Reviewer #1 (Public review):

Summary

Farkas and colleagues conducted a comparative neuroimaging study with domestic dogs and humans to explore whether social perception in both species is underpinned by an analogous distinction between animate and inanimate entities an established functional organizing principle in the primate and human brain. Presenting domestic dogs and humans with clips of three animate classes (dogs, humans, cats) and one inanimate control (cars), the authors also set out to compare how dogs and humans perceive their own vs other species. Both research questions have been previously studied in dogs, but the authors used novel dynamic stimuli and added animate and inanimate classes, which have not been investigated before (i.e., cats and cars). Combining univariate and multivariate analysis approaches, they identified functionally analogous areas in the dog and human occipito-temporal cortex involved in the perception of animate entities, largely replicating previous observations. This further emphasizes a potentially shared functional organizing principle of social perception in the two species. The authors also describe between-species divergencies in the perception of the different animate classes, arguing for a less generalized perception of animate entities in dogs, but this conclusion is not convincingly supported by the applied analyses and reported findings.

Strengths

Domestic dogs represent a compelling model species to study the neural bases of social perception and potentially shared functional organizing principles with humans and primates. The field of comparative neuroimaging with dogs is still young, with a growing but still small number of studies, and the present study exemplifies the reproducibility of previous research. Using dynamic instead of static stimuli and adding new stimuli classes, Farkas and colleagues successfully replicated and expanded previous findings, adding to the growing body of evidence that social perception is underpinned by a shared functional organizing principle in the dog and human occipito-temporal cortex.

Weaknesses

The study design is imbalanced, with only one category of inanimate objects vs. three animate entities. Moreover, based on the example videos, it appears that the animate stimuli also differed in the complexity of the content from the car stimuli, with often multiple agents interacting or performing goal-directed actions. Moreover, while dogs are familiar with cars, they are definitely of lower relevance and interest to them than the animate stimuli. Thus, to a certain extent, the results might also reflect differences in attention towards/salience of the stimuli.

The methods section and rationale behind the chosen approaches were often difficult to follow and lacked a lot of information, which makes it difficult to judge the evidence and the drawn conclusions, and it weakens the potential for reproducibility of this work. For example, for many preprocessing and analysis steps, parameters were missing or descriptions of the tools used, no information on anatomical masks and atlas used in humans was provided, and it is often not clear if the authors are referring to the univariate or multivariate analysis.

In regard to the chosen approaches and rationale, the authors generally binarize a lot of rich information. Instead of directly testing potential differences in the neural representations of the different animate entities, they binarize dissimilarity maps for, e.g. animate entity > inanimate cars and then calculate the overlap between the maps. The comparison of the overlap of these three maps between species is also problematic, considering that the human RSA was constricted to the occipital and temporal cortex (there is now information on how they defined it) vs. whole-brain in dogs. Considering that the stimuli do differ based on low-level visual properties (just not significantly within a run), the RSA would also allow the authors to directly test if some of the (dis)similarities might be driven by low-level visual features like they, e.g. did with the early visual cortex model. I do think RSA is generally an excellent choice to investigate the neural representation of animate (and inanimate) stimuli, but the authors should apply it more appropriately and use its full potential.

The authors localized some of the "animate areas" also with the early visual cortex model (e.g. ectomarginal gyrus, mid suprasylvian); in humans, it only included the known early visual cortex - what does this mean for the animate areas in dogs?

The results section also lacks information and statistical evidence; for example, for the univariate region-of-interest (ROI) analysis (called response profiles) comparing activation strength towards each stimulus type, it is not reported if comparisons were significant or not, but the authors state they conducted t-tests. The authors describe that they created spheres on all peaks reported for the contrast animate > inanimate, but they only report results for the mid suprasylvian and occipital gyrus (e.g. caudal suprasylvian gyrus is missing). Furthermore, considering that the ROIs were chosen based on the contrast animate > inanimate stimuli, activation strength should only be compared between animate entities (i.e., dogs, humans, cats), while cars should not be reported (as this would be double dipping, after selecting voxels showing lower activation for that category). The descriptive data in Figure 3B (pending statistical evidence) suggests there were no strong differences in activation for the three species in dog and human animate areas. Thus, the ROI analysis appears to contradict findings from the binary analysis approach to investigate species preference, but the authors only discuss the results of the latter in support of their narrative for conspecific preference in dogs and do not discuss research from other labs investigating own-species preference.

The authors also unnecessarily exaggerate novelty claims. Animate vs inanimate and own vs other species perceptions have both been investigated before in dogs (and humans), so any claims in that direction seem unsubstantiated - and also not needed, as novelty itself is not a sign of quality; what is novel, and a sign of theoretical advance besides the novelty, are as said the conceptual extension and replication of previous work.

Overall, more analyses and appropriate tests are needed to support the conclusions drawn by the authors, as well as a more comprehensive discussion of all findings.

Reviewer #2 (Public review):

Summary:

The manuscript reports an fMRI study looking at whether there is animacy organization in a non-primate, mammal, the domestic dog, that is similar to that observed in humans and non-human primates (NHPs). A simple experiment was carried out with four kinds of stimulus videos (dogs, humans, cats, and cars), and univariate contrasts and RSA searchlight analysis was performed. Previous studies have looked at this question or closely associated questions (e.g. whether there is face selectivity in dogs). The import of the present study is that it looks at multiple types of animate objects, dogs, humans, and cats, and tests whether there was overlapping/similar topography (or magnitude) of responses when these stimuli were compared to the inanimate reference class of cars. The main finding was of some selectivity for animacy though this was primarily driven by the dog stimuli, which did overlap with the other animate stimulus types, but far less so than in humans.

Strengths:

I believe that this is an interesting study in so far as it builds on other recent work looking at category-selectivity in the domestic dog. Given the limited number of such studies, I think it is a natural step to consider a number of different animate stimuli and look at their overlap. While some of the results were not wholly surprising (e.g. dog brains respond more selectively for dogs than humans or cats), that does not take away from their novelty, such as it is. The findings of this study are useful as a point of comparison with other recent work on the organization of high-level visual function in the brain of the domestic dog.

Weaknesses:

(1) One challenge for all studies like this is a lack of clarity when we say there is organization for "animacy" in the human and NHP brains. The challenge is by no means unique to the present study, but I do think it brings up two more specific topics.

First, one property associated with animate things is "capable of self-movement". While cognitively we know that cars require a driver, and are otherwise inanimate, can we really assume that dogs think of cars in the same way? After all, just think of some dogs that chase cars. If dogs represent moving cars as another kind of self-moving thing, then it is not clear we can say from this study that we have a contrast between animate vs inanimate. This would not mean that there are no real differences in neural organization being found. It was unclear whether all or some of the car videos showed them moving. But if many/most do, then I think this is a concern.

Second, there is quite a lot of potential complexity in the human case that is worth considering when interpreting the results of this study. In the human case, some evidence suggests that animacy may be more of a continuum (Sha et al. 2015), which may reflect taxonomy (Connolly et al. 2012, 2016). However moving videos seem to be dominated more by signals relevant to threat or predation relative to taxonomy (Nastase et al. 2017). Some evidence suggests that this purported taxonomic organization might be driven by gradation in representing faces and bodies of animals based on their relative similarity to humans (Ritchie et al. 2021). Also, it may be that animacy organization reflects a number of (partially correlated) dimensions (Thorat et al. 2019, Jozwik et al. 2022). One may wonder whether the regions of (partial) overlap in animate responses in the dog brain might have some of these properties as well (or not).

(2) It is stated that previous studies provide evidence that the dog brain shows selectivity to "certain aspects of animacy". One of these already looked at selectivity for dog and human faces and bodies and identified similar regions of activity (Boch et al. 2023). An earlier study by Dilks et al. (2015), not cited in the present work (as far as I can tell), also used dynamic stimuli and did not suffer from the above limitations in choosing inanimate stimuli (e.g. using toy and scene objects for inanimate stimuli). But it only included human faces as the dynamic animate stimulus. So, as far as stimulus design, it seems the import of the present study is that it included a *third* animate stimulus (cats) and that the stimuli were dynamic.

(3) I am concerned that the univariate results, especially those depicted in Figure 3B, include double dipping (Kriegesorte et al. 2009). The analysis uses the response peak for the A > iA contrast to then look at the magnitude of the D, H, C vs iA contrasts. This means the same data is being used for feature selection and then to estimate the responses. So, the estimates are going to be inflated. For example, the high magnitudes for the three animate stimuli above the inanimate stimuli are going to inherently be inflated by this analysis and cannot be taken at face value. I have the same concern with the selectivity preference results in Figure 3E.

I think the authors have two options here. Either they drop these analyses entirely (so that the total set of analyses really mirrors those in Figure 4), or they modify them to address this concern. I think this could be done in one of two ways. One would be to do a within-subject standard split-half analysis and use one-half of the data for feature selection and the other for magnitude estimation. The other would be to do a between-subject design of some kind, like using one subject for magnitude estimation based on an ROI defined using the data for the other subjects.

(4) There are two concerns with how the overlap analyses were carried out. First, as typically carried out to look at overlap in humans, the proportion is of overlapping results of the contrasts of interest, e.g, for face and body selectivity overlap (Schwarlose et al. 2006), hand and tool overlap (Bracci et al. 2012), or more recently, tool and food overlap (Ritchie et al. 2024). There are a number of ways of then calculating the overlap, with their own strengths and weaknesses (see Tarr et al. 2007). Of these, I think the Jaccard index is the most intuitive, which is just the intersection of two sets as a proportion of their union. So, for example, the N of overlapping D > iA and H > iA active voxels is divided by the total number of unique active voxels for the two contrasts. Such an overlap analysis is more standard and interpretable relative to previous findings. I would strongly encourage the authors to carry out such an analysis or use a similar metric of overlap, in place of what they have currently performed (to the extent the analysis makes sense to me).

Second, the results summarized in Figure 3A suggest multiple distinct regions of animacy selectivity. Other studies have also identified similar networks of regions (e.g. Boch et al. 2023). These regions may serve different functions, but the overlap analysis does not tell us whether there is overlap in some of these portions of the cortex and not in others. The overlap is only looked at in a very general sense. There may be more overlap locally in some portions of the cortex and not in others.

(5) Two comments about the RSA analyses. First, I am not quite sure why the authors used HMAX rather than layers of a standardly trained ImageNet deep convolutional neural network. This strikes me also as a missed opportunity since many labs have looked at whether later layers of DNNs trained on object categorization show similar dissimilarity structures as category-selective regions in humans and NHPs. In so far as cross-species comparisons are the motivation here, it would be genuinely interesting to see what would happen if one did a correlation searchlight with the dog brain and layers of a DNN, a la Cichy et al. (2016).

Second, from the text is hard to tell what the models for the class- and category-boundary effects were. Are there RDMs that can be depicted here? I am very familiar with RSA searchlight and I found the description of the methods to be rather opaque. The same point about overlap earlier regarding the univariate results also applies to the RSA results. Also, this is again a reason to potentially compare DNN RDMs to both the categorical models and the brains of both species.

(6) There has been emphasis of late on the role of face and body selective regions and social cognition (Pitcher and Ungerleider, 2021, Puce, 2024), and also on whether these regions are more specialized for representing whole bodies/persons (Hu et al. 2020, Taubert, et al. 2022). It may be that the supposed animacy organization is more about how we socialize and interact with other organisms than anything about animacy as such (see again the earlier comments about animacy, taxonomy, and threat/predation). The result, of a great deal of selectivity for dogs, some for humans, and little for cats, seems to readily make sense if we assume it is driven by the social value of the three animate objects that are presented. This might be something worth reflecting on in relation to the present findings.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors analyze electrophysiological data recorded bilaterally from the rat hippocampus to investigate the coupling of ripple oscillations across the hemispheres. Commensurate with the majority of previous research, the authors report that ripples tend to co-occur across both hemispheres. Specifically, the amplitude of ripples across hemispheres is correlated but their phase is not. These data corroborate existing models of ripple generation suggesting that CA3 inputs (coordinated across hemispheres via the commisural fibers) drive the sharp-wave component while the individual ripple waves are the result of local interactions between pyramidal cells and interneurons in CA1.

Strengths:

The manuscript is well-written, the analyses well-executed and the claims are supported by the data.

Weaknesses:

One question left unanswered by this study is whether information encoded by the right and left hippocampi is correlated.

Reviewer #2 (Public review):

Summary:

The authors completed a statistically rigorous analysis of the synchronization of sharp-wave ripples in the hippocampal CA1 across and within hemispheres. They used a publicly available dataset (collected in the Buzsaki lab) from 4 rats (8 sessions) recorded with silicon probes in both hemispheres. Each session contained approximately 8 hours of activity recorded during rest. The authors found that the characteristics of ripples did not differ between hemispheres, and that most ripples occurred almost simultaneously on all probe shanks within a hemisphere as well as across hemispheres. The differences in amplitude and exact timing of ripples between recording sites increased slightly with the distance between recording sites. However, the phase coupling of ripples (in the 100-250 Hz range), changed dramatically with the distance between recording sites. Ripples in opposite hemispheres were about 90% less coupled than ripples on nearby tetrodes in the same hemisphere. Phase coupling also decreased with distance within the hemisphere. Finally, pyramidal cell and interneuron spikes were coupled to the local ripple phase and less so to ripples at distant sites or the opposite hemisphere.

Strengths:

The analysis was well-designed and rigorous. The authors used statistical tests well suited to the hypotheses being tested, and clearly explained these tests. The paper is very clearly written, making it easy to understand and reproduce the analysis. The authors included an excellent review of the literature to explain the motivation for their study.

Weaknesses:

The authors state that their findings (highly coincident ripples between hemispheres), contradict other findings in the literature (in particular the study by Villalobos, Maldonado, and Valdes, 2017), but fail to explain why this large difference exists. They seem to imply that the previous study was flawed, without examining the differences between the studies.

The paper fails to mention the context in which the data was collected (the behavior the animals performed before and after the analyzed data), which may in fact have a large impact on the results and explain the differences between the current study and that by Villalobos et al. The Buzsaki lab data includes mice running laps in a novel environment in the middle of two rest sessions. Given that ripple occurrence is influenced by behavior, and that the neurons spiking during ripples are highly related to the prior behavioral task, it is likely that exposure to novelty changed the statistics of ripples. Thus, the authors should analyze the pre-behavior rest and post-behavior rest sessions separately. The Villalobos et al. data, in contrast, was collected without any intervening behavioral task or novelty (to my knowledge). Therefore, I predict that the opposing results are a result of the difference in recent experiences of the studied rats, and can actually give us insight into the memory function of ripples.

In one figure (5), the authors show data separated by session, rather than pooled. They should do this for other figures as well. There is a wide spread between sessions, which further suggests that the results are not as widely applicable as the authors seem to think. Do the sessions with small differences between phase coupling and amplitude coupling have low inter-hemispheric amplitude coupling, or high phase coupling? What is the difference between the sessions with low and high differences in phase vs. amplitude coupling? I noticed that the Buzsaki dataset contains data from rats running either on linear tracks (back and forth), or on circular tracks (unidirectionally). This could create a difference in inter-hemisphere coupling, because rats running on linear tracks would have the same sensory inputs to both hemispheres (when running in opposite directions), while rats running on a circular track would have different sensory inputs coming from the right and left (one side would include stimuli in the middle of the track, and the other would include closer views of the walls of the room). The synchronization between hemispheres might be impacted by how much overlap there was in sensory stimuli processed during the behavior epoch.

The paper would be a lot stronger if the authors analyzed some of the differences between datasets, sessions, and epochs based on the task design, and wrote more about these issues. There may be more publicly available bi-hemispheric datasets to validate their results.

Reviewer #1 (Public review):

Summary:

Chen and colleagues describe mechanisms by which UBA7 and UBE2L6 form disulfide bonds, disrupting the ISG15 transfer cascade. As other similar structures are currently available, the authors further note that the spontaneous formation of this disulfide suggests that it is a potential regulatory mechanism. Demonstrating that this mechanism occurs and is modulated in cells would greatly improve the impact of their work.

Strengths:

The various biochemical and structural experiments are largely convincing.

Weaknesses:

(1) The main point of the paper is that this covalent complex could occur and is potentially regulated in cells is limited. The authors even show an experiment in cells where this complex is formed by expressing UBE2L6-V5 and GFP-UBA7, awkwardly referenced in the discussion.

The authors should consider attempting an experiment with endogenous proteins and either modulate the formation of this complex in different cellular conditions or downplay this part of their story. For example, this sentence, "This redox-sensitive complex implies a link between oxidative stress and regulation of the immune response, highlighting a potential therapeutic target for modulating immune reactions arising from infections and inflammatory conditions." is in the abstract and should be excluded or rephrased considering the lack of cellular data.

Also, their one-cell-based experiment is shown in the discussion. This should be in the results as is standard practice but also repeated. It appears that the reduced lanes don't seem to have GFP or the GFP-UBA7. Without those controls, this experiment seems incomplete.

(2) Their intro sets up the paper to explain the disulfide formation they see in Figure 1, but a more fitting experiment would be to look at the disulfide formation between UBA7 and UBE2L6 at different pHs. It would nicely supplement the biochemical pKa data as this reaction is their focal point.

(3) While the biochemical data is extensive, it is not concise or easily accessible to a broad readership. The authors should try to clarify and simplify the text overall. Furthermore, many figure callouts are missing, interfering with the clarity of the text.

Minor

(1) Because the experiments are pKa dependent, knowing what buffers the proteins were finished in (final SEC purification step) is important. Similarly - for all assays, the buffers were not reported (SEC-MALS, biochemical assays).

(2) While the CBB and fluorescent gel assays look convincing, more controls are needed for their SEC experiments (Figure 1d), particularly because the authors definitively say the binding is because of S-S bonds. Using a reducing buffer like TCEP or DTT or their catalytic mutants to show reduced co-migration would be helpful. This is even more important given the reported high affinities between UBA7/UBE2L6 in Figure 6.

(3) Based on the data presented, it is unclear that the kinetic values are taken within initial velocity regimes. Some data in the supplement showing that the single time points represent initial velocities would be appreciated.

(4) As stated, "Previous experiments reveal an intriguing anomaly during the UBA7-UBE2L6-ISG15 thioester transfer reaction. Despite adding more ISG15 and UBE2L6, the level of UBE2L6~ISG15 remained the same." This experiment should be shown or the statement removed.

(5) Similarly, "Forty human E2 enzymes are classified in the InterProdatabase (https://www.ebi.ac.uk/interpro/), with the majority interacting with UBA1, whereas UBE2L6 and UBE2Z exclusively interact with UBA7 and UBA6, respectively." Is missing a reference.

Reviewer #2 (Public review):

Summary:

Chen et al. describe by different techniques that UBA7 and UBE2L6 readily form a complex that is covalently linked by a disulfide bond involving the active site cysteines of UBA6 and UBE2L6. Furthermore, they determined cryo-EM structures of the disulfide-linked UBY7-UBE2L6 complex in the absence and presence of ISG15. They propose that this disulfide-linked complex blocks ISGylation by temporarily rendering UBA7 inactive.

Strengths:

The authors employ a wide variety of techniques to study the formation of the binary Uba7-UBE2L6 and ternary UBA7-UBE2L6-ISG15 complexes including the structural characterization of the two complexes by cryo-EM. Despite the shortcomings (see below), the authors provide numerous valuable data that characterize the first steps of the ISGylation pathway, namely the activation of ISG15 and its transfer to UBE2L6.

Weaknesses:

(1) The authors correctly state that "Immune responses often entail the generation or reactive oxygen species, antioxidant defense mechanisms, and redox signaling" (1st sentence of 3rd paragraph in the Introduction). Based on the data presented in this study these cellular responses should lead to the formation of the covalent UBA7-UBE2L6. Since this complex renders UBA7 inactive, thus preventing it from initiating the ISGylation cascade in response to viral infections, the underlying cellular logic of complex formation remains a mystery.

The bulk of their work describes in vitro experiments, which will certainly not reflect the in vivo situation and hence one cannot rule out that this complex will not form inside cells. The authors have also observed this complex in HEK293T cells, however, this involved overexpression of both proteins and one can thus not rule out that the disulfide-linked complex will not form at physiological protein levels. Furthermore, this cellular model appears not to be a suitable system.

(2) The authors carried out a comparative analysis of E1-E2 disulfide bond formation with UBA1, the major activating enzyme for ubiquitin, and UBE2L3, a ubiquitin-specific E2. The choice of UBE2L3 was motivated by its close relationship to UBE2L6. From these studies, the authors conclude that UBA1 does not form the corresponding complex. Given that there are over 30 ubiquitin-specific E2s this conclusion does not rest on a very solid basis, since, as demonstrated for example in this study (PMID: 22949505), at least yeast Uba1 forms a disulfide-linked complex with Cdc34. Another study documenting the formation of a disulfide-linked complex between Uba1 and an E2 enzyme, in this case, Rad6, (PMID: 35613580) is even cited by the authors. If the authors want to make the argument that Uba1 does not form corresponding E1-E2 complexes, they need to repeat their experiments with a representative panel of human E2 enzymes and the two enzymes employed in the aforementioned studies (Cdc34 and Rad6) or, more precisely, their human counterparts represent obvious starting points. Depending on the outcome of these studies the experiments with the CCL mutants need to be revisited.

Reviewer #3 (Public review):

Summary:

In this manuscript, "Elucidating the mechanism underlying UBA7-UBE2L6 disulfide complex formation", Chen et al. describe the mechanism of spontaneous disulfide bond formation between the active site cysteines of UBA7 and UBE2L6. Employing state-of-the-art biochemistry, cryo-EM, and HDX mass spec approaches, the authors provide insights into how this mechanism occurs in UBA7/UBE2L6 but not in related ubiquitin enzymes. A central conclusion of the study is that the length of the catalytic cysteine loop (CCL) in UBA7 is insufficient to block access to the E1's catalytic cysteine, thereby facilitating UBE2L6 disulfide formation. In contrast, the CCL of UBA1 is sufficiently long and shields its catalytic cysteine, preventing access to the Ub E2 enzymes. In addition to the CCL, the authors also show that UBA7's specificity and strong binding affinity for UBE2L6 help promote this disulfide-linked E1-E2 complex.

Strengths:

The data within in manuscript is interesting and significantly contributes to our understanding of the mechanisms of the ISG15 conjugation pathway. Moreover, the biochemical and structural experiments were performed at an exceptionally high level and the data throughout the manuscript is convincing.

Weaknesses:

It is not clear whether this regulatory mechanism occurs in a biological context (e.g., during IFN signaling or oxidative stress). However, this weakness is somewhat offset by the last experiment of the manuscript which demonstrates the existence of UBA7-UBE2L6 disulfide complex formation in cells under overexpression conditions. If the authors could expand upon this finding, as outlined below it would further improve their study.

Reviewer #1 (Public review):

Summary:

The present work studies the coevolution of HIV-1 and the immune response in clinical patient data. Using the Marginal Path Likelihood (MPL) framework, they infer selection coefficients for HIV mutations from time-series data of virus sequences as they evolve in a given patient.

