecting a specific structural state. Although the inhibited kinase is no longer able to phosphorylate substrates, it can initiate signaling events functioning as scaffolds for other proteins. Therefore, by changing the chemistry of the inhibitors it may be possible to affect the MAP cascade in a predictable manner. This concept, recently introduced as proof of principle, finds here its significance and practical implications. The design of the next-generation inhibitors must be taken into account for these design principles. The research is well executed, and the data support the author's conclusions.

Reviewer #2 (Public Review):

Summary:

Artificial intelligence (AI) could be useful in some applications and could help humankind. Some forms of AI work on the platform of artificial neural networks (ANN). ANNs are inspired by real brains and real neurons. Therefore understanding the repertoire and logic of real neurons could potentially improve AANs. Cell bodies of real neurons, and axons of real neurons, fire nerve impulses (nerve impulses are very brief ~2 ms, and very tall ~100 mV). Dendrites, which comprise ~80% of the total neuronal membrane (80% of the total neuronal apparatus) typically generate smaller (~50 mV amplitude) but much longer (~100 ms duration) electrical transients, called glutamate-mediated dendritic plateau potentials. The authors have built artificial neurons capable of generating such dendritic plateau potentials, and through computer simulations the authors concluded that long-lasting dendritic signals (plateau potentials) reduce negative impact of temporal jitter occurring in real brain, or in AANs. The authors showed that in AANs equipped with neurons whose dendrites are capable of generating local dendritic plateau potentials, the sparse, yet reliable spiking computations may not require precisely synchronized inputs. That means, the real world can impose notable fluctuations in the network activity and yet neurons could still recognize and pair the related network events. In the AANs equipped with dendritic plateaus, the computations are very robust even when inputs are only partially synchronized. In summary, dendritic plateau potentials endow neurons with ability to hold information longer and connect two events which did not happen at the same moment of time. Dendritic plateaus circumvent the negative impact, which the short membrane time constants arduously inflict on the action potential generation (in both real neurons and model neurons). Interestingly, one of the indirect conclusions of the current study is that neurons equipped with dendritic plateau potentials may reduce the total number of cells (nodes, units) required to perform robust computations.

Strengths:<br /> The majority of published studies are descriptive in nature. Researchers report what they see or measure. A smaller number of studies embark on a more difficult task, which is to explain the logic and rationale of a particular natural design. The current study falls into that second category. The authors first recognize that conduction delays and noise make asynchrony unavoidable in communication between circuits in the real brain. This poses a fundamental problem for the integration of related inputs in real (noisy) world. Neurons with short membrane time constants can only integrate coincident inputs that arrive simultaneously within 2-3 ms of one another. Then the authors considered the role for dendritic plateau potentials. Glutamate-mediated depolarization events within individual dendritic branches, can remedy the situation by widening the integration time window of neurons. In summary, the authors recognized that one important feature of neurons, their dendrites, are built-in to solve the major problems of rapid signal processing: [1] temporal jitter, [2] variation, [3] stochasticity, and [4] reliability of computation. In one word, the dendritic plateau potentials have evolved in the central nervous systems to make rapid CNS computations robust.

Weaknesses:<br /> The authors made some unsupported statements, which should either be deleted, or thoroughly defended in the manuscript. But first of all, the authors failed to bring this study to the readers who are not experts in computational modeling or Artificial Neural Networks. Critical terms (syntax) and ideas have not been explained. For example: [1] binary feature space? [2] 13 dimensions binary vectors? [3] the binary network could still cope with the loss of information due to the binarization of the continuous coordinates? [4] accurate summation?

Reviewer #2 (Public Review):

Summary: The authors aim to learn about retinal cell-specific metabolic pathways, which could substantially improve the way retinal diseases are understood and treated. They culture ex vivo mouse retinas for 6 days with 2 - 4 days of various drug treatments targeting different metabolic pathways or by removing the RPE/choroid tissue from the neural retina. They then look at photoreceptor survival, stain for various metabolic enzymes, and quantify a broad panel of metabolites. While this is an important question to address, the results are not sufficient to support the conclusions.

Strengths: The questions the authors are exploring at extremely valuable and I commend the authors and working to learn more about retina metabolism. The different sensitivity of the cones to various drugs is interesting and may suggest key differences between rods and cones. The authors also provide a thoughtful discussion of various metabolic pathways in the context of previous publications.

Weaknesses: As the authors point out, ex vivo culture models allow for control over multiple aspects of the environment (such as drug delivery) not available in vivo. Ex vivo cultures can provide good hints as to what pathways are available between interacting tissues. However, there are many limitations to ex vivo cultures, including shifting to a very artificial culture media condition that is extremely different than the native environment of the retina. It is well appreciated that cells have flexible metabolism and will adapt to the conditions provided. Therefore, observations of metabolic responses obtained under culture conditions need to be interpreted with caution, they indicate what the tissue is doing under those specific conditions (which include cells adapting and dying).

Chen et al use pharmacological interventions to the impact of various metabolic pathways on photoreceptor survival and "long term" metabolic changes. The dose and timing of these drug treatments are not examined though. It is also hard to know how these drugs penetrate the tissue and it needs to be validated that the intended targets are being accurately hit. These relatively long-term treatments should be causing numerous downstream changes to metabolism, cell function, and survival, which makes looking at a snapshot of metabolite levels hard to interpret. It would be more valuable to look at multiple time points after drug treatment, especially easy time points (closer to 1 hr). The authors use metabolite ratios to make conclusions about pathway activity. It would be more valuable to directly measure pathway activity by looking a metabolite production rates in the media and/or with metabolic tracers again in time scales closer to minutes and hours instead of days.

It is not clear from the text if the ex vivo samples with RPE/choroid intact are analyzed for metabolomics with the RPE/choroid still intact or if this is removed. If it is not removed, the comparison to the retina without RPE/choroid needs to be re-interpreted for the contribution of metabolites from the added tissue. The composition of the tissue is different and cannot be disentangled from the changes to the neural retina specifically.

While the data is interesting and may give insights into some rod and cone-specific metabolic susceptibility, more work is needed to validate these conclusions. Given the limitations of the model the authors have over-interpreted their findings and the conclusions are not supported by the results. They need to either dramatically limit the scope of their conclusions or validate these hypotheses with additional models and tools.

Reviewer #2 (Public Review):

Summary:<br /> This study aims to address existing differences in the literature regarding the extent of reward versus aversive dopamine signaling in the prefrontal cortex. To do so, the authors chose to present mice with both a reward and an aversive stimulus during different trials each day. The authors used high spatial resolution two-photon calcium imaging of individual dopaminergic axons in the medial PFC to characterize the response of these axons to determine the selectivity of responses in unique axons. They also paired the reward (water) and an aversive stimulus (tail shock) with auditory tones and recorded across 12 days of associative learning.

The authors find that some axons respond to both reward and aversive unconditioned stimuli, but overall, there is a strong preference to respond to aversive stimuli consistent with expectations from prior studies that used other recording methods. The authors find that both of their two auditory stimuli initially drive responses in axons, but that with training axons develop more selective responses for the shock associated tone indicating that associative learning led to changes in these axon's responses. Finally, the authors use anticipatory behaviors during the conditioned stimuli and facial expressions to determine stimulus discrimination and relate dopamine axons signals with this behavioral evidence of discrimination. This study takes advantage of cutting-edge imaging approaches to resolve the extent to which dopamine axons in PFC respond appetitive or aversive stimuli. They conclude that there is a strong bias to respond to the aversive tail shock in most axons and weaker more sparse representation of water reward.

Strengths:<br /> The strength of this study is the imaging approach that allows for investigation of the heterogeneity of response across individual dopamine axons, unlike other common approaches such as fiber photometry which provide a measure of the average population activity. The use of appetitive and aversive stimuli to probe responses across individual axons is another strength.

Weaknesses:<br /> A weakness of this study is the design of the associative conditioning paradigm. The use of only a single reward and single aversive stimulus makes it difficult to know whether these results are specific to the valence of the stimuli versus the specific identity of the stimuli. Further, the reward presentations are more numerous than the aversive trials making it unclear how much novelty and habituation account for results. Moreover, the training seems somewhat limited by the low number of trials and did not result in strong associative conditioning. The lack of omission responses reported may reflect weak associative conditioning. Finally, the study provides a small advance in our understanding of dopamine signaling in the PFC and lacks evidence for if and what might be the consequence of these axonal responses on PFC dopamine concentrations and PFC neuron activity.

Reviewer #2 (Public Review):

The study presents an extensive computational approach to identify the motor neuron input from the characteristics of single motor neuron discharge patterns during a ramp up/down contraction. This reverse engineering approach is relevant due to limitations in our ability to estimate this input experimentally. Using well-established models of single motor neurons, a (very) large number of simulations were performed that allowed identification of this relation. In this way, the results enable researchers to measure motor neuron behavior and from those results determine the underlying neural input scheme. Overall, the results are very convincing and represent an important step forward in understanding the neural strategies for controlling movement.

Nevertheless, I would suggest that the authors consider the following recommendations to strengthen the message further. First, I believe that the relation between individual motor neuron behavioral characteristics (delta F, brace height etc.) and the motor neuron input properties can be illustrated more clearly. Although this is explained in the text, I believe that this is not optimally supported by figures. Figure 6 to some extent shows this, but figures 8 and 9 as well as Table 1 shows primarily the goodness of fit rather than the actual fit. Second, I would have expected the discussion to have addressed specifically the question of which of the two primary schemes (push-pull, balanced) is the most prevalent. This is the main research question of the study, but it is to some degree left unanswered. Now that the authors have identified the relation between the characteristics of motor neuron behaviors (which has been reported in many previous studies), why not exploit this finding by summarizing the results of previous studies (at least a few representative ones) and discuss the most likely underlying input scheme? Is there a consistent trend towards one of the schemes, or are both strategies commonly used?

In addition, it seems striking to me that highly non-linear excitation profiles are necessary to obtain a linear CST ramp in many model configurations. Although somewhat speculative, one may expect that an approximately linear relation is desired for robust and intuitive motor control. It seems to me that humans generally have a good ability to accurately grade the magnitude of the motor output, which implies that either a non-linear relation has been learnt (complex task), or that the central nervous system can generally rely on a somewhat linear relation between the neural drive to the muscle and the output (simpler task). Following this reasoning, it could be interesting to report also for which input scheme, the excitation profile is most linear. I understand that this is not the primary aim of the study, but it may be an interesting way to elaborate on the finding that in many cases non-linear excitation profiles were needed to produce the linear ramp.

Reviewer #2 (Public Review):

In this manuscript, Parrotta et al. tested whether it is possible to modulate pain perception and heart rate by providing false HR acoustic feedback before administering electrical cutaneous shocks. To this end, they performed two experiments. The first experiment tested whether false HR acoustic feedback alters pain perception and the cardiac anticipatory response. The second experiment tested whether the same perceptual and physiological changes are observed when participants are exposed to a non-interoceptive feedback. The main results of the first experiment showed a modulatory effect for faster HR acoustic feedback on pain intensity, unpleasantness, and cardiac anticipatory response compared to a control (acoustic feedback congruent to the participant's actual HR). However, the results of the second experiment also showed an increase in pain ratings for the faster non-interoceptive acoustic feedback compared to the control condition, with no differences in pain unpleasantness or cardiac response.

The main strengths of the manuscript are the clarity with which it was written, and its solid theoretical and conceptual framework. The researchers make an in-depth review of predictive processing models to account for the complex experience of pain, and how these models are updated by perceptual and active inference. They follow with an account of how pain expectations modulate physiological responses and draw attention to the fact that most previous studies focus on exteroceptive cues. At this point, they make the link between pain experience and heart rate changes, and introduce their own previous work showing that people may illusorily perceive a higher cardiac frequency when expecting painful stimulation, even though anticipating pain typically goes along with a decrease in HR. From here, they hypothesize that false HR acoustic feedback evokes more intense and unpleasant pain perception, although the actual HR actually decreases due to the orienting cardiac response. Furthermore, they also test the hypothesis that an exteroceptive cue will lead to no (or less) changes in those variables. The discussion of their results is also well-rooted in the existing bibliography, and for the most part, provides a credible account of the findings.

The main weaknesses of the manuscript lies in a few choices in methodology and data analysis that hinder the interpretation of the results and the conclusions as they stand. The first peculiar choice is the convoluted definition of the outcomes. Specifically, pain intensity and unpleasantness are first normalized and then transformed into variation rates (sic) or deltas, which makes the interpretation of the results unnecessarily complicated. This is also linked to the definitions of the smallest effect of interest (SESOI) in terms of these outcomes, which is crucial to determining the sample size and gauging the differences between conditions. However, the choice of SESOI is not properly justified, and strangely, it changes from the first experiment to the second.

Furthermore, the researchers propose the comparison of faster vs. slower delta HR acoustic feedback throughout the manuscript when the natural comparison is the incongruent vs. the congruent feedback. This could be influenced by the fact that the faster HR exteroceptive cue in experiment 2 also shows a significant modulatory effect on pain intensity compared to congruent HR feedback, which puts into question the hypothesized differences between interoceptive vs. exteroceptive cues. These results could also be influenced by the specific choice of exteroceptive cue: the researchers imply that the main driver of the effect is the nature of the cue (interoceptive vs. exteroceptive) and not its frequency. However, they attempt to generalize their findings using knocking wood sounds to all possible sounds, but it is possible that some features of these sounds (e.g., auditory roughness or loomingness) could be the drivers behind the observed effects. Finally, it is noteworthy that the researchers divided the study into two experiments when it would have been optimal to test all the conditions with the same subjects in a randomized order in a single cross-over experiment to reduce between-subject variability.

Taking this into consideration, I believe that the conclusions are only partially supported by the evidence. Despite of the outcome transformations, a clear effect of faster HR acoustic feedback can be observed in the first experiment, which is larger than the proposed exteroceptive counterpart. This work could be of broad interest to pain researchers, particularly those working on predictive coding of pain.

Reviewer #2 (Public Review):

Summary:<br /> This work explores the implication of astrocytes in the regulation of long-term potentiation of excitatory synapses onto inhibitory neurons in CA1 hippocampus. They found that astrocytes of a sub-region of CA1 regulate this plasticity through their activation of endocannabinoids that lead to the release of the NMDA receptor co-agonist, D-serine.

Strengths:<br /> The experiments are well considered and conceptualized, and use appropriate tools to explore the role of astrocytes in the tripartite synapse. The results highlight a novel role of astrocytes in an important aspect of the synaptic regulation of the hippocampal circuit. There are extensive levels of analysis for each experimental group of evidence.

Weaknesses:<br /> The authors underscore and used an oversimplified view of the heterogeneity of interneuron populations and their selective roles in the hippocampal network. Also, there is an uneven level of astrocyte-selective tools used in the different experiments which creates an uneven strength of arguments and conclusions regarding the role of glial cells. Finally, the wording used by the authors often lead to some confusion or sense of overinterpretation.

Reviewer #2 (Public Review):

Summary:<br /> Through a set of experiments and model simulations, the authors tested whether the commonly assumed world model of gravity was a faithful replica of the physical world. They found that participants did not model gravity as a single, fixed vector for gravity but instead as a distribution of possible vectors. Surprisingly, the width of this distribution was quite large (~20 degrees). While previous accounts had suggested that this uncertainty was due to perceptual noise or an inferred external perturbation, the authors suggest that this uncertainty simply arises from a noisy distribution of the representation of gravity's direction. A reinforcement learning model with an initial uniform distribution for gravity's direction ultimately converged to a precision in the same order as the human participants, which lends support to the authors' conclusion and suggests that this distribution is learned through experience. What's more, further simulations suggest that representing gravity with such a wide distribution may balance speed and accuracy, providing a potentially normative explanation for the world model with gravity as a distribution.

Strengths:<br /> The authors present surprising findings in a relatively straightforward way in a now classic experimental task. They provide a normative explanation based on a resource-rational framework for why people may have a stochastic world model instead of a deterministic world model.

Weaknesses:<br /> Support for gravity being represented as a Gaussian distribution (stochastic world model), as opposed to perceptual uncertainty or (inferred) external perturbations, is from an RL model simulation. It would be more convincing if the authors could experimentally demonstrate that potential external perturbations did not affect the distribution of gravity.

Reviewer #2 (Public Review):

Summary and strengths:<br /> The authors have developed a helpful resource for the community regarding hippocampal cell types and their interactions from many perspectives. There have been many updates to hippocampome v1.0 to v1.12, that are nicely summarized and explained (e.g., Table 1). The content and impact are also presented (Fig. 4).

Weaknesses:<br /> My main comment is that it is not completely clear and/or it is a bit buried as to what makes this v2.0 (rather than v1.13). The title would seem to encompass it ('... enabling data-driven spiking neural network simulations...), but in the introduction, the authors seem to emphasize "50 newly identified neuron types...". Is it the case that launching network simulations (using CARLsim) was not possible up to v1.12? I don't think so? I think that this research advance is to announce and summarize the various updates and to demonstrate how network simulations can be easily done? If so, this should and could be made more clear so that the reader does not necessarily have to go through all the previous versions to understand what is 'special' or different about v2.0. This could perhaps be achieved by situating their tool and its goals relative to other efforts (e.g., blue brain project) that are mentioned in the Discussion?

Reviewer #2 (Public Review):

Summary:<br /> Chromosome organization in E. coli and related species ('transversal') deviates starkly from the pattern more commonly found in bacteria ('longitudinal'). The underlying mechanisms and the physiological roles, however, are not well understood. This manuscript by Seba et al. investigates the activity and regulation of MukBEF in chromosome folding in E. coli. Using a construct for inducible expression of MukBEF, the authors first demonstrate that the initiation of long-range chromosome contacts (likely by loop extrusion) is not restricted to few positions on the chromosome and rather widely distributed but excluding the replication terminus region. Using ChIP-Seq, the authors show that the distribution of MukBEF over the chromosome is consistent with widely distributed loading and moreover indicate a connection of chromosome folding and DNA replication with newly replicated DNA shower an increased tendency for MukBEF binding. To dissect this further, they then redistribute matS sites on the chromosome by a clever strategy based on large-scale transpositions. The results reveal that matS-free DNA segments undergo MukBEF dependent folding regardless of their position relative to the origin of replication, being consistent with a broad distributed loading of MukBEF. By fine-mapping with smaller transposition events, they show that few matS sites are sufficient to impede MukBEF activity. Surprisingly, however, E. coli and most related genomes harbor many matS sites, which are particularly highly concentrated near the chromosome dimer resolution dif site (Fig. 5).

Strengths:<br /> This is a well-executed and well-presented study. The findings show that the MatP/matS system acts locally and independently of DNA replication to restrict MukBEF in the replication terminus region. Few of the many matS sites are sufficient for MukBEF restriction. The main conclusions of the work are clear and well supported by the data.

Weaknesses:<br /> The biological relevance of MukBEF restriction from the replication terminus region remains unresolved. The authors could speculate on possible functions.

Reviewer #2 (Public Review):

Studying the weakly electric brown ghost knifefish, the authors provide evidence that 'chirps' (brief modulations in the frequency and amplitude of the ongoing electric signal) function in active sensing (specifically homeoactive sensing) rather than communication. This is a behavior that has been very well studied, including numerous studies on the sensory coding of chirps and the neural mechanisms for chirp generation. Chirps are largely thought to function in communication behavior, so this alternative function is a very exciting possibility that could have a great impact on the field. The authors do provide convincing evidence that chirps may function in homeoactive sensing. However, their evidence arguing against a role for chirps in communication is not as strong, and neglects a large body of research. Ultimately, the manuscript has great potential but suffers from framing these two possibilities as mutually exclusive and dismissing evidence in favor of a communicative function.

(1) The specific underlying question of this study is not made clear in the abstract or introduction. It becomes apparent in reading through the manuscript that the authors seek to test the hypothesis that chirps function in active sensing (specifically homeoactive sensing). This should be made explicitly clear in both the abstract and introduction, along with the rationale for this hypothesis.

(2) My biggest issue with this manuscript is that it is much too strong in dismissing evidence that chirping correlates with context. This is captured in this sentence in the introduction, "We first show that the choice of different chirp types does not significantly correlate with any particular behavioral or social context." This very strong conclusion comes up repeatedly, and I disagree with it, for the following reasons:

In your behavioral observations, you found sex differences in chirping as well as differences between freely interacting and physically separated fish. Your model of chirp variability found that environmental experience, social experience, and beat frequency (DF) are the most important factors explaining chirp variability. Are these not all considered "behavioral or social context"? Beat frequency (DF) in particular is heavily downplayed as being a part of "context" but it is a crucial part of the context, as it provides information about the identity of the fish you're interacting with.

In your playback experiments, fish responded differently to small vs. large DFs, males chirped more than females, type 2 chirps became more frequent throughout a playback, and rises tended to occur at the end of a playback. These are all examples of context-dependent behavior.

Further, you only considered the identity of interacting fish or stimulated fish, not their behavior during the interaction or during playback. Such an analysis is likely beyond the scope of this study, but several other studies have shown correlations between social behavior and chirping. In the absence of such data here, it is too strong to claim that chirping is unrelated to context.