Strengths:

The authors analyze data from two human patients, consisting of HIV population sequence samples at various points in time during the infection. They infer selection coefficients from the observed changes in sequence abundance using MPL. Most beneficial mutations appear in viral envelop proteins. The authors also analyze SHIV samples in rhesus macaques, and find selection coefficients that are compatible with those found in the corresponding human samples.

The manuscript is well-written and organized.

Weaknesses:

The MPL method used by the authors considers only additive effects of mutations, thus ignoring epistasis.

Although the evolution of broadly neutralizing antibodies (bnAbs) is a motivating question in the introduction and discussion sections (and the title), the relevance of the analysis and results to better understanding how bnAbs arise is not clear. The only result presented in direct connection to bnAbs is Figure 6.

Questions or suggestions for further discussion:

I list here a number of points for which I believe the paper would benefit if additional discussion/results were included.

The MPL method used by the authors considers only additive effects of mutations, thus ignoring epistasis. In Sohail et al (2022) MBE 39(10), p. msac199 (https://doi.org/10.1093/molbev/msac199) an extension of MPL is developed allowing one to infer epistasis. Can the authors comment on why this was not attempted here?

I presume one possible reason is that epistasis inference requires considerably more computational effort (and more data). However, since the authors find most beneficial mutations occurring in Env, perhaps restricting the analysis to Env genes only (e.g. the trimer shown in Figure 2) can lead to tractable inference of epistasis within this segment (instead of the full genome).

Do the authors find correlations in the inferred selection coefficients of the two samples CH505 and CH848? I could not find any discussion of this in the manuscript. Only correlations between Humans and RM are discussed.

Reviewer #2 (Public review):

Summary

This paper combines a biological topic of interest with the demonstration of important theoretical/methodological advances. Fitness inference is the foundation of the quantitative analysis of adapting systems. It is a hard and important problem and this paper highlights a compelling approach (MPL) first presented in (1) and refined in (2), roughly summarized in equation 12.

(1) Sohail, M. S., Louie, R. H., McKay, M. R. & Barton, J. P. Mpl resolves genetic linkage in fitness inference from complex evolutionary histories. Nature biotechnology 39, 472-479 (2021).<br /> (2) Shimagaki, K. & Barton, J. P. Bézier interpolation improves the inference of dynamical models from data. Physical Review E 107, 024116 (2023).

The authors find that positive selection shapes the variable regions of env in shared patterns across two patient donors. The patterns of positive selection are interesting in and of themselves, they confirm the intuition that hyper-variation in env is the result of immune evasion rather than a broadly neutral landscape (flatness). They show that the immune evasion patterns due to CD8 T and naive B-cell selection are shared across patients. Furthermore, they suggest that a particular evolutionary history (larger flux to high fitness states) is associated with bNAb emergence. Mimicking this evolutionary pattern in vaccine design may help us elicit bNAbs in patients in the future.

There is a lot of information to be found in the full fitness landscape of env. The enormous strength of reversion-to-consensus in the patterns is a known pattern of HIV post-infection populations but they are nicely quantified here. Agreement between SHIV and HIV evolution is shown. They find selection is larger for autologous antibodies than the bNAbs themselves (perhaps bNAbs are just too small a component of the host response to drive the bulk of selection?), and that big fitness increases precede antibody breadth in rhesus macaques, suggesting that this fitness increase is the immune challenge required to draw forth a bNAb. This is all of high interest to HIV researchers.

Strength of evidence

One limitation is, of course, that the fitness model is constant in time when the immune challenge is variable and changing. This simplification may complicate some interpretations.

Equation 12 in the methods is really a beautiful tool because it is so simple, but accounts for linkage and can be solved precisely even in the presence of detailed mutational and selection models. However, the reliance on incomplete observations of the frequency leads to complications that must be carefully (re)addressed here.

For instance, the consistent finding of strong selection in hypervariable regions is biologically intuitive but so striking, that I worry that it might be the result of a bias for selection in high entropy regions. Mutational and covariance terms in equation 12 might be underestimated, due to finite sampling effect in highly diverse populations. Sampling effects lead to zeros in x(t) when actual frequency zeros might be rare at the population sizes of HIV viral loads and mutation rates. Both mutational flux and C underestimation will bias selection upward in eq. 12. The prior papers (1) and (2) seem to show robustness to finite sampling effects, but, again, more care needs to be shown that this robustness transfers to the amino acid inference under these conditions. That synonymous sites are rarely selected for in the nucleotide level is a good sign, and it may be a matter of simply fully explaining the amino-acid level model.

Uncertainty propagates to the later parts of the paper, eg. HIV and SIV shared patterns might be the result of shared biases in the method application. However, this worry does not extend to the apples-to-apples comparison of fitness trajectories across individuals (Figures 5 and 6) which I think are robust (for these sample sizes). The timing evidence is slightly weakened by the fact that bNAb detection is different from bNAb presence and the possibility that fitness increases occurred after the bNAbs appeared remains. Still, their conclusion is plausible and fits in with the other observations which form a coherent and compelling picture.

Overall this is a convincing paper, part of a larger admirable project of accurately inferring complete fitness landscapes.

Reviewer #3 (Public review):

Summary:

Shimagaki et al. investigate the virus-antibody coevolutionary processes that drive the development of broadly neutralizing antibodies (bnAbs). The study's primary goal is to characterize the evolutionary dynamics of HIV-1 within hosts that accompany the emergence of bnAbs, with a particular focus on inferring the landscape of selective pressures shaping viral evolution. To assess the generality of these evolutionary patterns, the study extends its analysis to rhesus macaques (RMs) infected with simian-human immunodeficiency viruses (SHIV) incorporating HIV-1 Env proteins derived from two human individuals.

Strengths:

A key strength of the study is its rigorous assessment of the similarity in evolutionary trajectories between humans and macaques. This cross-species comparison is particularly compelling, as it quantitatively establishes a shared pattern of viral evolution using a sophisticated inference method. The finding that similar selective pressures operate in both species adds robustness to the study's conclusions and suggests broader biological relevance.

Weaknesses:

However, the study has some limitations. The most significant weakness is that the authors do not sufficiently discuss the implications of the observed similarities. While the identification of shared evolutionary patterns (e.g., Figure 5) is intriguing, the study would benefit from a more explicit discussion of what these findings mean for instance, in the context of HIV vaccine design, immunotherapy, or fundamental viral-host interactions. Even speculative interpretations could provide valuable insights into the broader significance of these results.

A secondary, albeit less critical, limitation is the placement of methodological details in the Supplementary Information. While it is understandable that the authors focus on results in the main text - especially since the methodology is not novel and has been previously described in earlier publications - some readers might benefit from a more thorough presentation of the method within the main paper.

Conclusions:

Overall, the study presents a compelling analysis of HIV-1 evolution and its parallels in SHIV-infected macaques. While the quantitative comparison between species is a notable contribution, a deeper discussion of its broader implications would strengthen the paper's impact.

Reviewer #1 (Public review):

Summary:

The manuscript by Shi et al, has utilized multiple imaging datasets and one set of samples for analyzing serum EV-miRNAs & EV-RNAs to develop an EV miRNA signature associated with disease-relevant radiomics features for early diagnosis of pancreatic cancer. CT imaging features (in two datasets (UMMD & JHC and WUH) were derived from pancreatic benign disease patients vs pancreatic cancer cases), while circulating EV miRNAs were profiled from samples obtained from a different center (DUH). The EV RNA signature from external public datasets (GSE106817, GSE109319, GSE113486, GSE112264) were analyzed for differences in healthy controls vs pancreatic cancer cases. The miRNAs were also analyzed in the TCGA tissue miRNA data from normal adjacent tissue vs pancreatic cancer.

Strengths:

The concept of developing EV miRNA signatures associated with disease relevant radiomics features is a strength.

Weaknesses:

While the overall concept of developing EV miRNA signature associated with radiomics features is interesting, the findings reported are not convincing for the reasons outlined below:

(1) Discrepant datasets for analyzing radiomic features with EV-miRNAs: It is not justified how CT images (UMMD & JHC and WUH) and EV-miRNAs (DUH) on different subjects and centers/cohorts shown in Figures 1 &2 were analyzed for association. It is stated that the samples were matched according to age but there is no information provided for the stages of pancreatic cancer and the kind of benign lesions analyzed in each instance.

(2) The study is focused on low-abundance miRNAs with no adequate explanation of the selection criteria for the miRNAs analyzed.

(3) While EV-miRNAs were profiled or sequenced (not well described in the Methods section) with two different EV isolation methods, the authors used four public datasets of serum circulating miRNAs to validate the findings. It would be better to show the expression of the three miRNAs in the additional dataset(s) of EV-miRNAs and compare the expressions of the three EV-miRNAs in pancreatic cancer with healthy and benign disease controls.

(4) It is not clear how the 12 EV-miRNAs in Figure 4C were identified.

(5) Box plots in Figures 4D-F and G-I of three miRNAs in serum and tissue should show all quantitative data points.

(6) What is the GBM model in Figure 5?

(7) What are the AUCs of individual EV-miRNAs integrated as a panel of three EV-miRNAs?

(8) The authors could have compared the performance of CA19-9 with that of the three EV-miRNAs.

(9) How was the diagnostic performance of the three EV-miRNAs in the two molecular subtypes identified in Figure 6&7? Do the C1 & C2 clusters correlate with the classical/basal subtypes, staging, and imaging features?

Reviewer #2 (Public review):

Summary:

This study investigates a low abundance microRNA signature in extracellular vesicles to subtype pancreatic cancer and for early diagnosis. There are several major questions that need to be addressed. Numerous minor issues are also present.

Strengths:

The authors did a comprehensive job with numerous analyses of moderately sized cohorts to describe the clinical and translational significance of their miRNA signature.

Weaknesses:

There are multiple weaknesses of this study that should be addressed:

(1) The description of the datasets in the Materials and Methods lacks details. What were the benign lesions from the various hospital datasets? What were the healthy controls from the public datasets? No pancreatic lesions? No pancreatic cancer? Any cancer history or other comorbid conditions? Please define these better.

(2) It is unclear how many of the controls and cases had both imaging for radiomics and blood for biomarkers.

(3) The authors should define the imaging methods and protocols used in more detail. For the CT scans, what slice thickness? Was a pancreatic protocol used? What phase of contrast is used (arterial, portal venous, non-contrast)? Any normalization or pre-processing?

(4) Who performed the segmentation of the lesions? An experienced pancreatic radiologist? A student? How did the investigators ensure that the definition of the lesions was performed correctly? Raidomics features are often sensitive to the segmentation definitions.

(5) Figure 1 is full of vague images that do not convey the study design well. Numbers from each of the datasets, a summary of what data was used for training and for validation, definitions of all of the abbreviations, references to the Roman numerals embedded within the figure, and better labeling of the various embedded graphs are needed. It is not clear whether the graphs are real results or just artwork to convey a concept. I suspect that they are just artwork, but this remains unclear.

(6) The DF selection process lacks important details. Please reference your methods with the Boruta and Lasso models. Please explain what machine learning algorithms were used. There is a reference in the "Feature selection.." section of "the model formula listed below" but I do not see a model formula below this paragraph.

(7) In Figure 2, more quantitative details are needed. How are patients dichotomized into non-obese and obese? What does alcohol/smoking mean? Is it simply no to both versus one or the other as yes? These two risk factors should be separated and pack years of smoking should be reported. The details of alcohol use should also be provided. Is it an alcohol abuse history? Any alcohol use, including social drinking? Similarly, "diabetes" needs to be better explained. Type I, type II, type 3c? P values should be shown to demonstrate any statistically significant differences in the proportions of the patients from one dataset to another.

(8) In the section "Different expression radiomic features between pancreatic benign lesions and aggressive tumors", there is a reference to "MUJH" for the first time. What is this? There is also the first reference to "aggressive tumors" in the section. Do the authors just mean the cases? Otherwise there is no clear definition of "aggressive" (vs. indolent) pancreatic cancer. This terminology of tumor "aggressiveness" either needs to be removed or better defined.

(9) Figure 3 needs to have the specific radiomic features defined and how these features were calculated. Labeling them as just f1, f2, etc is not sufficient for another group to replicate the results independently.

(10) It is not clear what Figure 4A illustrates as regards model performance. What do the different colors represent, and what are the models used here? This is very confusing.

(11) Figure 5 shows results for many more model runs than the described 10, please explain what you are trying to convey with each row. What are "Test A" and "Test B"? There is no description in the manuscript of what these represent. In the figure caption, there is a reference to "our center data" which is not clear. Be more specific about what that data is.

(12) Figure 6 describes the subtypes identified in this study, but the authors do not show a multi-variable cox proportional hazards model to show that this subtype classification independently predicts DFS and OS when incorporating confounding variables. This is essential to show the subtypes are clinically relevant. In particular, the authors need to account for the stage of the patients, and receipt of chemotherapy, surgery, and radiation. If surgery was done, we need to know whether they had R1 or R0 resection. The details about the years in which patients were included is also important.

(13) How do these subtypes compare to other published subtypes?

Reviewer #3 (Public review):

Summary:

The authors appear to be attempting to identify which patients with benign lesions will progress to cancer using a liquid biomarker. They used radiomics and EV miRNAs in order to assess this.

Strengths:

It is a strength that there are multiple test datasets. Data is batch-corrected. A relatively large number of patients is included. Only 3 miRNAs are needed to obtain their sensitivity and specificity scores.

Weaknesses:

This manuscript is not clearly written, making interpretation of the quality and rigor of the data very difficult. There is no indication from the methods that the patients in their cohorts who are pancreatic cancer patients (from the CT images) had prior benign lesions, limiting the power of their analysis. The data regarding the cluster subtypes is very confusing. There is no discussion or comparison if these two clusters are just representing classical and basal subtypes (which have been well described).

Reviewer #1 (Public review):

Summary:

Dad et al. explored the roles of cytosolic carboxypeptidase 5（CCP5）in the development of ependymal multicilia in the brain. CCP family are erasers of polyglutamylation of ciliary-axoneme microtubules. The authors generated a new mutant mouse of Agbl5 gene, which encodes CCP5, with deletion of its N-terminus and partial carboxypeptidase (CP) domain (named AGBL5M1/M1).

Strengths:

The mutant mice revealed lethal hydrocephalus due to degeneration of ependymal multicilia. Interestingly, this is in contrast with the phenotype of Agbl5 mutants with disruption solely in the CP domain of CCP5 (named AGBL5M2/M2) that did not develop hydrocephalus despite increased glutamylation levels in ependymal cilia as observed for AGBL5M1/M1 mutants. The study has been well-performed and the findings suggest a unique function of the N-domain of CCP5 in ependymal multicilia stability.

Weaknesses:

The content of this article is relatively descriptive and lacks molecular insights.

Reviewer #2 (Public review):

Summary:

This study analyzed the consequences of Agbl5 mutation on ependymal cell development and function. The authors first characterize their mutant mouse line reporting a reduced lifespand and severe hydrocephalus. Next, they report a defect in ependymal cell cilia number and motility. They provide evidence for impaired basal body organisation and cilia glutamylation.

Strengths:

Description of a mutant mouse which implicates Cytosolic Carboxypeptidase 5 (the product of Agbl5 gene) for proper ependymal cells.

Weaknesses:

Description of phenotype is incomplete:

- Figure 3G - the sequence from the movie is not really informative. Providing beating frequencies as quantification of the data would be more informative.

- Figure 3 - the quantification of actin network would strengthen the message.

- Lines 219 -220 - the authors conclude «Taken together, in Agbl5M1/M1 ependymal cells, the expression of genes promoting multiciliogenesis were not impaired but certain proteins associated with differentiated ependymal cells are not properly expressed». However, they do not assess gene but protein expression (IF). In addition, their quantification shows differences in the number of FoxJ1 positive cells which indeed is an impaired expression.

- Microtubules are involved in the local organization of ciliary basal bodies (see Werner et al., Vladar et al.,2011; Boutin et al., 2014). It would be interesting for the authors to check whether the subapical network of microtubules is glutamylated or not during ependymal cell differentiation and how this network is affected in their mutants.

- Showing the data mentioned in the discussion on Cep110 would be a nice addition to the paper.

- Line 354: "The latter serves as a component of tissue polarity that is required for asymmetric PCP protein localization in each cell (Boutin et al., 2014; Vladar et al., 2012)." The cited reference did not demonstrate that this microtubule network is required for asymmetric PCP localization.

Reviewer #3 (Public review):

Summary:

The authors developed a new Agbl5 KO allele, extending the deletion to the N-terminus of CCP5 to explore its function in mouse ependymal cells.

Strengths:

They show that the KO mice exhibit severe hydrocephalus due to disorganized and mislocated basal bodies. Additionally, they present evidence of both impaired beating coordination and a reduction in ciliary beating.

Weaknesses:

The manuscript is well-written but lacks specific interpretations of the results presented. Further experiments are needed to be fully convincing.

Reviewer #1 (Public review):

Summary:

This manuscript describes a series of lab and field experiments to understand the role of tadpole transport in shaping the microbiome of poison frogs in early life. The authors conducted a cross-foster experiment in which R. variabilis tadpoles were carried by adults of their own species, carried by adults of another frog species, or not carried at all. After being carried for 6 hours, tadpole microbiomes resembled those of their caregiving species. Next, the authors reported higher microbiome diversity in tadpoles of two species that engage in transport-based parental care compared to one species that does not. Finally, they collected tadpoles either from the backs of an adult (i.e., they had recently been transported) or from eggs (i.e., not transported) but did not find significant overlap in microbiome composition between transported tadpoles and their parents.

Strengths:

The cross-foster experiment and the field experiment that reared transported and non-transported tadpoles are creative ways to address an important question in animal microbiome research. Together, they imply a small role for parental care in the development of the tadpole microbiome. The manuscript is generally well-written and easy to understand.

Weaknesses:

(1) Developmental time series:

It was not entirely clear how this experiment relates to the rest of the manuscript, as it does not compare any effects of transport within or across species.

(2) Cross-foster experiment:

The "heterospecific transport" tadpoles were manually brushed onto the back of the surrogate frog, while the "biological transport" tadpoles were picked up naturally by the parent. It is a little challenging to interpret the effect of caregiver species since it is conflated with the method of attachment to the parent. I noticed that the uptake of Os-associated microbes by Os-transported tadpoles seemed to be higher than the uptake of Rv-associated microbes by Rv-associated tadpoles (comparing the second box from the left to the rightmost boxplot in panel S2C). Perhaps this could be a technical artifact if manual attachment to Os frogs was more efficient than natural attachment to Rv frogs.

I was also surprised to see so much of the tadpole microbiome attributed to Os in tadpoles that were not transported by Os frogs (25-50% in many cases). It suggests that SourceTracker may not be effectively classifying the taxa.

(3) Cross-species analysis:

Like the developmental time series, this analysis doesn't really address the central question of the manuscript. I don't think it is fair for the authors to attribute the difference in diversity to parental care behavior, since the comparison only includes n=2 transporting species and n=1 non-transporting species that differ in many other ways. I would also add that increased diversity is not necessarily an expectation of vertical transmission. The similarity between adults and tadpoles is likely a more relevant outcome for vertical transmission, but the authors did not find any evidence that tadpole-adult similarity was any higher in species with tadpole transport. In fact, tadpoles and adults were more similar in the non-transporting species than in one of the transporting species (lines 296-298), which seems to directly contradict the authors' hypothesis. I don't see this result explained or addressed in the Discussion.

(4) Field experiment:

The rationale and interpretation of the genus-level network are not clear, and the figure is not legible. What does it mean to "visualize the microbial interconnectedness" or to be a "central part of the community"? The previous sentences in this paragraph (lines 337-343) seem to imply that transfer is parent-specific, but the genus-level network is based on the current adult frogs, not the previous generation of parents that transported them. So it is not clear that the distribution or co-distribution of these taxa provides any insight into vertical transmission dynamics.

Reviewer #2 (Public review):

Summary:

Here, Fischer et al. attempt to understand the role of parental care, specifically the transport of offspring, in the development of the amphibian microbiome. The amphibian microbiome is an important study system due to its association with host health and disease outcomes. This study provides vertical transfer of bacteria through parental transport of tadpoles as a mechanism influencing tadpole microbiome composition. This paper gives insight into the relative roles of the environment, species, and parental care in determining microbiome composition in amphibians.

The authors determine the time of bacterial colonization during tadpole development using PCR, observing that tadpoles were not colonized by bacteria prior to hatching from the vitelline membrane. By doing this, the impact of transport can be more accurately assessed in their laboratory experiments. The authors found that caregiver species influenced community composition, with transported tadpoles sharing a greater proportion of their skin communities with the transporting species.

In a comparison of three sympatric amphibian species that vary in their reproductive strategies, the authors found that tadpole community diversity was not reflective of habitat diversity, but may be associated with the different reproductive strategies of each species. Parental care explained some of the variance of tadpole microbiomes between species, however, transportation by conspecific adults did not lead to more similar microbiomes between tadpoles and adults compared to species that do not exhibit parental transport.

I did not find any major weaknesses in my review of this paper. The work here could potentially benefit from absolute abundance levels for shared ASVs between adults and tadpoles to more thoroughly understand the influences of vertical transmission that might be masked by relative abundance counts. This would only be a minor improvement as I think the conclusions from this work would likely remain the same, however.

Reviewer #1 (Public review):

Summary:

The novel advance by Wang et al is in the demonstration that, relative to a standard extinction procedure, the retrieval-extinction procedure more effectively suppresses responses to a conditioned threat stimulus when testing occurs just minutes after extinction. The authors provide some solid evidence to show that this "short-term" suppression of responding involves engagement of the dorsolateral prefrontal cortex.

Strengths:

Overall, the study is well-designed and the results are potentially interesting. There are, however, a few issues in the way that it is introduced and discussed. Some of the issues concern clarity of expression/communication. However, others relate to a theory that could be used to help the reader understand why the results should have come out the way that they did. More specific comments and questions are presented below.

Weaknesses:

INTRODUCTION & THEORY

(1) It is difficult to appreciate why the first trial of extinction in a standard protocol does NOT produce the retrieval-extinction effect. This applies to the present study as well as others that have purported to show a retrieval-extinction effect. The importance of this point comes through at several places in the paper. E.g., the two groups in Study 1 experienced a different interval between the first and second CS extinction trials; and the results varied with this interval: a longer interval (10 min) ultimately resulted in less reinstatement of fear than a shorter interval. Even if the different pattern of results in these two groups was shown/known to imply two different processes, there is nothing in the present study that addresses what those processes might be. That is, while the authors talk about mechanisms of memory updating, there is little in the present study that permits any clear statement about mechanisms of memory. The references to a "short-term memory update" process do not help the reader to understand what is happening in the protocol.

In reply to this point, the authors cite evidence to suggest that "an isolated presentation of the CS+ seems to be important in preventing the return of fear expression." They then note the following: "It has also been suggested that only when the old memory and new experience (through extinction) can be inferred to have been generated from the same underlying latent cause, the old memory can be successfully modified(Gershman et al., 2017). On the other hand, if the new experiences are believed to be generated by a different latent cause, then the old memory is less likely to be subject to modification. Therefore, the way the 1stand 2ndCS are temporally organized (retrieval-extinction or standard extinction) might affect how the latent cause is inferred and lead to different levels of fear expression from a theoretical perspective." This merely begs the question: why might an isolated presentation of the CS+ result in the subsequent extinction experiences being allocated to the same memory state as the initial conditioning experiences? This is not yet addressed in any way.

(2) The discussion of memory suppression is potentially interesting but, in its present form, raises more questions than it answers. That is, memory suppression is invoked to explain a particular pattern of results but I, as the reader, have no sense of why a fear memory would be better suppressed shortly after the retrieval-extinction protocol compared to the standard extinction protocol; and why this suppression is NOT specific to the cue that had been subjected to the retrieval-extinction protocol.

(3) Relatedly, how does the retrieval-induced forgetting (which is referred to at various points throughout the paper) relate to the retrieval-extinction effect? The appeal to retrieval-induced forgetting as an apparent justification for aspects of the present study reinforces points 2 and 3 above. It is not uninteresting but lacks clarification/elaboration and, therefore, its relevance appears superficial at best.

(4) I am glad that the authors have acknowledged the papers by Chalkia, van Oudenhove & Beckers (2020) and Chalkia et al (2020), which failed to replicate the effects of retrieval-extinction reported by Schiller et al in Reference 6. The authors have inserted the following text in the revised manuscript: "It should be noted that while our long-term amnesia results were consistent with the fear memory reconsolidation literature, there were also studies that failed to observe fear prevention (Chalkia, Schroyens, et al., 2020; Chalkia, Van Oudenhove, et al., 2020; Schroyens et al., 2023). Although the memory reconsolidation framework provides a viable explanation for the long-term amnesia, more evidence is required to validate the presence of reconsolidation, especially at the neurobiological level (Elsey et al., 2018). While it is beyond the scope of the current study to discuss the discrepancies between these studies, one possibility to reconcile these results concerns the procedure for the retrieval-extinction training. It has been shown that the eligibility for old memory to be updated is contingent on whether the old memory and new observations can be inferred to have been generated by the same latent cause (Gershman et al., 2017; Gershman and Niv, 2012). For example, prevention of the return of fear memory can be achieved through gradual extinction paradigm, which is thought to reduce the size of prediction errors to inhibit the formation of new latent causes (Gershman, Jones, et al., 2013). Therefore, the effectiveness of the retrieval-extinction paradigm might depend on the reliability of such paradigm in inferring the same underlying latent cause." Firstly, if it is beyond the scope of the present study to discuss the discrepancies between the present and past results, it is surely beyond the scope of the study to make any sort of reference to clinical implications!!! Secondly, it is perfectly fine to state that "the effectiveness of the retrieval-extinction paradigm might depend on the reliability of such paradigm in inferring the same underlying latent cause..." This is not uninteresting, but it also isn't saying much. Minimally, I would expect some statement about factors that are likely to determine whether one is or isn't likely to see a retrieval-extinction effect, grounded in terms of this theory.

CLARIFICATIONS, ELABORATIONS, EDITS

(5) Some parts of the paper are not easy to follow. Here are a few examples (though there are others):

(a) In the abstract, the authors ask "whether memory retrieval facilitates update mechanisms other than memory reconsolidation"... but it is never made clear how memory retrieval could or should "facilitate" a memory update mechanism.

(b) The authors state the following: "Furthermore, memory reactivation also triggers fear memory reconsolidation and produces cue specific amnesia at a longer and separable timescale (Study 2, N = 79 adults)." Importantly, in study 2, the retrieval-extinction protocol produced a cue-specific disruption in responding when testing occurred 24 hours after the end of extinction. This result is interesting but cannot be easily inferred from the statement that begins "Furthermore..." That is, the results should be described in terms of the combined effects of retrieval and extinction, not in terms of memory reactivation alone; and the statement about memory reconsolidation is unnecessary. One can simply state that the retrieval-extinction protocol produced a cue-specific disruption in responding when testing occurred 24 hours after the end of extinction.

(c) The authors also state that: "The temporal scale and cue-specificity results of the short-term fear amnesia are clearly dissociable from the amnesia related to memory reconsolidation, and suggest that memory retrieval and extinction training trigger distinct underlying memory update mechanisms." ***The pattern of results when testing occurred just minutes after the retrieval-extinction protocol was different to that obtained when testing occurred 24 hours after the protocol. Describing this in terms of temporal scale is unnecessary; and suggesting that memory retrieval and extinction trigger different memory update mechanisms is not obviously warranted. The results of interest are due to the combined effects of retrieval+extinction and there is no sense in which different memory update mechanisms should be identified with the different pattern of results obtained when testing occurred either 30 min or 24 hours after the retrieval-extinction protocol (at least, not the specific pattern of results obtained here).

(d) The authors state that: "We hypothesize that the labile state triggered by the memory retrieval may facilitate different memory update mechanisms following extinction training, and these mechanisms can be further disentangled through the lens of temporal dynamics and cue-specificities." *** The first part of the sentence is confusing around usage of the term "facilitate"; and the second part of the sentence that references a "lens of temporal dynamics and cue-specificities" is mysterious. Indeed, as all rats received the same retrieval-extinction exposures in Study 2, it is not clear how or why any differences between the groups are attributed to "different memory update mechanisms following extinction".

DATA

(6A) The eight participants who were discontinued after Day 1 in Study 1 were all from the no reminder group. The authors should clarify how participants were allocated to the two groups in this experiment so that the reader can better understand why the distribution of non-responders was non-random (as it appears to be).

(6B) Similarly, in study 2, of the 37 participants that were discontinued after Day 2, 19 were from Group 30 min and 5 were from Group 6 hours. The authors should comment on how likely these numbers are to have been by chance alone. I presume that they reflect something about the way that participants were allocated to groups: e.g., the different groups of participants in studies 1 and 2 could have been run at quite different times (as opposed to concurrently). If this was done, why was it done? I can't see why the study should have been conducted in this fashion - this is for myriad reasons, including the authors' concerns re SCRs and their seasonal variations.

(6C) In study 2, why is responding to the CS- so high on the first test trial in Group 30 min? Is the change in responding to the CS- from the last extinction trial to the first test trial different across the three groups in this study? Inspection of the figure suggests that it is higher in Group 30 min relative to Groups 6 hours and 24 hours. If this is confirmed by the analysis, it has implications for the fear recovery index which is partly based on responses to the CS-. If not for differences in the CS- responses, Groups 30 min and 6 hours are otherwise identical. That is, the claim of differential recovery to the CS1 and CS2 across time may simply an artefact of the way that the recovery index was calculated. This is unfortunate but also an important feature of the data given the way in which the fear recovery index was calculated.

(6D) The 6 hour group was clearly tested at a different time of day compared to the 30 min and 24 hour groups. This could have influenced the SCRs in this group and, thereby, contributed to the pattern of results obtained.

(6E) The authors find different patterns of responses to CS1 and CS2 when they were tested 30 min after extinction versus 24 h after extinction. On this basis, they infer distinct memory update mechanisms. However, I still can't quite see why the different patterns of responses at these two time points after extinction need to be taken to infer different memory update mechanisms. That is, the different patterns of responses at the two time points could be indicative of the same "memory update mechanism" in the sense that the retrieval-extinction procedure induces a short-term memory suppression that serves as the basis for the longer-term memory suppression (i.e., the reconsolidation effect). My pushback on this point is based on the notion of what constitutes a memory update mechanism; and is motivated by what I take to be a rather loose use of language/terminology in the reconsolidation literature and this paper specifically (for examples, see the title of the paper and line 2 of the abstract).

Reviewer #2 (Public review):

Summary

The study investigated whether memory retrieval followed soon by extinction training results in a short-term memory deficit when tested - with a reinstatement test that results in recovery from extinction - soon after extinction training. Experiment 1 documents this phenomenon using a between-subjects design. Experiment 2 used a within-subject control and saw that the effect is also observed in a control condition. In addition, it also revealed that if testing is conducted 6 hours after extinction, there is not effect of retrieval prior to extinction as there is recovery from extinction independently of retrieval prior to extinction. A third Group also revealed that retrieval followed by extinction attenuates reinstatement when the test is conducted 24 hours later, consistent with previous literature. Finally, Experiment 3 used continuous theta-burst stimulation of the dorsolateral prefrontal cortex and assessed whether inhibition of that region (vs a control region) reversed the short-term effect revealed in Experiments 1 and 2. The results of control groups in Experiment 3 replicated the previous findings (short-term effect), and the experimental group revealed that these can be reversed by inhibition of the dorsolateral prefrontal cortex.

Strengths

The work is performed using standard procedures (fear conditioning and continuous theta-burst stimulation) and there is some justification of the sample sizes. The results replicate previous findings - some of which have been difficult to replicate and this needs to be acknowledged - and suggest that the effect can also be observed in a short-term reinstatement test.

The study establishes links between the memory reconsolidation and retrieval-induced forgetting (or memory suppression) literatures. The explanations that have been developed for these are distinct and the current results integrate these, by revealing that the DLPFC activity involved in retrieval-extinction short-term effect. There is thus some novelty in the present results, but numerous questions remain unaddressed.

Weakness

The fear acquisition data is converted to a differential fear SCR and this is what is analysed (early vs late). However, the figure shows the raw SCR values for CS+ and CS- and therefore it is unclear whether acquisition was successful (despite there being an "early" vs "late" effect - no descriptives are provided).

In Experiment 1 (Test results) it is unclear whether the main conclusion stems from a comparison of the test data relative to the last extinction trial ("we defined the fear recovery index as the SCR difference between the first test trial and the last extinction trial for a specific CS") or the difference relative to the CS- ("differential fear recovery index between CS+ and CS-"). It would help the reader assess the data if Fig 1e presents all the indexes (both CS+ and CS-). In addition, there is one sentence which I could not understand "there is no statistical difference between the differential fear recovery indexes between CS+ in the reminder and no reminder groups (P=0.048)". The p value suggests that there is a difference, yet it is not clear what is being compared here. Critically, any index taken as a difference relative to the CS- can indicate recovery of fear to the CS+ or absence of discrimination relative to the CS-, so ideally the authors would want to directly compare responses to the CS+ in the reminder and no-reminder groups. In the absence of such comparison, little can be concluded, in particular if SCR CS- data is different between groups. The latter issue is particularly relevant in Experiment 2, in which the CS- seems to vary between groups during the test and this can obscure the interpretation of the result.

In experiment 1, the findings suggest that there is a benefit of retrieval followed by extinction in a short-term reinstatement test. In Experiment 2, the same effect is observed to a cue which did not undergo retrieval before extinction (CS2+), a result that is interpreted as resulting from cue-independence, rather than a failure to replicate in a within-subjects design the observations of Experiment 1 (between-subjects). Although retrieval-induced forgetting is cue-independent (the effect on items that are suppressed [Rp-] can be observed with an independent probe), it is not clear that the current findings are similar, and thus that the strong parallels made are not warranted. Here, both cues have been extinguished and therefore been equally exposed during the critical stage.

The findings in Experiment 2 suggest that the amnesia reported in Experiment 1 is transient, in that no effect is observed when the test is delayed by 6 hours. The phenomena whereby reactivated memories transition to extinguished memories as a function of the amount of exposure (or number of trials) is completely different from the phenomena observed here. In the former, the manipulation has to do with the number of trials (or total amount of time) that the cues are exposed. In the current Experiment 2, the authors did not manipulate the number of trials but instead the retention interval between extinction and test. The finding reported here is closer to a "Kamin effect", that is the forgetting of learned information which is observed with intervals of intermediate length (Baum, 1968). Because the Kamin effect has been inferred to result from retrieval failure, it is unclear how this can be explained here. There needs to be much more clarity on the explanations to substantiate the conclusions.<br /> There are many results (Ryan et al., 2015) that challenge the framework that the authors base their predictions on (consolidation and reconsolidation theory), therefore these need to be acknowledged. These studies showed that memory can be expressed in the absence of the biological machinery thought to be needed for memory performance. The authors should be careful about statements such as "eliminate fear memores" for which there is little evidence.

The parallels between the current findings and the memory suppression literature are speculated in the general discussion, and there is the conclusion that "the retrieval-extinction procedure might facilitate a spontaneous memory suppression process". Because one of the basic tenets of the memory suppression literature is that it reflects an "active suppression" process, there is no reason to believe that in the current paradigm the same phenomenon is in place, but instead it is "automatic". In other words, the conclusions make strong parallels with the memory suppression (and cognitive control) literature, yet the phenomena that they observed is thought to be passive (or spontaneous/automatic). Ultimately, it is unclear why 10 mins between the reminder and extinction learning will "automatically" suppress fear memories. Further down in the discussion it is argued that "For example, in the well-known retrieval-induced forgetting (RIF) phenomenon, the recall of a stored memory can impair the retention of related long-term memory and this forgetting effect emerges as early as 20 minutes after the retrieval procedure, suggesting memory suppression or inhibition can occur in a more spontaneous and automatic manner". I did not follow with the time delay between manipulation and test (20 mins) would speak about whether the process is controlled or automatic. In addition, the links with the "latent cause" theoretical framework are weak if any. There is little reason to believe that one extinction trial, separated by 10 mins from the rest of extinction trials, may lead participants to learn that extinction and acquisition have been generated by the same latent cause.

Among the many conclusions, one is that the current study uncovers the "mechanism" underlying the short-term effects of retrieval-extinction. There is little in the current report that uncovers the mechanism, even in the most psychological sense of the mechanism, so this needs to be clarified. The same applies to the use of "adaptive".

Whilst I could access the data in the OFS site, I could not make sense of the Matlab files as there is no signposting indicating what data is being shown in the files. Thus, as it stands, there is no way of independently replicating the analyses reported.

The supplemental material shows figures with all participants, but only some statistical analyses are provided, and sometimes these are different from those reported in the main manuscript. For example, the test data in Experiment 1 is analysed with a two-way ANOVA with main effects of group (reminder vs no-reminder) and time (last trial of extinction vs first trial of test) in the main report. The analyses with all participants in the sup mat used a mixed two-way ANOVA with group (reminder vs no reminder) and CS (CS+ vs CS-). This makes it difficult to assess the robustness of the results when including all participants. In addition, in the supplementary materials there are no figures and analyses for Experiment 3.

One of the overarching conclusions is that the "mechanisms" underlying reconsolidation (long term) and memory suppression (short term) phenomena are distinct, but memory suppression phenomena can also be observed after a 7-day retention interval (Storm et al., 2012), which then questions the conclusions achieved by the current study.

References:

Baum, M. (1968). Reversal learning of an avoidance response and the Kamin effect. Journal of Comparative and Physiological Psychology, 66(2), 495.<br /> Chalkia, A., Schroyens, N., Leng, L., Vanhasbroeck, N., Zenses, A. K., Van Oudenhove, L., & Beckers, T. (2020). No persistent attenuation of fear memories in humans: A registered replication of the reactivation-extinction effect. Cortex, 129, 496-509.<br /> Ryan, T. J., Roy, D. S., Pignatelli, M., Arons, A., & Tonegawa, S. (2015). Engram cells retain memory under retrograde amnesia. Science, 348(6238), 1007-1013.<br /> Storm, B. C., Bjork, E. L., & Bjork, R. A. (2012). On the durability of retrieval-induced forgetting. Journal of Cognitive Psychology, 24(5), 617-629.

Comments on revisions:

The authors have revised the manuscript but most of my concerns have remained unaddressed.

(1) There are still no descriptive statistics to substantiate learning in Experiment 1.

(2) In the revised analyses, the authors now show that CS- changes in different groups (for example, Experiment 2) so this means that there is little to conclude from the differential scores because these depend on CS-. It is unclear whether the effects arise from CS+ performance or the differential which is subject to CS- variations.

(3) The notion that suppression is automatic is speculative at best

(4) It still struggle with the parallels between these findings and the "limbo" literature. Here you manipulated the retention interval, whereas in the cited studies the number of extinction (exposure) was varied. These are two completely different phenomena.

(5) My point about the data problematic for the reconsolidation (and consolidation) frameworks is that they observed memory in the absence of the brain substrates that are needed for memory to be observed. The answer did not address this. I do not understand how the latent cause model can explain this, if the only difference is the first ITI. Wouldn't participants fail to integrate extinction with acquisition with a longer ITI?

(6) The materials in the OSF site are the same as before, they haven't ben updated.

(7) Concerning supplementary materials, the robustness tests are intended to prove that you 1) can get the same results by varying the statistical models or 2) you can get the same results when you include all participants. Here authors have done both so this does not help. Also, in the rebuttal letter, they stated "Please note we did not include non-learners in these analyses " which contradicts what is stated in the figure captions "(learners + non learners)"

(8) Finally, the literature suggesting that reconsolidation interference "eliminates" a memory is not substantiated by data nor in line with current theorising, so I invite a revision of these strong claims.

Overall, I conclude that the revised manuscript did not address my main concerns.

Joint Public Review:

The central theme of the manuscript is the structure of SBPase - an enzyme central to the photosynthetic Calvin-Benson-Bassham cycle. The authors claim that the structure is first of its kind from a chlorophyte Chlamydomonas reinhardtii, a model unicellular green microalga. The authors use a number of methods like protein expression, purification, enzymatic assays, SAXS, molecular dynamics simulations and xray crystallography to resolve a 3.09 A crystal structure of the oxidized and partially reduced state. The results are supported by the claims made in the manuscript. While the structure is the first from a chlorophyte, it is not unique. Several structures of SBPase are available and a comparison has been made between the structure reported here and others that have been previously published.

Reviewer #1 (Public review):

First, the authors confirm the up-regulation of the main genes involved in the three branches of the Unfolded Protein Response (UPR) system in diet-induced obese mice in AT, observations that have been extensively reported before. Not surprisingly, IRE1a inhibition with STF led to an amelioration of the obesity and insulin resistance of the animals. Moreover, non-alcoholic fatty liver disease was also improved by the treatment. More novel are their results in terms of thermogenesis and energy expenditure, where IRE1a seems to act via activation of brown AT. Finally, mice treated with STF exhibited significantly fewer metabolically active and M1-like macrophages in the AT compared to those under vehicle conditions. Overall, the authors conclude that targeting IRE1a has therapeutical potential for treating obesity and insulin resistance.

The study has some strengths, such as the detailed characterization of the effect of STF in different fat depots and a thorough analysis of macrophage populations. However, the lack of novelty in the findings somewhat limits the study´s impact on the field.

Reviewer #3 (Public review):

Summary:

The manuscript by Wu D. et al. explores an innovative approach in immunometabolism and obesity by investigating the potential of targeting macrophage Inositol-requiring enzyme 1α (IRE1α) in cases of overnutrition. Their findings suggest that pharmacological inhibition of IRE1α could influence key aspects such as adipose tissue inflammation, insulin resistance, and thermogenesis. Notable discoveries include the identification of High-Fat Diet (HFD)-induced CD9+ Trem2+ macrophages and the reversal of metabolically active macrophages' activity with IRE1α inhibition using STF. These insights could significantly impact future obesity treatments.

Strengths:

The study's key strengths lie in its identification of specific macrophage subsets and the demonstration that inhibiting IRE1α can reverse the activity of these macrophages. This provides a potential new avenue for developing obesity treatments and contributes valuable knowledge to the field.

Weaknesses:

The research lacks an in-depth exploration of the broader metabolic mechanisms involved in controlling diet-induced obesity (DIO). Addressing this gap would strengthen the understanding of how targeting IRE1α might fit into the larger metabolic landscape.

Impact and Utility:

The findings have the potential to advance the field of obesity treatment by offering a novel target for intervention. However, further research is needed to fully elucidate the metabolic pathways involved and to confirm the long-term efficacy and safety of this approach. The methods and data presented are useful, but additional context and exploration are required for broader application and understanding.

Comments on revisions:

The authors have satisfactorily addressed all of my previous concerns.

Reviewer #1 (Public review):

Bacterial effectors that interfere with the inner molecular workings of eukaryotic host cells are of great biological significance across disciplines. On the one hand they help us to understand the molecular strategies that bacteria use to manipulate host cells. On the other hand, they can be used as research tools to reveal molecular details of the intricate workings of the host machinery that is relevant for the interaction/defence/symbiosis with bacteria. The authors investigate the function and biological impact of a rhizobial effector that interacts with and modifies, and curiously is modified by, legume receptors essential for symbiosis. The molecular analysis revealed a bacterial effectorthat cleaves a plant symbiosis signaling receptor to inhibit signaling and the host counterplay by phosphorylation via a receptor kinase. These findings have potential implications beyond bacterial interactions with plants. Bao and colleagues investigated how rhizobial effector proteins can regulate the legume root nodule symbiosis.

Bao and colleagues investigated how rhizobial effector proteins can regulate the legume root nodule symbiosis. A rhizobial effector is described to directly modify symbiosis-related signaling proteins, altering the outcome of the symbiosis. Overall, the paper presents findings that will have a wide appeal beyond its primary field.

Out of 15 identified effectors from Sinorhizobium fredii, they focus on the effector NopT, which exhibits proteolytic activity and may therefore cleave specific target proteins of the host plant. They focus on two Nod factor receptors of the legume Lotus japonicus, NFR1 and NFR5, both of which were previously found to be essential for the perception of rhizobial nod factor, and the induction of symbiotic responses such as bacterial infection thread formation in root hairs and root nodule development (Madsen et al., 2003, Nature; Tirichine et al., 2003; Nature). The authors present evidence for an interaction of NopT with NFR1 and NFR5. The paper aims to characterize the biochemical and functional consequences of these interactions and the phenotype that arises when the effector is mutated.

Evidence is presented that in vitro NopT can cleave NFR5 at its juxtamembrane region. NFR5 appears also to be cleaved in vivo, and NFR1 appears to inhibit the proteolytic activity of NopT by phosphorylating NopT. When NFR5 and NFR1 are ectopically over-expressed in leaves of the non-legume Nicotiana benthamiana, they induce cell death (Madsen et al., 2011, Plant Journal). Bao et al. found that this cell death response is inhibited by the coexpression of nopT. Mutation of nopT alters the outcome of rhizobial infection in L. japonicus. These conclusions are well supported by the data.

The presented data support the interaction of NopT with NFR1 and NFR5. In particular, there is solid support for cleavage of NFR5 by NopT (Figure 3) and the identification of NopT phosphorylation sites that inhibit its proteolytic activity (Figure 4C). Cleavage of NFR5 upon expression in N. benthamiana (Figure 3A) requires appropriate controls (inactive mutant versions), since Agrobacterium as a closely rhizobia related bacterium might increase defense related proteolytic activity in the plant host cells, and these controls are provided.