In summary, it is simply too strong to say that chirping does not correlate with context. Importantly, however, this does not detract from your hypothesis that chirping functions in homeoactive sensing. A given EOD behavior could serve both communication and homeoactive sensing. I actually suspect that this is quite common in electric fish. The two are not mutually exclusive, and there is no reason for you to present them as such. I recommend focusing more on the positive evidence for a homeoactive function and less on the negative evidence against a communication function.

(3) The results were generally challenging to follow. In the first 4 sections, it is not made clear what the specific question is, what the approach to addressing that question is, and what specific experiment was carried out (the last two sections of the results were much clearer). The independent variables (contexts) are not clearly established before presenting the results. Instead they are often mentioned in passing when describing the results. They come across as an unbalanced hodgepodge of multiple factors, and it is not made clear why they were chosen. This makes it challenging to understand why you did what you did, the results, and their implications. For each set of major results, I recommend: First, pose a clear question. Then, describe the general approach to answering that question. Next, describe the specifics of the experimental design, with a rationale that appeals to the general approach described. Finally, describe the specific results.

(4) Results: "We thus predicted that, if behavioral meaning can be attributed to different types of chirps, as posed by the prevailing view (e.g., Hagedorn and Heiligenberg, 1985; Larimer and MacDonald, 1968; Rose, 2004)..." It should be made clear why this is the prevailing view, and this description should likely be moved to the introduction. There is a large body of evidence supporting this view and it is important to be complete in describing it, especially since the authors seem to seek to refute it.

(5) I am not convinced of the conclusion drawn by the analysis of chirp transitions. The transition matrices show plenty of 1-2 and 2-1 transitions occurring. Further, the cross-correlation analysis only shows that chirp timing between individuals is not phase-locked at these small timescales. It is entirely possible that chirp rates are correlated between interacting individuals, even if their precise timing is not.

Reviewer #2 (Public Review):

Kandola et al. explore the important and difficult question regarding the initiating event that triggers (nucleates) amyloid fibril growth in glutamine-rich domains. The researchers use a fluorescence technique that they developed, dAMFRET, in a yeast system where they can manipulate the expression level over several orders of magnitude, and they can control the length of the polyglutamine domain as well as the insertion of interfering non-glutamine residues. Using flow cytometry, they can interrogate each of these yeast 'reactors' to test for self-assembly.

In the introduction, the authors provide a fairly thorough yet succinct review of the relevant literature into the mechanisms of polyglutamine-mediated aggregation over the last two decades, as well as a fairly clear description of the experimental techniques they developed.

Their assay shows that the fraction of cells with AmFRET signal increases strongly with an increase in polyQ length, with a threshold around 35-40 glutamines. This roughly correlates with the Q-length dependence of disease. The experiments in which asparagine or other amino acids are inserted at variable positions in the glutamine repeat are creative and thorough, and the data along with the simulations provide compelling support for the proposed Q zipper model. The experiments are strongly supportive of a model where formation of the beta-sheet nucleus is within a monomer. This is a potentially important result, as there are conflicting data in the literature as to whether the nucleus in polyQ is monomer.

The authors present convincing data that there are differences in the structural stability of their "QU" versus "QB" aggregates. However, the conclusion that "QB" must have multilamellar architecture versus "QU" was feasible but less compelling.

The authors present intriguing data showing that amyloid formation does not monotonically increase with increasing concentration, and their conclusion that high concentrations of polyQ can 'self-poison' amyloid growth is supported by the experimental data. The discussion surrounding the mechanism by which 'self-poisoning' occurs is confusing. The authors variously discuss that soluble oligomers must be the inhibitory species, that dead-end products of Q zipper nuclei are the inhibitory species, or that self-poisoning occurs because conformational conversion at the templating surface is slow relative to the rate of arrival of new molecules to the surface. The data seem consistent with an argument that, at high concentrations, non-structured polyQ oligomers form which interfere with elongation into structured amyloid assemblies - but it is not clear why such oligomers would be zippers.

Overall, this is a very valuable and thorough exploration of the fundamental question as to the nature and identity of the nucleating species in polyglutamine aggregation.

Reviewer #2 (Public Review):

Summary:<br /> The EAG family of ion channels is associated with many pathological conditions and are considered a target for the treatment of disease such as cancer. In this study, Abdelaziz et. al. examine the role of interaction between PAS domain and CNBHD in voltage-dependent gating of EAG channels. Based on their data, the authors conclude that they have identified a hidden open state that is only accessible in the mutant channels but not in the wild type. This hidden open state O1 can distinguished from the canonical open state O2 because it exhibits very different voltage-dependence. Although it is clear that the kinetics of these two open states are different, I have concerns about whether the data presented in this manuscript rule out alternate explanations. The idea that PAS domain deletions uncover a hidden open state is an extraordinary claim and if established, it has the potential to open a completely new approach to studying early gating transitions of these channels.

Strengths:<br /> 1. The study has identified a number of potentially interesting mutants that modulate voltage-dependent gating.<br /> 2. The discovery of a hidden open state due to mutations in the cytosolic domains is quite astonishing.

Weaknesses:<br /> 1. WT EAG currents are far right shifted compared to previously published data. It is not clear whether it is the recording conditions but at 0 mV very few channels are open. Compare this with recordings reported previously of the same channel hEAG1 by Gail Robertson's lab ( Zhao et. al. (2017) JGP). In that case, most of the channels are open at 0 mV. There must be at least 25 mV shift in voltage-dependence. These differences are unusually large.

2. In most of the mutants, O2 state becomes more prevalent at potentials above +50 mV. At these potentials, endogenous voltage-dependent currents are often observed in xenopus oocytes. The observed differences between the various mutants might simply be a function of the expression level of the channel versus endogenous currents.

3. Voltage-dependence of the kinetics of WT currents appears a bit strange. Why is the voltage-dependence saturated at 0 mV even though very few channels have activated at that point? I cannot imagine any kinetic model that can lead to such unusual voltage-dependence of kinetics.

4. One of the other concerns I have is that in many cases, it is clear that the pulse is too short to measure steady-state voltage-dependence. For instance, the currents in -160 mV and -100 mV in Figure 6A and 6B are not saturated.

Reviewer #2 (Public Review):

The manuscript starts with a demonstration of pantoate binding to ASBTnm using a thermostability assay and ITC, and follows with structure determinations of ASBTnm with or without pantoate. The structure of ASBTnm in the presence of pantoate pinpoints the binding site of pantoate to the "crossover" region formed by partially unwinded helices TMs 4 and 9. Binding of pantoate induces modest movements of side chain and backbone atoms at the crossover region that are consistent with providing coordination of the substrate. The structures also show movement of TM1 that opens the substrate binding site to the cytosol and mobility of loops between the TMs. MD simulations of the ASBT structure embedded in lipid bilayer suggests a stabilizing effect of the two sodium ions that are known to co-transport with the substrate. Binding study on pantoate analogs further demonstrate the specificity of pantoate as a substrate.

Overall, the structural, functional and computational studies are solid and rigorous, and the conclusions are well justified. In addition, the authors discussed the significance of the current study in a broader perspective relevant to recent structures of mammalian BASS members.

Reviewer #2 (Public Review):

Summary:<br /> The paper sought to determine the number of myosin 10 molecules per cell and localized to filopodia, where they are known to be involved in formation, transport within, and dynamics of these important actin-based protrusions. The authors used a novel method to determine the number of molecules per cell. First, they expressed HALO tagged Myo10 in U20S cells and generated cell lysates of a certain number of cells and detected Myo10 after SDS-PAGE, with fluorescence and a stained free method. They used a purified HALO tagged standard protein to generate a standard curve which allowed for determining Myo10 concentration in cell lysates and thus an estimate of the number of Myo10 molecules per cell. They also examined the fluorescence intensity in fixed cell images to determine the average fluorescence intensity per Myo10 molecule, which allowed the number of Myo10 molecules per region of the cell to be determined. They found a relatively small fraction of Myo10 (6%) localizes to filopodia. There are hundreds of Myo10 in each filopodia, which suggests some filopodia have more Myo10 than actin binding sites. Thus, there may be crowding of Myo10 at the tips, which could impact transport, the morphology at the tips, and dynamics of the protrusions themselves. Overall, the study forms the basis for a novel technique to estimate the number of molecules per cell and their localization to actin-based structures. The implications are broad also for being able to understand the role of myosins in actin protrusions, which is important for cancer metastasis and wound healing.

Strengths:<br /> The paper addresses an important fundamental biological question about how many molecular motors are localized to a specific cellular compartment and how that may relate to other aspects of the compartment such as the actin cytoskeleton and the membrane. The paper demonstrates a method of estimating the number of myosin molecules per cell using the fluorescently labeled HALO tag and SDS-PAGE analysis. There are several important conclusions from this work in that it estimates the number of Myo10 molecules localized to different regions of the filopodia and the minimum number required for filopodia formation. The authors also establish a correlation between number of Myo10 molecules filopodia localized and the number of filopodia in the cell. There is only a small % of Myo10 that tip localized relative to the total amount in the cell, suggesting Myo10 have to be activated to enter the filopodia compartment. The localization of Myo10 is log-normal, which suggest a clustering of Myo10 is a feature of this motor.

Weaknesses:<br /> One main critique of this work is that the Myo10 was overexpressed. Thus, the amount in the cell body compared to the filopodia is difficult to compare to physiological conditions. The amount in the filopodia was relatively small - 100s of molecules per filopodia so this result is still interesting regardless of the overexpression. However, the overexpression should be addressed in the limitations.<br /> The authors have not addressed the potential for variability in transfection efficiency. The authors could examine the average fluorescence intensity per cell and if similar this may address this concern.<br /> The SDS PAGE method of estimating the number of molecules is quite interesting. I really like this idea. However, I feel there are a few more things to consider. The fraction of HALO tag standard and Myo10 labeled with the HALO tagged ligand is not determined directly. It is suggested that since excess HALO tagged ligand was added we can assume nearly 100% labeling. If the HALO tag standard protein is purified it should be feasible to determine the fraction of HALO tagged standard that is labeled by examining the absorbance of the protein at 280 and fluorophore at its appropriate wavelength. The fraction of HALO tagged Myo10 labeled may be more challenging to determine, since it is in a cell lysate, but there may be some potential approaches (e.g. mass spec, HPLC).<br /> In Figure 1B, the stain free gel bands look relatively clean. The Myo10 is from cell lysates so it is surprising that there are not more bands. I am not surprised that the bands in the TMR fluorescence gel are clean, and I agree the fluorescence is the best way to quantitate.<br /> In Figure 3C, the number of Myo10 molecules needed to initiate a filopodium was estimated. I wonder if the authors could have looked at live cell movies to determine that these events started with a puncta of Myo10 at the edge of the cell, and then went on to form a filopodia that elongated from the cell. How was the number of Myo10 molecules that were involved in the initiation determined? Please clarify the assumptions in making this conclusion.<br /> It is stated in the discussion that the amount of Myo10 in the filopodia exceeds the number of actin binding sites. However, since Myo10 contains membrane binding motifs and has been shown to interact with the membrane it should be pointed that the excess Myo10 at the tips may be interacting with the membrane and not actin, which may prevent traffic jams.

Reviewer #2 (Public Review):

The authors suggest that the African trypanosome endomembrane system has unusual organisation, in that the entire system is a single reticulated structure. It is not clear if this is thought to extend to the lysosome or MVB. There is also a suggestion that this unusual morphology serves as a trans-(post)Golgi network rather than the more canonical arrangement.

The work is based around very high-quality light and electron microscopy, as well as utilising several marker proteins, Rab5A, 11 and 7. These are deemed as markers for early endosomes, recycling endosomes and late or pre-lysosomes. The images are mostly of high quality but some inconsistencies in the interpretation, appearance of structures and some rather sweeping assumptions make this less easy to accept. Two perhaps major issues are claims to label the entire endosomal apparatus with a single marker protein, which is hard to accept as certainly this reviewer does not really even know where the limits to the endosomal network reside and where these interface with other structures. There are several additional compartments that have been defined by Rob proteins as well, and which are not even mentioned. Overall I am unconvinced that the authors have demonstrated the main things they claim.

The approaches taken are state-of-the-art but not novel, and because of the difficulty in fully addressing the central tenet, I am not sure how much of an impact this will have beyond the trypanosome field. For certain this is limited to workers in the direct area and is not a generalisable finding.

Reviewer #2 (Public Review):

The authors use Xenopus embryos to study feedback interactions between the planar cell polarity (PCP) proteins in the context of convergence and extension. They show that binding of the cytoplasmic polarity protein Pk2 to Vangl2 is needed for them to synergistically suppress defects in convergence and extension caused by Dvl overexpression. They then examine protein localizations in animal cap cells, and show that Wnt11-induced accumulation of Fzd7, Ror2 and Dvl into plasma membrane patches is disrupted by the functional Vangl2/Pk complex. This disperses Fzd and causes its endocytosis, while Dvl remains at the plasma membrane.

This is a potentially interesting paper, showing mechanisms by which Vangl2/Pk can functionally antagonize Fzd/Dvl during planar cell polarity.

The protein localization experiments in animal cap assays are for the most part convincing, but with the caveat that the authors assume that the proteins are acting within the same cell. As Fzd and Vangl2 are thought to localize to opposite cell ends in many contexts, can the authors be sure that the effects they observe are not due to trans interactions?

The authors propose a model whereby Vangl2 acts as an adaptor between Dvl and Ror, to first prevent ectopic activation of signaling, and then to relay Dvl to Fzd upon Wnt stimulation. This is based on the observation that Ror2 can be co-IPed with Vangl2 but not Dvl; and secondly that the distribution of Ror2 in membrane patches after Wnt11 stimulation is broader than that of Fzd7/Dvl, while Vangl2 localizes to the edges of these patches. The data for both these points is not wholly convincing. The co-IP of Ror2 and Vangl2 is very weak, and the input of Dvl into the same experiment is very low, so any direct interaction could have been missed. Secondly, the broader distribution of Ror2 in membrane patches is very subtle, and further analysis would be needed to firm up this conclusion.

A final caveat to these experiments is that in the animal cap assays, loss of function and gain of function both cause convergence and extension defects, so any genetic interactions need to be treated with caution i.e. two injected factors enhancing a phenotype does not imply they act in the same direction in a pathway, in particular as there are both cis/trans and positive/negative feedbacks between the PCP proteins.

Reviewer #2 (Public Review):

Where this study is interesting is that the authors do a meta-analysis of studies in which metabolic rate was experimentally manipulated and both this rate and glucocorticoid levels were simultaneously measured. Unsurprisingly, there are relatively few such studies and many are from a single lab. More studies are needed. While the results of the analysis are compelling, they are not surprising. That said, this work is important.

Reviewer #2 (Public Review):

Prime editing is a major gene editing technique because it allows for the introduction of all possible substitutions, as well as small insertions and deletions, without causing double strand breaks. However, its efficiency is often limited. In a previous study, the authors showed that prime editing could be performed in zebrafish using recombinant PE2 protein and pegRNAs generated by in vitro transcription, but at many of the sites tested, gene editing efficiency remained relatively low.

In this current paper, the authors find that when pegRNAs were combined with Cas9, many induced much less indels than their corresponding guide RNAs and propose that this is due to the complementarity between the 5' and 3' regions of pegRNAs. Two methods aiming to reduce the resulting circularization of pegRNAs were next shown to increase the efficiency of prime editing: a slow refolding protocol (which was previously shown to be useful for inefficient guide RNAs), and the introduction of a substitution at position +2 of the reverse transcriptase template sequence. The data obtained and analyzed is solid and convincing.

These methods are remarkably straightforward and proved beneficial for most of the pegRNAs tested. Consequently, they represent important advances for the prime editing technique.

It should be noted, however, that despite these advances, prime editing activity remained relatively low for a significant proportion of pegRNAs tested (with less than 2% sequencing reads exhibiting the expected sequence change). This shows that further improvements are still needed for this important gene editing technique.

Reviewer #2 (Public Review):

Summary:<br /> This is a solid study that dissects the thermodynamics of lipopolysaccharide (LPS) transporter MsbA and LPS. Native ESI-MS and the novel strategies developed by the authors were employed to quantify the affinities of LPS-MsbA interactions and its temperature dependence. Here, the equilibrium of lipid-protein interactions occurs in the micellar phase. The double-/triple-mutant cycle analysis and van't Hoff analysis allowed a full thermodynamic description of the lipid-protein interactions and the analysis of thermodynamic coupling between LPS binding sites. The most notable result would be that LPS-MsbA interaction is largely driven by entropy involving the negative heat capacity, a signature of the solvent reorganization effect (here authors attribute the solvent effect to "water" reorganization). The entropy driven lipid binding has been previously reported by the same authors for Kir1,2-PIP2 interactions.

Strengths:

1) This is overall a very thorough and rigorous study providing the detailed thermodynamic principles of LPS-MsbA interaction.

2) The double and triple-mutant cycle approaches are newly applied to lipid-protein interactions, enabling detailed thermodynamics between LPS binding sites.

3) The entropy-driven protein-lipid interaction is surprising. The binding seems to be mainly mediated by the electrostatic interaction between the positively charged residues on the protein and the negatively charged or polar headgroup of LPS, which could be thought of as "enthalpic" (making of a strong bond relative to that with solvent).

Weaknesses:

1. This study is a good contribution to the field, but it was difficult to find novel biological insights or methodological novelty from this study.

1a) Thermodynamic analysis of lipid-protein interactions, an example of entropy-driven lipid-protein interactions, and the cooperativity between lipid binding sites have been reported by the author's group. Also, the cooperativity between binding sites in general have been reported from numerous studies of biomolecular interactions.

1b) It is not clear how this study provides new insights into the understanding of LPS transport mechanisms. Probably, authors could strengthen the Discussion by providing biological insights-how the residue coupling.

2) One to three LPS molecules bind to MsbA, but it is unclear whether bound KDL occupies inner or outer cavities, or both and how a specific mutation affects the affinity of specific LPS (i.e., to inner or to outer cavities). Based on the known structures, the maximal number of LPS is three. It is possible that the inner and outer cavities have different LPS affinities. Also, there can be multiple one-LPS-bound states, two-LPS-bound states if LPS strictly binds to the binding sites indicated by the structures. This aspect is beyond the scope of this study and difficult to address, but without this information, it seems hard to tell what is going on in the system.

3) If a single mutation is introduced to the inner cavity, its effect will be "doubled" because the inner cavity is shared by two identical subunits. This effect needs to be clarified in the result section.

4) In the result section, "Mutant cycle analysis of KDL binding to vanadate-trapped MsbA.":

4a) It seems necessary to show the mass spectra for Msb-ADP-vanadate complex as well as its lipid bound forms.

4b) The rationale of this section (i.e., what mechanistic insights can be obtained from this study) is unclear. For example, it is not sure what meaningful information can be obtained from a single type (ADP/vanadate) of the bound state regarding the ATP-driven function of MsbA.

Reviewer #2 (Public Review):

Previously, using bioinformatics study, authors have identified potential sequence motifs that are common to a large subset of beta-barrel outer membrane proteins in gram negative bacteria. Interestingly, in that study, some of those motifs are located in the internal strands of barrels (not near the termini), in addition to the well-known "beta-signal" motif in the C-terminal region.

Here, the authors carried out rigorous biochemical, biophysical, and genetic studies to prove that the newly identified internal motifs are critical to the assembly of outer membrane proteins and the interaction with the BAM complex. The author's approaches are rigorous and comprehensive, whose results reasonably well support the conclusions. While overall enthusiastic, I have some scientific concerns with the rationale of the neutron refractory study, and the distinction between "the intrinsic impairment of the barrel" vs "the impairment of interaction with BAM" that the internal signal may play a role in. I hope that the authors will be able to address this.

Strengths:

1. It is impressive that the authors took multi-faceted approaches using the assays on reconstituted, cell-based, and population-level (growth) systems.

2. Assessing the role of the internal motifs in the assembly of model OMPs in the absence and presence of BAM machinery was a nice approach for a precise definition of the role.

Weaknesses:

1. The result section employing the neutron refractory (NR) needs to be clarified and strengthened in the main text (from line 226). In the current form, the NR result seems not so convincing.

What is the rationale of the approach using NR?<br /> What is the molecular event (readout) that the method detects?<br /> What are "R"-y axis and "Q"-x axis and their physical meanings (Fig. 5b)?<br /> How are the "layers" defined from the plot (Fig. 5b)?<br /> What are the meanings of "thickness" and "roughness" (Fig. 5c)?<br /> What are the meanings of the increases in thickness and roughness?<br /> What does "SLD" stand for?

2. In the result section, "The internal signal is necessary for insertion step of assembly into OM"

This section presents an important result that the internal beta-signal is critical to the intrinsic propensity of barrel formation, distinct from the recognition by BAM complex. However, this point is not elaborated in this section. For example, what is the role of these critical residues in the barrel structure formation? That is, are they involved in any special tertiary contacts in the structure or in membrane anchoring of the nascent polypeptide chains?

Reviewer #2 (Public Review):

Summary: The authors seek to elucidate the early evolution of cnidarians through computer modeling of fluid flow in the oral region of very small, putative medusozoan polyps. They propose that the evolutionary advent of the free-swimming medusoid life stage was preceded by a sessile benthic life stage equipped with circular muscles that originally functioned to facilitate feeding and that later became co-opted for locomotion through jet propulsion.

Strengths: Assumptions of the modeling exercise laid out clearly; interpretations of the results of the model runs in terms of functional morphology plausible. An intriguing investigation that should stimulate further discussion and research.

Weaknesses: Speculation on the origin of the medusoid life stage in cnidarians heavily dependent on prior assumptions concerning the soft part anatomy and material properties of the skeleton of the modeled fossil organism that may be open to alternative interpretations.

Reviewer #2 (Public Review):

This is a thorough and convincing body of work that represents an incremental but significant improvement on iterations of this method of CRISPR-based Sterile Insect Technique ('pgSIT'). In this version, compared to previous, the authors target more genes than previously, in order to induce both female inviability (targeting the genes intersex and doublesex, compared to fem-myo previously) and male sterility (targeting a beta-tubulin, as previously in the release generation.<br /> The characterization of the lines is extensive and this data will be useful to the field. However, what is lacking is some context as to how this formulation compares to the previous iteration. Mention is made of the possible advantage of removing most females, compared to just making them flightless (as previously) but there is no direct comparison, either experimental, or theoretical i.e. imputing the life history traits into a model. For me this is a weakness, yet easily addressed. In a similar vein, much is made in alluding to the 'safety concerns of gene drive' and how this is a more palatable half-way house, just because it has CRISPR component within it; it is not. It would be much more sensible, and more informative, to compare this pgSIT technology to RIDL (release of insects carrying a dominant lethal), which is essentially a transgene-based version of the Sterile Insect Technique, as is the work presented here.

The authors achieve impressive results and show that these strains, under a scenario of high levels of release ratios compared to WT, could achieve significant local suppression of mosquito populations. The sensitivity analysis that examines the effect of changing different biological or release parameters is well performed and very informative.

The authors are honest in acknowledging that there are still challenges in bringing this to field release, namely in developing sexing strains and optimizing release strategies - a question I have here is how to actually release eggs, and could variability in the efficiency of this aspect be modelled in the sensitivity analysis? It seems to me like this could be a challenge and inherently very variable.

Reviewer #2 (Public Review):

The authors were trying to survey reservoir viral sequences in different anatomical sites in the body, with the brain being of special interest. This is a study that is technically demanding and here is well done, providing insights that prompt new and more sophisticated questions.

The authors use end-point dilution PCR to identify individual proviruses that can then be sequenced with high accuracy. These are high quality data sets but given the technical requirements of this approach the number of sequenced proviruses is limiting given the scope of questions this study addresses. Nonetheless, there is a lot of data here to draw many useful conclusions.

It will be important to realize how clones of infected T cells can move around the body, including into the CNS compartment. It will also be important to remember that there are limits in sampling depth of proviruses in any one tissue meaning the failure to detect something has a limit in sensitivity of detection when trying to interpret a negative result.

As noted in the next section, it is important to emphasize that there is another entry phenotype beyond X4 that will ultimately be important in interpreting these results. Macrophage-tropic viruses are often found in the CNS compartment and it will be important to understand whether these CNS-derived sequences are macrophage-tropic viruses there infecting macrophages and microglia or if they are all T-tropic viruses brought in by wandering infected T cells (or both).

Reviewer #2 (Public Review):

Summary:<br /> In the current study, the authors tested the hypothesis that Aβ42 toxicity arises from its proven affinity for γ-secretases. Specifically, the increases in Aβ42, particularly in the endolysosomal compartment, promote the establishment of a product feedback inhibitory mechanism on γ-secretases, and thereby impair downstream signaling events. They showed that human Aβ42 peptides, but neither murine Aβ42 nor human Aβ17-42 (p3), inhibit γ-secretases and trigger accumulation of unprocessed substrates in neurons, including (CTFs of APP, p75 and pan-cadherin. Moreover, Aβ42 dysregulated cellular homeostasis by inducing p75-dependent neuronal death. Because γ-secretases process many other membrane proteins, including NOTCH, ERB-B2<br /> receptor tyrosine kinase 4 (ERBB4), N-cadherin (NCAD) and p75 neurotrophin receptor (p75-NTR), revealing a broad range of downstream signaling pathways, including those critical for neuronal structure and function. Hence, they propose to identification of a selective role for the Aβ42 peptide, and raise the intriguing possibility that compromised γ-secretase activity against the CTFs of APP and/or other neuronal substrates contributes to the pathogenesis of AD. Overall, the data are not very convincing to support the main claim.

Strengths.

Different in vitro and cellular approaches are employed to test the hypothesis.

Weaknesses.

The experimental concentrations for Aβ42 peptide in the assay are too high, which are far beyond the physiological concentrations or pathological levels. The artificial observations are not supported by any in vivo experimental evidence.

Reviewer #2 (Public Review):

The authors describe the synthesis and testing of the anti-cancer activity of a new molecule CK21 against pancreatic cancer mouse models. This part of the study is very strong showing regression of pancreatic tumors at non-toxic concentrations, which is very hard to achieve for practically uncurable pancreatic cancer. Authors synthesized CK21 as an analog of a known inhibitor of RNA synthesis which is very toxic. The authors did very little attempt to understand whether the mechanism of anti-cancer efficacy of CK2 is similar to this known inhibitor of transcription or not. One cannot compare gene expression profiles between untreated and CK21-treated cells, taking into account that CK2 may inhibit the expression of all genes. The effect of CK2 on general transcription needs to be tested first, and then based on this data absolute changes in the expression of genes may be considered for the revealing of the mechanism of activity of CK21.

Reviewer #2 (Public Review):

In this manuscript, Ruesseler and colleagues use a continuous task to examine how neural correlates of decision-making change when subjects face conditions with different durations and frequencies of occurrence of signals embedded in noise. The authors develop a novel task where subjects must report the direction of relatively sustained (3 or 5 s) signal changes in average coherence of a random dot kinetogram that are intermittent among relatively transient noise fluctuations (<1 s) of motion coherence that is continuous. Subjects adjust their behavior to changes in the duration of signal events and the frequency of their occurrence. The authors estimate a decay time constant of leaky integration of evidence based on the average coherence leading up to decision responses. Interestingly, there is considerable inter-subject variability in decay time constants even under identical conditions. In addition, the average time constants are shorter when signal periods occur more frequently as opposed to when they are more rare. The authors use EEG to find that a component of the Centroparietal Positivity (CPP) regressed to the magnitude of changes in the noise coherence is larger in conditions when the signal periods occur less frequently. Using a control condition, the authors show that this component of the CPP is not simply based on surprise because it is smaller for changes in motion coherence in irrelevant directions with matched statistics as the changes in relevant directions. The authors also find that a different component of the CPP related to the magnitude of the motion coherence co-varies with the inter-subject variability in decay time constants estimated from behavior.

Overall, the authors use a clever experimental design and approach to tackle an important set of questions in the field of decision-making. The manuscript is easy to follow with clear writing. The analyses are well thought-out and generally appropriate for the questions at hand. From these analyses, the authors have a number of intriguing results. So, there is considerable potential and merit in this work. That said, I have a number of important questions and concerns that largely revolve around putting all the pieces together. I describe these below.

1) Quite sensibly, the authors hypothesize that "decay time constant" for past evidence and "decision threshold" would be altered between the different task conditions. They find clear and compelling evidence of behavioral alterations with the conditions. They also have a method to estimate the decay time constant. However, it is unclear to what extent the decision threshold is changing between subjects and conditions, how that might affect the empirical integration kernel, and how well these two factors can together explain the overall changes in behavior.

To be more specific, the authors state that the lower false alarm rates and slower reaction times for the LONG condition are consistent with a more cautious response threshold for LONG. The empirical integration kernels lead to the suggestion that the decay time constant is not changing between SHORT and LONG, while it is changing between FREQUENT and RARE. Does the lack of change in false alarm rate between FREQUENT and RARE imply no change in the decision threshold? Is this consistent with the behavior shown in Figure 2? I would expect that less decay in RARE would have led to more false alarms, higher detection rates, and faster RTs unless the decision threshold also increased (or there was some other additional change to the decision process). The CPP for motor preparatory activity reported in Fig. 5 is also potentially consistent with a change in the decision threshold between RARE and FREQUENT. If the decision threshold is changing, how would that affect the empirical integration kernel? These are important questions on their own and also for interpreting the EEG changes.

2) The authors find an interesting difference in the CPP for the FREQUENT vs RARE conditions where they also show differences in the decay time constant from the empirical integration kernel. As mentioned above, I'm wondering what else may be different between these conditions. Do the authors have any leverage in addressing whether the decision threshold differs? What about other factors that could be important for explaining the CPP difference between conditions? Big picture, the change in CPP becomes increasingly interesting the more tightly it can be tied to a particular change in the decision process.

I'll note that I'm also somewhat skeptical of the statements by the authors that large shifts in evidence are less frequent in the RARE compared to FREQUENT conditions (despite the names) - a central part of their interpretation of the associated CPP change. The FREQUENT condition obviously has more frequent deviations from the baseline, but this is countered to some extent by the experimental design that has reduced the standard deviation of the coherence for these response periods. I think a calculation of overall across-time standard deviation of motion coherence between the RARE and FREQUENT conditions is needed to support these statements, and I couldn't find that calculation reported. The authors could easily do this, so I encourage them to check and report it.

3) The wide range of decay time constants between subjects and the correlation of this with another component of the CPP is also interesting. However, in trying to interpret this change in CPP, I'm wondering what else might be changing in the inter-subject behavior. For instance, it looks like there could be up to 4 fold changes in false alarm rates. Are there other changes as well? Do these correlate with the CPP? Similar to my point above, the changes in CPP across subjects become increasingly interesting the more tightly it can be tied to a particular difference in subject behavior. So, I would encourage the authors to examine this in more depth.

Reviewer #2 (Public Review):

The study by Yang et al. examines the interactions between a model host, the nematode C. elegans, and its gut bacteria during aging, focusing on how the host responds to progressing bacterial colonization. In a sense, this work follows up on a previous report describing the activation of DAF-16 in middle-aged worms. Here they test the importance of DAF-16 for aging-dependent accumulation of E. coli in the worm gut, as a model for responses to, and mitigation of, dysbiosis, which in humans is associated with pathology.

The mechanism unraveled in this study includes the sensing of increasing concentrations of indole, a tryptophan metabolite that is secreted by the accumulating gut bacteria, which dependent on the neuronal cation channel TRPA-1 (and NOT through the known indole receptor AHR-1), activates intestinal DAF-16, driving its nuclear translocation and leading to subsequent induction of downstream targets, of which LYS-7 and LYS-8 are essential for diminishing bacterial colonization and mitigating the associated damage.

The authors provide very clean and very strong evidence to support the described mechanism, clean identification of indole as the metabolite responsible for DAF-16 nuclear localization, and good indole supplementation experiments and measurements of indole levels inside of worms to support its function. At the same time, some of the methods are not completely clear - for example, how did the authors obtain pure bioactive fraction to run their NMR analysis and identify indole as the activating molecule (this should be clarified in, or added to the method section); or how were indole supplementation experiments carried out? On solid media, i.e. NGM plates, or in solution; with live bacteria, or heat-killed ones? (this is important for figuring out if indole sensing is from the outside or from the gut); and in a few cases the results appear too clear-cut, like the contribution of lys-7 and lys-8 to controlling gut bacteria - these two lysozymes seem to be sufficient to account for the entire contribution of DAF-16, which is surprising considering the large number of downstream targets this transcription factor has, as well as the very redundant nature of innate immune protection, which would have suggested the partial ability to protect at best; this should be considered and discussed.

Overall, though, the study is strong, and the conclusions are well supported. Given this, its potential impact is high, to inform our understanding of how animals respond to dysbiosis and the mechanisms aimed at mitigating potential detrimental effects of dysbiosis. Here, dysbiosis is manifested as increased colonization of aging worms by bacteria that cannot colonize young adults. In humans, dysbiosis manifests as imbalances in microbiome composition, which may include the proliferation of some gut bacteria at the expense of others. Thus, the mechanisms characterized here, which are conserved in humans, may play similar roles in human pathology and may offer handles to try and mitigate the detrimental effects of dysbiosis.

Reviewer #2 (Public Review):

Hybridization events between species are known to result in substantial genomic upheaval, requiring subsequent coordination between gene copies to ensure proper control of gene expression and embryonic viability. An example of such an event happened over 18 million years ago between two frog species that resulted in Xenopus laevis-an allotetraploid that has largely retained copies of both genes from this event, known as L-alleles and S-alleles. Often, the presence of both copies presents an experimental and bioinformatic hurdle for researchers and is a feature of the biology of X. laevis that renders cross-species comparisons difficult. Phelps et al, however, take advantage of this feature of Xenopus biology and use it to their advantage to ask how the hybridization event in this species altered gene regulatory architecture. They find that a handful of pluripotency genes are largely responsible for activating gene expression in the early embryo, but that L and S alleles are differentially activated in many cases. Moreover, they find extensive differences in cis-regulatory architecture between L/S alleles. Despite these differences in alleles, however, they find that their combined gene expression output is largely conserved, possibly reflecting strong selection pressures acting to maintain gene expression output at specific levels. This work represents a significant advance in how hybridization events are something greatly understudied in developmental biology-influence gene regulatory programs and how evolutionary pressures have shaped these programs in response to such events.

Reviewer #2 (Public Review):

Zou et al. presented a comprehensive study where they generated single-cell RNA profiling of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC, and their matched normal tissues, covering comprehensive clinical courses of cSCC. Using bioinformatics analysis, they identified keratinocytes, CAFs, immune cells, and their subpopulations. The authors further compared signatures within subpopulations of keratinocytes along with the clinical progression, especially basal cells, and identified many interesting genes. They also further validate some of the markers in an independent cohort using IHC, followed by some knockdown experiments using cSCC cell lines.

The strength of this study is the unique data set they have created, providing the community with invaluable resources to study and validate their findings. However, a lot of analyses were not robust enough to support the claims and conclusions in the paper. More clarification and cross-comparison with polished data are needed to further strengthen the study and claims.

1) Stemness markers were used. The authors used COL17A1, TP63, ITGB1, and ITGA3 to represent stemness markers. However, these were not common classic stemness markers used in cSCC. What is the source claiming these genes were stemness markers in cSCC? TP63 is a master regulator and early driver event in SCC, while COL17A1, ITGB1, and ITGA3 are all ECM genes. The authors need to use commonly well-known stem cell markers in cSCC, e.g., LGR5, to mark stem-like cells.

2) Cell proportion analysis. The authors used the mean proportions to compare different clinical groups for subpopulations of keratinocytes, e.g., Figure 2B, and Figure 5B. This is not robust, as no statistics can be derived from this. For example, from Fig 2A, it is clearly shown there is a high level of heterogeneity of cellular compositions for normal samples. One cannot say which group is higher or lower simply based on mean not variance as well.

3) Basal tumour cells in SCCIS and SCC. To make the findings valid, authors need to compare these cells/populations with the keratinocyte cell populations defined by Ji et al. Cell 2020. Do basal-SCCIS-tumours cells, also in SCC samples, resemble any of the population defined in Ji et al. Ji et al. also had 10 match normal, thus the authors need to validate their findings of SCC vs normal analysis using the Ji et al. dataset.

4) Copy number analysis. Authors used inferCNV to perform copy number analysis using scRNA-seq data and identified CNVs in subpopulations of keratinocytes in SCCIS and SCC. To ensure these CNVs were not artefacts, were some of the CNVs identified by inferCNV well-known copy number changes previously reported in cSCC?

5) Pseudotime analysis lines 308-313. Not sure the pseudotime analysis added much as, as it is unclear two distinct subgroups were identified from this analysis. Suggest removing this to keep it neater

6) Selection of candidate genes for validation using IHC and cell line work. For example, lines 205-206, lines 352-356 and lines 437-441, authors selected several genes associated with AK and SCC to further validate using IHC and cell line knockdown work. What are the criteria for selecting those genes for validation? It is unclear to readers how these were selected. It reads like a fishing experiment, then followed by a knockdown. Clear rationale/criteria need to be elaborated.

7) TME. Compared to keratinocytes populations, the investigation of TME cells was weak. (a) can authors produce UMAP files just for T cells, DC cells, and fibroblasts separately? Figure 7B is not easy to see those subclusters. (b) similar to what was done for keratinocytes, can authors find differentially expressed clusters and genes among the different clinical groups, associated with disease progression? (c) where are the myeloid cell populations, also B cells?

8) Heat shock protein genes line 327-329. HSP signature was well-known to be induced via tissue dissociation and library prep during the scRNA experiment. How could the authors be sure these were not artefacts induced by the experiment? If authors regress their gene expression against HSP gene signatures, would this cluster still be identified?

9) Cell-cell communication analysis. The authors claimed that that cell-to-cell interaction was significantly enhanced in poorly-differentiated cSCC, and multiple interaction pathways were significantly active. How was this kind of analysis carried out? How did the authors define significance? what statistical method was used? these were all unclear. Furthermore, it is difficult to judge the robustness of the cell-cell communication analysis. Were these findings also supported by another method, such as celltalker, and cellphoneDB?

10) Statistics and significance. In general, the detail of statistics and significance was lacking throughout the paper. Authors need to specify what statistical tests were used, and the p-values. It is difficult to judge the correctness of the test, and robustness without seeing the stats.

11) Overall, this manuscript needs a lot of re-writing. A lot of discussion was also included in the results, making it really difficult to read overall. The authors should simplify the results sections, remove the discussion bits, and further highlight and streamline with the key results of this paper.

Reviewer #2 (Public Review):

The manuscript employs multiple approaches, including molecular docking, molecular dynamic simulations, and functional experiments to uncover a distinct uridine diphosphate-sugar-binding site on P2Y14 - a key drug target for inflammation and immune responses. Overall, the manuscript is clearly written and the experimental techniques are well-documented. However, it may benefit from further analysis, particularly in terms of validating the binding pose.

Reviewer #2 (Public Review):

There currently are several hundreds of kinase inhibitors described and available for purchase. However, most of the target the ATP binding site of the protein kinase domain and, since it is pretty well conserved across the whole protein family, it means that the inhibitors are rarely selective, and most are able to simultaneously inhibit several kinases with, sometimes, different binding affinities. In this m/s, the authors present a strategy to combine kinase inhibitors with the aim of reducing off-target effects while preserving the inhibition potency in the intended target. To develop the methodology, the authors have used a set of publicly available data (protein kinase inhibitor set-2, or PKIS-2) containing affinity data on 406 kinases and 645 inhibitors. The authors run a series of simulations suggesting that, in a few cases, the identified combination of inhibitors is superior to the most specific single kinase inhibitor (i.e. show fewer off-target effects while maintaining the inhibition of the on-target). Finally, they test one of these examples in cells using nanoBRET.

The manuscript tackles an interesting problem (i.e. poor selectivity of kinase inhibitors) that, in some cases, has important clinical bearings. The approach is novel, interesting, and well-executed. However, unfortunately, I am not convinced that the strategy presents a real advantage over the most selective inhibitor.

I believe the author refers to the open-sources of llama-2 model. It allows quick and specific fine-tuning of the original big model.

Reviewer #2 (Public Review):

Respiratory chain complexes assemble in higher-ordered structures termed supercomplexes or respirasomes. The functional significance of these assemblies is currently investigated, there are two main hypothesis tested, namely that supercomplexes provide kinetic advantages or structural stability. Here, the authors use the fruitfly to reveal that, while the respiratory chain in the organism normally does not form higher-order assemblies, it does so under conditions when their assembly is impaired. Because the rather moderate increase in supercomplex formation does not change oxygen consumption stimulated by CI or CII substrate, the authors conclude that supercomplex formation has more a structural than a functional role. The main strength of this work is that the technical quality of the experiments is high and that the authors induced defects in respiratory chain assembly through sets of well-controlled genetic models. The obtained data are mostly descriptive using standard approaches and are very well executed. The authors claim that their experiments allow to conclude that the role of supercomplex formation is restricted to a structural role and, hence, exclude a function directly related to electron transport efficiency. However, while the authors can show convincingly that supercomplexes form in the mutants, but not in the wild type, the main questions still remain, namely what is the structural mechanism of supercomplex formation and what is the significance of their formation. Given that the fly system does not show supercomplex formation under normal conditions, it is likely that it evolved functionally to work different than systems having supercomplexes. Because these differences are yet unknown, it remains questionable whether the fly system can be used to inform about the general significance of supercomplexes found in the other systems.

Reviewer #2 (Public Review):

This manuscript by Martin-Flores et al. has examined the role of DKK3 in Alzheimer's disease, focusing on the regulation of synaptic numbers. By using human AD brain databases and tissue samples, the authors showed that DKK3 protein and mRNA levels are increased in the brains of AD patients. DKK3 is expressed in the excitatory neurons in WT mouse brains and accumulates at atrophic neurites around amyloid plaques in AD mouse brains. Interestingly, secretion of DKK3 appears to be regulated by NMDAR antagonist as well as chemical LTD. Through gain and loss of function studies, the authors showed that DKK3 regulates the number of excitatory as well as inhibitory synapses with distinct downstream pathways. Finally, the authors investigated the contribution of DKK3 to synaptic changes in AD and found that DKK3 loss of function rescues both the excitatory and inhibitory synaptic defects, resulting in the improvement of memory function in J20 mice.