Key results from N. benthamiana appear consistent with data from recombinant protein expression in bacteria. For the analysis in the host legume L. japonicus transgenic hairy roots were included. To demonstrate that the cleavage of NFR5 occurs during the interaction in plant cells, the authors build largely on Western blots. Regardless of whether Nicotiana leaf cells or Lotus root cells are used as the test platform, the Western blots indicate that only a small proportion of NFR5 is cleaved when co-expressed with nopT, and most of the NFR5 persists in its full-length form (Figures 3A-D). The authors discuss how the loss of NFR5 function (loss of cell death, impact on symbiosis) can be explained despite this vast excess of intact NFR5, but do not further explore the impact of this ratio on downstream signaling.

Reviewer #2 (Public review):

Summary:

This manuscript presents data demonstrating NopT's interaction with Nod Factor Receptors NFR1 and NFR5 and its impact on cell death inhibition and rhizobial infection. The identification of a truncated NopT variant in certain Sinorhizobium species adds an interesting dimension to the study. These data try to bridge the gaps between classical Nod-factor-dependent nodulation and T3SS NopT effector-dependent nodulation in legume-rhizobium symbiosis. Overall, the research provides interesting insights into the molecular mechanisms underlying symbiotic interactions between rhizobia and legumes.

Strengths:

The manuscript nicely demonstrates NopT's proteolytic cleavage of NFR5, regulated by NFR1 phosphorylation, promoting rhizobial infection in L. japonicus. Intriguingly, authors also identify a truncated NopT variant in certain Sinorhizobium species, maintaining NFR5 cleavage but lacking NFR1 interaction. These findings bridge the T3SS effector with the classical Nod-factor-dependent nodulation pathway, offering novel insights into symbiotic interactions.

Weaknesses:

(1) In the previous study, when transiently expressed NopT alone in Nicotiana tobacco plants, proteolytically active NopT elicited a rapid hypersensitive reaction. However, this phenotype was not observed when expressing the same NopT in Nicotiana benthamiana (Figure 1A). Conversely, cell death and a hypersensitive reaction were observed in Figure S8. This raises questions about the suitability of the exogenous expression system for studying NopT proteolysis specificity.

(2) NFR5 Loss-of-function mutants do not produce nodules in the presence of rhizobia in lotus roots, and overexpression of NFR1 and NFR5 produces spontaneous nodules. In this regard, if the direct proteolysis target of NopT is NFR5, one could expect the NGR234's infection will not be very successful because of the Native NopT's specific proteolysis function of NFR5 and NFR1. Conversely, in Figure 5, authors observed the different results.

(3) In Figure 6E, the model illustrates how NopT digests NFR5 to regulate rhizobia infection. However, it raises the question of whether it is reasonable for NGR234 to produce an effector that restricts its own colonization in host plants.

(4) The failure to generate stable transgenic plants expressing NopT in Lotus japonicus is surprising, considering the manuscript's claim that NopT specifically proteolyzes NFR5, a major player in the response to nodule symbiosis, without being essential for plant development.

Comments on the revised version:

My concerns regarding the potential function of NopT during nodule symbiosis have been adequately addressed in the revised manuscript. Therefore, I have no further questions about this version, aside from a few minor suggestions:

(1) Please carefully check the text formatting throughout the manuscript to ensure consistency with scientific conventions and the journal's standards. For example, Line 105-117 and line119-131.<br /> (2) The term "detrimental" in line 624 may not accurately describe the function of NopT in rhizobial infection. Since the authors propose that NopT proteolytically cleaves NFR5 and suppresses NF signaling as a potential fine-tuning mechanism for legume symbiosis, a more precise term may be needed.<br /> (3) Lines 632-634 are somewhat unclear. If NopT serves as a strategy for rhizobia to evade detection by plant immunity, then knocking out NopT should, in theory, inhibit rhizobial infection. Clarification on this point would be beneficial.

Reviewer #1 (Public review):

Summary:

The authors used a subset of a very large, previously generated 16S dataset to: 1) assess age-associated features; and 2) develop a fecal microbiome clock, based on extensive longitudinal sampling of wild baboons for which near-exact chronological age is known. They further seek to understand deviation from age-expected patterns and uncover if and why some individuals have an older or younger microbiome than expected, and the health and longevity implications of such variation. Overall, the authors compellingly achieved their goals to discover age-associated microbiome features and develop a fecal microbiome clock. They also showed clear and exciting evidence for sex and rank-associated variation in the pace of gut microbiome aging and impacts of seasonality on microbiome age in females. These data add to a growing understanding of modifiers of the pace of age in primates, and links among different biological indicators of age, with implications for understanding and contextualizing human variation. However, in the current version there are gaps in the analyses with respect to the social environment, and in comparisons with other biological indicators of age. Despite this, I anticipate this work will be impactful, generate new areas of inquiry and fuel additional comparative studies.

Strengths:

The major strengths of the paper are the size and sampling depth of the study population, including ability to characterize of the social and physical environments, and the application of recent and exciting methods to characterize the microbiome clock. An additional strength was the ability of the authors to compare and contrast the relative age-predictive power of the fecal microbiome clock to other biological methods of age estimation available for the study population (dental wear, blood cell parameters, methylation data). Furthermore, the writing and support materials are clear and informative and visually appealing.

Revisions made following initial review have further improved the content and clarity.

Weaknesses:

Revisions to the manuscript clarified some of the analysis decisions and limitations regarding drawing comparisons between the microbiome clock and other metrics of biological age, and on the impact of sociality on microbiome metrics. Hopefully these interesting topics will be further addressed in forthcoming publications.

Reviewer #2 (Public review):

Summary:

Dasari et al present an interesting study investigating the use of 'microbiota age' as an alternative to other measures of 'biological age'. The study provides several curious insights into biological ageing. Although 'microbiota age' holds potential as a proxy of biological age, it comes with limitations considering the gut microbial community can be influenced various non-age related factors, and various age-related stressors may not manifest in changes in the gut microbiota.

Strengths:

The dataset this study is based on is impressive, and can reveal various insights into biological ageing and beyond. The analysis implemented is extensive and of high level.

Weaknesses:

The key weakness is the use of microbiota age instead of e.g., DNA-methylation based epigenetic age as a proxy of biological ageing, for reasons stated in the summary. DNA methylation levels can be measured from faecal samples, and as such epigenetic clocks too can be non-invasive.

In the first round of review, I provided authors a list of minor edits, which they have implemented in the revised version of the manuscript.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors sought to build upon their prior work, which suggested the presence of an outer retinal metabolic microenvironment using ex vivo and in vitro systems, by using in vivo methods and a multitude of genetic models. The authors convincingly demonstrate that the retina prefers circulating glucose to some other circulating fuel sources and that photoreceptors are the main consumers of glucose in the retina. However, the claims regarding the ability of photoreceptors to utilize lactate as a fuel source, that lactate exported specifically from photoreceptors is taken up by RPE and further utilized to support the TCA cycle in the RPE are incomplete or inadequate and would benefit from further experimentation to convince the reader of such biological processes. Considering alternative explanations and performing key experiments to confirm or refute these claims would substantially improve the impact of this study.

Strengths:

The major strengths of this study are its in vivo infusion methodologies and utilization of mouse models that are devoid of photoreceptors or are photoreceptor-specific conditional knockouts to provide convincing evidence that the retina utilizes circulating glucose to a significant degree and photoreceptors are the main consumers of glucose in the retina. These in vivo studies are complemented by ex vivo experiments in retinal explants.

Weaknesses:

While the in vivo infusion methodologies are a clear strength, not utilizing these techniques or other in vivo methodologies with the genetic models that lack photoreceptors or photoreceptor-specific proteins and not providing in vivo metabolomics data from these infusions in the RPE is a major weakness. Also, some circulating fuel sources may not get into the retina in appreciable amounts, impacting some of the authors' claims. Another major weakness is that for many of the claims noted by the authors, alternative explanations have not been considered nor have the proper experiments been conducted to fully support or refute these claims. For example, the authors claim it is photoreceptors that utilize lactate upon knockout of Glut1. However, other cells in the retina, such as Muller glia, may be the ones actually catabolizing lactate based on prior studies and enzyme expression patterns and their kinetics to support photoreceptors via the production of other metabolites from lactate. This alternative has not been considered nor have experiments been conducted to refute this possibility. Additionally, the authors claim lactate exported from photoreceptors is being taken up by RPE. The models used to support this claim lack photoreceptors, or their ability to take up glucose. None of the models specifically address lactate export from photoreceptors. Finally, the authors claim lactate exported from photoreceptors can be oxidized to TCA cycle intermediates in the RPE in vivo. No experiments specifically addressed the downstream path of lactate exported by photoreceptors in RPE TCA cycle metabolism in vivo, so this conclusion is also not well supported. Hence, the claims need to be significantly amended with an acknowledgment of potential alternatives or with some key experiments performed.

Reviewer #2 (Public review):

Hass et al. use in vivo and ex vivo mouse models to explore and validate the use of glucose and lactate by the outer retina. While the authors' conclusions are not totally novel, their work uses powerful in vivo models to validate, strengthen, and support their conclusions. This data is an important step forward in the field's understanding of retinal metabolism.

They performed in vivo metabolite tracing with 5 different fuel sources and found that glucose was the primary fuel for TCA in the retina. While performing these experiments they measured the circulating levels of the tracer metabolites to ensure steady-state labeling which aids in the interpretation of the results. Showing the levels of the labeled tracer in the retina would be a nice addition to establishing if the tracer is getting into the target tissue.

To support their conclusions that the photoreceptors are the primary consumers of glucose in the retina, the authors used multiple mouse models either with photoreceptor degeneration or a retina lacking the primary glucose transporter. While the photoreceptor degeneration mouse model has some caveats that make interpreting the data challenging, the glucose transporter KO models are a powerful tool to show the changes in metabolite levels between the retina and RPE in a retina. These retinas are not degenerated and have more subtle metabolic rearrangements. Therefore decreases in glucose consumption and lactate export can confidently be attributed to the changes in the photoreceptor metabolism. This model also allowed the authors to show that when glucose uptake is limited the photoreceptors can use lactate.

The authors show in vivo data to support that the RPE uses lactate from the photoreceptors as a fuel source. They do very short-term tracing in vivo to show that the RPE has reduced lactate levels and TCA labeling in a mouse model lacking photoreceptors. There is no deficiency when the RPE is measured ex vivo. These data clearly show that the adjacent photoreceptor activity is impacting RPE metabolism.

The manuscript is well-written, and thorough and does a very good job detailing and explaining methods and concepts that are not straightforward. The authors address (and do not bury) confusing data that does not necessarily support their conclusions (for example glycolytic intermediates in Figure 3C being elevated. The authors even perform additional experiments to clarify artifacts they observed in the tracing of the degeneration model due to short-term ischemia.

Reviewer #3 (Public review):

This work addresses the metabolic interplay between photoreceptors and the adjacent supporting layer of the vertebrate retina, the retinal pigment epithelium (RPE). Prior work from the Hurley lab and others provided evidence, mainly in acutely dissected mouse retina and in cell culture, for the idea that although glucose enters the retina via the RPE, the photoreceptors use most of this glucose via glycolysis, producing lactate that is used by other cells such as Müller cells and RPE cells. In the current study, they build on this by showing that these same principles hold true in vivo, using organism-level stable isotope tracing, as well as in intact retina preparations. They also use several mutant mice that lack photoreceptors, or that lack glucose transporters in either rods or the whole retina, to examine the contribution of photoreceptors to retinal glucose uptake. While many of the concepts were introduced in earlier work, it is an important expansion of this work to show these same mechanisms function in vivo. The authors also use other labeled fuels, lactate, and palmitate, to characterize their use in the presence or absence of glucose transport.

The paper presents a nice combination of in vivo experiments (with a steady infusion of labeled metabolites into the circulation of a living mouse) with ex vivo experiments that allow the monitoring of lactate production and temporal control of labeling.

Overall, the work provides convincing evidence that in the eye of a living mouse, photoreceptors are the main consumers of glucose in the retina, and the main producers of lactate. It seems less clear that the incorporation of labeled glucose into TCA metabolites in the RPE is dependent on the photoreceptor processing of glucose to lactate. Figure 5D is cited as the evidence that "much less m+3 lactate reaches the RPE-choroid in AIPL-/- mice than in controls," and indeed there is much less labeled lactate; but the downstream labeling of citrate is not substantially affected. It is also hard to discern whether these in vivo experiments provide evidence that photoreceptor-derived lactate suppresses glucose oxidation in RPE cells (as shown in vitro in Kanow et al., 2017).

Reviewer #1 (Public review):

This paper presents a comprehensive study of how neural tracking of speech is affected by background noise. Using five EEG experiments and Temporal response function (TRF), it investigates how minimal background noise can enhance speech tracking even when speech intelligibility remains very high. The results suggest that this enhancement is not attention-driven but could be explained by stochastic resonance. These findings generalize across different background noise types, listening conditions, and speech features (envelope onset and envelope), offering insights into speech processing in real-world environments.

I find this paper well-written, the experiments and results are clearly described.

Comments on revisions:

I thank the author for thoughtful revisions and for adequately addressing my comments. The new version is much clearer and improved. I have no further questions.

Reviewer #2 (Public review):

The author investigates the role of background noise on EEG-assessed speech tracking in a series of five experiments. In the first experiment the influence of different degrees of background noise is investigated and enhanced speech tracking for minimal noise levels is found. The following four experiments explore different potential influences on this effect, such as attentional allocation, different noise types and presentation mode.

The step-wise exploration of potential contributors to the effect of enhanced speech tracking for minimal background noise is compelling. The motivation and reasoning for the different studies is clear and logical and therefore easy to follow. The results are discussed in a concise and clear way. While I specifically like the conciseness, one inevitable consequence is that not all results are equally discussed in depth.

Based on the results of the five experiments, the authors conclude that the enhancement of speech tracking for minimal background noise is likely due to stochastic resonance. Given broad conceptualizations of stochasitc resonance as noise benefit this is a reasonable conclusion.

This study will likely impact the field as it provides compelling support questioning the relationship between speech tracking and speech processing.

Comments on revisions:

All my previous comments were addressed nicely. Some of the comments were mere curiosity questions that were nicely entertained, even though they were not of direct relevance to the manuscript. I like the addition of the amplitude envelope analysis to the supplementary material as it offers direct comparison of those different methods. My only tiny tiny critic is (which bears no significance), that due to the many rearrangement changes in the marked changes document, the changes of content get buried and hard to see.

Joint Public Review:

This paper examines the role of MLCK (myosin light chain kinase) and MLCP (myosin light chain phosphatase) in axon regeneration. Using loss-of-function approaches based on small molecule inhibitors and siRNA knockdown, the authors explore axon regeneration in cell culture and in animal models from central and peripheral nervous systems. Their evidence shows that MLCK activity facilitates axon extension/regeneration, while MLCP prevents it. Additionally, they show that when the MLCK/MLCP pathway is experimentally intervened, F-actin is redistributed in the growth cone.

Strengths:

This manuscript presents a wide range of experimental models to address its hypothesis and biological question. Notably, the use of multiple in vivo models significantly enhances the overall validity of the study.

What follows is a discussion of the merits and limitations of different claims of the manuscript in light of the evidence presented.

(1) The authors combine MLCK inhibitors with Bleb (Figure 6), trying to verify if both pairs of inhibitors act on the same target/pathway. MLCK may regulate axon growth independent of NMII activity. However, this has very important implications for the understanding not only on how NMII works and affects axon extension but also in trying to understand what MLCP is doing. One wonders if MLCP actions, which are opposite of MLCK, also independent of NMII activity? The authors try to address this controversial issue in the discussion section. The reviewers consider that it is still an open question, and acknowledge that it would require a significant amount of experimental work to solve the issue, that goes well beyond the main goal of the present study.

(2) Using western blot and immunohistochemical analyses, authors first show that MLCK expression is increased in DRG sensory neurons following peripheral axotomy, concomitant to an increase in MLC phosphorylation, suggesting a causal effect (Figure 1). The authors claim that it is common that axon growth-promoting genes are upregulated. It would have been interesting at<br /> this point to study in this scenario the regulation of MLCP.

(3) Using DRG cultures and sciatic nerve crush in the context of MLCK inhibition (ML-7) and down-regulation, authors conclude that MLCK activity is required for mammalian peripheral axon regeneration both in vitro and in vivo (Figure 2). In parallel, the authors show that these treatments affect, as expected, the phosphorylation levels of MLC.

(4) The authors then examined the role of the phosphatase MLCP in axon growth during regeneration. The authors first use a known MLCP blocker, phorbol 12,13-dibutyrate (PDBu), to show that is able to increase the levels of p-MLC, with a concomitant increase in the extent of axon regrowth of DRG neurons, both in permissive as well as non-permissive substrates. The authors repeat the experiments using the knockdown of MYPT1, a key component of the MLC-phosphatase, and again can observe a growth-promoting effect (Figure 3).

(5) In the next set of experiments (presented in Figure 4) authors extend the previous observations in primary cultures from the CNS. For that, they use cortical and hippocampal cultures, and pharmacological and genetic loss-of-function using the above-mentioned strategies. The expected results were obtained in both CNS neurons: inhibition or knockdown of the kinase decreases axon growth, whereas inhibition or knockdown of the phosphatase increases growth. A main weakness in this set is that drugs were used from the beginning of the experiment, and hence, they would also affect axon specification. As pointed out in Materials and Method (lines 143-145) authors counted as "axons" neurites longer than twice the diameter of the cell soma, and hence would not affect the variable measured. In any case, to be sure one is only affecting axon extension in these cells, the drugs should have been used after axon specification and maturation, which occurs at least after 3 DIV. Taking this into account, the conclusions with this experimental design are limited.

Reviewer #1 (Public review):

Summary:

Desveaux et al. describe human mAbs targeting protein from the Pseudomonas aeruginosa T3SS, discovered by employing single cell B cell sorting from cystic fibrosis patients. The mAbs were directed at the proteins PscF and PcrV. They particularly focused on two mAbs binding the T3SS with the potential of blocking activity. The supplemented biochemical analysis was crystal structures of P3D6 Fab complex. They also compared the blocking activity with mAbs that were described in previous studies, using an assay that evaluated the toxin injection. They conducted mechanistic structure analysis and found that these mAbs might act through different mechanisms by preventing PcrV oligomerization and disrupting PcrVs scaffolding function.

Strengths:

The antibiotic resistance crisis requires the development of new solutions to treat infections caused by MDR bacteria. The development of antibacterial mAbs holds great potential. In that context, this report is important as it paves the way for the development of additional mAbs targeting various pathogens that harbor the T3SS. In this report, the authors present a comparative study of their discovered mAbs vs. a commercial mAb currently in clinical testing resulting in valuable data with applicative implications. The authors investigated the mechanism of action of the mAbs using advanced methods and assays for the characterization of antibody and antigen interaction, underlining the effort to determine the discovered mAbs suitability for downstream application.

Weaknesses:

Although the information presented in this manuscript is important, previous reports regarding other T3SS structures complexed with antibodies, reduce the novelty of this report. Nevertheless, we provide several comments that may help to improve the report. The structural analysis of the presented mAbs is incomplete and unfortunately, the authors did not address any developability assessment. With such vital information missing, it is unclear if the proposed antibodies are suited for diagnostic or therapeutic usage. This vastly reduces the importance of the possibly great potential of the authors' findings. Moreover, the structural information does not include the interacting regions on the mAb which may impede the optimization of the mAb if it is required to improve its affinity.

Reviewer #2 (Public review):

Summary:

Desveaux et al. performed Elisa and translocation assays to identify among 34 cystic fibrosis patients which ones produced antibodies against P. aeruginosa type three secretion system (T3SS). The authors were especially interested in antibodies against PcrV and PcsF, two key components of the T3SS. The authors leveraged their binding assays and flow cytometry to isolate individual B cells from the two most promising sera, and then obtained monoclonal antibodies for the proteins of interest. Among the tested monoclonal antibodies, P3D6 and P5B3 emerged as the best candidates due to their inhibitory effect on the ExoS-Bla translocation marker (with 24% and 94% inhibition, respectively). The authors then showed that P5B3 binds to the five most common variants of PcrV, while P3D6 seems to recognize only one variant. Furthermore, the authors showed that P3D6 inhibits translocon formation, measured as cell death of J774 macrophages. To get insights into the P3D6-PcrV interaction, the authors defined the crystal structure of the P3D6-PcrV complex. Finally, the authors compared their new antibodies with two previous ones (i.e., MEDI3902 and 30-B8).

Strengths:

(1) The article is well written.

(2) The authors used complementary assays to evaluate the protective effect of candidate monoclonal antibodies.

(3) The authors offered crystal structure with insights into the P3D6 antibody-T3SS interaction (e.g., interactions with monomer vs pentamers).

(4) The authors put their results in context by comparing their antibodies with respect to previous ones.

Weaknesses:

(1) The authors used a similar workflow to the one previously reported in Simonis et al. 2023 (antibodies from cystic fibrosis patients that included B cell isolation, antibody-PcrV interaction modeling, etc.) but the authors do not clearly explain how their work and findings differentiate from previous work.

(2) Although new antibodies against P. aerugisona T3SS expand the potential space of antibody-based therapies, it is unclear if P3D6 or P5B3 are better than previous antibodies. In fact, in the discussion section authors suggested that the 30-B8 antibody seems to be the most effective of the tested antibodies.

(3) The authors should explain better which of the two antibodies they have discovered would be better suited for follow-up studies. It is confusing that the authors focused the last sections of the manuscript on P3D6 despite P3D6 having a much lower ExoS-Bla inhibition effect than P5B3 and the limitation in the PcrV variant that P3D6 seems to recognize. A better description of this comparison and the criteria to select among candidate antibodies would help readers identify the main messages of the paper.

(4) This work could strongly benefit from two additional experiments:<br /> a) In vivo experiments: experiments in animal models could offer a more comprehensive picture of the potential of the identified monoclonal antibodies. Additionally, this could help to answer a naïve question: why do the patients that have the antibodies still have chronic P. aeruginosa infections?<br /> b) Multi-antibody T3SS assays (i.e., a combination of two or more monoclonal antibodies evaluated with the same assays used for characterization of single ones). This could explore the synergistic effects of combinatorial therapies that could address some of the limitations of individual antibodies.

Reviewer #1 (Public review):

Summary:

Phytophathogens including fungal pathogens such as F. graminearum remain a major threat to agriculture and food security. Several agriculturally relevant fungicides including the potent Quinofumelin have been discovered to date, yet the mechanisms of their action and specific targets within the cell remain unclear. This paper sets out to contribute to addressing these outstanding questions.

Strengths:

The paper is generally well-written and provides convincing data to support their claims for the impact of Quinofumelin on fungal growth, the target of the drug, and the potential mechanism. Critically the authors identify an important pyrimidine pathway dihydroorotate dehydrogenase (DHODH) gene FgDHODHII in the pathway or mechanism of the drug from the prominent plant pathogen F. graminearum, confirming it as the target for Quinofumelin. The evidence is supported by transcriptomic, metabolomic as well as MST, SPR, molecular docking/structural biology analyses.