Overall, the data is clearly presented and deals with novel roles of DKK3 in controlling excitatory and inhibitory synapses. The finding that shRNA expression of DKK3 in AD model mice rescues synaptic phenotypes and memory impairment is potentially interesting and may provide a new strategy for AD treatment.

Reviewer #2 (Public Review):

Summary:<br /> Zung et al. use a comparative approach to examine the volatile headspace of diverse mammals and host species to understand the differences in chemical profiles that may provide mosquitoes with signatures of appropriate hosts. The authors collect the volatiles from hair samples and conduct qualitative analyses of the headspace composition. The authors' results suggest that mammals share overlapping volatile signatures, although the sampling method and statistical approaches reduce the veracity of the authors' findings. Additional comparisons between mammalian and floral odours were conducted, although the datasets were limited.

The inter-species comparisons will be helpful in the field, although the data pipeline and approaches may underestimate the headspace chemical diversity, and sampling artifacts and contaminants occur in the datasets, which further weakens the study's findings.

Strengths:<br /> The comparative approach is a strength of the manuscript. The authors identify an important gap in mosquito natural history by attempting to characterize the odours from various mammalian, bird, and reptile species that mosquitoes may use as blood hosts. Although others have compared the skin volatiles of humans, apes, and ungulates (Verhulst et al., 2018, not cited in the current manuscript), Zung and coworkers expand this sampling by using hair samples from collections and zoos. Unfortunately, the sampling approach leads to potential artifacts associated with the collected volatiles and statistical analyses.

Weaknesses:<br /> There are three major points of weakness associated with the manuscript: (1) sampling approach and analysis pipeline; (2) statistical analyses; and (3) premise and prior work.

1. Sampling approach and pipeline<br /> A. The authors have described their sampling and analysis as quantitative, but they use a qualitative approach by not quantifying their samples and using a low-res MS. I outline several approaches that would allow the authors to quantitate their samples. The authors must run synthetic standards for peak verification (the mass spectra alone are insufficient for compound identification). The authors are also encouraged to run the standards in a concentration curve to allow quantification of the compounds. The authors have only tentatively identified 120 compounds. Using an autosampler and standard analyses in the software, the authors could easily quantify their samples which would take less than a week's time (this is not impossible, as the authors state in the methods). Based on the volatile fragmentation and the MS detector, the compounds will differ in their relative abundances - running calibration curves, co-injection of authentic standards, and using multiple column types are necessary for the resulting statistical analyses to prevent mischaracterization of the abundances in the hair samples. Using an internal standard, by spiking the Tenax before collection, would also allow determination if column conditions change over the course of the experiment. These measurements would provide some quantitative measures to explore the differences in host odors. Details on these approaches can be found in Methods in Chemical Ecology, Techniques in Pheromone Research, and article reviews that describe more recent approaches and analyses (Tholl and Rose, 2006; Stashenko and Martínez, 2008; Spicer et al., 2017; Tholl et al., 2020; Eisen et al., 2021; Schulz and Mollerke, 2022).

B. Abundant contaminants in the samples. In the supplemental table of partially identified compounds, many contaminants are associated with the headspace collection method and environmental contaminants. Under thermal deadsorption, Tenax degradation produces many compounds, including quinolones and benzenoid compounds. Phenyl-substituted carbonyl compounds (benzaldehyde, acetophenone, benzene acetaldehyde) are formed as artifacts from the oxidation of Tenax with environmental contaminants. Other compounds, like phenol or -ethyl and methylated benzene compounds, are known to be released from the Tenax traps. The authors' pipeline and blank subtraction should have identified these compounds.

C. Hair and live headspace volatiles. I appreciate the authors' experiments comparing the composition and abundance of volatiles from live collections and hair samples. However, the results demonstrate that the hair does not always match the volatiles from the live animal. Humans 1, 3, and 4 differ significantly in their aldehyde abundances, especially nonanal. The hamster and mice samples also differ significantly. The matrix of the hair will adsorb and modify the emissions and ratios of compounds, which makes the inter-species comparisons difficult if not impossible if the headspace collection approaches differ. The authors need to change their phrasing of the host odours to "hair odours", and soften their statements associated with the complete host odour profile, and use hair samples as a standard matrix for the headspace collections. The comparison of human odour collections relative to hair samples is like the comparison of apples and oranges.

D. The authors need to use another column type to characterize their peaks further. Some of the compounds are enantiomers or closely elute from the column. Although the authors suggest their methods may separate these compounds, they may be misidentified without a different GC temperature ramp or column.

E. The authors should replace their retention indices with KRI values to further identify their compounds. The methods section does not describe whether the alkane standards were run parallel to the hair samples, and the manuscript's retention indices do not match published KRI values.

F. The number of compounds across species (including flower compounds) is very low (approximately 120 compounds) and surprising. This suggests that the analysis pipeline and thresholding may miss many compounds in the headspace. I would encourage the authors to lower their threshold to 10^-5 AU, or to perform a sensitivity analysis on their ability to identify the peaks. Running authentic standards would also allow the identification of compounds missed in the analysis.

G. I understand the difficulty in obtaining these samples across the different species. However, additional information is needed for those species that are limited in the number of replicates (individuals). Sampling the individual multiple times may indicate the variability in the hair volatiles. Although the authors and many others have shown the reproducibility of human skin volatiles through time, additional sampling would indicate this also occurs for other mammals while strengthening the authors' approach.

H. An important measure of natural odour statistics is the odor emission rates, and normalizing across samples by the sample mass. More information on the methods would have clarified these aspects. It needs to be clarified why the samples were collected for different time periods (5 to 80 minutes). The sample mass for each specimen should also be included as this would allow normalization by time and mass, and should be described in the methods. This would allow quantitative measurements of the samples.

I. A critical missing component in the headspace is the acids. Tenax does not perform well at collecting these compounds. However, Gerstel Twisters and other collection matrices can capture those compounds. The authors must use these other collection methods to sample the hair specimens and identify those compounds to include in their table and analyses. Without this information, the manuscript lacks a critical dimension in the human odour landscape that is critical for mosquito attraction.

2. Statistical Analyses<br /> A. Sampling effort and the replicate numbers used in the analyses is an important consideration that the authors do not address, but should be discussed in more detail. In many subfields of chemical ecology, a minimum of ten replicates per species has been suggested to accurately identify the composition of compounds, and even with ten samples, this may not be enough to characterize the volatile profile (Raguso and Pellmyr, 1998; Campbell et al 2019). The authors could perform a power analysis, or an accumulation curve to represent the needed sample number to identify the number of compounds in the hair headspace accurately.

B. It would be worthwhile for the authors to provide more detail on their supervised and unsupervised approaches, and how their data fits the assumptions of the analyses. The PCA parametric method may require log or square root transformation of the data to make residuals fit the normality assumption, but it's unclear if this was the case with the authors' datasets.

C. PCA is also not appropriate when many samples have zero values in the data matrix, which occurs in the authors' data. In such a case, the approaches of NMDS or canonical analysis of principal coordinates would be more appropriate, and allow distance measures (the Bray-Curtis distance) to define dissimilarity of different groups. An analysis of similarity (ANOSIM) could be used to determine if the data clustered significantly by species or by mosquito host.

D. The authors are encouraged to use alternate approaches, such as random forest (ML) approach, to determine if the odor classification is based on host or non-host. This method has been used for the last fifteen years in chemical ecology and human odor analysis (Cutler et al, 2007, Kwak et al 2008).

E. The authors use a phylogenetic framework for their analyses. Multivariate methods are now available to test evolutionary hypotheses about scent composition in a phylogenetic framework (Goolsby, 2017), and the authors are encouraged to use these approaches.

F. Comparison to floral odour space section. I would encourage the authors to examine other datasets of plant headspace samples, including plants used by mosquitoes. There are many datasets out there that the authors could use (El-Sayed 2021, Farré-Armengol et al 2020). Expanding the authors' dataset would provide more statistical power, and provide control of differences in plant visitor and plant phylogenetic relatedness.

G. Adding context related to mosquito olfaction. The authors describe how their work could provide insight into the coding of olfactory information by the mosquito. I would encourage the authors to analyze their data further by collapsing the host volatiles into groups based on biochemical pathways, or knowledge of the detection of the volatiles by the mosquitoes (such as using electroantennogram responses) to filter and identify only those responsive volatiles to keep in their dataset.

Premise and Background Knowledge<br /> A. Analyses of odour headspace have been known for the last three decades, e.g. (Methods in Chemical Ecology, Techniques in Pheromone Research, George Petri's work, Tholl and Rose, 2006; Stashenko and Martínez, 2008; Spicer et al., 2017; Tholl et al., 2020; Eisen et al., 2021; Schulz and Mollerke, 2022). But in many places, the paper conveys the impression that these are new discoveries and analyses. For example,<br /> -"Yet we remain remarkably ignorant of the composition of the chemical world."<br /> -"Our work provides one of the first quantitative descriptions of a natural odour space"<br /> -"Progress in understanding natural odours has also been hindered by the technical challenges of capturing and analyzing odour, especially the complex blends that constitute most natural odours"<br /> The Introduction and Discussion are rife with these overblown statements. I found this frustrating as the authors were not giving due credit to prior work on that topic while (maybe unintentionally) giving an impression that this specific idea was a new contribution. More care is needed to delineate which aspects of the study are 1) based on prior understanding, or 2) totally new). The authors are adding to an already extensive field of chemical ecology and olfactory processing of mixtures, and are contributing to this knowledge by adding datasets related to mammalian odor. I plead that the authors clearly describe these gaps, and place their results into proper context.

B. Similarly to the above statements relating to chemical ecology, the authors have numerous statements about gaps in odour processing. Mixture processing has been an important topic of study for the last forty years (Shorey, 1973, Caprio, 1988, Riffell et al 2009, Su et al 2009, Rokni et al 2014, Mathis et al 2016), which is based on encoding the temporal and concentration-dependent statistics of the odour.<br /> -"Yet compared to visual and auditory scenes, we know very little about the statistics of natural olfactory scenes"<br /> As described above, this is surprising and frustrating because of the rich literature on these topics (searching for "odour mixtures" provides 32,000 articles). In their manuscript, the authors are providing a strawman argument for their analyses by focusing on single odorant signatures, when the literature has repeatedly demonstrated the importance of odour mixtures for behavior and combinatorial processing.

C. There are increasing studies examining the mosquito behavioral and electrophysiological responses to hosts and other odours. However, this literature is not cited or included in the authors' analyses. The chemical ecology of mosquito attractants and natural odours has been studied in the Carde, Leal, Ignell, Carlson, Kline, Riffell, Takken, Torto, Verlhurst, Vosshall labs, and many others. The authors could use this information in their analyses and cite the literature.

Reviewer #2 (Public Review):

It is well known that DMRT proteins and more specifically, DMRT1 plays a key role in the sex determination processes of many species. While DMRT1 has been shown to be critical for the sex determination of fish, birds, and reptiles, it seems less crucial at the sex determination stages of the mice. It is important though for adult sex maintenance in mice.

Unlike its minor role in mouse sex determination, it seems that variants in DMRT1 in humans cause 46, XY DSD and sex reversal.

The paper by Dujardin et al. is a beautiful study that provides an answer to this long-lasting discrepancy of the difference between the two common mammal species: human and mouse. It is a really nice example of how working with other mammal species, like the rabbit, could serve as a nice model for understanding mammalian sex determination.

In this study the researchers first described the expression patterns of DMRT1 in the rabbit XY and XX gonads throughout the window of sex determination.

They then used CRISPR/Cas9 to generate DMRT1 KO rabbits and analysed the phenotype in XY and XX rabbits. They show that XY rabbits present with complete XY male-to-female sex reversal, very similar to what observed in human 46, XY DSD patients (but not the mice model). They further show that in the XY sex reversed gonads, germ cells fail to enter meiosis. They next analysed XX gonads and while there is no major effect on sex determination (as expected), the germ cells in these ovaries fail to enter meiosis, highlighting the critical role that DMRT1 has in germ cells.

I think it is really important that we start to embrace other mammal models that are not the mouse as we find many instances that the mouse is not the optimal system for understanding human sex determination.

The study is well explained and presented. The data is clear, and the paper is fluent to read.

Reviewer #2 (Public Review):

Summary:<br /> The authors used next-generation sequencing approaches combined with ribosome trapping to investigate gene expression in neurons and glia in the heads of adult fruit flies. Ribosome footprinting was further used to investigate the translational efficiency (TE) of particular RNAs in these two tissues. The evidence convincingly demonstrated that translation of specific messages is repressed in glia while others are repressed in neurons. Further evidence suggests that cis-acting elements within the 5'UTR of neuronal transcripts cause the repression of translation in glia. For instance, a fluorescent reporter using the 5'UTR of Rhodopsin-1 is highly translated in neurons but fluorescence from this reporter is nearly undetectable in glia. Furthermore, pausing of ribosomes on start codons of upstream Open Reading Frames (uORFs) is seen on the 5'UTR of this and other messages in glia but not in neurons.

Strengths:<br /> The main strength of the manuscript is its use of cutting-edge next-generation sequencing and bioinformatic approaches to investigate the tissue-specific translatome of Drosophila.

Weaknesses:<br /> A minor weakness is that little insight is provided into the mechanism that leads to ribosome stalling on uORFs in glia but not in neurons. The manuscript could be improved by some discussion on potential pathways that might control the differential TE through uORF pausing.

Reviewer #2 (Public Review):

Summary:<br /> This manuscript by Xu et al., is an interesting study aiming to identify novel features of macaque cortical development. This study serves as a valuable atlas of single cell data during macaque neurogenesis, which extends the developmental stages previously explored. Overall, the authors have achieved their aim of collecting a comprehensive dataset of macaque cortical neurogenesis and have identified a few unknown features of macaque development.

Strengths:<br /> The authors have accumulated a robust dataset of developmental time points and have applied a variety of informatic approaches to interrogate this dataset. One interesting finding in this study is the expression of previously unknown receptors on macaque oRG cells. Another novel aspect of this paper is the temporal dissection of neocortical development across species. The identification that the regulome looks quite different, despite similar expression of transcription factors in discrete cell types, is intriguing.

Weaknesses:<br /> Due to the focus on demonstrating the robustness of the dataset, the novel findings in this manuscript are underdeveloped. There is also a lack of experimental validation. This is a particular weakness for newly identified features (like receptors in oRG cells). It's important to show expression in relevant cell types and, if possible, perform functional perturbations on these cell types. The presentation of the data highlighting novel findings could also be clarified at higher resolution, and dissected through additional informatic analyses. Additionally, the presentation of ideas and goals of this manuscript should be further clarified. A major gap in the study rationale and results is that the data was collected exclusively in the parietal lobe, yet the rationale and interpretation of what this data indicates about this specific cortical area was not discussed. Last, a few textual errors about neural development are also present and need to be corrected.

Reviewer #2 (Public Review):

Summary:<br /> The authors examined several defensive responses elicited during Pavlovian conditioning using a serial compound stimulus (SCS) as the conditioned stimulus (CS) and a shock unconditioned stimulus (US) in male and female mice. The SCS consisted of tone pips followed by white noise. Their design included 3 treatment groups that were either exposed to the CS and US in a paired fashion, in an unpaired fashion, or only exposed to the shock US. They compared freezing, jumping, darting, and tail rattling across all groups during conditioning and extinction. During conditioning, strong freezing responses to the tone pips followed by strong jumping and darting responses to the white noise were present in the paired group but less robust or not present in the unpaired or shock only groups. During extinction, tone-induced freezing diminished while the jumping was replaced by freezing and darting in the paired group. Together, these findings support the idea that associative pairings are necessary for conditioned defensive responses.

Strengths:<br /> The study has strong control groups including a group that receives the same stimuli in an unpaired fashion and another control group that only receives the shock US and no CS to test the associative value of the SCS to the US. The authors examine a wide variety of defensive behaviors that emerge during conditioning and shift throughout extinction: in addition to the standard freezing response, jumping, darting, and tail rattling were also measured.

Weaknesses:<br /> This study could have greater impact and significance if additional conditions were added (e.g., using other stimuli of differing salience during the SCS), and determining the neural correlates or brain regions that are differentially recruited during different phases of the task across the different groups.

Reviewer #2 (Public Review):

The manuscript investigates the function of basal forebrain cholinergic axons in mouse primary visual cortex (V1) during locomotion using two-photon calcium imaging in head-fixed mice. Cholinergic modulation has previously been proposed to mediate the effects of locomotion on V1 responses. The manuscript concludes that the activity of basal forebrain cholinergic axons in visual cortex provides a signal which is more correlated with binary locomotion state than locomotion velocity of the animal. Cholinergic axons did not seem to respond to grating stimuli or visuomotor prediction error. Optogenetic stimulation of these axons increased the amplitude of responses to visual stimuli and decreased the response latency of layer 5 excitatory neurons, but not layer 2/3 neurons. Moreover, optogenetic or chemogenetic stimulation of cholinergic inputs reduced pairwise correlation of neuronal responses. These results provide insight into the role of cholinergic modulation to visual cortex and demonstrate that it affects different layers of visual cortex in a distinct manner. The experiments are well executed and the data appear to be of high quality. However, further analyses are required to fully support several of the study's conclusions.

1) In experiments analysing the activity of V1 neurons, GCaMP6f was expressed using a ubiquitous Ef1a promoter, which is active in all neuronal cell types as well as potentially non-neuronal cells. The manuscript specifically refers to responses of excitatory neurons but it is unclear how excitatory neuron somata were identified and distinguished from that of inhibitory neurons or other cell types.

2) The manuscript concludes that cholinergic axons convey a binary locomotion signal and are not tuned to running speed. The average running velocity of mice in this study is very slow - slower than 15 cm/s in the example trace in Figure 1D and speeds <6 cm/s were quantified in Figure 2E. However, mice can run at much faster speeds both under head-fixed and freely moving conditions (see e.g. Jordan and Keller, 2020, where example running speeds are ~35 cm/s). Given that the data in the present manuscript cover such a narrow range of running speeds, it is not possible to determine whether cholinergic axons are tuned to running speed or convey a binary locomotion signal.

3) The analyses in Figure 4 only consider the average response to all grating orientations and directions. Without further analysing responses to individual grating directions it is unclear how stimulation of cholinergic inputs affects visual responses. Previous work (e.g. Datarlat and Stryker, 2017) has shown that locomotion can have both additive and multiplicative effects and it would be valuable to determine the type of modulation provided by cholinergic stimulation.

4) The difference between the effects of locomotion and optogenetic stimulation of cholinergic axons in Figure 5 may be confounded by differences in the visual stimulus. These experiments are carried out under open-loop conditions, where mice may adapt their locomotion based on the speed of the visual stimulus. Consequently, locomotion onsets are likely to occur during periods of higher visual flow. Since optogenetic stimulation is presented randomly, it is likely to occur during periods of lower visual flow speed. Consequently, the difference between the effect of locomotion and optogenetic stimulation may be explained by differences in visual flow speed and it is important to exclude this possibility.

5) It is unclear why chemogenetic manipulations of cholinergic inputs had no effect on pairwise correlations of L2/3 neuronal responses while optogenetic stimulation did.

6) The effects of locomotion and optogenetic stimulation on the latency of L5 responses in Figure 7 are very large - ~100 ms. Indeed, typical latencies in mouse V1 measured using electrophysiology are themselves shorter than 100 ms (see e.g. Durand et al., 2016). Visual response latencies in stationary conditions or without optogenetic stimulation appear surprisingly long - much longer than reported in previous studies even under anaesthesia. Such large and surprising results require careful analysis to ensure they are not confounded by artefacts. However, as in Figure 4, this analysis is based only on average responses across all gratings and no individual examples are shown.

Reviewer #2 (Public Review):

Summary:

The authors develop a computational approach-avoidance-conflict (AAC) task, designed to overcome the limitations of existing offer based AAC tasks. The task incorporated likelihoods of receiving rewards/ punishments that would be learned by the participants to ensure computational validity and estimated model parameters related to reward/punishment and task induced anxiety. Two independent samples of online participants were tested. In both samples participants who experienced greater task induced anxiety avoided choices associated with greater probability of punishment. Computational modelling revealed that this effect was explained by greater individual sensitivities to punishment relative to rewards.

Strengths:

Large internet-based samples, with discovery sample (n = 369), pre-registered replication sample (n = 629) and test-retest sub group (n = 57). Extensive compliance measures (e.g. audio checks) seek to improve adherence.

There is a great need for RL tasks that model threatening outcomes rather than simply loss of reward. The main model parameters show strong effects and the additional indices with task based anxiety are a useful extension. Associations were broadly replicated across samples. Fair to excellent reliability of model parameters is encouraging and badly needed for behavioral tasks of threat sensitivity.

The task seems to have lower approach bias than some other AAC tasks in the literature.

Appraisal and impact:<br /> Overall this is a very strong paper, describing a novel task that could help move the field of RL forward to take account of threat processing more fully. The large sample size with discovery, replication and test-retest gives confidence in the findings. The task has good ecological validity and associations with task-based anxiety and clinical self-report demonstrate clinical relevance. Test-retest of the punishment learning parameter is the only real concern. Overall this task provides an exciting new probe of reward/threat that could be used in mechanistic disease models.

Additional context:

The sex differences between the samples are interesting as effects of sex are commonly found in AAC tasks. It would be interesting to look at the main model comparison with sex included as a covariate.

Reviewer #2 (Public Review):

This manuscript links the distinctive stinging behavior of sea anemones in different ecological niches to varying inactivation properties of voltage-gated calcium channels that are conferred by the identity of auxiliary Cavbeta subunits. Previous work from the Bellono lab established that the burrowing anemone, Nematostella vectensis, expresses a CaV channel that is strongly inactivated at rest which requires a simultaneous delivery of prey extract and touch to elicit a stinging response, reflecting a precise stinging control adapted for predation. They show here that by contrast, the anemone Exaiptasia diaphana which inhabits exposed environments, indiscriminately stings for defense even in the absence of prey chemicals, and that this is enabled by the expression of a CaVbeta splice variant that confers weak inactivation. They further use the heterologous expression of CaV channels with wild type and chimeric anemone Cavbeta subunits to infer that the variable N-termini are important determinants of Cav channel inactivation properties.

Reviewer #2 (Public Review):

Summary:

C. difficile infection (CDI) is clinically important as a hospital-acquired infection and a frequent cause of antibiotic-associated diarrhea, which is associated with high morbidity and mortality and increases in prevalence. It is also the prime example of a disease that is associated with gut microbiome dysbiosis and successfully treated with fecal microbiota transfer, highlighting the important but unclear functional or structural role of this bacterial pathogen and the condition of CDI for the gut microbiome, which is the focus of this study.

Ferretti et al. assembled an impressive gut metagenome dataset from previous and ongoing microbiome studies, which involves a large number of samples from patients with CDI or other diarrheal and non-diarrheal diseases and from healthy individuals, as well as from infants, adolescents, and adults. The authors analyze the prevalence and relative abundance of C. difficile in this dataset in relation to CDI diagnosis, host age and disease background, and the composition of the remaining microbiota. They detect C. difficile only in a minority of samples labelled as originating from CDI patients but frequently identify other pathogens and their toxin genes in the same samples. In infants, they detect C. difficile at high frequency and relative abundance in samples without clinical symptoms. They associate C. difficile presence in infant samples with "multiple indicators of healthy gut microbiome maturation' and suggest 'distinct biotic and physiological contexts in infants and adults' for C. difficile.

Strengths:

The manuscript provides an important overview of the complex relationship of C. difficile with the gut microbiome of healthy and diseased infants and adults, mostly due to the large studied dataset and convincing applied analysis that underlies the presented findings. This includes a number of interesting findings including, for example, that CDI can be reliably predicted based on taxonomic microbiota compositions, without including C. difficile itself or that C. difficile in infants appears not to originate from maternal sources.

Weaknesses:

Inconsistent associations of C. difficile with what is clinically labeled CDI, as well as the frequent detection of C. difficile in healthy infants, have been reported before and the manuscript does not reveal to what extent this bacterium reflects or even directly influences the gut microbiome of infants and adults. Whether the increased microbiota diversity, richness, and compositional similarity of C. difficile-positive infants to their mothers is sufficient to associate this bacterium with "healthy gut microbiome maturation" seems questionable, since C. difficile was also found to be more prevalent in preterm infants, formula-fed or antibiotically treated infants, and infants born by C-section, all of which are typically considered detrimental influences on microbiota development. The conclusion that "C. difficile may be a transient hallmark of healthy gut microbiome maturation" therefore appears too strong.

In addition, the statement that "its asymptomatic carriage in adults depends on microbial context" is not sufficiently supported by the presented data. Apparently, the authors are unable to define or measure "asymptomatic carriage", as they convincingly show that many patients diagnosed with "CDI" appear not to carry C. difficile, suggesting that neither asymptomatic nor symptomatic "CDI" conditions are necessarily linked to C. difficile.

The manuscript includes a large number of samples from poorly defined, but diverse patient backgrounds. It might be helpful to better define these samples (e.g. fecal samples vs. other gut samples) and to specify subcategories for samples from "diseased control subjects without CDI". Maybe this information could help validate the interesting suggestion from the manuscript that C. difficile may be (one of several) dysbiosis marker rather than the cause of (CDI) dysbiosis.

The phylogenetic analysis of C. difficile from metagenomic sequence data seems to suggest that there is a large mostly toxin gene-free cluster that is only identified in infants (Supplementary Figure 13). Could this indicate that there are, in fact, less pathogenic C. difficile lineages that are more prevalent in infants?

The authors argue in the Discussion that "Differential diagnosis against multiple enteropathogens may therefore stratify patients with CDI-like symptoms, towards adapted therapeutic interventions." It might be helpful to expand this discussion of different clinical options that could be adapted to highlight the clinical applicability of the presented findings.

Reviewer #2 (Public Review):

In this work, the authors reported cryo-EM structures of four types of zinc-binding site mutants of a bacterial Zn2+/H+ antiporter YiiP, and proposed distinct structural/functional roles of each of the binding sites in the intramolecular Zn2+ relay and the integrity of the homodimeric structure of YiiP. MST analysis using the mutants with a single Zn2+-binding site at different pH further clarified the pH dependence of Zn2+ binding affinity of each site. Moreover, the inverse Multibind approach refined the CpHMD pKa values of the key Zn2+-binding residues so that they agreed with the MST data. Consequently, energetic coupling of Zn2+ export to the proton-motive force has been suggested. These findings definitely provide new mechanistic insight into this Zn2+/H+ antiporter.

Reviewer #2 (Public Review):

This paper makes important and novel advances that significantly enhance our understanding of the ClC-2 channel. The EM data are of high quality, and the most important argument, concerning the role of the N-terminus of the protein as an occluding inactivation gate, is very well supported by structural, computational, and functional data (some of which is previously published). The proposal that the "run up" observed in patch clamp experiments represents relief of inactivation is interesting and compelling. The model predicts that mutations at the hairpin binding site should influence this "run up", which should be tested in the near future. Finally, the confirmation of the AK-42 binding site further solidifies evidence that this is a pore-blocking compound; the authors' argument about determinants of specificity is convincing.

Reviewer #2 (Public Review):

Using standard and widely used tools, the author revealed the factors (cultural, phenotypic, phylogenetic, etc.) shaping societal and scientific interest in natural species around the globe. The strength of this ms (and the authors) lies in its command of the available literature, database and variable management and analysis, and its solid discussion. The authors thus achieved a manuscript that was pleasant to read.

While I agree that doing a global study requires losing details of local patterns, maybe this is exactly the biggest shortcoming of the manuscript, oblivious to how different cultures (compare USA to PNG, for example) are reflected in these global patterns.

Reviewer #2 (Public Review):

The paper presents new mitochondrial sequence data from baboons from a museum collection and from one ancient Egyptian mummified baboon. By comparing the mitochondrial sequence of the mummified baboon with the new and existing data, they conclude that it originated from present-day Eritrea, specifically the ancient city of Adulis.

The paper is well-written and an interesting read. The background and details of the study are well-described and logical. Not knowing much about the history of the region I learned a lot. The data also seem sound and the analysis robust, with the exception of one check that should be added (in particular, to assess contamination by looking at mismatching reads).

The main limitation of the paper is just down to the N=1 sample and the limits of mitochondrial phylogeography. Based on the present-day distribution of hamadryas, the baboon must either come from the area of Africa around present-day Eritrea/Ethiopia/Sudan, or from Arabia. All the authors can really reasonably establish here is that this particular baboon did not come from Arabia. But beyond that, there is not much more they can say. Fig 2b makes it clear that the G3Y clade extends over a large range. Given the limited sampling, this is a minimum bound for the range, which probably includes most of the non-Arabian hamadryas range. The link to Adulis is speculative. There may be historical or archaeological evidence to support this but the genetic data really do not come close to establishing this. The authors do acknowledge this in the text, though the abstract makes a much stronger claim. And of course, it also remains possible that other baboons in the assemblage came from other places.

Reviewer #2 (Public Review):

The study by Ciabatti et al examined the mutation issue for self-inactivating rabies (SiR), which was found by other labs. The authors identified the mutations in the rabies genome and showed that this mutation occurred more frequently after multiple passage of production cell lines with suboptimal TEVp expressions. The authors further showed that such mutation did not accumulate in vivo and that SiR-labeled cells remained alive across longitudinal imaging in vivo.

In this study, the rabies genome is rigorously examined by sequencing many viral particles from independent preparations. The rabies with point mutation in the PEST domain is directly engineered for sequencing and infection test. Overall, the mutation issue is well addressed by the authors and the conclusions are well supported, but some more aspects of discussion and data analysis need to be extended for an easier production of SiR in a condition not that optimal.

1) The authors stated that one should produce SiR from cDNA in order to avoid the potential mutation in SiR. From a practical point of view, it would be much better to amplify the rabies from a stock virus directly in the production cell lines. Any discussion or exploration on this direction would be appreciated in the field.

2) 6 passages of production cell lines are not that extensive. In Fig.2C, there was already some level of TEVp activity reduction at 2nd passage. It is not clear to me that how the TEVp activity reduction naturally happens. Is there some room to play around puromycin concentration to maintain high TEVp activity?

Reviewer #2 (Public Review):

Wang et al. investigate the LGN in the tree shrew as a potential target for artificial vision. They report that (a) animals pre-trained on a visual detection task can generalize from visual to optogenetic detection and (b) optogenetic activation of the LGN results in reliable field potential activity in V1.

In this revised version of the manuscript, the authors have done a commendable job of addressing the critiques from the previous round of reviews.

Among the new results, the analysis of V1 LFP entrainment with optogenetic stimulation in the LGN is quite interesting and convincing. However, I found the spiking results in V1 to be underwhelming (which the authors also acknowledge). I find this a little surprising, given the robustness of the LFP results. Was this a matter of finding a better alignment of LGN and V1 sites? Might the authors have found more convincing spiking activity results if they use laminar electrodes in V1 to find monosynaptic connectivity between the LGN injection sites and their targets in V1?

Reviewer #2 (Public Review):

While the hypothesis that MEMO1 plays a key role in cell iron homeostasis remains to be directly tested, the data presented herein clearly support further delineation of the underlying mechanisms. The key findings in this regard are the facts, as established herein, that: 1) MEMO1 binds ferrous iron (the appropriate valence state for cell iron) along with glutathione (Fig. 5A); 2) the structure of MEMO1 in complex with Fe(II)-GSH reveals the coordination site within the protein for this complex (Fig. 5B/c); 3) oxidative stress and sensitivity to ferroptosis correlate with MEMO1 protein abundance in a consistent fashion (Fig. 4); and 4) while the effect is limited, there are data that indicate a relation between cell iron content and MEMO1 abundance (Fig. 4A/B).

Experimentally, it is thorough and well-documented and offers a new look at a protein that has been at the edges of iron metabolism (and copper, but I agree with the authors that this is not likely to be the case). This work and its subject will stimulate much further research.

Reviewer #2 (Public Review):

In this study, the authors validated a positive feedback loop between ZEB2 and ACSL4 in breast cancer, which regulates lipid metabolism to promote metastasis.

Overall, the study is original, well structured, and easy to read.

Reviewer #2 (Public Review):

Summary:

Molecular dynamics (MD) data is deposited in public, non-specialist repositories. This work starts from the premise that these data are a valuable resource as they could be used by other researchers to extract additional insights from these simulations; it could also potentially be used as training data for ML/AI approaches. The problem is that mining these data is difficult because they are not easy to find and work with. The primary goal of the authors was to discover and index these difficult-to-find MD datasets, which they call the "dark matter of the MD universe" (in contrast to data sets held in specialist databases).

The authors developed a search strategy that avoided the use of ill-defined metadata but instead relied on the knowledge of the restricted set of file formats used in MD simulations as a true marker for the data they were looking for. Detection of MD data marked a data set as relevant with a follow-up indexing strategy of all associated content. This "explore-and-expand" strategy allowed the authors for the first time to provide a realistic census of the MD data in non-specialist repositories.

As a proof of principle, they analyzed a subset of the data (primarily related to simulations with the popular Gromacs MD package) to summarize the types of simulated systems (primarily biomolecular systems) and commonly used simulation settings.

Based on their experience they propose best practices for metadata provision to make MD data FAIR (findable, accessible, interoperable, reusable).

A prototype search engine that works on the indexed datasets is made publicly available. All data and code are made freely available as open source/open data.

Strengths:

- The novel search strategy is based on relevant data to identify full datasets instead of relying on metadata and thus is likely to have many true positives and few false positives.

- The paper provides a first glimpse at the potential hidden treasures of MD simulations and force field parametrizations of molecules.

- Analysis of parameter settings of MD simulations from how researchers *actually* run simulations can provide valuable feedback to MD code developers for how to document/educate users. This approach is much better than analyzing what authors write in the Methods sections.

- The authors make a prototype search engine available.

- The guidelines for FAIR MD data are based on experience gained from trying to make sense of the data.

Weaknesses:

- So far the work is a proof-of-concept that focuses on MD data produced by Gromacs (which was prevalent under all indexed and identified packages).

As discussed in the manuscript, some types of biomolecules are likely underrepresented because different communities have different preferences for force fields/MD codes (for example: carbohydrates with AMBER/GLYCAM using AMBER MD instead of Gromacs).

- Materials sciences seem to be severely under-represented --- commonly used codes in this area such as LAMMPS are not even detected, and only very few examples could be identified. As it is, the paper primarily provides an insight into the *biomolecular* MD simulation world.

The authors succeed in providing a first realistic view on what MD data is available in public repositories. In particular, their explore-expand approach has the potential to be customized for all kinds of specialist simulation data, whereby specific artifacts are<br /> used as fiducial markers instead of metadata. The more detailed analysis is limited to Gromacs simulations and primarily biomolecular simulations (even though MD is also widely used in other fields such as the materials sciences). This restricted view may simply be correlated with the user community of Gromacs and hopefully, follow-up studies from this work will shed more light on this shortcoming.

The study quantified the number of trajectories currently held in structured databases as ~10k vs ~30k in generalist repositories. To go beyond the proof-of-principle analysis it would be interesting to analyze the data in specialist repositories in the same way as the one in the generalist ones, especially as there are now efforts underway to create a database for MD simulations (Grant 'Molecular dynamics simulation for biology and chemistry research' to establish MDDB' DOI 10.3030/101094651). One should note that structured databases do not invalidate the approach pioneered in this work; if anything they are orthogonal to each other and both will likely play an important role in growing the usefulness of MD simulations in the future.

Reviewer #2 (Public Review):

Summary:<br /> This work investigates how increased temperature affects pollen production and fertility of Arabidopsis thaliana plants grown at selected temperature conditions ranging from 16C to 30C. They report that pollen production and fertility decline with increasing temperature. To identify the cause of reduced pollen and fertility, they resort to living cell imaging of male meiotic cells to identify that the duration of meiosis increases with an increase in temperature. They also show that pollen sterility is associated with the increased presence of micronuclei likely originating from heat stress-induced impaired meiotic chromosome segregation. They correlate abnormal meiosis to weakened centromere caused by meiosis-specific defective loading of the centromere-specific histone H3 variant (CenH3) to the meiotic centromeres. Similar is the case with kinetochore-associated spindle assembly checkpoint(SAC) protein BMF1. Intriguingly, they observe a reverse trend of strong CENH3 presence in the somatic cells of the tapetum in contrast to reduced loading of CENH3 in male meiocytes with increasing temperature. In contrast to CENH3 and BMF1, the SAC protein BMF3 persists for longer periods than the WT control, based on which authors conclude that the heat stress prolongs the duration of SAC at metaphase I, which in turn extends the time of chromosome biorientation during meiosis I. The study provides preliminary insights into the processes that affect plant reproduction with increasing temperatures which may be relevant to develop climate-resilient cultivars.

Strengths:<br /> The authors have mastered the live cell imaging of male meiocytes which is a technically demanding exercise, which they have successfully employed to examine the time course of meiosis in Arabidopsis thaliana plants exposed to different temperature conditions. In continuation, they also monitor the loading dynamics and resident time of fluorescently tagged centromere/kinetochore proteins and spindle assembly checkpoint proteins to precisely measure the time duration of respective proteins to study their precise dynamics and function in male meiosis.

Weaknesses:<br /> Here the authors use only one representative centromere protein CENH3, one kinetochore-associated SAC protein BMF1, and the SAC protein BMF3 to conclude that heat stress impairs centromere function and prolongs SAC with increased temperatures. Centromere and its associated protein complex the kinetochores and the SAC contain a multitude of proteins, some of which are well characterized in Arabidopsis thaliana. Hence the authors could have used additional such tagged proteins to further strengthen their claim. Though the results presented here are interesting and solid, the study lacks a deeper mechanistic understanding of what causes the defective loading of CenH3 to the centromeres, and why the SAC protein BMF3 persists only at meiotic centromeres to prolong the spindle assembly checkpoint. Also, this observation should be interpreted in light of the fact that SAC is not that robust in plants as several null mutants of plant SAC components are known to grow as healthy as wild-type plants at normal growth conditions without any vegetative and reproductive defects. One of the immediate responses to heat stress is the production of heat shock proteins(Hsps), which act as molecular chaperones to safeguard the proteome. It will be interesting to see if the expression levels of known HsPs can be correlated with their role in stabilizing the structure of SAC proteins like BMF1 to prolong its presence at the meiotic kinetochores.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript highlights a mechanistic insight into meiotic initiation in budding yeast. In this study, the authors addressed a genetic link between mitotic cell cycle regulator SBF (the Swi4-Swi6 complex) and a meiosis inducing regulator Ime1 in the context of meiotic initiation. The authors' comprehensive analyses with cytology, imaging, RNA-seq using mutant strains lead the authors to conclude that Swi4 levels regulates Ime1-Ume6 interaction to activate expression of early meiosis genes for meiotic initiation. The major findings in this paper are that (1) the higher level of Swi4, a subunit of SBF transcription factor for mitotic cell cycle regulation, is the limiting factor for mitosis-to-meiosis transition; (2) G1 cyclins (Cln1, Cln2), that are expressed under SBF, inhibit Ime1-Ume6 interaction under overexpression of SWI4, which consequently leads to downregulation of early meiosis genes; (3) expression of SWI4 is regulated by LUTI-based transcription in the SWI4 locus that impedes expression of canonical SWI4 transcripts; (4) expression of SWI4 LUTI is likely negatively regulated by Ime1; (5) Action of Swi4 is negatively regulated by Whi5 (homologous to Rb)-mediated inhibition of SBF, which is required for meiotic initiation. Thus, the authors proposed that meiotic initiation is regulated under the balance of mitotic cell cycle regulator SBF and meiosis-specific transcription factor Ime1.

Strengths:<br /> The most significant implication in their paper is that meiotic initiation is regulated under the balance of mitotic cell cycle regulator and meiosis-specific transcription factor. This finding will provide a mechanistic insight in initiation of meiosis not only into the budding yeast also into mammals. The manuscript is overall well written, logically presented and raises several insights into meiotic initiation in budding yeast. Therefore, the manuscript should be open for the field. I would like to raise the following concerns, though they are not mandatory to address. However, it would strengthen their claims if the authors could technically address and revise the manuscript by putting more comprehensive discussion.

Weaknesses:<br /> The authors showed that increased expression of the SBF targets, and reciprocal decrease in expression of meiotic genes upon SWI4 overexpression at 2 h in SPO (Figure 2F). However, IME1 was not found as a DEG in Supplemental Table 1. Meanwhile, IME1 transcript level was decreased at 2 h SPO condition in pATG8-CLN2 cells in Fig S4C.

Now this reviewer still wonders with confusion whether expression of IME1 transcripts per se is directly or in directly suppressed under SBF-activated gene expression program at 2 h SPO in pATG8-SWI4 and pATG8-CLN2 cells. This reviewer wonders how Fig S4C data reconciles with the model summarized in Fig 6F.

One interpretation could be that persistent overexpression of G1 cyclin caused active mitotic cell cycle, and consequently delayed exit from mitotic cell cycle, which may have given rise to an apparent reduction of cell population that was expressing IME1. For readers to better understand, it would be better to explain comprehensively this issue in the main text.

The % of cells with nuclear Ime1 was much reduced in pATG8-CLN2 cells (Fig 2B) than in pATG8-SWI4 cells (Fig 4C). Is the Ime1 protein level comparable or different between pATG8-CLN2 strain and pATG8-SWI4 strain? Since it is difficult to compare the quantifications of Ime1 levels in Fig S1D and Fig S4B, it would be better to comparably show the Ime1 protein levels in pATG8-CLN2 and pATG8-SWI4 strains.<br /> Further, it is uncertain how pATG8-CLN2 cells mimics the phenotype of pATG8-SWI4 cells in terms of meiotic entry. It would be nice if the authors could show RNA-seq of pATG8-CLN2/WT and/or quantification of the % of cells that enter meiosis in pATG8-CLN2.