Weaknesses:

Whilst the study adds to our knowledge about this drug, it is, however, worth stating that previous reports (although in different organisms) by Higashimura et al., 2022 https://pmc.ncbi.nlm.nih.gov/articles/PMC9716045/ had already identified DHODH as the target for Quinofumelin and hence this knowledge is not new and hence the authors may want to tone down the claim that they discovered this mechanism and also give sufficient credit to the previous authors work at the start of the write-up in the introduction section rather than in passing as they did with reference 25? other specific recommendations to improve the text are provided in the recommendations for authors section below.

Reviewer #2 (Public review):

Summary:

In the current study, the authors aim to identify the mode of action/molecular mechanism of characterized a fungicide, quinofumelin, and its biological impact on transcriptomics and metabolomics in Fusarium graminearum and other Fusarium species. Two sets of data were generated between quinofumelin and no treatment group, and differentially abundant transcripts and metabolites were identified. The authors further focused on uridine/uracil biosynthesis pathway, considering the significant up- and down-regulation observed in final metabolites and some of the genes in the pathways. Using a deletion mutant of one of the genes and in vitro biochemical assays, the authors concluded that quinofumelin binds to the dihydroorotate dehydrogenase.

Strengths:

Omics datasets were leveraged to understand the physiological impact of quinofumelin, showing the intracellular impact of the fungicide. The characterization of FgDHODHII deletion strains with supplemented metabolites clearly showed the impact of the enzyme on fungal growth.

Weaknesses:

Some interpretation of results is not accurate and some experiments lack controls. The comparison between quinofumelin-treated deletion strains, in the presence of different metabolites didn't suggest the fungicide is FgDHODHII specific. A wild type is required in this experiment.

Potential Impact: Confirming the target of quinofumelin may help understand its resistance mehchanism, and further development of other inhibitory molecules against the target.

The manuscript would benefit more in explaining the study rationale if more background on previous characterization of this fungicide on Fusarium is given.

Reviewer #3 (Public review):

Summary:

The manuscript shows the mechanism of action of quinofumelin, a novel fungicide, against the fungus Fusarium graminearum. Through omics analysis, phenotypic analysis, and in silico approaches, the role of quinofumelin in targeting DHODH is uncovered.

Strengths:

The phenotypic analysis and mutant generation are nice data and add to the role of metabolites in bypassing pyrimidine biosynthesis.

Weaknesses:

The role of DHODH in this class of fungicides has been known and this data does not add any further significance to the field. The work of Higashimura et al is not appreciated well enough as they already showed the role of quinofumelin upon DHODH II.

There is no mention of the other fungicide within this class ipflufenoquin, as there is ample data on this molecule.

Reviewer #1 (Public review):

Summary:

In this study, the authors examined the function of CLIP in exercise-mediate inhibition of osteoarthritis using an ACL transection rat model. The authors rely on rigorous experimental design and methods to demonstrate that CLIP is downregulated in osteoarthritic cartilage tissue and that CLIP expression can be rescued by moderate treadmill exercise. They further show that activation of Nrf2 signaling occurs through CLIP inhibition of Keap1-Nrf2. The results are novel as they suggest a new role for CLIP in OA pathogenesis. The following points need to be addressed in order to bring additional clarity to this work.

Strengths:

This is an interesting study that addresses an important global health issue. The significance is high and the work is novel and mechanistic.

Weaknesses:

A major concern is that a direct link between exercise and CLIP-mediated inhibition of ferroptosis via Keap1-Nrf2 pathway is not supported by the provided data. The ferroptosis studies were performed in vitro, whereas the effect of exercise was demonstrated in an OA animal model. Therefore, the data suggest a potential correlation between CLIP-Keap1-Nrf2 and exercise. This must be described as a limitation in the discussion section. Consequently, the title of the manuscript needs to better reflect the interpretation of these data.

Figure 1: Radiomics data are not described in the text. OARSI scoring of damaged and undamaged sections is not presented in the figure.

Figure 2: Data presentation is very dense in this figure. It is recommended that Figure 2 be split into two figures. Also, the histology and IHC images in Figure 2A are of poor resolution. These data do not sufficiently demonstrate early OA pathology. Clearer images to substantiate the authors' statement need to be provided.

Figure 3: The superficial zone appears to be misrepresented; it should include only the top 2-3 layers of flat chondrocyte cells.

Figure 4: This Figure should be listed as supplementary data. CTS is not spelled out in the legend. Also, a rationale for using low, medium, and high CTS needs to be provided.

Figure 5: Please describe positive and negative controls. Please elaborate on the findings of the yeast hybrid experiment in the results. Please expand KD-02 experimental condition in the legend and results.

Figure 6: Please move Figure S2 into the main Figures and describe the results in section 2.9 which describes ferroptosis.

In the results section, it is recommended that the authors describe all panels of the figures appropriately in sequential order. The authors are advised to provide publication-quality figures and, in some cases, to split figure panels into new figures as well as to ensure that the fonts and data are legible. Finally, the use of non-conventional abbreviations (such as G3 for passage-3 chondrocytes, CG for the control condition, and OE for overexpression) may confuse the readership, and describing each abbreviation when used for the first time is required.

Reviewer #2 (Public review):

Summary:

Recent studies indicate a beneficial role for moderate-intensity exercise in early osteoarthritis (OA). This manuscript by Jia et al. investigates the role of cartilage intermediate layer protein (CILP) and moderate exercise in maintaining hyaline cartilage integrity following anterior cruciate ligament transection (ACLt) in rats. Single-cell RNA-sequencing of OA and OA+ exercise knee joints from rats at 4 weeks post-ACLt revealed the upregulation of CILP and a higher Col2/Col1 ratio in OA knee chondrocytes from ACLt rats that exercised on a treadmill. CILP was downregulated in the damaged portions, compared to healthy regions of knee cartilage of patients undergoing total knee arthroplasty. In the rat ACLt model, CILP is downregulated in the OA cartilage but not in OA + exercise cartilage. Using CLIP1 over-expression and knockdown in passage 3 cultures of primary rat chondrocytes, the authors demonstrate that the loss of CILP is associated with higher ROS, lipid peroxidation, and iron content in chondrocytes whereas its overexpression is protective against these changes. CILP binds to Keap1, and its overexpression disrupts Keap1/Nrf2 interaction and attenuates Nrf2 ubiquitination. The authors conclude that exercise protects the articular cartilage intermediate zone and the associated upregulation of CILP facilitates Keap1-Nrf2 interaction to prevent chondrocyte ferroptosis and hyaline cartilage fibrosis.

Strengths:

The study is interesting, and the experiments are conducted well. The methodology is well-described. The data presented strongly support the downregulation of CILP in human OA cartilage and its potential role in regulating Keap1/Nrf2 interaction and chondrocyte ferroptosis.

Weaknesses:

The data do not support a role for CILP in exercise-mediated inhibition of hyaline cartilage fibrosis in early OA. The reason for selecting CILP from the ScRNA-seq for further analysis is not clear. The manuscript is put together sloppily. The abstract, introduction, and results were written confusingly, and hard to follow. Some of the figures were confusing as well. Still, the study is interesting.

Reviewer #2 (Public review):

Summary:

Liu et al investigated the performance of a novel imaging technique called RIM-Deep to enhance the imaging depth for cleared samples. Usually, the imaging depth using the classical confocal microscopy sample chamber is limited due to optical aberrations, resulting in loss of resolution and image quality. To overcome this limitation and increase depth, they generated a special imaging chamber, that is affixed to the objective and filled with a solution matching the refractive indices to reduce aberrations. Importantly, the study was conducted using a standard confocal microscope, that has not been modified apart from exchanging the standard sample chamber with the RIM-Deep sample holder. Upon analysing the imaging depth, the authors claim that the RIM-Deep method increased the depth from 2 mm to 5 mm. In summary, RIM-Deep has the potential to significantly enhance imaging quality of thick samples on a low budget, making in-depth measurements possible for a wide range of researchers that have access to an inverted confocal microscope.

Strengths:

The authors used different clearing methods to demonstrate the suitability of RIM-Deep for various sample preparation protocols with clearing solutions of different refractive indices. They clearly demonstrate that the RIM-Deep chamber is compatible with all 3 methods. Brain samples are characterized by complex networks of cells and are often hard to visualize. Despite the dense, complex structure of brain tissue, the RIM-Deep method generated high-quality images of all 3 samples given. As the authors already stated, increasing imaging depth often goes hand in hand with purchasing expensive new equipment, exchanging several microscopy parts or purchasing a new microscopy set-up. Innovations, such as the RIM-Deep chamber, hence, might pave the way for cost-effective imaging and expand the applicability of an inverted confocal microscope.

Weaknesses:

(1) However, since this study introduces a novel imaging technique, and therefore, aims to revolutionize the way of imaging large samples, additional control experiments would strengthen the data. From the 3 clearing protocol used (CUBIC, MACS and iDISCO), only the brain section from Macaca fascicularis cleared with iDISCO was imaged with the standard chamber and the RIM-Deep method. This comparison indeed shows that the imaging depth thereby increases more than 2-fold, which is a significant enhancement in terms of microscopy. However, it would have been important to evaluate and show the difference of the imaging depth also on the other two samples, since they were cleared with different protocols and, thus, treated with clearing solutions of different refractive indices compared to iDCISCO.

(2) The description of the figures and figure panels should be improved for a better understanding of the experiments performed and the thus resulting images/data.

(3) While the authors used a Nikon AX inverted laser scanning confocal microscope, the study would highly benefit from evaluating the performance of the RIM-Deep method using other inverted confocal microscopes or even wide-field microscopes.

Comments on Revision:

Regarding point 1)<br /> Within the revised manuscript, Liu et al focussed on a more detailed comparison of the standard vs the RIM-Deep method of samples cleared with the 3 different methods.

Regarding point 2)<br /> The revised description of the figures results in a better understanding of the data.

Regarding point 3)<br /> The authors tested their method on different microscopic setups to show the compatibility.

Summary: the revised manuscript addressed all previously mentioned points.

Reviewer #1 (Public review):

This study by Popli et al. evaluated the function of Atg14, an autophagy protein, in reproductive function using a conditional knockout mouse model. The authors showed that female mice lacking Atg14 were infertile partly due to defective embryo transport function of the oviduct and faulty uterine receptivity and decidualization using PgrCre/+;Atg14f/f mice. The findings from this work are exciting and novel. The authors demonstrated that a loss of Atg14 led to an excessive pyroptosis in the oviductal epithelial cells that compromises cellular integrity and structure, impeding the transport function of the oviduct. In addition, the authors use both genetic and pharmacological approaches to test the hypothesis. Therefore, the findings from this study are high-impact and likely reproducible.

Comments on revisions: Thank you for your time revising the manuscript. The authors have addressed all of my previous concerns.

Reviewer #2 (Public review):

In this manuscript, Popli et al investigated the roles of autophagy related gene, Atg14, in the female reproductive tract (FRT) using conditional knockout mouse models. By ablation of Atg14 in both oviduct and uterus with PR-Cre (Atg14 cKO), authors discovered that such females are completely infertile. They went on to show that Atg14 cKO females have impaired embryo implantation as well as embryo transport from oviduct to uterus. Further analysis showed that Atg14 cKO leads to increased pyroptosis in oviduct, which disrupts oviduct epithelial integrity and leads to obstructive oviduct lumen and impaired embryo transport. Authors concluded that Atg14 is critical for maintaining the oviduct homeostasis and keeping the inflammation under check to enable proper embryo transport.

Comments on revisions: Authors have addressed all my concerns in this revised version, which is substantial improved compared to the original version. I have no further comments.

Reviewer #3 (Public review):

The manuscript by Pooja Popli and co-authors tested importance of Atg14 in female reproductive tract by conditionally deleting Atg14 use PrCre and also Foxj1cre. The authors showed that loss of Atg14 leads to infertility due to retention of embryos within the oviduct. The authors further concluded that the retention of embryos within the oviduct is due to pyroptosis in oviduct cells leading to defective cellular integrity. This revised version of the manuscript has addressed the remaining concerns that were raised earlier. The manuscript is now a convincing one.

Reviewer #1 (Public review):

Summary:

Work by Brosseau et. al. combines NMR, biochemical assays, and MD simulations to characterize the influence of the C-terminal tail of EmrE, a model multi-drug efflux pump, on proton leak. The authors compare the WT pump to a C-terminal tail deletion, delta_107, finding that the mutant has increased proton leak in proteoliposome assays, shifted pH dependence with a new titratable residue, faster-alternating access at high pH values, and reduced growth, consistent with proton leak of the PMF.

Strengths:

The work combines thorough experimental analysis of structural, dynamic, and electrochemical properties of the mutant relative to WT proteins. The computational work is well aligned in vision and analysis. Although all questions are not answered, the authors lay out a logical exploration of the possible explanations.

Weaknesses:

There are a few analyses that are missing and important data left out. For example, the relative rate of drug efflux of the mutant should be reported to justify the focus on proton leak. Additionally, the correlation between structural interactions should be directly analyzed and the mutant PMF also analyzed to justify the claims based on hydration alone. Some aspects of the increased dynamics at high pH due to a potential salt bridge are not clear.

Reviewer #2 (Public review):

Summary:

This manuscript explores the role of the C-terminal tail of EmrE in controlling uncoupled proton flux. Leakage occurs in the wild-type transporter under certain conditions but is amplified in the C-terminal truncation mutant D107. The authors use an impressive combination of growth assays, transport assays, NMR on WT and mutants with and without key substrates, classical MD, and reactive MD to address this problem. Overall, I think that the claims are well supported by the data, but I am most concerned about the reproducibility of the MD data, initial structures used for simulations, and the stochasticity of the water wire formation. These can all be addressed in a revision with more simulations as I point out below. I want to point out that the discussion was very nicely written, and I enjoyed reading the summary of the data and the connection to other studies very much.

Strengths:

The Henzler-Wildman lab is at the forefront of using quantitative experiments to probe the peculiarities in transporter biophysics, and the MD work from the Voth lab complements the experiments quite well. The sheer number of different types of experimental and computational approaches performed here is impressive.

Weaknesses:

The primary weaknesses are related to the reproducibility of the MD results with regard to the formation of water wires in the WT and truncation mutant. This could be resolved with simulations starting from structures built using very different loops and C-terminal tails.

The water wire gates identified in the MD should be tested experimentally with site-directed mutagenesis to determine if those residues do impact leak.

Reviewer #1 (Public review):

The origin recognition complex (ORC) is an essential loading factor for the replicative Mcm2-7 helicase complex. Despite ORC's critical role in DNA replication, there have been instances where the loss of specific ORC subunits has still seemingly supported DNA replication in cancer cells, endocycling hepatocytes, and Drosophila polyploid cells. Critically, all tested ORC subunits are essential for development and proliferation in normal cells. This presents a challenge, as conditional knockouts need to be generated, and a skeptic can always claim that there were limiting but sufficient ORC levels for helicase loading and replication in polyploid or transformed cells. That being said, the authors have consistently pushed the system to demonstrate replication in the absence or extreme depletion of ORC subunits.

Here, the authors generate conditional ORC2 mutants to counter a potential argument with prior conditional ORC1 mutants that Cdc6 may substitute for ORC1 function based on homology. They also generate a double ORC1 and ORC2 mutant, which is still capable of DNA replication in polyploid hepatocytes. While this manuscript provides significantly more support for the ability of select cells to replicate in the absence or near absence of select ORC subunits, it does not shed light on a potential mechanism.

The strengths of this manuscript are the mouse genetics and the generation of conditional alleles of ORC2 and the rigorous assessment of phenotypes resulting from limiting amounts of specific ORC subunits. It also builds on prior work with ORC1 to rule out Cdc6 complementing the loss of ORC1.

The weakness is that it is a very hard task to resolve the fundamental question of how much ORC is enough for replication in cancer cells or hepatocytes. Clearly, there is a marked reduction in specific ORC subunits that is sufficient to impact replication during development and in fibroblasts, but the devil's advocate can always claim minimal levels of ORC remaining in these specialized cells.

The significance of the work is that the authors keep improving their conditional alleles (and combining them), thus making it harder and harder (but not impossible) to invoke limiting but sufficient levels of ORC. This work lays the foundation for future functional screens to identify other factors that may modulate the response to the loss of ORC subunits.

This work will be of interest to the DNA replication, polyploidy, and genome stability communities.

Reviewer #2 (Public review):

This manuscript proposes that primary hepatocytes can replicate their DNA without the six-subunit ORC. This follows previous studies that examined mice that did not express ORC1 in the liver. In this study, the authors suppressed expression of ORC2 or ORC1 plus ORC2 in the liver.

Comments:

(1) I find the conclusion of the authors somewhat hard to accept. Biochemically, ORC without the ORC1 or ORC2 subunits cannot load the MCM helicase on DNA. The question arises whether the deletion in the ORC1 and ORC2 genes by Cre is not very tight, allowing some cells to replicate their DNA and allow the liver to develop, or whether the replication of DNA proceeds via non-canonical mechanisms, such as break-induced replication. The increase in the number of polyploid cells in the mice expressing Cre supports the first mechanism, because it is consistent with few cells retaining the capacity to replicate their DNA, at least for some time during development.

(2) Fig 1H shows that 5 days post infection, there is no visible expression of ORC2 in MEFs with the ORC2 flox allele. However, at 15 days post infection, some ORC2 is visible. The authors suggest that a small number of cells that retained expression of ORC2 were selected over the cells not expressing ORC2. Could a similar scenario also happen in vivo?

(3) Figs 2E-G show decreased body weight, decreased liver weight and decreased liver to body weight in mice with recombination of the ORC2 flox allele. This means that DNA replication is compromised in the ALB-ORC2f/f mice.

(4) Figs 2I-K do not report the number of hepatocytes, but the percent of hepatocytes with different nuclear sizes. I suspect that the number of hepatocytes is lower in the ALB-ORC2f/f mice than in the ORC2f/f mice. Can the authors report the actual numbers?

(5) Figs 3B-G do not report the number of nuclei, but percentages, which are plotted separately for the ORC2-f/f and ALB-ORC2-f/f mice. Can the authors report the actual numbers?

(6) Fig 5 shows the response of ORC2f/f and ALB-ORC2f/f mice after partial hepatectomy. The percent of EdU+ nuclei in the ORC2-f/f (aka ALB-CRE-/-) mice in Fig 5H seems low. Based on other publications in the field it should be about 20-30%. Why is it so low here? The very low nuclear density in the ALB-ORC2-f/f mice (Fig 5F) and the large nuclei (Fig 5I) could indicate that cells fire too few origins, proceed through S phase very slowly and fail to divide.

(7) Fig 6F shows that ALB-ORC1f/f-ORC2f/f mice have very severe phenotypes in terms of body weight and liver weight (about on third of wild-type!!). Fig 6H and 6I, the actual numbers should be presented, not percentages. The fact that there are EYFP negative cells, implies that CRE was not expressed in all hepatocytes.

(8) Comparing the EdU+ cells in Fig 7G versus 5G shows very different number of EdU+ cells in the control animals. This means that one of these images is not representative. The higher fraction of EdU+ cells in the double-knockout could mean that the hepatocytes in the double-knockout take longer to complete DNA replication than the control hepatocytes. The control hepatocytes may have already completed DNA replication, which can explain why the fraction of EdU+ cells is so low in the controls. The authors may need to study mice at earlier time points after partial hepatectomy, i.e. sacrifice the mice at 30-32 hours, instead of 40-52 hours.

(9) Regarding the calculation of the number of cell divisions during development: the authors assume that all the hepatocytes in the adult liver are derived from hepatoblasts that express Alb. Is it possible to exclude the possibility that pre-hepatoblast cells that do not express Alb give rise to hepatocytes? For example, the cells that give rise to hepatoblasts may proliferate more times than normal giving rise to a higher number of hepatoblasts than in wild-type mice.

(10) My interpretation of the data is that not all hepatocytes have the ORC1 and ORC2 genes deleted (eg EYFP-negative cells) and that these cells allow some proliferation in the livers of these mice.

My comments regarding the previous version still stand, since the authors did not perform experiments to address them.

Reviewer #3 (Public review):

Summary:

The authors address the role of ORC in DNA replication and that this protein complex is not essential for DNA replication in hepatocytes. They provide evidence that ORC subunit levels are substantially reduced in cells that have been induced to delete multiple exons of the corresponding ORC gene(s) in hepatocytes. They evaluate replication both in purified isolated hepatocytes and in mice after hepatectomy. In both cases, there is clear evidence that DNA replication does not decrease at a level that corresponds with the decrease in detectable ORC subunit and that endoreduplication is the primary type of replication observed. It remains possible that small amounts of residual ORC are responsible for the replication observed, although the authors provide arguments against this possibility. The mechanisms responsible for the DNA replication observed in the absence of ORC are not examined, including why such replication would primarily be due to endoreduplication.

Strengths:

The authors clearly show that there are dramatic reductions in the amount of the targeted ORC subunits in the cells that have been targeted for deletion. They also provide clear evidence that there is replication in a subset of these cells and that it is likely due to endoreduplication. Although there is no replication in MEFs derived from cells with the deletion, there is clearly DNA replication occurring in hepatocytes (both isolated in culture and in the context of the liver). Interestingly, the cells undergoing replication exhibit enlarged cell sizes and elevated ploidy indicating endoreduplication of the genome. These findings raise the interesting possibility that endoreduplication does not require ORC while normal replication does.

Weaknesses:

There remain two significant weaknesses in this manuscript. The first is that although there is clearly robust reduction of the targeted ORC subunit, the authors cannot confirm that it is deleted in all cells. For example, the analysis in Fig. 4B would suggest that a substantial number of cells have not lost the targeted region of ORC2. In their response, the authors suggest that this is due to contaminating non-hepatocyte cells but do not provide evidence that this is the case. Although the western blots show stronger effects, this type of analysis is notorious for non-linear response curves and no standards are not provided. The second weakness is that there is no evaluation of the molecular nature of the replication observed. In response to the initial review the authors point out that a previous publication mapped Mcm2-7 loading in the absence of ORC1, ORC2 and ORC5 and saw no deficit or altered location. Unfortunately, this is not done for the mutants discussed here and this previous data supports a model that limiting residual ORC is responsible for the replication observed rather than some novel mechanism (which would be expected to alter location or amounts of loading). The manuscript provides no exploration of why "ORC-independent" replication would drive endoreduplicaiton (which is the strongest evidence for an alternative mechanism of initiation but is unique to this experiment and not the previously mutants analyzed for Mcm2-7 loading). Most importantly, it remains true that after numerous papers from this lab and others claiming that ORC is not required for eukaryotic DNA replication, we still have no information about an alternative pathway that could explain Mcm2-7 loading in the absence of ORC. Without some insights in this area, studies such as these will remain controversial.

Reviewer #1 (Public review):

Summary:

In this paper, Bruter and colleagues report effects of inducible deletion of the genes encoding the two paralogous kinases of the Mediator complex in adult mice. The physiological roles of these two kinases, CDK8 and CDK19, are currently rather poorly understood; although conserved in all eukaryotes, and among the most highly conserved kinases in vertebrates, individual knockouts of genes encoding CDK8 homologues in different species have revealed generally rather mild and specific effects, in contrast to Mediator itself. Here, the authors provide evidence that neither CDK8 nor CDK19 are required for adult homeostasis but they are functionally redundant for maintenance of reproductive tissue morphology and fertility in males.

Strengths:

The morphological data on atrophy of the male reproductive system and arrest of spermatocyte meiosis are solid and are reinforced by single cell transcriptomics data, which is a challenging technique to implement in vivo. The main findings are important and will be of interest to scientists in the fields of transcription and developmental biology.

Weaknesses:

There are several weaknesses.

The first is that data comparing general health of mice with single and double knockouts is not shown, and data on effects in other tissues are sparse and very preliminary. The only strong phenotype of double knockouts that is described is in the male reproductive system. Furthermore, data for the genitourinary system in single knockouts are very sparse; data are described for fertility in figure 1E, ploidy and cell number in figure 3B and C, plasma testosterone and luteinizing hormone levels in figure 6C and 6D and morphology of testis and prostate tissue for single Cdk8 knockout in supplementary figure 1E (although in this case the images do not appear very comparable between control and CDK8 KO), but, for example, there is no analysis of different meiotic stages or of gene expression in single knockouts. Given that the authors have shown that CDK8 and CDK19 expression levels differ widely between different cell types, such an analysis would be interesting. This might have provided insight into the sterility of induced CDK8 knockout.

The second weakness is that the correlation between double knockout and reduced expression of genes involved in steroid hormone biosynthesis is hypothesized to be a causal mechanism for the phenotypes observed. While this is a possibility, there are no experiments performed to provide evidence that this is the case. Furthermore, there is no evidence shown that CDK8 and/or CDK19 are directly responsible for transcription of the genes concerned.

Finally, the authors propose that the phenotypes are independent of the kinase activity of CDK8 or CDK19 because treatment of mice for a month with an inhibitor does not recapitulate the effects of the knockout, and nor does expression of two steroidogenic genes change in cultured Leydig cells upon treatment with an inhibitor. However, there are no controls for effective target inhibition shown.

Comments on revisions:

This manuscript is slightly improved compared to the previous version, though it still does not address the weaknesses that were highlighted in the first version, which largely remain relevant. Please note the typo in the abstract (line 30) and the absence of response to the query of how many crypts and villi were counted in the experiment shown in Suppl Fig 1D.

Reviewer #2 (Public review):

Summary:

The authors tried to test the hypothesis that Cdk8 and Cdk19 stabilize the cytoplasmic CcNC protein, the partner protein of Mediator complex including CDK8/19 and Mediator protein via a kinase-independent function by generating induced double knockout of Cdk8/19. However the evidence presented suffer from a lack of focus and rigor and does not support their claims.

Strengths:

This is the first comprehensive report on the effect of a double knockout of CDK8 and CDK19 in mice on male fertility, hormones and single cell testicular cellular expression. The inducible knockout mice led to male sterility with severe spermatogenic defects, and the authors attempted to use this animal model to test the kinase-independent function of CDK8/19, previously reported for human. Single cell RNA-seq of knockout testis presented a high resolution of molecular defects of all the major cell types in the testes of the inducible double knockout mice. The authors also have several interesting findings such as reentry into cell cycles by Sertoli cells, loss of Testosterone in induced dko that could be investigated further.

Weaknesses:

The claim of reproductive defects in the induced double knockout of CDK8/19 resulted from the loss of CCNC via a kinase-independent mechanism is interesting but was not supported by the data presented. While the construction and analysis of the systemic induced knockout model of Cdk8 in Cdk19KO mice is not trivial, the analysis and data is weakened by systemic effect of Cdk8 loss, making it difficult to separate the systemic effect from the local testis effect.

The analysis of male sterile phenotype is also inadequate with poor image quality, especially testis HE sections. Male reproductive tract picture is also small and difficult to evaluate. The mice crossing scheme is unusual as you have three mice to cross to produce genotypes, while we could understand that it is possible to produce pups of desired genotypes with different mating schemes, such vague crossing scheme is not desirable and of poor genetics practice. Also using TAM treated wild type as control is ok, but a better control will be TAM treated ERT2-cre; CDK8f/f or TAM treated ERT2 Cre CDK19/19 KO, so as to minimize the impact from well-recognized effect of TAM.

While the authors proposed that the inducible loss of CDK8 in the CDK19 knockout background is responsible for spermatogenic defects, it was not clear in which cells CDK8/19 genes are interested and which cell types might have a major role in spermatogenesis. The authors also put forward the evidence that reduction/loss of Testosterone might be the main cause of spermatogenic defects, which is consistent with the expression change in genes involved in steroigenesis pathway in Leydig cells of inducible double knockout. But it is not clear how the loss of Testosterone contributed to the loss of CcnC protein.

The authors should clarify or present the data on where CDK8 and CDK19 as well as CcnC are expressed so as to help the readers to understand which tissues that both CDK might be functioning and cause the loss of CcnC. It should be easier to test the hypothesis of CDK8/19 stabilize CcnC protein using double knock out primary cells, instead of the whole testis.

Since CDK8KO and CDK19KO both have significantly reduced fertility in comparison with wildtype, it might be important to measure the sperm quantity and motility among CDK8 KO, CDK19KO and induced DKO to evaluate spermatogenesis based on their sperm production.

Some data for the inducible knockout efficiency of Cdk8 were presented in Supplemental figure 1, but there is no legend for the supplemental figures, it was not clear which band represented deletion band, which tissues were examined? Tail or testis? It seems that two months after the injection of Tam, all the Cdk8 were completely deleted, indicating extremely efficient deletion of Tam induction by two-month post administration. Were the complete deletion of Cdk8 happening even earlier ? an examination of timepoints of induced loss would be useful and instructional as to when is the best time to examine phenotypes.

The authors found that Sertoli cells re-entered cell cycle in the inducible double knockout but stop short of careful characterization other than increased expression of cell cycle genes.

Overall this work suffered from a lack of focus and rigor in the analysis and lack of sufficient evidence to support their main conclusions.

Comments on revisions:

This reviewer appreciated the authors' effort in improving the quality of this manuscript during their revision. While some concerns remain, the revision is a much improved work and the authors addressed most of my major concerns.<br /> Figure 2E CDK8 and CDK19 immunofluorescent staining images seem to show CDK8 and CDK19 location are completely distinct and in different cells, the authors need to elaborate on this results and discuss what such a distinct location means in line of their double knockout data.

Reviewer #1 (Public review):

Summary

The manuscript by Chen et al. presents a detailed metabolic characterization of male and female WT and Ctrp10 knockout mice. The main finding is that female KO mice become obese on both low-fat and high-fat diets, but without evidence of marked insulin resistance, hepatic steatosis, dyslipidemia, or increased inflammatory markers. The authors performed a detailed transcriptomic analysis and identified differentially-expressed genes that distinguish high-fat diet -fed Ctrp10 KO from WT control mice. They further show that this set of genes exhibits cross correlation in human tissues, and that this is greater in females than in males. The data indicate that the Ctrp10 KO model may be useful to understand how obesity and metabolic dysfuction are coupled to each other, and how this occurs by a sex-biased mechanism.

Strengths

The work presents a large amount of data, which has been carefully acquired and is convincing. The transcriptomic analysis will further help to define what pathways are associated with obesity, but not necessarily with metabolic dysfunction. The manuscript will be of interest to investigators studying metabolic diseases, and to those studying sex-specific differences in metabolic physiology. The limitations of the study are acknowledged, including that a whole-body knockout was used. The cause of the increased body weight is not entirely clear, despite the careful and detailed analysis that was performed. Notwithstanding these limitations, the phenotype is interesting, and this work will establish basis for further work to understand the mechanisms that are involved.

Weaknesses

The main weaknesses are that no antibody is available to detect Ctrp10, and the knockout is a global knockout since no conditional allele is available. These limitations are discussed in the manuscript. Despite these weaknesses, the current work establishes the intriguing phenotype and its sex-specificity, and will provide a solid foundation for future studies.

Reviewer #2 (Public review):

Summary:

Here the authors have shown the role of sex differences in MHO phenotype, which increases the scope for research in this area.

Strengths:

The study provides a detailed idea of how the genes are regulated in sex sex-dependent manner.

Weaknesses:

The mechanistic details are missing

Reviewer #3 (Public review):

Summary:

This study examines the impact of CTRP10/C1QL2 absence on obesity and metabolic health in mice. Female mice lacking CTRP10 tend to develop obesity, particularly on a high-fat diet. Surprisingly, they do not display the typical metabolic traits associated with obesity, like fatty liver or glucose intolerance. This indicates a disconnection between weight gain and metabolic issues in these female mice. The research underscores the need to understand sex-specific factors in how obesity influences metabolic health.

Strengths:

The study provides compelling evidence regarding Ctrp10's role in female-specific metabolic regulation in mice, shedding light on its potential significance in metabolically healthy obese (MHO) individuals.

Weaknesses:

-The analysis and description of sex-specific human data require more details to highlight the relevance of Ctrp10 mouse data and the analysis of differentially expressed genes in humans.<br /> -There's a lack of analysis regarding secreted Ctrp10 under various dietary conditions.

Reviewer #1 (Public review):

Summary:

In this article, Nedbalova et al. investigate the biochemical pathway that acts in circulating immune cells to generate adenosine, a systemic signal that directs nutrients toward the immune response, and S-adenosylmethionine (SAM), a methyl donor for lipid, DNA, RNA, and protein synthetic reactions. They find that SAM is largely generated through uptake of extracellular methionine, but that recycling of adenosine to form ATP contributes a small but important quantity of SAM in immune cells during the immune response. The authors propose that adenosine serves as a sensor of cell activity and nutrient supply, with adenosine secretion dominating in response to increased cellular activity. Their findings of impaired immune action but rescued larval developmental delay when the enzyme Ahcy is knocked down in hemocytes are interpreted as due to effects on methylation processes in hemocytes and reduced production of adenosine to regulate systemic metabolism and development, respectively. Overall this is a strong paper that uses sophisticated metabolic techniques to map the biochemical regulation of an important systemic mediator, highlighting the importance of maintaining appropriate metabolite levels in driving immune cell biology.

Strengths:

The authors deploy metabolic tracing - no easy feat in Drosophila hemocytes - to assess flux into pools of the SAM cycle. This is complemented by mass spectrometry analysis of total levels of SAM cycle metabolites to provide a clear picture of this metabolic pathway in resting and activated immune cells.

The experiments show that recycling of adenosine to ATP, and ultimately SAM, contributes meaningfully to the ability of immune cells to control infection with wasp eggs.

This is a well-written paper, with very nice figures showing metabolic pathways under investigation. In particular, the italicized annotations, for example "must be kept low", in Figure 1 illustrate a key point in metabolism - that cells must control levels of various intermediates to keep metabolic pathways moving in a beneficial direction.

Experiments are conducted and controlled well, reagents are tested, and findings are robust and support most of the authors' claims.

Weaknesses:

The authors posit that adenosine acts a sensor of cellular activity, with increased release indicating active cellular metabolism and insufficient nutrient supply. The authors have provided a discussion of how generalizable they think this may be across different cell types or organs, but mechanisms for the role of adenosine in specific cell types, and whether cell autonomous or cell-nonautonomous mechanisms may be employed in sensing, are largely unknown.

Reviewer #2 (Public review):

Summary:

In this work, the authors wish to explore the metabolic support mechanisms enabling lamellocyte encapsulation, a critical antiparasitic immune response of insects. They show that S-adenosylmethionine metabolism is specifically important in this process through a combination of measurements of metabolite levels and genetic manipulations of this metabolic process.

Strengths:

The metabolite measurements and the functional analyses are generally very strong, and clearly show that the metabolic process under study is important in lamellocyte immune function.

Previous weaknesses:

The previous version of the manuscript contained RNAseq data that were inadequately explained. In this version, the treatment and representation of these data are significantly improved, such that they no longer represent a significant weakness. This version also contains increased evidence that SAM transmethylation is directly required for encapsulation.

Reviewer #3 (Public review):

Summary:

The authors of this study provides evidence that Drosophila immune cells show upregulated SAM transmethylation pathway and adenosine recycling upon wasp infection. Blocking this pathway compromises the lamellocyte formation, developmental delay and the host survival, suggesting its physiological relevance.

Strengths:

Snapshot quantification of the metabolite pool does not provide evidence that the metabolic pathway is active or not. The authors use an ex vivo isotope labelling to precisely monitor the SAM and adenosine metabolism. During infection, the methionine metabolism and adenosine recycling are upregulated, which is necessary to support the immune reaction. By combining the genetic experiment, they successfully show that the pathway is activated in immune cells.

Weaknesses:

The authors knocked down Ahcy to prove the importance of SAM methylation pathway. However, Ahcy-RNAi produces massive accumulation of SAH, in addition to block adenosine production. To further validate the phenotypic causality, it is important to manipulate other enzymes in the pathway, such as Sam-S, Cbs, SamDC, etc. The authors do not demonstrate how infection stimulates the metabolic pathway given the gene expression of metabolic enzymes is not upregulated by infection stimulus.

Reviewer #1 (Public review):

Summary:

Wang et al. created a series of specific FLIM-FRET sensors to measure the activity of different Rab proteins in small cellular compartments. They apply the new sensors to monitor Rab activity in dendritic spines during induction of LTP. They find sustained (30 min) inactivation of Rab10 and transient (5 min) activation of Rab4 after glutamate uncaging in zero Mg. NMDAR function and CaMKII activation are required for these effects. Knock-down of Rab4 reduced spine volume change while knock-down of Rab10 boosted it and enhanced functional LTP (in KO mice). To test Rab effects on AMPA receptor exocytosis, the authors performed FRAP of fluorescently labeled GluA1 subunits in the plasma membrane. Within 2-3 min, new AMPARs appear on the surface via exocytosis. This process is accelerated by Rab10 knock-down and slowed by Rab4 knock-down. The authors conclude that CaMKII promotes AMPAR exocytosis by i) activating Rab4, the exocytosis driver and ii) inhibiting Rab10, possibly involved in AMPAR degradation.

Strengths:

The work is a technical tour de force, adding fundamental insights to our understanding of the crucial functions of different Rab proteins in promoting/preventing synaptic plasticity. The complexity of compartmentalized Ras signaling is poorly understood and this study makes substantial inroads. The new sensors are thoroughly characterized, seem to work very well and will be quite useful for the neuroscience community and beyond (e.g. cancer research). The use of FLIM for read-out is compelling for precise activity measurements in rapidly expanding compartments (i.e., spines during LTP). In addition to structural changes, evidence for functional LTP is provided, too.

Weaknesses:

The interpretation of the FRAP experiments (Fig. 5, Ext. Data Fig. 13) is not straightforward as spine volume and surface area greatly expand during uncaging. I appreciate the correction for added spine membrane shown in Extended Data Fig. 14i.<br /> Pharmacological experiments were not conducted or analyzed blind, risking bias in the selection/exclusion of experiments for analysis.

Reviewer #2 (Public review):

Summary:

Wang et al. developed a set of optical sensors to monitor Rab protein activity. Their investigation into Rab activity in dendritic spines during structural long-term plasticity (sLTP) revealed sustained Rab10 inactivation (>30min) and transient Rab4 activation (~5 min). Through pharmacological and genetic manipulation to constitutively activate or inhibit Rab proteins, the authors discovered that Rab10 negatively regulates sLTP and AMPA receptor trafficking, while Rab4 positively influences sLTP but only during the transient phase. These optical sensors provide new tools for studying Rab activity in cell biology and neurobiology. The distinct kinetics and functions of Rab proteins are important for understanding synaptic plasticity. However, there are some concerns regarding result inconsistencies within this manuscript and with prior work.

Strengths:

(1) The introduction of a series of novel sensors that can address numerous questions in Rab biology.<br /> (2) The use of multiple methods to manipulate Rab proteins to reveal the roles of Rab10 and Rab4 in LTP.<br /> (3) The discovery of Rab4 activation and Rab10 inhibition with different kinetics during sLTP, correlating with their functional roles in the transient (Rab4) and both transient and sustained (Rab10) phases of sLTP.

Weaknesses:

(1) The discrepancy between spine phenotype and sLTP potential with Rab10 perturbation remains unexplained (refer to previous Weakness #4). The basal state is the outcome of many activity-dependent processes that are physiologically relevant. It is also unclear why different preparations would yield different results. These can be experimentally addressed, and it is at least important to highlight and discuss the discrepancies.<br /> (2) In the response, the authors estimated that the bleed-through from mEGFP-Rab is ~3% and the red channel signal from FRET changes is ~20%. The context of these percentages is unclear. Are they percentages of the total signal in the red channel, or does 3% refer to 3% of the green channel signal? Additionally, there is no explanation of how these numbers were estimated.<br /> (3) The changes in the fEPSP slope in response to theta burst stimulation (a decrease followed by a gradual increase) differ from prior publications (e.g. PMID: 1359925, 3967730, 19144965, 20016099). The explanation of these differences due to different conditions in response to Reviewer's recommendation #6 does not seem sufficient.

Reviewer #3 (Public review):

Summary:

This study examines the roles of Rab10 and Rab4 proteins in structural long-term potentiation (sLTP) and AMPA receptor (AMPAR) trafficking in hippocampal dendritic spines using various different methods and organotypic slice cultures as the biological model.<br /> The paper shows that Rab10 inactivation enhances AMPAR insertion and dendritic spine head volume increase during sLTP, while Rab4 supports the initial stages of these processes. The key contribution of this study is identifying Rab10 inactivation as a previously unknown facilitator of AMPAR insertion and spine growth, acting as a brake on sLTP when active. Rab4 and Rab10 seems to be playing opposing roles, suggesting a somewhat coordinated mechanism that precisely controls synaptic potentiation, with Rab4 facilitating early changes and Rab10 restricting the extent and timing of synaptic strengthening.

Strengths:

The study combines multiple techniques such as FRET/FLIM imaging, pharmacology, genetic manipulations and electrophysiology to dissect the roles of Rab10 and Rab4 in sLTP. The authors developed highly sensitive FRET/FLIM-based sensors to monitor Rab protein activity in single dendritic spines. This allowed them to study the spatiotemporal dynamics of Rab10 and Rab4 activity during glutamate uncaging induced sLTP. They also developed various controls to ensure the specificity of their observations. For example, they used a false acceptor sensor to verify the specificity of the Rab10 sensor response.

This study reveals previously unknown roles for Rab10 and Rab4 in synaptic plasticity, showing their opposing functions in regulating AMPAR trafficking and spine structural plasticity during LTP.

Weaknesses:

In the first round of revision I raised these points:

(1) In sLTP, the initial volume of stimulated spines is an important determinant of induced plasticity. To address changes in initial volume and those induced by uncaging, the authors present Extended Data Figure 2. In my view, the methods of fitting, sample selection, or both may pose significant limitations for interpreting the overall results. While the initial spine size distribution for Rab10 experiments spans ~0.1-0.4 fL (with an unusually large single spine at the upper end), Rab4 spine distribution spans a broader range of ~0.1-0.9 fL. If the authors applied initial size-matched data selection or used polynomial rather than linear fitting, panels a, b, e, f, and g might display a different pattern. In that case, clustering analysis based on initial size may be necessary to enable a fair comparison between groups-not only for this figure but also for main Figures 2 and 3.

- The authors responded to this point as follows: For sensor uncaging experiments, we usually uncaged glutamate at large mushroom spines because we need to have a good signal-to-noise ratio. We just happen to choose these spines with different initial sizes for Rab4 sensor and Rab10 sensor uncaging experiments.

Even if they happen to choose these spine sizes, it is possible to compare only those that match in size. This does not require any additional experiments. Because of this, I do not find this response satisfactory.

(2) Another limitation is the absence of in vivo validation, as the experiments were performed in organotypic hippocampal slices, which may not fully replicate the complexity of synaptic plasticity in an intact brain, where excitatory and inhibitory processes occur concurrently. High concentrations of MNI-glutamate (4 mM in this study) are known to block GABAergic responses due to its antagonistic effect on GABA-A receptors, thereby precluding the study of inhibitory network activity or connectivity, which is already known to be altered in organotypic slice cultures.

- I found the Authors following response reasonable and useful:

We appreciate the reviewer's comments and would like to clarify that we have conducted experiments in acute slices for LTP using conditional Rab10 knockout (Fig. 4k, 4l), and we obtained similar results. Additionally, we have recently published findings on the behavioral deficits observed in heterozygous Rab10 knockout mice (PubMed 37156612). These studies further support our conclusions and provide additional context for our findings.

Reviewer #1 (Public review):

SNeuronal activity spatiotemporal fine-tuning of cerebral blood flow balances metabolic demands of changing neuronal activity with blood supply. Several 'feed-forward' mechanisms have been described that contribute to activity-dependent vasodilation as well as vasoconstriction leading to a reduction in perfusion. Involved messengers are ionic (K+), gaseous (NO), peptides (e.g., NPY, VIP) and other messengers (PGE2, GABA, glutamate, norepinephrine) that target endothelial cells, smooth muscle cells, or pericytes. Contributions of the respective signaling pathways likely vary across brain regions or even within specific brain regions (e.g., across cortex) and are likely influenced by the brain's physiological state (resting, active, sleeping) or pathological departures from normal physiology.

The manuscript "Elevated pyramidal cell firing orchestrates arteriolar vasoconstriction through COX-2-derived prostaglandin E2 signaling" by B. Le Gac, et al. investigates mechanisms leading to activity-dependent arteriole constriction. Here, mainly working in brain slices from mice expressing channelrhodopsin 2 (ChR2) in all excitatory neurons (Emx1-Cre; Ai32 mice), the authors show that strong optogenetic stimulation of cortical pyramidal neurons is leading to constriction that is mediated through the cyclooxygenase-2 / prostaglandin E2 / EP1 and EP3 receptor pathway with contribution of NPY-releasing interneurons and astrocytes releasing 20-HETE. Specifically, using patch clamp, the authors show that 10-s optogenetic stimulation at 10 and 20 Hz leads to vasoconstriction (Figure 1), in line with a stimulation frequency-dependent increase in somatic calcium (Figure 2). The vascular effects were abolished in presence in TTX and significantly reduced in presence of glutamate receptor antagonists (Figure 3). The authors further show with RT-PCR on RNA isolated from patched cells that ~50% of analyzed cells express COX-1 or -2 and other enzymes required to produce PGE2 or PGF2a (Figure 4). Further, blockade of COX-1 and -2 (indomethacin), or COX-2 (NS-398) abolishes constriction. In animals with chronic cranial window that were anesthetized with ketamine and medetomidine, 10-s long optogenetic stimulation at 10 Hz leads to considerable constriction, which is reduced in presence of indomethacin. Blockade of EP1 and EP3 receptors leads to significant reduction of the constriction in slices (Figure 5). Finally, the authors show that blockade of 20-HETE synthesis caused moderate and NPY Y1 receptor blockade a complete reduction of constriction.