The authors stated that reduced Ime1-Ume6 interaction is a primary cause of meiotic entry defect by CLN2 overexpression (Line 320-322, Fig 4J-L). This data is convincing. However, the authors also showed that GFP-Ime1 protein level was decreased compared to WT in pATG8-CLN2 cells by WB (Fig S4A). Further, GFP-Ime1 signals were overall undetectable through nuclei and cytosol in pATG8-CLN2 cells (Fig 4B), and accordingly cells with nuclear Ime1 were reduced (Fig 4C). Although the authors raised a possibility that the meiotic entry defect in the pATG8-CLN2 mutant arises from downregulation of IME1 expression (Line 282-283), causal relationship between meiotic entry defect and CLN2 overexpression is still not clear. Is the Ime1 protein level reduced in the pATG8-CLN2;UME6-⍺GFP strain compared to WT? It would be better to comparably show the Ime1 protein levels in the pATG8-CLN2 strain and the pATG8-CLN2;UME6-⍺GFP strain by WB. Also, it would be nice if the authors could show quantification of the % of cells that enter meiosis in the pATG8-CLN2;UME6-⍺GFP strain to see how and whether artificial tethering of Ime1 to Ume6 rescued normal meiosis program rather than simply showing % sporulation in Fig4A.

The authors showed Ume6 binding at the SWI4LUTI promoter (Figure 5K). However, since Ume6 forms a repressive form with Rpd3 and Sin3a and binds to target genes independently of Ime1, Ume6 binding at the SWI4LUTI promoter bind does not necessarily represent Ime1-Ume6 binding there. Instead, it would be better to show Ime1 ChIP-seq at the SWI4LUTI promoter.

The authors showed ∆LUTI mutant and WHI5-AA mutant did not significantly change the expression of SBF targets nor early meiotic genes relative to wildtype (Figure 6A, C). Accordingly, they concluded that LUTI- or Whi5-based repression of SBF alone was not sufficient to cause a delay in meiotic entry (Line451-452), and perturbation of both pathways led to a significant delay in meiotic entry (Figure 6E). This reviewer wonders whether Ime1 expression level and nuclear localization of Ime1 was normal in ∆LUTI mutant and WHI5-AA mutant.

Reviewer #2 (Public Review):

Nagy et al investigated the role of volume increase and swelling in neutrophils in response to the chemoattractant. Authors show that following chemoattractant response cells lose their volume slightly owing to the cell spreading phase and then have a relatively rapid increase in the cell volume that is concomitant with cell migration. The authors performed an impressive genome-wide CRISPR screen and buoyant density assay to identify the regulators of neutrophil swelling. This assay showed that stimulating cells with chemoattractant fMLP led to an increase in the cell volume that was abrogated with the FPR1 receptor knockout. The screen revealed a cascade that could potentially be involved in cell swelling including NHE1 (sodium-proton antiporter) and PI3K. NHE1 and PI3K are required for chemoattractant-induced swelling in human primary neutrophils. Authors also suggest slightly different functions of NHE1 and PI3K activity where PI3K is also required to maintain chemoattractant-induced cell shape changes. The authors convincingly show that chemoattractant-induced cell swelling is linked to cell migration and NHE1 is required for swelling at the later stages of swelling since the cells at the early point work on low-volume and low-velocity regime. Interestingly, the authors also show that lack of swelling in NHE1-inhibited cells could be rescued by mild hypo-osmotic swelling strengthening the argument that water influx followed chemoattractant stimulation is important for potentiation for migration.

The conclusions of this paper are mostly well supported by data and are pretty convincing, but some aspects of image acquisition and data analysis need to be clarified and extended.

Weaknesses<br /> 1) It would really help if the authors could add the missing graph for the footprint area when cells are treated with Latranculin. Graph S1F for volume changes with Lat treatment should be compared with DMSO-treated controls.<br /> 2) The authors show inhibition of NHE1 blocked cell swelling using Coulter counter, a similar experiment should be done with PI3K inhibitions especially since they see PI3K inhibition impact chemoattractant-induced cell shape change.<br /> 3) It would be more convincing visually if the authors could also include the movie of cell spreading (footprint) and then mobility with PI3K inhibition.<br /> 4) It is not clear how cell spreading and later volume increase are linked to overall mobility of neutrophils. Are authors suggesting that cell spreading is not required for cell mobility in neutrophils?<br /> 5) Volume fluctuations associated with motility were impacted by NHE1 inhibition at the baselines, what about PI3K inhibitions? Does that impact the actual fluctuations?<br /> 6) It would really help if the authors compared similar analyses and drew conclusions from that, for example, it is unclear what the authors mean by they found no change in the angular persistence of WT and NHE1 inhibited cells which is in contrast to PI3K inhibition since they do not really have an analysis for angular persistence in PI3K inhibited cells. (S4A and S4B).

Reviewer #2 (Public Review):

The authors present a pipeline for generating strain-specific genome-scale metabolic models for bacteria using Klebsiella spp. as the demonstrative data. This paper claims to provide a high-throughput tool for generating strain-specific models for bacteria. However, in reality, the tool requires a reference pan-genome-based complete model to generate the strain-specific model of the species of interest, which in this study is Klebsiella pneumoniae. This requirement renders the tool redundant for high-throughput purposes since the process of building or generating the pan-genome reference model is performed separately. Additionally, the quality of the newly built strain-specific model will depend on the reference model used. Therefore, this tool, on its own, can only work specifically with the available pan-genome model of reference, which in this case is only applicable to Klebsiella pneumoniae. Its effectiveness with other bacteria has not been proven. I would suggest that the authors either reframe the performance and results to be applicable only to Klebsiella or consider adding more reference pan-genome models for the study.

Reviewer #2 (Public Review):

In this manuscript, Funabiki and colleagues investigated the co-evolution of DNA methylation and nucleosome remolding in eukaryotes. This study is motivated by several observations: (1) despite being ancestrally derived, many eukaryotes lost DNA methylation and/or DNA methyltransferases; (2) over many genomic loci, the establishment and maintenance of DNA methylation relies on a conserved nucleosome remodeling complex composed of CDCA7 and HELLS; (3) it remains unknown if/how this functional link influenced the evolution of DNA methylation. The authors hypothesize that if CDCA7-HELLS function was required for DNA methylation in the last eukaryote common ancestor, this should be accompanied by signatures of co-evolution during eukaryote radiation.

To test this hypothesis, they first set out to investigate the presence/absence of putative functional orthologs of CDCA7, HELLS and DNMTs across major eukaryotic clades. They succeed in identifying homologs of these genes in all clades spanning 180 species. To annotate putative functional orthologs, they use similarity over key functional domains and residues - such as ICF related mutations for CDCA7 and SNF2 domains for HELLS - as well as maximum likelihood phylogenetic analyses. Using established eukaryote phylogenies, the authors conclude that the CDCA7-HELLS-DNMT axis arose in the last common ancestor to all eukaryotes. Importantly, they found recurrent loss events of CDCA7-HELLS-DNMT in at least 40 eukaryotic species, most of them lacking DNA methylation.

Having identified these factors, they successfully identify signatures of co-evolution between DNMTs, CDCA7 and HELLS using CoPAP analysis - a probabilistic model inferring the likelihood of interactions between genes given a set of presence/absence patterns. As a control, such interactions are not detected with other remodelers or chromatin modifying pathways also found across eukaryotes. Expanding on this analysis, the authors found that CDCA7 was more likely to be lost in species without DNA methylation.

In conclusion, the authors suggest that the CDCA7-HELLS-DNMT axis is ancestral in eukaryotes and raise the hypothesis that CDCA7 becomes quickly dispensable upon the loss of DNA methylation and/or that CDCA7 might be the first step toward the switch from DNA methylation-based genome regulation to other modes.

The data and analyses reported are significant and solid. Overall, this work is a conceptual advance in our understanding of the evolutionary coupling between nucleosome remolding and DNA methylation. It also provides a useful resource to study the early origins of DNA methylation related molecular process. Finally, it brings forward the interesting hypothesis that since eukaryotes are faced with the challenge of performing DNA methylation in the context of nucleosome packed DNA, loosing factors such as CDCA7-HELLS likely led to recurrent innovations in chromatin-based genome regulation.

Strengths:<br /> - The hypothesis linking nucleosome remodeling and the evolution of DNA methylation.<br /> - Deep mapping of DNA methylation related process in eukaryotes.<br /> - Identification and evolutionary trajectories of novel homologs/orthologs of CDCA7.<br /> - Identification of CDCA7-HELLS-DNMT co-evolution across eukaryotes.

Reviewer #2 (Public Review):

In this manuscript, Funabiki and colleagues investigated the co-evolution of DNA methylation and nucleosome remolding in eukaryotes. This study is motivated by several observations: (1) despite being ancestrally derived, many eukaryotes lost DNA methylation and/or DNA methyltransferases; (2) over many genomic loci, the establishment and maintenance of DNA methylation relies on a conserved nucleosome remodeling complex composed of CDCA7 and HELLS; (3) it remains unknown if/how this functional link influenced the evolution of DNA methylation. The authors hypothesize that if CDCA7-HELLS function was required for DNA methylation in the last eukaryote common ancestor, this should be accompanied by signatures of co-evolution during eukaryote radiation.

To test this hypothesis, they first set out to investigate the presence/absence of putative functional orthologs of CDCA7, HELLS and DNMTs across major eukaryotic clades. They succeed in identifying homologs of these genes in all clades spanning 180 species. To annotate putative functional orthologs, they use similarity over key functional domains and residues - such as ICF related mutations for CDCA7 and SNF2 domains for HELLS - as well as maximum likelihood phylogenetic analyses. Using established eukaryote phylogenies, the authors conclude that the CDCA7-HELLS-DNMT axis arose in the last common ancestor to all eukaryotes. Importantly, they found recurrent loss events of CDCA7-HELLS-DNMT in at least 40 eukaryotic species, most of them lacking DNA methylation.

Having identified these factors, they successfully identify signatures of co-evolution between DNMTs, CDCA7 and HELLS using CoPAP analysis - a probabilistic model inferring the likelihood of interactions between genes given a set of presence/absence patterns. As a control, such interactions are not detected with other remodelers or chromatin modifying pathways also found across eukaryotes. Expanding on this analysis, the authors found that CDCA7 was more likely to be lost in species without DNA methylation.

In conclusion, the authors suggest that the CDCA7-HELLS-DNMT axis is ancestral in eukaryotes and raise the hypothesis that CDCA7 becomes quickly dispensable upon the loss of DNA methylation and/or that CDCA7 might be the first step toward the switch from DNA methylation-based genome regulation to other modes.

The data and analyses reported are significant and solid. Overall, this work is a conceptual advance in our understanding of the evolutionary coupling between nucleosome remolding and DNA methylation. It also provides a useful resource to study the early origins of DNA methylation related molecular process. Finally, it brings forward the interesting hypothesis that since eukaryotes are faced with the challenge of performing DNA methylation in the context of nucleosome packed DNA, loosing factors such as CDCA7-HELLS likely led to recurrent innovations in chromatin-based genome regulation.

Strengths:<br /> - The hypothesis linking nucleosome remodeling and the evolution of DNA methylation.<br /> - Deep mapping of DNA methylation related process in eukaryotes.<br /> - Identification and evolutionary trajectories of novel homologs/orthologs of CDCA7.<br /> - Identification of CDCA7-HELLS-DNMT co-evolution across eukaryotes.

Reviewer #2 (Public Review):

Summary:<br /> This work follows previous work from the group where they have demonstrated the role of TASK1 in the regulation of glucose-stimulated insulin secretion. Moreover, a recent study links a mutation in KCNK16, the gene encoding TALK-1 channels to MODY. Here the authors have constructed a mouse model with the specific mutation (TALK-1 L114P mutation) and investigated the phenotype. They have to perform a couple of breeding tricks to find a model that is lethal in adult which might complicate the conclusions, however, the phenotype of the heterozygote model used has a MODY-like phenotype. The study is convincing and solid.

Strengths:<br /> 1) The work is a natural follow-up from previous studies from the groups.

2) The authors present convincing and solid data that in the long perspective will help patients with these mutations.

3) Both in vivo and in vitro data are presented to give the full picture of the phenotype.

4) Data from both female and male mice are presented.

Weaknesses:<br /> 1) The authors perform an RNA-sequencing showing that the cAMP amplifying pathway is upregulated. A weakness is that this is not further followed up. The remaining questions include; Is this also true in humans with this mutation? Would treatment with incretins improve glucose-stimulated insulin secretion and and lower blood glucose?<br /> 2) The authors avoid further investigating what it means that the glucagon area and secretion are increased in the model.<br /> 3) The performance of measurements in both male and female mice is praiseworthy. However, despite differences in the response, the authors do not investigate the potential reason for this. Are hormonal differences of importance?

Reviewer #2 (Public Review):

Summary:

The paper presents a novel approach to expand iPSC-derived pdx1+/nkx6.1+ pancreas progenitors, making them potentially suitable for GMP-compatible protocols. This advancement represents a significant breakthrough for diabetes cell replacement therapies, as one of the current bottlenecks is the inability to expand PP without compromising their differentiation potential. The study employs a robust dataset and state-of-the-art methodology, unveiling crucial signaling pathways (eg TGF, Notch...) responsible for sustaining pancreas progenitors while preserving their differentiation potential in vitro.

Strengths:

This paper has strong data, guided omics technology, clear aims, applicability to current protocols, and beneficial implications for diabetes research. The discussion on challenges adds depth to the study and encourages future research to build upon these important findings.

Weaknesses:

The paper does have some weaknesses that could be addressed to improve its overall clarity and impact. The writing style could benefit from simplification, as certain sections are explained in a convoluted manner and difficult to follow, in some instances, redundancy is evident. Furthermore, the legends accompanying figures should be self-explanatory, ensuring that readers can easily understand the presented data without the need to be checking along the paper for information.

The culture conditions employed in the study might benefit from more systematic organization and documentation, making them easier to follow.

Another important aspect is the functionality of the expanded cells after differentiation. While the study provides valuable insights into the expansion of pancreas progenitors in vitro and does the basic tests to measure their functionality after differentiation the paper could be strengthened by exploring the behavior and efficacy of these cells deeper, and in an in vivo setting.

Quantifications for immunofluorescence (IF) data should be displayed.

Some claims made in the paper may come across as somewhat speculative.

Additionally, while the paper discusses the potential adaptability of the method to GMP-compatible protocols, there is limited elaboration on how this transition would occur practically or any discussion of the challenges it might entail.

Reviewer #2 (Public Review):

Summary: Walker et al have proposed that the tumor suppressor TMEM127 converges with RET activation to drive adrenal phenochromocytoma. RET is a common oncogene both in familial and sporadic forms of this cancer, and TMEM127 has also been observed as a loss of function mutation in sporadic disease. The authors hypothesize that loss of the TMEM127 might signal stabilization of RET on the cell surface, mimicking an activating mutation. Through a nice set of experiments, they show that TMEM127 loss impairs endosome function and promotes RET surface accumulation. This expression was resistant to GDNF, suggesting that recycling via endosome recirculation was impaired such that the half-life of RET on the cell surface was extended. RET interaction with clathrin-coated pits was also disrupted, as the CCPs themselves were significantly smaller, and plasma membrane organization was affected by the impaired endosome recycling. Notably, a number of proteins were found to be accumulating on the cell surface via the purported mechanism, EGFR, TFR1, N cadherin, integrin beta 3. The authors applied a RET inhibitor to cells, showing decreased cellular proliferation.

Strengths: In summary, this is an interesting finding, that is preliminary in nature and is incompletely validated currently. It is certainly worth further investigation as a central feature linking TMEM127 mutations and pheochromocytoma through a common pathway of RET activation by fixing this factor in an active state on the cell surface.

Weaknesses: Although this is a provocative finding, and the authors test the interaction in a number of ways, there are several factors that limit the enthusiasm for this work as currently presented. The work is limited to one isogenic cell line with limited validation.

Reviewer #2 (Public Review):

The authors tried to diagnose cancers and pinpoint tissues of origin using cfDNA. To achieve this goal, they developed a framework to assess methylation, CNA, and other genomic features. They established discovery and validation cohorts for systematic assessment and successfully achieved robust prediction power.

Reviewer #2 (Public Review):

Summary:<br /> This study is quite thorough, tackling this NO-dependent UV avoidance circuit with both breadth and depth. There are several novel discoveries throughout, but the whole package represents perhaps even more than the sum of these parts.

Strengths:<br /> The presentation of the work is compelling. The introduction sets up the question and the state of the field very nicely. The discovery of the non-canonical NO receptor pathway in the ciliary photoreceptors is fascinating and will likely open up new avenues for future research into NO-pathways in different species. The use of genetic and pharmacological manipulations of circuit components was well thought-out. The authors applied different experimental techniques expertly throughout the study so that they could develop a comprehensive view from the molecular to the behavioral levels.

Weaknesses:<br /> While I appreciate the intent of bringing together a large set of measurements from connectomics and calcium imaging in the framework of a model, the model seemed rather poorly constrained. How many parameters are in the model shown in Figure 6A? How many of them are well constrained by experimental measurements? The authors also don't perform sensitivity analysis on the parameters of the model. And ultimately, the conclusion over the model in Figure 7 is somewhat trivial within the unitless construction: larger amplitude and longer duration stimuli lead to increased activation of the downstream neuron thought to lead to the downward swim behavior. I could imagine that a large family of models would arrive at this same result, and without units, there is no way to really test it with new behavioral experiments.

Reviewer #2 (Public Review):

Kleinman and colleagues conducted an analysis of two datasets, one recorded from DLPFC in one monkey and the other from PMD in two monkeys. They also performed similar analyses on trained RNNs with various architectures.

The study revealed four main findings. (1) All task variables (color coherence, target configuration, and choice direction) were found to be encoded in DLPFC. (2) PMD, an area downstream of PFC, only encoded choice direction. (3) These empirical findings align with the celebrated 'information bottleneck principle,' which suggests that FF networks progressively filter out task-irrelevant information. (4) Moreover, similar results were observed in RNNs with three modules.

While the analyses supporting results 1 and 2 were convincing and robust, I have some concerns and recommendations regarding findings 3 and 4, which I will elaborate on below. It is important to note that findings 2 and 4 had already been reported in a previous publication by the same authors (ref. 43).

Major recommendation/comments:<br /> The interpretation of the empirical findings regarding the communication subspace in relation to the information bottleneck theory is very interesting and novel. However, it may be a stretch to apply this interpretation directly to PFC-PMd, as was done with early vs. late areas of a FF neural network.

In the RNN simulations, the main finding indicates that a network with three or more modules lacks information about the stimulus in the third or subsequent modules. The authors draw a direct analogy between monkey PFC and PMd and Modules 1 and 3 of the RNNs, respectively. However, considering the model's architecture, it seems more appropriate to map Area 1 to regions upstream of PFC, such as the visual cortex, since Area 1 receives visual stimuli. Moreover, both PFC and PMd are deep within the brain hierarchy, suggesting a more natural mapping to later areas. This contradicts the CCA analysis in Figure 3e. It is recommended to either remap the areas or provide further support for the current mapping choice.

Reviewer #2 (Public Review):

Summary:<br /> One often wishes to combine activation of a neural population via red light with simultaneous modulation of a different population via blue light, or simultaneous imaging of a blue-excited fluorescent reporter. The problem is that all red-shifted opsins have an action spectrum with a long blue tail, leading to spurious opsin activation by blue light.

This valuable paper presents a clever solution to this problem, by pairing an engineered blue-shifted inhibitory chloride-conducting opsin with a red-shifted excitatory opsin. The combined effect is excitation by red light and shunting inhibition by blue light. The paper is very thorough, with convincing spectroscopic and patch clamp characterization of the tools, and tests in brain slices and in vivo. This tool is likely to be useful in the neuroscience community.

Strengths:<br /> The methods are solid, including the complete characterization of each tool separately, as well as the combination in vivo. The array of testing gives a strong degree of confidence that this tool will work as expected.

Weaknesses:<br /> There are two discussion points and one experimental point which would make the paper stronger.

1) In the Introduction or Discussion, the authors could better motivate the need for a red-shifted actuator that lacks blue crosstalk, by giving some specific examples of how the tool could be productively used, e.g. pairing with another blue-shifted excitatory opsin in a different population, or pairing with a GFP-based fluorescent indicator, e.g. GCaMP. The motivation for the current tool is not obvious to non-experts.

2) Simultaneous excitation and inhibition are not the same as non-excitation. The authors mentioned shunting briefly. Another possible issue is changes in osmotic balance. Activation of a Na+ channel and a Cl- channel will lead to net import of NaCl into the cell, possibly changing osmotic pressure. Please discuss.

3) The authors showed that in ZipT-IvfChr, orange light drives excitation and blue light does not. But what about simultaneous blue and orange light? Can the blue light overwhelm the effect of the orange light? Since the stated goal is to open the blue part of the spectrum for other applications, one is now worried about "negative" crosstalk. Please discuss and, ideally, characterize this phenomenon.<br /> 3.1) Does the use of the new tool require careful balancing of the expression levels of the ZipT and the IvfChr? Does it require careful balancing of blue and orange light intensities?<br /> 3.2) Also, many opsins show complex and nonlinear responses to dual-wavelength illumination, so each component should be characterized individually under simultaneous blue + orange light.<br /> 3.3) I was expecting to see photocurrents at different holding potentials as a function of illumination wavelength for the co-expressed construct (i.e. to see at what wavelength it switches from being excitatory to inhibitory); and also to see I-V curves of the photocurrent at blue and orange wavelengths for the co-expressed constructs (i.e. to see the reversal potential under blue excitation). Overall, the patch clamp and spectroscopic characterization of the individual constructs was stronger than that of the combined constructs.