The mechanistic analysis of neurovascular coupling mechanisms as exemplified here will guide further in-vivo studies and has important implications for human neuroimaging in health and disease. Most of the data in this manuscript uses brain slices as experimental model which contrasts with neurovascular imaging studies performed in awake (headfixed) animals. However, the slice preparation allows for patch clamp as well as easy drug application and removal. Further, the authors discuss their results in view of differences between brain slices and in vivo observations experiments, including the absence of vascular tone as well as blood perfusion required for metabolite (e.g., PGE2) removal, and the presence of network effects in the intact brain. The manuscript and figures present the data clearly; regarding the presented mechanism, the data supports the authors conclusions. Some of the data was generated in vivo in head-fixed animals under anesthesia; in this regard, the authors should revise introduction and discussion to include the important distinction between studies performed in slices, or in acute or chronic in-vivo preparations under anesthesia (reduced network activity and reduced or blockade of neuromodulation, or in awake animals (virtually undisturbed network and neuromodulatory activity). Further, while discussed to some extent, the authors could improve their manuscript by more clearly stating if they expect the described mechanism to contribute to CBF regulation under 'resting state conditions' (i.e., in absence of any stimulus), during short or sustained (e.g., visual, tactile) stimulation, or if this mechanism is mainly relevant under pathological conditions; especially in context of the optogenetic stimulation paradigm being used (10-s long stimulation of many pyramidal neurons at moderate-high frequencies) and the fact that constriction leading to undersupply in response to strongly increased neuronal activity seems counterintuitive?

The authors have addressed all comments, and I appreciate their insightful discussion and revision of the manuscript.

Reviewer #2 (Public review):

Summary:

The present study by Le Gac et al. investigates the vasoconstriction of cerebral arteries during neurovascular coupling. It proposes that pyramidal neurons firing at high frequency lead to prostaglandin E2 (PGE2) release and activation of arteriolar EP1 and EP3 receptors, causing smooth muscle cell contraction. The authors further claim that interneurons and astrocytes also contribute to the vasoconstriction via neuropeptide Y (NPY) and 20-hydroxyeicosatetraenoic acid (20-HETE) release, respectively. The study mainly uses brain slices and pharmacological tools in combination with Emx1-Cre;Ai32 transgenic mice expressing the H134R variant of channelrhodopsin-2 (ChR2) in the cortical glutamatergic neurons for precise photoactivation. Stimulation with 470 nm light using 10-second trains of 5-ms pulses at frequencies from 1-20 Hz revealed small constrictions at 10 Hz and robust constrictions at 20 Hz, which were abolished by TTX and partially inhibited by a cocktail of glutamate receptor antagonists. Inhibition of cyclooxygenase-1 (COX-1) or -2 (COX-2) by indomethacin blocked the constriction both ex vivo (slices) and in vivo (pial artery), and inhibition of EP1 and EP3 showed the same effect ex vivo. Single-cell RT-PCR from patched neurons confirmed the presence of the PGE2 synthesis pathway. While the data are convincing, the overall experimental setting presents some limitations. How is the activation protocol comparable to physiological firing frequency? The delay (minutes) between the stimulation and the constriction appears contradictory to the proposed pathway, which would be expected to occur rapidly. The experiments are conducted in the absence of vascular "tone," which further questions the significance of the findings. Some of the targets investigated are expressed by multiple cell types, which makes the interpretation difficult; for example, cyclooxygenases are also expressed by endothelial cells. Finally, how is the complete inhibition of the constriction by the NPY Y1 receptor antagonist BIBP3226 consistent with a direct effect of PGE2 and 20-HETE in arterioles? Overall, the manuscript is well-written with clear data, but the interpretation and physiological relevance have some limitations. However, vasoconstriction is a rather understudied phenomenon in neurovascular coupling, and the present findings may be of significance in the context of pathological brain hypoperfusion.

Reviewer #1 (Public review):

Summary of what the authors were trying to achieve:

In this manuscript, the authors investigated the role of β-CTF on synaptic function and memory. They report that β-CTF can trigger the loss of synapses in neurons that were transiently transfected in cultured hippocampal slices and that this synapse loss occurs independently of Aβ. They confirmed previous research (Kim et al, Molecular Psychiatry, 2016) that β-CTF-induced cellular toxicity occurs through a mechanism involving a hexapeptide domain (YENPTY) in β-CTF that induces endosomal dysfunction. Although the current study also explores the role of β-CTF in synaptic and memory function in the brain using mice chronically expressing β-CTF, the studies are inconclusive because potential effects of Aβ generated by γ-secretase cleavage of β-CTF were not considered. Based on their findings, the authors suggest developing therapies to treat Alzheimer's disease by targeting β-CTF. While they acknowledge that clinical trials of potent BACE1 inhibitors - which also target β-CTF - have failed to show clinical improvement, their study lacks in vivo evidence directly linking β-CTF to brain function, which weakens its significance.

Major strengths and weaknesses of the methods and results:

The conclusions of the in vitro experiments using cultured hippocampal slices were well supported by the data, but aspects of the in vivo experiments need additional clarification.<br /> In contrast to the in vitro experiments in which a γ-secretase inhibitor was used to exclude possible effects of Aβ, this possibility was not examined in in vivo experiments assessing synapse loss and function (Fig. 3) and cognitive function (Fig. 4). The absence of plaque formation (Fig. 4C) is not sufficient to exclude the possibility that Aβ is involved. The potential involvement of Aβ is an important consideration given the 4-month duration of protein expression in the in vivo studies. This issue could be addressed using γ-secretase modulators to avoid the off-target effects of inhibitors. Evidence that the detrimental effects in mice are directly caused by β-CTF rather than indirectly via Aβ is critical to support the authors' conclusion.

Appraisal of whether the authors achieved their aims, and whether the results support their conclusion:

See above

Discussion of likely impact of the work on the field, and the utility of the methods and data to the community:

The authors' use of sparse expression to examine the role of β-CTF on spine loss could be a useful general tool for examining synapses in brain tissue.

Any additional context that might help readers interpret or understand the significance of the work:

The discovery of BACE1 stimulated an international effort to develop BACE1 inhibitors to treat Alzheimer's disease. BACE1 inhibitors block the formation of β-CTF which, in turn, prevents the formation of Aβ and other fragments. Unfortunately, BACE1 inhibitors not only did not improve cognition in patients with Alzheimer's disease, they appeared to worsen it, suggesting that β-CTF could facilitate learning and memory. Therefore, it seems unlikely that the disruptive effects of β-CTF on endosomes plays a significant role in the human disease.

Comments on revisions:

The authors may be interested in the study by Ma et al., PNAS 2007 titled "Involvement of β-site APP cleaving enzyme 1 (BACE1) in amyloid precursor protein-mediated enhancement of memory and activity-dependent synaptic plasticity," which provides significant insights into the physiological role of BACE1 in synaptic function. The researchers demonstrated that BACE1-mediated cleavage of amyloid precursor protein (APP) is essential for enhancing learning, memory, and synaptic plasticity in vivo. They observed that overexpression of APP in transgenic mice led to improved spatial memory retention and potentiation of synaptic plasticity, effects that were abolished when one or both copies of the BACE1 gene were eliminated. This suggests that BACE1's cleavage of APP facilitates activity-dependent synaptic modifications, potentially through the production of APP intracellular domain (AICD) via β-CTF, rather than amyloid-β (Aβ) or soluble APPα (sAPPα). These findings highlight a physiological mechanism where BACE1-mediated APP processing leading to β-CTF supports cognitive functions, potentially explaining the detrimental effects of BACE1 inhibitors on cognitive function in clinical trials.

Reviewer #3 (Public review):

Summary:

Most previous studies have focused on the contributions of Abeta and amyloid plaques in the neuronal degeneration associated with Alzheimer's disease, especially in the context of impaired synaptic transmission and plasticity which underlies the impaired cognitive functions, a hallmark in AD. But processes independent of Abeta and plaques are much less explored, and to some extent, the contributions of these processes are less well understood. Luo et all addressed this important question with an array of approaches, and their findings generally support the contribution of beta-CTF-dependent but non-Abeta dependent process to the impaired synaptic properties in the neurons. Interestingly, the above process appears to operate in a cell-autonomous manner. This cell-autonomous effect of beta-CTF as reported here may facilitate our understanding of some potential important cellular processes related to neurodegeneration. Although these findings are valuable, it is key to understand the probability of this process occurring in a more natural condition, such as when this process occurring in many neurons at the same time. This will put the authors' findings into a context for a better understanding of their contribution to either physiological or pathological processes, such as Alzheimer's. The experiments and results using cell system are quite solid, but the in vivo results are incomplete and hence less convincing (see below). The mechanistic analysis is interesting but primitive, and does not add much more weight to the significance. Hence, further efforts from the authors are required to clarify, and solidify their results, in order to provide a complete picture and support for the authors' conclusions.

Strengths:

(1) The authors have addressed an interesting and potentially important question<br /> (2) The analysis using the cell system are solid and provides strong support for the authors' major conclusions. This analysis has used various technical approaches to support the authors' conclusions from different aspects and most of these results are consistent with each other.

Weaknesses:

(1) The relevance of the authors' major findings to the pathology, especially the Abeta-dependent processes is less clear, and hence the importance of these findings may be limited.<br /> (2) In vivo analysis is incomplete, with certain caveats in the experimental procedures and some of the results need to be further explored to confirm the findings.<br /> (3) The mechanistic analysis is rather primitive and does not add further significance.

Comments on revisions:

The authors have satisfactorily addressed my main questions.

Reviewer #1 (Public review):

Summary:

This study investigated the mechanism underlying Congenital NAD Deficiency Disorder (CNDD) using a mouse model with loss of function of the HAAO enzyme which mediates a key step in the NAD de novo synthesis pathway. This study builds on the observation that the kynurenine pathway is required in the conceptus, as HAAO null embryos are sensitive to maternal deficiency of NAD precursors (vitamin B3) and tryptophan, and narrows the window of sensitivity to a 3 day period.

An important finding is that de novo NAD synthesis occurs in an extra-embryonic tissue, the visceral yolk sac, before the liver develops in the embryo. It is suggested that lack of this yolk sac activity leads to impaired NAD supply in the embryo leading to structural abnormalities found later in development.

Strengths:

Previous studies show a requirement for HAOO activity for normal development of the embryos develop abnormalities under conditions of maternal vitamin B3 deficiency, indicating a requirement for NAD synthesis in the conceptus. Analysis of scRNA-seq datasets combined with metabolite analysis of yolk sac tissue shows that the NAD synthesis pathway is expressed and functional in the yolk sac from E10.5 onwards (prior to liver development).

HAOO enzyme assay enabled quantification of enzyme activity in relevant tissues including liver (from E12.5), embryo, placenta and yolk sac (from E11.5).<br /> Comprehensive metabolite analysis of the NAD synthesis pathway supports the predicted effects of HAOO knockout and provides analysis of yolk sac, placenta and embryo at a series of stages.

The dietary study (with lower vitamin B3 in maternal diet from E7.5-10.5) is an incremental addition to previous studies which imposed similar restrictions from E7.5-12.5. Nevertheless, this emphasises the importance of the synthesis pathway on the conceptus at stages before liver activity is prominent.

Weaknesses:

The current dietary study narrows the period when deficiency can cause malformations (analysed at E18.5), and altered metabolite profiles (eg, increased 3HAA, lower NAD) are detected in yolk sac and embryo at E10.5.

More importantly, there is still a question of whether in addition to the yolks sac, there is HAAO activity within the embryo itself has been assayed as early as E11.5, with minimal activity prior to E12.5 (when it is assayed in liver). These findings support the hypothesis that within the conceptus (embryo, chorioallantoic placenta and visceral yok sac) the embryo is unlikely to be the site of NAD synthesis prior to liver development.

Evidence for lack of function of the NAD synthesis pathway in the embryos itself from kynurenine at E7.5-10.5 comes from reanalysis of scRNA-seq. This suggests low or absent expression of HAAO in the embryo prior to E10.5 (corresponding to the period when the authors have demonstrated that de novo NAD synthesis in the conceptus is needed). The caveat to this conclusion is that additional analysis of RNA and/or protein expression in the embryos at E7.5-10.5 has not been performed to validate the scRNA-seq data.

Reviewer #2 (Public review):

Summary:

Disruption of the nicotinamide adenine dinucleotide (NAD) de novo Synthesis Pathway, by which L-tryptophan is converted to NAD results in multi-organ malformations which collectively has been termed Congenital NAD Deficiency Disorder (CNDD).

While NAD de novo synthesis is primarily active in the liver postnatally, the site of activity prior to and during organogenesis is unknown. However, mouse embryos are susceptible to CNDD between E7.5-E12.5, before the embryo has developed a functional liver. Therefore, NAD de novo synthesis is likely active in another cell or tissue during this time window of susceptibility.

The body of work presented in this paper continues the corresponding author's labs investigation of the cause and effects of NAD Deficiency and the primary goal was to determine the cell or tissue responsible for NAD de novo synthesis during early embryogenesis.

The authors conclude that visceral yolk sac endoderm is the source of NAD de novo synthesis, which is essential for mouse embryonic development, and furthermore that the dynamics of NAD synthesis are conserved in human equivalent cells and tissues, the perturbation of which results in CNDD.

Strengths:

Overall, the primary findings regarding the source of NAD synthesis, the temporal requirement and conservation between rodent and human species is quite novel and important for our understanding of NAD synthesis and function and role in CNDD.

The authors used UHPLC-MS/MS to quantify NAD+ and NAD-related metabolites and showed convincingly that the NAD salvage pathway can compensate for the loss of NAD synthesis in Haao-/- embryos, then determined that Haao activity was present in the yolk sac prior to hepatic development identifying this organ as the site of de novo NAD synthesis. Dietary modulation between E7.5-10.5 was sufficient to induce CNDD phenotypes, narrowing the window of susceptibility, and then re-analysis of RNA-seq datasets suggested the endoderm was the cell source of NAD synthesis.

Weaknesses:

Page 4 and Table S4. The descriptors for malformations of organs such as the kidney and vertebrae are quite vague and uninformative. More specific details are required to convey the type and range of anomalies observed as a consequence of NAD deficiency.

Can the authors define whether the role for the NAD pathway in a couple of tissue or organ systems is the same. By this I mean is the molecular or cellular effect of NAD deficiency the same in the vertebrae and organs such as the kidney. What unifies the effects on these specific tissues and organs and are all tissues and organs affected. If some are not, can the authors explain why they escape the need for the NAD pathway.

Page 5 and Figure 6C. The expectation and conclusion for whether specific genes are expressed in particular cell types in scRNA-seq datasets depends on number of cells sequenced, the technology (methodology) used, the depth of sequencing and also the resolution of the analysis. It is therefore essential to perform secondary validation of the analysis of scRNA-seq data. At a minimum, the authors should perform in situ hybridization or immunostaining for Tdo2, Afmid, Kmo, Kynu, Haao, Qprt and Nadsyn1 or some combination thereof at multiple time points during early mouse embryogenesis to truly understand the spatiotemporal dynamics of expression and NAD synthesis.

Absolute functional proof of the yolk sac endoderm as being essential and required for NAD synthesis in the context of CNDD might require conditional deletion of Haao in the yolk sac versus embryo using appropriate Cre driver lines or in the absence of a conditional allele, could be performed by tetraploid embryo-ES cell complementation approaches. But temporal dietary intervention can also approximate the same thing by perturbing NAD synthesis then the yolk sac is the primary source versus when the liver becomes the primary source in the embryo.

In further revisions, the authors have added data to Supp Table 4 and Supplemental Figures 1 and 2

Although the authors did not perform in situ hybridization for some of the genes requested to define the critical cell type of expression, available scRNA-sequencing suggests the yolk sac endoderm are the only likely source of NAD synthesis prior to its synthesis in the liver. Absolute functional proof of the yolk sac endoderm as being essential and required for NAD synthesis in the context of CNDD still requires validation but nonetheless it seems likely given the absence of a functional liver in embryos prior to E12.5. The authors provided some additional data pertaining to the type of kidney and vertebral anomalies observed which makes this data more complete.

Reviewer #1 (Public review):

In this paper by Brickwedde et al., the authors observe an increase in posterior alpha when anticipating auditory as opposed to visual targets. The authors also observe an enhancement in both visual and auditory steady-state sensory evoked potentials in anticipation of auditory targets, in correlation with enhanced occipital alpha. The authors conclude that alpha does not reflect inhibition of early sensory processing, but rather orchestrates signal transmission to later stages of the sensory processing stream. However, there are several major concerns that need to be addressed in order to draw this conclusion.

First, I am not convinced that the frequency tagging method and the associated analyses are adequate for dissociating visual vs auditory steady-state sensory evoked potentials.

Second, if the authors want to propose a general revision for the function of alpha, it would be important to show that alpha effects in the visual cortex for visual perception are analogous to alpha effects in the auditory cortex for auditory perception.

Third, the authors propose an alternative function for alpha - that alpha orchestrates signal transmission to later stages of the sensory processing stream. However, the supporting evidence for this alternative function is lacking. I will elaborate on these major concerns below.

(1) Potential bleed-over across frequencies in the spectral domain is a major concern for all of the results in this paper. The fact that alpha power, 36Hz and 40Hz frequency-tagged amplitude and 4Hz intermodulation frequency power is generally correlated with one another amplifies this concern. The authors are attaching specific meaning to each of these frequencies, but perhaps there is simply a broadband increase in neural activity when anticipating an auditory target compared to a visual target?

(2) Moreover, 36Hz visual and 40Hz auditory signals are expected to be filtered in the neocortex. Applying standard filters and Hilbert transform to estimate sensory evoked potentials appears to rely on huge assumptions that are not fully substantiated in this paper. In Figure 4, 36Hz "visual" and 40Hz "auditory" signals seem largely indistinguishable from one another, suggesting that the analysis failed to fully demix these signals.

(3) The asymmetric results in the visual and auditory modalities preclude a modality-general conclusion about the function of alpha. However, much of the language seems to generalize across sensory modalities (e.g., use of the term 'sensory' rather than 'visual').

(4) In this vein, some of the conclusions would be far more convincing if there was at least a trend towards symmetry in source-localized analyses of MEG signals. For example, how does alpha power in the primary auditory cortex (A1) compare when anticipating auditory vs visual target? What do the frequency-tagged visual and auditory responses look like when just looking at the primary visual cortex (V1) or A1?

(5) Blinking would have a huge impact on the subject's ability to ignore the visual distractor. The best thing to do would be to exclude from analysis all trials where the subjects blinked during the cue-to-target interval. The authors mention that in the MEG experiment, "To remove blinks, trials with very large eye-movements (> 10 degrees of visual angle) were removed from the data (See supplement Fig. 5)." This sentence needs to be clarified since eye-movements cannot be measured during blinking. In addition, it seems possible to remove putative blink trials from EEG experiments as well, since blinks can be detected in the EEG signals.

(6) It would be interesting to examine the neutral cue trials in this task. For example, comparing auditory vs visual vs neutral cue conditions would be indicative of whether alpha was actively recruited or actively suppressed. In addition, comparing spectral activity during cue-to-target period on neutral-cue auditory correct vs incorrect trials should mimic the comparison of auditory-cue vs visual-cue trials. Likewise, neutral-cue visual correct vs incorrect trials should mimic the attention-related differences in visual-cue vs auditory-cue trials.

(7) In the abstract, the authors state that "This implies that alpha modulation does not solely regulate 'gain control' in early sensory areas but rather orchestrates signal transmission to later stages of the processing stream." However, I don't see any supporting evidence for the latter claim, that alpha orchestrates signal transmission to later stages of the processing stream. If the authors are claiming an alternative function to alpha, this claim should be strongly substantiated.

Reviewer #2 (Public review):

Brickwedde et al. investigate the role of alpha oscillations in allocating intermodal attention. A first EEG study is followed up with a MEG study that largely replicates the pattern of results (with small to be expected differences). They conclude that a brief increase in the amplitude of auditory and visual stimulus-driven continuous (steady-state) brain responses prior to the presentation of an auditory - but not visual - target speaks to the modulating role of alpha that leads them to revise a prevalent model of gating-by-inhibition.

Overall, this is an interesting study on a timely question, conducted with methods and analysis that are state-of-the-art. I am particularly impressed by the author's decision to replicate the earlier EEG experiment in MEG following the reviewer's comments on the original submission. Evidently, great care was taken to accommodate the reviewer's suggestions.

Nevertheless, I am struggling with the report for two main reasons: It is difficult to follow the rationale of the study, due to structural issues with the narrative and missing information or justifications for design and analysis decisions, and I am not convinced that the evidence is strong, or even relevant enough for revising the mentioned alpha inhibition theory. Both points are detailed further below.

Strength/relevance of evidence for model revision: The main argument rests on 1) a rather sustained alpha effect following the modality cue, 2) a rather transient effect on steady-state responses just before the expected presentation of a stimulus, and 3) a correlation between those two. Wouldn't the authors expect a sustained effect on sensory processing, as measured by steady-state amplitude irrespective of which of the scenarios described in Figure 1A (original vs revised alpha inhibition theory) applies? Also, doesn't this speak to the role of expectation effects due to consistent stimulus timing? An alternative explanation for the results may look like this: Modality-general increased steady-state responses prior to the expected audio stimulus onset are due to increased attention/vigilance. This effect may be exclusive (or more pronounced) in the attend-audio condition due to higher precision in temporal processing in the auditory sense or, vice versa, too smeared in time due to the inferior temporal resolution of visual processing for the attend-vision condition to be picked up consistently. As expectation effects will build up over the course of the experiment, i.e., while the participant is learning about the consistent stimulus timing, the correlation with alpha power may then be explained by a similar but potentially unrelated increase in alpha power over time.

Structural issues with the narrative and missing information: Here, I am mostly concerned with how this makes the research difficult to access for the reader. I list the major points below:

In the introduction the authors pit the original idea about alpha's role in gating against some recent contradictory results. If it's the aim of the study to provide evidence for either/or, predictions for the results from each perspective are missing. Also, it remains unclear how this relates to the distinction between original vs revised alpha inhibition theory (Fig. 1A). Relatedly if this revision is an outcome rather than a postulation for this study, it shouldn't be featured in the first figure.

The analysis of the intermodulation frequency makes a surprise entrance at the end of the Results section without an introduction as to its relevance for the study. This is provided only in the discussion, but with reference to multisensory integration, whereas the main focus of the study is focussed attention on one sense. (Relatedly, the reference to "theta oscillations" in this sections seems unclear without a reference to the overlapping frequency range, and potentially more explanation.) Overall, if there's no immediate relevance to this analysis, I would suggest removing it.

Reviewer #3 (Public review):

Brickwedde et al. attempt to clarify the role of alpha in sensory gain modulation by exploring the relationship between attention-related changes in alpha and attention-related changes in sensory-evoked responses, which surprisingly few studies have examined given the prevalence of the alpha inhibition hypothesis. The authors use robust methods and provide novel evidence that alpha likely exhibits inhibitory control over later processing, as opposed to early sensory processing, by providing source-localization data in a cross-modal attention task.