Reviewer #2 (Public Review):

Summary:<br /> Silva et al. describe an experimental study conducted on cerebellar parallel fiber-to-molecular interneuron synapses to investigate the size of the readily releasable pool (RRP) of synaptic vesicles (SVs) per docking site in response to trains of action potentials. The study aims to determine whether there are multiple binding sites for SVs at each docking site, which could lead to a higher RRP size than previously thought.

The researchers used this glutamatergic synapse to conduct their experiments. They employed various techniques and manipulations to enhance release probability, docking site occupancy, and synaptic depression. By counting the number of released SVs in response to action potential trains and normalizing the results based on the number of docking sites, they estimated the RRP size per docking site.

The key findings and observations in the manuscript are as follows:

Docking Site Occupancy and Release Probability Enhancement: The researchers used 4-amidopyridine (4-AP) and post-tetanic potentiation (PTP) protocols to enhance the release probability of docked SVs and the occupancy of docking sites, respectively.

Synchronous and Asynchronous Release: Synchronous release refers to SVs released in response to individual action potentials, while asynchronous release involves SVs released after the initial release response due to calcium elevation. The study observed changes in the balance between synchronous and asynchronous release under different conditions, revealing the degree of filling of the RRP.

Modeling of Release Dynamics: The researchers employed a modeling approach based on the "replacement site/docking site" (RS/DS) model, where SVs bind to a replacement site before moving to a docking site and eventually undergoing release. The model was adjusted to experimental conditions to estimate parameters like docking site occupancy and release probabilities.

Comparison of Different Models: The study compared the RS/DS model with an alternative model known as the "loosely docked/tightly docked" (LS/TS) model. The LS/TS model assumes that a docking site can only accommodate one SV at a time, while the RS/DS model considers the possibility of accommodating multiple SVs.

Maximum RRP Size: Through a combination of experimental results and model simulations, the study revealed that the maximum RRP size per docking site reached close to two SVs under certain conditions, supporting the idea that each docking site can accommodate multiple SVs.

Strengths:<br /> The study is rigorously conducted and takes into consideration the previous work on RRP size and SV docking site estimation. The study addresses a long-standing question in synaptic physiology.

Weaknesses:<br /> It remains unclear how generalizable the findings are to other types of synapses.

Reviewer #2 (Public Review):

Pak et al. report on a study using a computational method to assess differences in the relative proportion of six canonical brain cell types, across eleven neurodegenerative classes (defined as both clinical syndromes (e.g. FTD, PD), groups of neurogenerative diseases (e.g. 4-repeat tauopathies) or distinct neuropathological entities (e.g. FTLD-TDP type C), as they relate to a standard map of class-dependent volume loss. The study uses innovative methods and is commendable in its goal to highlight the contribution of non-neuronal cell types to the pathobiology of neurodegeneration. The findings of the study are in part contradicting expected results based on extensive literature on the biology of these diseases. The authors based their methodology on the use of a deconvolutional cell classifier; however, do not extensively recognize that their data on gene expression are based on normal brain levels rather than on diseased ones. Also, while predicted levels are uniquely based on patterns of brain atrophy, it is not possible to know whether this strategy is generalizable to all diseases (for instance, it is known that pure DLB, PD and ALS are not associated with extensive brain atrophy), or even adequately comparable between subtypes of diseases within the same class (e.g., different forms of FTLD). The authors do not acknowledge that only data based on true neuropathological assessment may prove whether their findings are true. Subject characteristics, numbers, and diagnostic criteria are hard to assess and only described in the methods section. This format prevents the reader from assessing data robustness while going through the results, especially when fundamental biological bases of nomenclature and differences between clinical syndromes and pathological entities are omitted or uncharacteristically provided.

Reviewer #2 (Public Review):

Summary:<br /> This study links rare human loss of function mutations in the zinc transporter family member SLC39A5 to increased circulating and hepatic concentrations of this trace element. Beneficial metabolic changes were observed in a corresponding convincing mouse model relevant to the development of NASH.

Strengths:<br /> Authors combine human exome sequencing data, meta-analysis of four large European cohorts, and a patient recall approach to link the rare loss of function variants of SLC39A5 to the phenotype and protection from T2DM.

Using a SLC39A5-null mouse model challenged either by cross-breeding with Lepr-/- mice or diet-induced obesity they unravel the metabolic impact of elevated circulating and hepatic zinc concentration with respect to T2DM, glucose homeostasis, hepatic steatosis, and NASH development. Some mechanistic aspects and a remarkable sex difference in the outcome are identified from mouse ex vivo readouts and supported by in vitro hepatocyte cellular studies. Authors present evidence that increased hepatic zinc concentrations inhibit zinc-regulated phosphatases resulting in activation of AMPK and AKT signalling with consequences for lipid and glucose metabolism and insulin sensitivity.

Weaknesses:<br /> The reasons for the observed sex differences in the metabolic consequences of SLC39A5 inactivation in the mouse models remain unclear. While heterozygous rare SLC39A5 variants show distinct phenotypes only SLC39A5-null mice and no heterozygous mice are studied. The role of SLC39A5 in pancreatic islets and on insulin secretion remains unclear because authors do not address data published recently that claim a relevant role of SLC39A5 in b-cell function and glucose tolerance.

Reviewer #2 (Public Review):

Medwig-Kinney et al. explore the role of the transcription factor NHR-67 in distinguishing between AC and VU cell identity in the C. elegans gonad. NHR-67 is expressed at high levels in AC cells where it induces G1 arrest, a requirement for the AC fate invasion program (Matus et al., 2015). NHR-67 is also present at low levels in the non-invasive VU cells and, in this new study, the authors suggest a role for this residual NHR-67 in maintaining VU cell fate. What this new role entails, however, is not clear.

The authors present two models: 1) That NHR-67 switches from a transcriptional activator in ACs to a transcriptional repressor in VUs by virtue of recruiting translational repressors, or 2) that these interactions sequester NHR-67 away from its transcription targets in VU cells. Neither model is fully supported by the data, leaving a paper with extensive data but no single compelling conclusions, and leaving open the question of what is the function, if any, of NHR-67 condensates in VU cells?

While the authors report on interesting observations, in particular the co-localization of NHR-67 with UNC-37/Groucho and POP-1 in nuclear puncta, the functional significance of these observations remains unclear. The authors have not demonstrated that the "repressive condensates" are functional and play a role in the suppression of AC fate in VU cells as claimed. The colocalization data suggest that NHR-67 interacts with repressors, but additional experiments are needed to demonstrate that these interactions are specific to VUs, impact VU fate, and sequester NHR-67 from its targets or transform NHR-67 into a transcriptional repressor.

[Editor's note: we feel that the current state of the data with respect to this question is best captured in the response by the authors to the original concerns expressed by reviewer 2, which we include in abbreviated form here]

1) The authors report that NHR-67 forms "repressive condensates" (aka. puncta) in the nuclei of VU cells and imply that these condensates prevent VU cells from becoming ACs. However, there are also examples of AC cells presented that have NHR-67 puncta (these are less obvious simply due to the higher levels of NHR-67 in ACs). Similarly, there also are UNC-37 and LSY-22 also puncta in ACs. The presence of NHR-67 puncta in the AC seems to directly contradict the author's assumption that the puncta repress the AC fate.

RESPONSE: The puncta formed by NHR-67 in the AC are different in appearance than those observed in the VU cells and furthermore do not exhibit strong colocalization with that of UNC-37 or LSY-22. The Manders' overlap coefficient between NHR-67 and UNC-37 is 0.181 in the AC, whereas it is 0.686 in the VU cells. Likewise, the Manders' overlap coefficient between NHR-67 and LSY-22 is 0.189 in the AC compared to 0.741 in the VU cells. We speculate that the areas of NHR-67 subnuclear enrichment in the AC may represent concentration around transcriptional targets, but testing this would require knowledge of direct targets of NHR-67.

2) While a pool of NHR-67 localizes to "repressive condensates", it appears that a substantial portion of NHR-67 also exists diffusively in the nucleoplasm. This would appear to contradict a "sequestration model" since, for such a model to work, a majority of NHR-67 should be in puncta? What proportion of NHR-67 is in puncta? Is the concentration of NHR-67 in the nucleoplasm lower in VUs compared to ACs and does this depend on the puncta?

RESPONSE: The proportion of NHR-67 localizing to puncta versus the nucleoplasm is dynamic, as these puncta form and dissolve over the course of the cell cycle. However, we estimate that approximately 25-40% of NHR-67 protein resides in puncta based on segmentation and quantification of fluorescent intensity. We also measured NHR-67 concentration in the nucleoplasm of VU cells and found that it is only 28% of what is observed in ACs (n = 10). We also disagree with the notion that the majority of NHR-67 protein should be located in puncta to support the sequestration model. As one example, previously published work examining phase separation of endogenous YAP shows that it is present in the nucleoplasm in addition to puncta (Cai et al., 2019, doi: 10.1038/s41556-019-0433-z). In our system, it is possible that the combination of transcriptional downregulation and partial sequestration away from DNA is sufficient to disrupt the normal activity of NHR-67.

3) The authors do not report whether NHR-67, UNC-37, LSY-22, or POP-1 localization to puncta is interdependent, as implied by their model.

RESPONSE: We based our model, shown in Fig. 7E, on known or predicted protein-protein interactions, which we confirmed through yeast two-hybrid analyses (Fig. 7D; Fig. 7-figure supplement 1). It is difficult to test whether localization of these proteins to puncta is interdependent, as a perturbation of UNC-37, LSY-22, and POP-1 result in ectopic ACs. Trying to determine if loss of puncta results in VU-to-AC transdifferentiation or vice versa becomes a chicken-egg argument. It is also possible that UNC-37 and LSY-22 are at least partially redundant in this context.

4) The evidence that the "repressor condensates" suppress AC fate in VUs is presented in Fig. 4D where the authors deplete the presumed repressor LSY-22. First, the authors do not examine whether NHR-67 forms puncta under these conditions. Second, the authors rely on a single marker (cdh-3p::mCherry::moeABD) to score AC fate: this marker shows weak expression in cells flanking one bright cell (presumably the AC) which the authors interpret as a VU AC transformation. The authors, however, do not identify the cells that express the marker by lineage analyses and dismiss the possibility that the marker-positive cells could arise from the division of an AC-committed cell. Finally, the authors did not test whether marker expression was dependent on NHR-67, as predicted by the model shown in Fig. 7.

RESPONSE: For the auxin-inducible degron experiments, strains contained labeled AID-tagged proteins, a labeled TIR1 transgene, and a labeled AC marker. Thus, we were limited by the number of fluorescent channels we could covisualize and therefore could not also visualize NHR-67 (to assess for puncta formation) or another AC marker (such as LAG-2). We could have generated an AID-tagged LSY-22 strain without a fluorescent protein, but then we would not be able to quantify its depletion, which this reviewer points out is important to measure. We did visualize NHR-67::GFP expression following RNAi-induced knockdown of POP-1 and observed consistent loss of puncta in ectopic ACs. However, it is unclear whether cell fate change causes loss of puncta or vice-versa.

5) Interaction between NHR-67 and UNC-37 is shown using Y2H, but not verified in vivo. Furthermore, the functional significance of the NHR-67/UNC-37 interaction is not tested.

We attempted to remove the intrinsically disordered region found at the C-terminus of the endogenous nhr-67 locus, using CRISPR/Cas9, as this would both confirm the NHR-67/UNC-37 interaction in vivo and allow us to determine the functional significance of this interaction. However, we were unable to recover a viable line after several attempts, suggesting that this region of the protein is vital.

6) Throughout the manuscript, the authors do not use lineage analysis to confirm fate transformation as is the standard in the field. There are 4 multipotential gonadal cells with the potential to differentiate into VUs or ACs. Which ones contribute to the extra ACs in the different genetic backgrounds examined was not determined, which complicates interpretation. The authors should consider and test the following possibilities: disruption of NHR-67 regulation causes 1) extra pluripotent cells to directly become ACs early in development, 2) causes VU cells to gradually trans-fate to an AC-like fate after VU fate specification (as implied by the authors), or 3) causes an AC to undergo extra cell division(s)? In Fig. 1F, 5 cells are designated as ACs, which is one more that the 4 precursors depicted in Fig. 1A, implying that some of the "ACs" were derived from progenitors that divided.

The timing between AC/VU cell fate specification and AC invasion (the point at which we look for differentiated ACs) is approximately 10-12 hours at 25 {degree sign}C. With our imaging setup, we are limited to approximately 3-4 hours of live-cell imaging. Therefore, lineage tracing was not feasible for our experiments. Instead, we relied on visualization of established markers of AC and VU cell fate to determine how ectopic ACs arose. In Fig. 6B,C we show that the expression of two AC markers (cdh-3 and lag-2) turn on while a VU marker (lag-1) gets downregulated within the same cell. In our opinion, live-imaging experiments that show in real time changes in cell fate via reporters was the most definitive way to observe the phenotype.

7) There are 4 multipotential gonadal cells with the potential to differentiate into VUs or ACs. Which ones contribute to the extra ACs in the different genetic backgrounds examined was not determined, which complicates interpretation. The authors should consider and test the following possibilities: disruption of NHR-67 regulation causes 1) extra pluripotent cells to directly become ACs early in development, 2) causes VU cells to gradually trans-fate to an AC-like fate after VU fate specification (as implied by the authors), or 3) causes an AC to undergo extra cell division(s)?? In Fig. 1F, 5 cells are designated as ACs, which is one more that the 4 precursors depicted in Fig. 1A, implying that some of the "ACs" were derived from progenitors that divided.

RESPONSE: When trying to determine the source of the ectopic ACs, we considered the three possibilities noted by the reviewer: (1) misspecification of AC/VU precursors, (2) VU-to-AC transdifferentiation, or (3) proliferation of the AC. We eliminated option 3 as a possibility, as the ectopic ACs we observed here were invasive and all of our previous work has shown that proliferating ACs cannot invade and that cell cycle exit is necessary for invasion (Matus et al., 2015; MedwigKinney & Smith et al., 2020; Smith et al., 2022). Specifically, NHR-67 is upstream of the cyclin dependent kinase CKI-1 and we found that induced expression of NHR-67 resulted in slow growth and developmental arrest, likely because of inducing cell cycle exit. For our experiment using hsp::NHR-67, we induced heat shock after AC/VU specification. For POP-1 perturbation, we explicitly acknowledged that misspecification of the AC/VU precursors could also contribute to ectopic ACs (Fig. 6A; lines 368-385). We could not achieve robust protein depletion through delayed RNAi treatment, so instead we utilized timelapse microscopy and quantification of AC and VU cell markers (Fig. 6B,C; see response 2.7 above).

Reviewer #2 (Public Review):

This work clarifies neural mechanisms that can lead to a phenomenology consistent with motor preparation in its broader sense. In this context, motor preparation refers to an activity that occurs before the corresponding movement. Another property often associated with preparatory activity is a correlation with global movement characteristics such as reach speed (Churchland et al., Neuron 2006), reach angle (Sun et al., Nature 2022), or grasp type (Meirhaeghe et al., Cell Reports 2023). Such activity has notably been observed in premotor and primary motor cortices, and it has been hypothesized to serve as an input to a motor execution circuit. The timing and mechanisms by which such 'preparatory' inputs are made available to motor execution circuits remain however unclear in general, especially in light of the presence of a 'trigger-like' signal that appears to relate to the transition from preparatory dynamics to execution activity (Kaufman et al. eNeuron 2016, Iganaki et al., Cell 2022, Zimnik and Churchland, Nature Neuroscience 2021).

The preparatory inputs have been hypothesized to fulfill one or several (non-mutually-exclusive) possible objectives. Two notable hypotheses are that these inputs could be shaped to maximize output accuracy under regularization of the input magnitude; or that they may help the flexible re-use of the neural machinery involved in the control of movements in different contexts.

Here, the authors investigate in detail how the former hypothesis may be compatible with the presence of early inputs in recurrent network models driving arm movements, and compare models to data.

Strengths:

The authors are able to deploy an in-depth evaluation of inputs that are optimized for producing an accurate output at a pre-defined time while using a regularization term on the input magnitude, in the case of movements that are thought to be controlled in a quasi-open loop fashion such as reaches.

First, the authors have identified that optimal control theory is a great framework to study this question as it provides methods to find and analyze exact solutions to this cost function in the case of models with linear dynamics. The authors not only use this framework to get an exact assessment of how much activity before movement start happens in large recurrent networks, but also give insight into the mechanisms by which it happens by dissecting in detail low-dimensional networks. The authors find that two key network properties - observability of the readout's nullspace and limited controllability - give rise to optimal inputs that are large before the start of the movement (while the corresponding network activity lies in the nullspace of the readout). Further, the authors numerically investigate the timing of optimized inputs in models with nonlinear dynamics, and find that pre-movement inputs can also arise in these more general networks. Finally, the authors point out some coarse-grained similarities between the pre-movement activity driven by the optimized inputs in some of the models they studied, and the phenomenology of preparation observed in the brain during single reaches and reach sequences. Overall, the authors deploy an impressive arsenal of tools and a very in-depth analysis of their models.

Limitations:

1. Though the optimal control theory framework is ideal to determine inputs that minimize output error while regularizing the input norm, it however cannot easily account for some other varied types of objectives - especially those that may lead to a complex optimization landscape. For instance, the reusability of parts of the circuit, sparse use of additional neurons when learning many movements, and ease of planning (especially under uncertainty about when to start the movement), may be alternative or additional reasons that could help explain the preparatory activity observed in the brain. It is interesting to note that inputs that optimize the objective chosen by the authors arguably lead to a trade-off in terms of other desirable objectives. Specifically, the inputs the authors derive are time-dependent, so a recurrent network would be needed to produce them and it may not be easy to interpolate between them to drive new movement variants. In addition, these inputs depend on the desired time of output and therefore make it difficult to plan, e.g. in circumstances when timing should be decided depending on sensory signals. Finally, these inputs are specific to the full movement chain that will unfold, so they do not permit reuse of the inputs e.g. in movement sequences of different orders.

2. Relatedly, if the motor circuits were to balance different types of objectives, the activity and inputs occurring before each movement may be broken down into different categories that may each specialize into one objective. For instance, previous work (Kaufman et al. eNeuron 2016, Iganaki et al., Cell 2022, Zimnik and Churchland, Nature Neuroscience 2021) has suggested that inputs occurring before the movement could be broken down into preparatory inputs 'stricto sensu' - relating to the planned characteristics of the movement - and a trigger signal, relating to the transition from planning to execution - irrespective of whether the movement is internally timed or triggered by an external event. The current work does not address which type(s) of early input may be labeled as 'preparatory' or may be thought of as a part of 'planning' computations.

3. While the authors rightly point out some similarities between the inputs that they derive and observed preparatory activity in the brain, notably during motor sequences, there are also some differences. For instance, while both the derived inputs and the data show two peaks during sequences, the data reproduced from Zimnik and Churchland show preparatory inputs that have a very asymmetric shape that really plummets before the start of the next movement, whereas the derived inputs have larger amplitude during the movement period - especially for the second movement of the sequence. In addition, the data show trigger-like signals before each of the two reaches. Finally, while the data show a very high correlation between the pattern of preparatory activity of the second reach in the double reach and compound reach conditions, the derived inputs appear to be more different between the two conditions. Note that the data would be consistent with separate planning of the two reaches even in the compound reach condition, as well as the re-use of the preparatory input between the compound and double reach conditions. Therefore, different motor sequence datasets - notably, those that would show even more coarticulation between submovements - may be more promising to find a tight match between the data and the author's inputs. Further analyses in these datasets could help determine whether the coarticulation could be due to simple filtering by the circuits and muscles downstream of M1, planning of movements with adjusted curvature to mitigate the work performed by the muscles while permitting some amount of re-use across different sequences, or - as suggested by the authors - inputs fully tailored to one specific movement sequence that maximize accuracy and minimize the M1 input magnitude.

4. Though iLQR is a powerful optimization method to find inputs optimizing the author's cost function, it also has some limitations. First, given that it relies on a linearization of the dynamics at each timestep, it has a limited ability to leverage potential advantages of nonlinearities in the dynamics. Second, the iLQR algorithm is not a biologically plausible learning rule and therefore it might be difficult for the brain to learn to produce the inputs that it finds. It remains unclear whether using alternative algorithms with different limitations - for instance, using variants of BPTT to train a separate RNN to produce the inputs in question - could impact some of the results.

5. Under the objective considered by the authors, the amount of input occurring before the movement might be impacted by the presence of online sensory signals for closed-loop control. It is therefore an open question whether the objective and network characteristics suggested by the authors could also explain the presence of preparatory activity before e.g. grasping movements that are thought to be more sensory-driven (Meirhaeghe et al., Cell Reports 2023).

Reviewer #2 (Public Review):

Summary<br /> In this experiment, Voltage Sensitive Dye Imaging (VSDI) was used to measure neural activity in macaque primary visual cortex in monkeys trained to detect an oriented grating target that was presented either alone or against an oriented mask. Monkeys' ability to detect the target (indicated by a saccade to its location) was impaired by the mask, with the greatest impairment observed when the mask was matched in orientation to the target, as is also the case in human observers. VSDI signals were examined to test the hypothesis that the target-evoked response would be maximally suppressed by the mask when it matched the orientation of the target. In each recording session, fixation trials were used to map out the spatial response profile and orientation domains that would then be used to decode the responses on detection trials. VSDI signals were analyzed at two different scales: a coarse scale of the retinotopic response to the target and a finer scale of orientation domains within the stimulus-evoked response. Responses were recorded in three conditions: target alone, mask alone, and target presented with mask. Analyses were focused on the target evoked response in the presence of the mask, defined to be the difference in response evoked by the mask with target (target present) versus the mask alone (target absent). These were computed across five 50 msec bins (total, 250 msec, which was the duration of the mask (target present trials, 50% of trials) / mask + target (target present trials, 50% of trials). Analyses revealed that in an initial (transient) phase the target evoked response increased with similarity between target and mask orientation. As the authors note, this is surprising given that this was the condition where the mask maximally impaired detection of the target in behavior. Target evoked responses in a later ('sustained') phase fell off with orientation similarity, consistent with the behavioral effect. When analyzed at the coarser scale the target evoked response, integrated over the full 250 msec period showed a very modest dependence on mask orientation. The same pattern held when the data were analyzed on the finer orientation domain scale, with the effect of the mask in the transient phase running counter to the perceptual effect of the mask and the sustained response correlating the perceptual effect. The effect of the mask was more pronounced when analyzed at the scale.

Strengths<br /> The work is on the whole very strong. The experiments are thoughtfully designed, the data collection methods are good, and the results are interesting. The separate analyses of data at a coarse scale that aggregates across orientation domains and a more local scale of orientation domains is a strength and it is reassuring that the effects at the more localized scale are more clearly related to behavior, as one would hope and expect. The results are strengthened by modeling work shown in Figure 8, which provides a sensible account of the population dynamics. The analyses of the relationship between VSDI data and behavior are well thought out and the apparent paradox of the anti-correlation between VSDI and behavior in the initial period of response, followed by a positive correlation in the sustained response period is intriguing.

Points to Consider / Possible Improvements<br /> The biphasic nature of the relationship between neural and behavioral modulation by the mask and the surprising finding that the two are anticorrelated in the initial phase are left as a mystery. The paper would be more impactful if this mystery could be resolved.

The finding is based on analyses of the correlation between behavior and neural responses. This appears in the main body of the manuscript and is detailed in Figures S1 and S2, which show the correlation over time between behavior and target response for the retinotopic and columnar scale.

One possible way of thinking of this transition from anti- to positive correlation with behavior is that it might reflect the dynamics of a competitive interaction between mask and target, with the initial phase reflecting predominantly the mask response, with the target emerging, on some trials, in the latter phase. On trials when the mask response is stronger, the probability of the target emerging in the latter phase, and triggering a hit, might be lower, potentially explaining the anticorrelation in the initial phase. The sustained response may be a mixture of trials on which the target response is or is not strong enough to overcome the effect of the mask sufficiently to trigger target detection.

It would, I think, be worth examining this by testing whether target dynamics may vary, depending on whether the monkey detected the target (hit trials) or failed to detect the target (miss trials). Unless I missed it I do not think this analysis was done. Consistent with this possibility, the authors do note (lines 226-229) that "The trajectories in the target plus mask conditions are more complex. For example, when mask orientation is at +/- 45 deg to the target, the population response is initially dominated by the mask, but then in mid-flight, the population response changes direction and turns toward the direction of the target orientation." This suggests (to this reviewer, at least) that the emergence of a positive correlation between behavioral and neural effects in the latter phase of the response could reflect either a perceptual decision that the target is present or perhaps deployment of attention to the location of the target.

It may be that this transition reflected detection, in which it might be more likely on hit trials than miss trials. Given the SNR it would presumably be difficult to do this analysis on a trial-by-trial basis, but the hit and miss trials (which make each make up about 1/2 of all trials) could be averaged separately to see if the mid-flight transition is more prominent on hit trials. If this is so for the +/- 45 degree case it would be good to see the same analysis for other combinations of target and mask. It would also be interesting to separate correct reject trials from false alarms, to determine whether the mid-flight transition tends to occur on false alarm trials.

If these analyses do not reveal the predicted pattern, they might still merit a supplemental figure, for the sake of completeness.

Reviewer #2 (Public Review):

The authors of this study investigated the relationship between (under)confidence and the anxious-depressive symptom dimension in a longitudinal intervention design. The aim was to determine whether confidence bias improves in a state-like manner when symptoms improve. The primary focus was on patients receiving internet-based CBT (iCBT; n=649), while secondary aims compared these changes to patients receiving antidepressants (n=82) and a control group (n=88).

The results support the authors' conclusions, and the authors convincingly demonstrated a weak link between changes in confidence bias and anxious-depressive symptoms (not specific to the intervention arm)

The major strength and contribution of this study is the use of a longitudinal intervention design, allowing the investigation of how the well-established link between underconfidence and anxious-depressive symptoms changes after treatment. Furthermore, the large sample size of the iCBT group is commendable. The authors employed well-established measures of metacognition and clinical symptoms, used appropriate analyses, and thoroughly examined the specificity of the observed effects.

However, due to the small expected effect sizes, the comparisons with the antidepressant and control groups were underpowered, reducing comparability between interventions and the generalizability of the results. The lack of interaction effect with treatment makes it harder to interpret the observed differences in confidence.

Reviewer #2 (Public Review):

This work explored the biological functions of a small family of RNA-binding proteins that was previously studied in animals, but was uncharacterized in plants. Combinatorial T-DNA insertional mutants disrupting the expression of the four Mushashi-like (MSIL) genes in Arabidopsis revealed that only the msil2 msil4 double mutant visibly alters plant development. The msil2/4 plants produced stems that could not stand upright. Transgene complementation, site-directed mutagenesis of MSIL4 conserved RNA-binding motifs, and in vitro RNA binding assays support the conclusion that the loss of MSIL2 and MISL4 function is responsible for the observed morphological defects. MSIL2/4 interact with proteins associated with mRNA 3'UTR binding and translational regulation.

The authors present compelling biochemical evidence that Mushashi-like2 (MSIL2) and MSIL4 jointly regulate secondary cell wall biosynthesis in the Arabidopsis stem. Quantitative analyses of proteins and transcripts in msil2/4 stems uncovered transcriptional upregulation of several xylan-related enzymes (despite WT-like RNA levels). Consistent with MALDI-TOF data for released xylan oligosaccharides, the authors propose a model in which MSIL2/4 negatively regulate the translation of GXM (glucuronoxylan methyltransferase), a presumed rate-limiting step. The molecular links between overmethylated xylans and the observed stem defects (which include subtle reductions in lignin and increases beta-glucan polymer distribution) warrants further investigation in future studies. Similarly, as the authors point out, it is intriguing that the loss of the broadly expressed MSIL2/4 genes only significantly affects specific cell types in the stem.

Reviewer #2 (Public Review):

Summary: The authors provide a nice summary on the possibility to study genetic heterogeneity and how to measure the dynamics of stem cells. By combining single cell and bulk sequencing analyses, they aim to use a stochastic process and inform on different aspects of genetic heterogeneity.

Strengths: Well designed study and strong methods

Weaknesses: Minor<br /> Further clarification to Figure 3 legend would be good to explain the 'no association' of number of samples and mutational burden estimate as per line 180-182 p.8

Reviewer #2 (Public Review):

Summary:<br /> The authors set out to characterise "trust" in terms of a spatial pattern of neural responses, and then validate whether different tasks, in different datasets, express this pattern or do not express it, according to their hypotheses. They based their approach on linear classifiers (Support Vector Machines), which they trained to distinguish trust from distrust in an investment game, and then applied the classifier to other datasets. Additionally, they performed visualisations of the similarity among participants and among tasks in their neural responses, using dimensionality reduction techniques.

Strengths:<br /> The key strength of this study is the use of multiple datasets to test whether a single study's characterisation of trust, in terms of a spatial pattern of neural responses, generalises to other tasks and populations. This is a nice use for existing data, which bolsters the interpretation of fMRI results, demonstrating that they are generalisable. While I am not a specialist in decoding methods, the analyses appear to have been performed conscientiously and to a high standard. The manuscript is also clearly written.

Weaknesses:<br /> It's worth noting an obvious but important statistical point. In this study, the *inability* of a classifier to distinguish between conditions in particular datasets is taken as evidence that those conditions do not differ in terms of the effect of interest (trust). In this case, these results make sense, in that they are consistent with the authors' hypotheses. However, there are various reasons why the classifier may not work well on particular datasets - e.g. differences in noise, or a lack of linear separability between patterns (which might mandate a non-linear classifier or a different SVM kernel). Therefore, any null result obtained with classical statistics should be interpreted with caution.

Reviewer #2 (Public Review):

Summary:

This study by Park and Gross investigates the spatiotemporal neural representation of semantic information most pertinent to the gist of speech materials presented to subjects as magnetoencephalography was recorded. Participants heard and saw naturalistic continuous speech recordings (with the auditory component presented to one ear), while also presented with distractor auditory speech (presented in the other ear). Participants were instructed to attend to the speech stream that matched the video of the speaker. The stimuli were semantically parsed to create short segments to which topic probabilities were assigned. These segments were then organized into high and low topic probabilities for each of the four topics (determined using Latent Dirichlet Allocation (LDA) analysis). The results suggest clear differences in the fidelity of neural encoding of the speech envelope during high-topic probability segments, which is interpreted as the brain representing key information for a story whether that information is explicitly attended to.

Strengths:<br /> The use of LDA analysis makes possible the quantification of whether a particular speech segment is relevant to a particular topic and enables analysis based on this high-temporal resolution of semantic salience. The authors show clear differences between attended and unattended speech conditions, as well as, surprisingly, differences between semantically salient unattended speech and attended, less semantically relevant speech.

Weaknesses:<br /> Though the effect sizes of the results of this study show clear differences between stimulus conditions, clarification of the experimental methods is needed to appreciate their interpretation. Broadly, I would suggest adding a clearer description of the task during data collection, even though it has been published elsewhere.

One key piece of information that is missing is how semantically relevant topics are assigned, so that salient semantic information can be compared between attended and unattended stories. It's unclear to me how results are combined across topics and stories. If a particular speech segment is assigned 4 topic probabilities, that segment has both a high probability of belonging to one topic and a low probability of belonging to another. I understand how this can be used to create the experimental conditions for a single topic, but how are results combined across topics?

I think some discussion of using the encoding and decoding of the speech envelope as a measure of what is semantically relevant is warranted. The fidelity with which the speech envelop is represented has been used as a proxy for how well that speech is attended to, but it is unclear to me whether we should expect to see high-fidelity encoding of speech envelop outside of the primary and secondary auditory regions of the brain, or how it relates to the semantic information contained in the speech signal.

Additionally, I wonder if it might be more informative to decode the topic labels themselves directly by building a model to predict the topic probabilities from the neural data? This might give a more direct measure of where and when semantically relevant information is represented.

Reviewer #2 (Public Review):

In the current study, Fischer and colleagues extensively examined the role of parthenolide in inhibiting microtubule detyrosination and making the mechanistic link for the compound to facilitate the role of IL6 and PTEN/KO in promoting neurite outgrowth and axon regeneration. The in vitro and mechanistic work laid the foundation for the authors to reach several key predictions that such detyrosination can be applied for in vivo applications. Thus the authors extended the work to optic nerve regeneration and spinal cord recovery. The in vivo compound that the authors utilized is DMAPT, which plays a synergistic role with existing pro-regeneration therapies, such as Il6 treatment.

The major strength of the work is the first half of the mechanistic inquiries, where the authors combined cell biology and biochemistry approaches to dissect the mechanistic link from parthenolide to microtube dynamics. The shortcoming is that the in vivo data is limited, and the effects might be considered mild, especially by benchmarking with other established and effective strategies.

The work is solid and prepares a basis for others to test the role of DMAPT in other settings, especially in the setting of other effective pro-regenerative approaches. With the goal of comprehensive and functional recovery in vivo, the impact of the work and the utilities of the methods remain to be tested broadly in other models in vivo.

Reviewer #2 (Public Review):

Place cells fire sequentially during hippocampal theta oscillations, forming a spatial representation of behavioral experiences in a temporally-compressed manner. The firing sequences during theta cycles are widely considered as essential assemblies for learning, memory, and planning. Many theoretical studies have investigated the mechanism of hippocampal theta firing sequences; however, they are either entirely extrinsic or intrinsic. In other words, they attribute the theta sequences to external sensorimotor drives or focus exclusively on the inherent firing patterns facilitated by the recurrent network architectures. Both types of theories are inadequate for explaining the complexity of the phenomena, particularly considering the observations in a previous paper by the authors: theta sequences independent of animal movement trajectories may occur simultaneously with sensorimotor inputs (Yiu et al., 2022).

In this manuscript, the authors concentrate on the CA3 area of the hippocampus and develop a model that accounts for both mechanisms. Specifically, the model generates extrinsic sequences through the short-term facilitation of CA3 cell activities, and intrinsic sequences via recurrent projections from the dentate gyrus. The model demonstrates how the phase precession of place cells in theta sequences is modulated by running direction and the recurrent DG-CA3 network architecture. To evaluate the extent to which firing sequences are induced by sensorimotor inputs and recurrent network architecture, the authors use the Pearson correlation coefficient to measure the "intrinsicity" and "extrinsicity" of spike pairs in their simulations.

I find this research topic to be both important and interesting, and I appreciate the clarity of the paper. The idea of combining intrinsic and extrinsic mechanisms for theta sequences is novel, and the model effectively incorporates two crucial phenomena: phase precession and directionality of theta sequences. I particularly commend the authors' efforts to integrate previous theories into their model and conduct a systematic comparison. This is exactly what our community needs: not only the development of new models, but also understanding the critical relationships between different models.

Reviewer #2 (Public Review):

Summary:<br /> This work investigates the effects of various antipsychotic drugs on cortical responses during visuomotor integration. Using wide-field calcium imaging in a virtual reality setup, the researchers compare neuronal responses to self-generated movement during locomotion-congruent (closed loop) or locomotion-incongruent (open loop) visual stimulation. Moreover, they probe responses to unexpected visual events (halt of visual flow, sudden-onset drifting grating). The researchers find that, in contrast to a variety of excitatory and inhibitory cell types, genetically defined layer 5 excitatory neurons distinguish between the closed and the open loop condition and exhibit activity patterns in visual cortex in response to unexpected events, consistent with unsigned prediction error coding. Motivated by the idea that prediction error coding is aberrant in psychosis, the authors then inject the antipsychotic drug clozapine, and observe that this intervention specifically affects closed loop responses of layer 5 excitatory neurons, blunting the distinction between the open and closed loop conditions. Clozapine also leads to a decrease in long-range correlations between L5 activity in different brain regions, and similar effects are observed for two other antipsychotics, aripripazole and haloperidol, but not for saline or the stimulant amphetamine. The authors suggest that altered prediction error coding in layer 5 excitatory neurons due to reduced long-range correlations in L5 neurons might be a major effect of antipsychotic drugs and speculate that this might serve as a new biomarker for drug development.

Strengths:<br /> - Relevant and interesting research question:<br /> The distinction between expected and unexpected stimuli is blunted in psychosis but the neural mechanisms remain unclear. Therefore, it is critical to understand whether and how antipsychotic drugs used to treat psychosis affect cortical responses to expected and unexpected stimuli. This study provides important insights into this question by identifying a specific cortical cell type and long-range interactions as potential targets. The authors identify layer 5 excitatory neurons as a site where functional effects of antipsychotic drugs manifest. This is particularly interesting as these deep layer neurons have been proposed to play a crucial role in computing the integration of predictions, which is thought to be disrupted in psychosis. This work therefore has the potential to guide future investigations on psychosis and predictive coding towards these layer 5 neurons, and ultimately improve our understanding of the neural basis of psychotic symptoms.

- Broad investigation of different cell types and cortical regions:<br /> One of the major strengths of this study is quasi-systematic approach towards cell types and cortical regions. By analysing a wide range of genetically defined excitatory and inhibitory cell types, the authors were able to identify layer 5 excitatory neurons as exhibiting the strongest responses to unexpected vs. expected stimuli and being the most affected by antipsychotic drugs. Hence, this quasi-systematic approach provides valuable insights into the functional effects of antipsychotic drugs on the brain, and can guide future investigations towards the mechanisms by which these medications affect cortical neurons.

- Bridging theory with experiments<br /> Another strength of this study is its theoretical framework, which is grounded in the predictive coding theory. The authors use this theory as a guiding principle to motivate their experimental approach connecting visual responses in different layers with psychosis and antipsychotic drugs. This integration of theory and experimentation is a powerful approach to tie together the various findings the authors present and to contribute to the development of a coherent model of how the brain processes visual information both in health and in disease.

Weaknesses:<br /> - Unclear relevance for psychosis research<br /> From the study, it remains unclear whether the findings might indeed be able to normalise altered predictive coding in psychosis. Psychosis is characterised by a blunted distinction between predicted and unpredicted stimuli. The main results of this study indicate that antipsychotic drugs further blunt the distinction between predicted and unpredicted stimuli, which would suggest that antipsychotic drugs would deteriorate rather than ameliorate the predictive coding deficit found in psychosis. However, these findings were based on observations in wild-type mice at baseline. Given that antipsychotics are thought to have little effects in health but potent antipsychotic effects in psychosis, it seems possible that the presented results might be different in a condition modelling a psychotic state, for example after a dopamine-agonistic or a NMDA-antagonistic challenge. Therefore, future work in models of psychotic states is needed to further investigate the translational relevance of these findings.

- Incomplete testing of predictive coding interpretation<br /> While the investigation of neuronal responses to different visual flow stimuli is interesting, it remains open whether these responses indeed reflect internal representations in the framework of predictive coding. While the responses are consistent with internal representation as defined by the researchers, i.e., unsigned prediction error signals, an alternative interpretation might be that responses simply reflect sensory bottom-up signals that are more related to some low-level stimulus characteristics than to prediction errors. Moreover, this interpretational uncertainty is compounded by the fact that the used experimental paradigms were not suited to test whether behaviour is impacted as a function of the visual stimulation which makes it difficult to assess what the internal representation of the animal actually was. For these reasons, the observed effects might reflect simple bottom-up sensory processing alterations and not necessarily have any functional consequences. While this potential alternative explanation does not detract from the value of the study, future work would be needed to explain the effect of antipsychotic drugs on responses to visual flow. For example, experimental designs that systematically vary the predictive strength of coupled events or that include a behavioural readout might be more suited to draw from conclusions about whether antipsychotic drugs indeed alter internal representations.

Conclusion:<br /> Overall, the results support the idea that antipsychotic drugs affect neural responses to predicted and unpredicted stimuli in deep layers of cortex. Although some future work is required to establish whether this observation can indeed be explained by a drug-specific effect on predictive coding, the study provides important insights into the neural underpinnings of visual processing and antipsychotic drugs, which is expected to guide future investigations on the predictive coding hypothesis of psychosis. This will be of broad interest to neuroscientists working on predictive coding in health and disease.

Reviewer #2 (Public Review):

Bilgic et al first explored cellular diversity in the developing cerebral cortex of ferret, honing in on progenitor cell diversity by employing FACS sorting of HES5-positive cells. They have generated a novel single cell transcriptomic dataset capturing the diversity of cells in the developing ferret cerebral cortex, including diverse radial glial and excitatory neuron populations. Unexpectedly, this analysis revealed the presence of CRYAB-positive truncated radial glia previously described only in humans. Using bioinformatic analyses, the investigators proposed that truncated radial glia produce ependymal cells, astrocytes, and to a lesser degree, neurons. Of particular interest to the field, they identify enriched expression of FOXJ1 in late truncated radial glia strongly indicating that towards the end of neurogenesis, these cells likely give rise to ependymal cells. This study represents a major advancement in the field of cortical development and a valuable dataset for future studies of ferret cortical development.

Reviewer #2 (Public Review):

Summary:<br /> In this article, the authors provide a method of evaluating the safety of orthopedic implants in relation to radiofrequency-induced heating issues. The authors provide an open-source computational heterogeneous human model and explain computational techniques in a finite element method solver to predict the RF-induced temperature increase due to an orthopedic implant while being exposed to MRI RF fields at 1.5 T.

Strengths:<br /> The open-access computational human model along with their semiautomatic algorithm to position the implant can help realistically model the implant RF exposure in patients avoiding over- or under-estimation of RF heating measured using rectangular box phantoms such as ASTM phantom. Additionally, using numerical simulation to predict radiofrequency-induced heating will be much easier compared to the experimental measurements in an MRI scanner, especially when the scanner availability is limited.

Weaknesses:<br /> The proposed method only used radiofrequency (RF) field exposure to evaluate the heating around the implant. However, in the case of bulky implants, the rapidly changing gradient field can also produce significant heating due to large eddy currents. So the gradient-induced heating still remains an issue to be evaluated to decide on the safety of the patient. Moreover, the method is limited to a single human model and might not be representative of patients with different age, sex, and body weights. Additionally, the authors compare the temperature rise predicted by their method to an earlier study. However, there is no information about how they controlled the input power in their simulation testbed compared to the earlier study in showing validation of the method.