This paper seems very strong, particularly given that the follow-up MEG study both (a) clarifies the task design and separates the effect of distractor stimuli into other experimental blocks, and (b) provides source-localization data to more concretely address whether alpha inhibition is occurring at or after the level of sensory processing, and (c) replicates most of the EEG study's key findings.

There are some points that would be helpful to address to bolster the paper. First, the introduction would benefit from a somewhat deeper review of the literature, not just reviewing when the effects of alpha seem to occur, but also addressing how the effect can change depending on task and stimulus design (see review by Morrow, Elias & Samaha (2023). Additionally, the discussion could benefit from more cautionary language around the revision of the alpha inhibition account. For example, it would be helpful to address some of the possible discrepancies between alpha and SSEP measures in terms of temporal specificity, SNR, etc. (see Peylo, Hilla, & Sauseng, 2021). The authors do a good job speculating as to why they found differing results from previous cross-modal attention studies, but I'm also curious whether the authors think that alpha inhibition/modulation of sensory signals would have been different had the distractors been within the same modality or whether the cues indicated target location, rather than just modality, as has been the case in so much prior work?

Overall, the analyses and discussion are quite comprehensive, and I believe this paper to be an excellent contribution to the alpha-inhibition literature.

Reviewer #1 (Public review):

Summary:

The authors explore associations between plasma metabolites and glaucoma, a primary cause of irreversible vision loss worldwide. The study relies on measurements of 168 plasma metabolites in 4,658 glaucoma patients and 113,040 controls from the UK Biobank. The authors show that metabolites improve the prediction of glaucoma risk based on polygenic risk score (PRS) alone, albeit weakly. The authors also report a "metabolomic signature" that is associated with a reduced risk (or "resilience") for developing glaucoma among individuals in the highest PRS decile (reduction of risk by an estimated 29%). The authors highlight the protective effect of pyruvate, a product of glycolysis, for glaucoma development and show that this molecule mitigates elevated intraocular pressure and optic nerve damage in a mouse model of this disease.

Strengths:

This work provides additional evidence that glycolysis may play a role in the pathophysiology of glaucoma. Previous studies have demonstrated the existence of an inverse relationship between intraocular pressure and retinal pyruvate levels in animal models (Hader et al. 2020, PNAS 117(52)) and pyruvate supplementation is currently being explored for neuro-enhancement in patients with glaucoma (De Moraes et al. 2022, JAMA Ophthalmology 140(1)). The study design is rigorous and relies on validated, standard methods. Additional insights gained from a mouse model are valuable.

Weaknesses:

Caution is warranted when examining and interpreting the results of this study. Among all participants (cases and controls) glaucoma status was self-reported, determined on the basis of ICD codes or previous glaucoma laser/surgical therapy. This is problematic as it is not uncommon for individuals in the highest PRS decile to have undiagnosed glaucoma (as shown in previous work by some of the authors of this article). The authors acknowledge a "relatively low glaucoma prevalence in the highest decile group" but do not explore how undiagnosed glaucoma may affect their results. This also applies to all controls selected for this study. The authors state that "50 to 70% of people affected [with glaucoma] remain undiagnosed". Therefore, the absence of self-reported glaucoma does not necessarily indicate that the disease is not present. Validation of the findings from this study in humans is, therefore, critical. This should ideally be performed in a well-characterized glaucoma cohort, in which case and control status has been assessed by qualified clinicians.

The authors indicate that within the top decile of PRS participants with glaucoma are more likely to be of white ethnicity, while they are more likely to be of Black and Asian ethnicity if they are in the bottom half of PRS. Have the authors explored how sensitive their predictions are to ethnicity? Since their cohort is predominantly of European ancestry (85.8%), would it make sense to exclude other ethnicities to increase the homogeneity of the cohort and reduce the risk for confounders that may not be explicitly accounted for?

The authors discuss the importance of pyruvate, and lactate for retinal ganglion cell survival, along with that of several lipoproteins for neuroprotection. However, there is a distinction to be made between locally produced/available glycolysis end products and lipoproteins and those circulating in the blood. It may be useful to discuss this in the manuscript, and for the authors to explore if plasma metabolites may be linked to metabolism that takes place past the blood-retinal barrier.

Reviewer #2 (Public review):

Summary:

The authors have used the UK Biobank data to interrogate the association between plasma metabolites and glaucoma.

(1) They initially assessed plasma metabolites as predictors of glaucoma: The addition of NMR-derived metabolomic data to existing models containing clinical and genetic data was marginal.

(2) They then determined whether certain metabolites might protect against glaucoma in individuals at high genetic risk: Certain molecules in bioenergetic pathways (lactate, pyruvate, and citrate) conferred protection.

(3) They provide support for protection conferred by pyruvate in a murine model.

Strengths:

(1) The huge sample size supports a powerful statistical analysis and the opportunity for the inclusion of multiple covariates and interactions without overfitting the models.

(2) The authors have constructed a robust methodology and statistical design.

(3) The manuscript is well written, and the study is logically presented.

(4) The figures are of good quality.

(5) Broadly, the conclusions are justified by the findings.

Weaknesses:

(1) Although it is an invaluable treasure trove of data, selection bias and self-reporting are inescapable problems when using the UK Biobank data for glaucoma research. The high-impact glaucoma-related GWAS publications (references 26 and 27) referenced in support of the method suffer the same limitations. This doesn't negate the conclusions but must be taken into consideration. The authors might note that it is somewhat reassuring that the proportion of glaucoma cases (4%) is close to what would be expected in a population-based study of 40-69-year-olds of predominantly white ethnicity.

(2) As noted by the authors, a limitation is the predominantly white ethnicity profile that comprises the UK Biobank.

(3) Also as noted by the authors, the study is cross-sectional and is limited by the "correlation does not imply causation" issue.

(4) The optimal collection, transport, and processing of the samples for NMR metabolite analysis is critical for accurate results. Strict policies were in place for these procedures, but deviations from protocol remain an unknown influence on the data.

(5) In addition, all UK Biobank blood samples had unintended dilution during the initial sample storage process at UK Biobank facilities. (Julkunen, H. et al. Atlas of plasma NMR biomarkers for health and disease in 118,461 individuals from the UK Biobank. Nat Commun 14, 604 (2023) Samples from aliquot 3, used for the NMR measurements, suffered from 5-10% dilution. (Allen, Naomi E., et al. Wellcome Open Research 5 (2021): 222.) Julkunen et al. report that "The dilution is believed to come from mixing of participant samples with water due to seals that failed to hold a system vacuum in the automated liquid handling systems. While this issue is likely to have an impact on some of the absolute biomarker concentration values, it is expected to have limited impact on most epidemiological analyses."

Impact:

The findings advance personalized prognostics for glaucoma that combine metabolomic and genetic data. In addition, the protective effect of certain metabolites influences further research on novel therapeutic strategies.

Reviewer #1 (Public review):

Summary:

The study addresses how faces and bodies are integrated in two STS face areas revealed by fMRI in the primate brain. It builds upon recordings and analysis of the responses of large populations of neurons to three sets of images, that vary face and body positions. These sets allowed the authors to thoroughly investigate invariance to position on the screen (MC HC), to pose (P1 P2), to rotation (0 45 90 135 180 225 270 315), to inversion, to possible and impossible postures (all vs straight), to the presentation of head and body together or in isolation. By analyzing neuronal responses, they found that different neurons showed preferences for body orientation, head orientation, or the interaction between the two. By using a linear support vector machine classifier, they show that the neuronal population can decode head-body angle presented across orientations, in the anterior aSTS patch (but not middle mSTS patch), except for mirror orientation.

Strengths:

These results extend prior work on the role of Anterior STS fundus face area in face-body integration and its invariance to mirror symmetry, with a rigorous set of stimuli revealing the workings of these neuronal populations in processing individuals as a whole, in an important series of carefully designed conditions.

Minor issues and questions that could be addressed by the authors:

(1) Methods. While monkeys certainly infer/recognize that individual pictures refer to the same pose with varying orientations based on prior studies (Wang et al.), I am wondering whether in this study monkeys saw a full rotation of each of the monkey poses as a video before seeing the individual pictures of the different orientations, during recordings.

(2) Experiment 1. The authors mention that neurons are preselected as face-selective, body-selective, or both-selective. Do the Monkey Sum Index and ANOVA main effects change per Neuron type?

(3) I might have missed this information, but the correlation between P1 and P2 seems to not be tested although they carry similar behavioral relevance in terms of where attention is allocated and where the body is facing for each given head-body orientation.

(4) Is the invariance for position HC-MC larger in aSTS neurons compared to mSTS neurons, as could be expected from their larger receptive fields?

(5) L492 "The body-inversion effect likely results from greater exposure to upright than inverted bodies during development". Monkeys display more hanging upside-down behavior than humans, however, does the head appear more tilted in these natural configurations?

(6) Methods in Experiment 1. SVM. How many neurons are sufficient to decode the orientation?

(7) Figure 3D 3E. Could the authors please indicate for each of these neurons whether they show a main effect of face, body, or interaction, as well as their median corrected correlation to get a flavor of these numbers for these examples?

(8) Methods and Figure 1A. It could be informative to precise whether the recordings are carried in the lateral part of the STS or in the fundus of the STS both for aSTS and mSTS for comparison to other studies that are using these distinctions (AF, AL, MF, ML).

Wang, G., Obama, S., Yamashita, W. et al. Prior experience of rotation is not required for recognizing objects seen from different angles. Nat Neurosci 8, 1768-1775 (2005). https://doi-org.insb.bib.cnrs.fr/10.1038/nn1600

Reviewer #2 (Public review):

Summary:

This paper investigates the neuronal encoding of the relationship between head and body orientations in the brain. Specifically, the authors focus on the angular relationship between the head and body by employing virtual avatars. Neuronal responses were recorded electrophysiologically from two fMRI-defined areas in the superior temporal sulcus and analyzed using decoding methods. They found that: (1) anterior STS neurons encode head-body angle configurations; (2) these neurons distinguish aligned and opposite head-body configurations effectively, whereas mirror-symmetric configurations are more difficult to differentiate; and (3) an upside-down inversion diminishes the encoding of head-body angles. These findings advance our understanding of how visual perception of individuals is mediated, providing a fundamental clue as to how the primate brain processes the relationship between head and body - a process that is crucial for social communication.

Strengths:

The paper is clearly written, and the experimental design is thoughtfully constructed and detailed. The use of electrophysiological recordings from fMRI-defined areas elucidated the mechanism of head-body angle encoding at the level of local neuronal populations. Multiple experiments, control conditions, and detailed analyses thoroughly examined various factors that could affect the decoding results. The decoding methods effectively and consistently revealed the encoding of head-body angles in the anterior STS neurons. Consequently, this study offers valuable insights into the neuronal mechanisms underlying our capacity to integrate head and body cues for social cognition-a topic that is likely to captivate readers in this field.

Weaknesses:

I did not identify any major weaknesses in this paper; I only have a few minor comments and suggestions to enhance clarity and further strengthen the manuscript, as detailed in the Private Recommendations section.

Reviewer #3 (Public review):

Summary:

Zafirova et al. investigated the interaction of head and body orientation in the macaque superior temporal sulcus (STS). Combining fMRI and electrophysiology, they recorded responses of visual neurons to a monkey avatar with varying head and body orientations. They found that STS neurons integrate head and body information in a nonlinear way, showing selectivity for specific combinations of head-body orientations. Head-body configuration angles can be reliably decoded, particularly for neurons in the anterior STS. Furthermore, body inversion resulted in reduced decoding of head-body configuration angles. Compared to previous work that examined face or body alone, this study demonstrates how head and body information are integrated to compute a socially meaningful signal.

Strengths:

This work presents an elegant design of visual stimuli, with a monkey avatar of varying head and body orientations, making the analysis and interpretation straightforward. Together with several control experiments, the authors systematically investigated different aspects of head-body integration in the macaque STS. The results and analyses of the paper are mostly convincing.

Weaknesses:

(1) Using ANOVA, the authors demonstrate the existence of nonlinear interactions between head and body orientations. While this is a conventional way of identifying nonlinear interactions, it does not specify the exact type of the interaction. Although the computation of the head-body configuration angle requires some nonlinearity, it's unclear whether these interactions actually contribute. Figure 3 shows some example neurons, but a more detailed analysis is needed to reveal the diversity of the interactions. One suggestion would be to examine the relationship between the presence of an interaction and the neural encoding of the configuration angle.

(2) Figure 4 of the paper shows a better decoding of the configuration angle in the anterior STS than in the middle STS. This is an interesting result, suggesting a transformation in the neural representation between these two areas. However, some control analyses are needed to further elucidate the nature of this transformation. For example, what about the decoding of head and body orientations - dose absolute orientation information decrease along the hierarchy, accompanying the increase in configuration information?

(3) While this work has characterized the neural integration of head and body information in detail, it's unclear how the neural representation relates to the animal's perception. Behavioural experiments using the same set of stimuli could help address this question, but I agree that these additional experiments may be beyond the scope of the current paper. I think the authors should at least discuss the potential outcomes of such experiments, which can be tested in future studies.

Reviewer #1 (Public review):

Summary:

In this manuscript, the authors describe a new computational method (SegPore), which segments the raw signal from nanopore-direct RNA-Seq data to improve the identification of RNA modifications. In addition to signal segmentation, SegPore includes a Gaussian Mixture Model approach to differentiate modified and unmodified bases. SegPore uses Nanopolish to define a first segmentation, which is then refined into base and transition blocks. SegPore also includes a modification prediction model that is included in the output. The authors evaluate the segmentation in comparison to Nanopolish and Tombo, and they evaluate the impact on m6A RNA modification detection using data with known m6A sites. In comparison to existing methods, SegPore appears to improve the ability to detect m6A, suggesting that this approach could be used to improve the analysis of direct RNA-Seq data.

Strengths:

SegPore addresses an important problem (signal data segmentation). By refining the signal into transition and base blocks, noise appears to be reduced, leading to improved m6A identification at the site level as well as for single-read predictions. The authors provide a fully documented implementation, including a GPU version that reduces run time. The authors provide a detailed methods description, and the approach to refine segments appears to be new.

Weaknesses:

In addition to Nanopolish and Tombo, f5c and Uncalled4 can also be used for segmentation, however, the comparison to these methods is not shown. The overall improvement in accuracy appears to be relatively small. The run time and resources that are required to run SegPore are not shown, however, it appears that the GPU version is essential, which could limit the application of this method in practice. The method was only applied to data from the RNA002 direct RNA-Sequencing version, which is not available anymore, currently, it remains unclear if the methods still work on RNA004.

Reviewer #2 (Public review):

Summary:

The work seeks to improve the detection of RNA m6A modifications using Nanopore sequencing through improvements in raw data analysis. These improvements are said to be in the segmentation of the raw data, although the work appears to position the alignment of raw data to the reference sequence and some further processing as part of the segmentation, and result statistics are mostly shown on the 'data-assigned-to-kmer' level.

As such, the title, abstract, and introduction stating the improvement of just the 'segmentation' does not seem to match the work the manuscript actually presents, as the wording seems a bit too limited for the work involved.

The work itself shows minor improvements in m6Anet when replacing Nanopolish eventalign with this new approach, but clear improvements in the distributions of data assigned per kmer. However, these assignments were improved well enough to enable m6A calling from them directly, both at site-level and at read-level.

Strengths:

A large part of the improvements shown appear to stem from the addition of extra, non-base/kmer specific, states in the segmentation/assignment of the raw data, removing a significant portion of what can be considered technical noise for further analysis. Previous methods enforced the assignment of all raw data, forcing a technically optimal alignment that may lead to suboptimal results in downstream processing as data points could be assigned to neighbouring kmers instead, while random noise that is assigned to the correct kmer may also lead to errors in modification detection.

For an optimal alignment between the raw signal and the reference sequence, this approach may yield improvements for downstream processing using other tools.<br /> Additionally, the GMM used for calling the m6A modifications provides a useful, simple, and understandable logic to explain the reason a modification was called, as opposed to the black models that are nowadays often employed for these types of tasks.

Weaknesses:

The work seems limited in applicability largely due to the focus on the R9's 5mer models. The R9 flow cells are phased out and not available to buy anymore. Instead, the R10 flow cells with larger kmer models are the new standard, and the applicability of this tool on such data is not shown. We may expect similar behaviour from the raw sequencing data where the noise and transition states are still helpful, but the increased kmer size introduces a large amount of extra computing required to process data and without knowledge of how SegPore scales, it is difficult to tell how useful it will really be. The discussion suggests possible accuracy improvements moving to 7mers or 9mers, but no reason why this was not attempted.

The manuscript suggests the eventalign results are improved compared to Nanopolish. While this is believably shown to be true (Table 1), the effect on the use case presented, downstream differentiation between modified and unmodified status on a base/kmer, is likely limited as during actual modification calling the noisy distributions are usually 'good enough', and not skewed significantly in one direction to really affect the results too terribly.

Furthermore, looking at alternative approaches where this kind of segmentation could be applied, Nanopolish uses the main segmentation+alignment for a first alignment and follows up with a form of targeted local realignment/HMM test for modification calling (and for training too), decreasing the need for the near-perfect segmentation+alignment this work attempts to provide. Any tool applying a similar strategy probably largely negates the problems this manuscript aims to improve upon.

Finally, in the segmentation/alignment comparison to Nanopolish, the latter was not fitted(/trained) on the same data but appears to use the pre-trained model it comes with. For the sake of comparing segmentation/alignment quality directly, fitting Nanopolish on the same data used for SegPore could remove the influences of using different training datasets and focus on differences stemming from the algorithm itself.

Appraisal:

The authors have shown their method's ability to identify noise in the raw signal and remove their values from the segmentation and alignment, reducing its influences for further analyses. Figures directly comparing the values per kmer do show a visibly improved assignment of raw data per kmer. As a replacement for Nanopolish eventalign it seems to have a rather limited, but improved effect, on m6Anet results. At the single read level modification modification calling this work does appear to improve upon CHEUI.

Impact:

With the current developments for Nanopore-based modification largely focusing on Artificial Intelligence, Neural Networks, and the like, improvements made in interpretable approaches provide an important alternative that enables a deeper understanding of the data rather than providing a tool that plainly answers the question of whether a base is modified or not, without further explanation. The work presented is best viewed in the context of a workflow where one aims to get an optimal alignment between raw signal data and the reference base sequence for further processing. For example, as presented, as a possible replacement for Nanopolish eventalign. Here it might enable data exploration and downstream modification calling without the need for local realignments or other approaches that re-consider the distribution of raw data around the target motif, such as a 'local' Hidden Markov Model or Neural Networks. These possibilities are useful for a deeper understanding of the data and further tool development for modification detection works beyond m6A calling.

Reviewer #3 (Public review):

Summary:

Nucleotide modifications are important regulators of biological function, however, until recently, their study has been limited by the availability of appropriate analytical methods. Oxford Nanopore direct RNA sequencing preserves nucleotide modifications, permitting their study, however, many different nucleotide modifications lack an available base-caller to accurately identify them. Furthermore, existing tools are computationally intensive, and their results can be difficult to interpret.

Cheng et al. present SegPore, a method designed to improve the segmentation of direct RNA sequencing data and boost the accuracy of modified base detection.

Strengths:

This method is well-described and has been benchmarked against a range of publicly available base callers that have been designed to detect modified nucleotides.

Weaknesses:

However, the manuscript has a significant drawback in its current version. The most recent nanopore RNA base callers can distinguish between different ribonucleotide modifications, however, SegPore has not been benchmarked against these models.

I recommend that re-submission of the manuscript that includes benchmarking against the rna004_130bps_hac@v5.1.0 and rna004_130bps_sup@v5.1.0 dorado models, which are reported to detect m5C, m6A_DRACH, inosine_m6A and PseU.

A clear demonstration that SegPore also outperforms the newer RNA base caller models will confirm the utility of this method.

Reviewer #1 (Public review):

Summary:

Insects inhabit diverse environments and have neuroanatomical structures appropriate to each habitat. Although the molecular mechanism of insect neural development has been mainly studied in Drosophila, the beetle, Tribolium castaneum has been introduced as another model to understand the differences and similarities in the process of insect neural development. In this manuscript, the authors focused on the origin of the central complex. In Drosophila, type II neuroblasts have been known as the origin of the central complex. Then, the authors tried to identify those cells in the beetle brain. They established a Tribolium fez enhancer trap line to visualize putative type II neuroblasts and successfully identified 9 of those cells. In addition, they also examined expression patterns of several genes that are known to be expressed in the type II neuroblasts or their lineage in Drosophila. They concluded that the putative type II neuroblasts they identified were type II neuroblasts because those cells showed characteristics of type II neuroblasts in terms of genetic codes, cell diameter, and cell lineage.

Strengths:

The authors established a useful enhancer trap line to visualize type II neuroblasts in Tribolium embryos. Using this tool, they have identified that there are 9 type II neuroblasts in the brain hemisphere during embryonic development. Since the enhancer trap line also visualized the lineage of those cells, the authors found that the lineage size of the type II neuroblasts in the beetle is larger than that in the fly. They also showed that several genetic markers are also expressed in the type II neuroblasts and their lineages as observed in Drosophila.

Comments on revisions:

The revisions have improved the manuscript greatly. However, I still have some concerns about the lack of examination of the expression of NB markers. Without examining the expression of at least one unequivocal neuroblast marker, no one can say confidently that it is a neuroblast. However, it is acknowledged that such a marker is currently not available for Tribolium.

Reviewer #2 (Public review):

The authors address the question of differences in the development of the central complex (Cx), a brain structure mainly controlling spatial orientation and locomotion in insects, which can be traced back to the neuroblast lineages that produce the Cx structure. The lineages are called type-II neuroblast (NB) lineages and assumed to be conserved in insects. While Tribolium castaneum produces a functional larval Cx that only consists of one part of the adult Cx structure, the fan-shaped body, in Drosophila melanogaster a non-functional neuropile primordium is formed by neurons produced by the embryonic type-II NBs which then enter a dormant state and continue development in late larval and pupal stages.

The authors present a meticulous study demonstrating that type-II neuroblast (NB) lineages are indeed present in the developing brain of Tribolium castaneum. In contrast to type-I NB lineages, type-II NBs produce additional intermediate progenitors. The authors generate a fluorescent enhancer trap line called fez/earmuff which prominently labels the mushroom bodies but also the intermediate progenitors (INPs) of the type-II NB lineages. This is convincingly demonstrated by high resolution images that show cellular staining next to large pointed labelled cells, a marker for type-II NBs in Drosophila melanogaster. Using these and other markers (e.g. deadpan, asense), the authors show that the cell type composition and embryonic development of the type-II NB lineages are similar to their counterparts in Drosophila melanogaster. Furthermore, the expression of the Drosophila type-II NB lineage markers six3 and six4 in subsets of the Tribolium type-II NB lineages (anterior 1-4 and 1-6 type-II NB lineages) and the expression of the Cx marker skh in the distal part of most of the lineages provide further evidence that the identified NB lineages are equivalent to the Drosophila lineages that establish the central complex. However, in contrast to Drosophila, there are 9 instead of 8 embryonic type-II NB lineages per brain hemisphere and the lineages contain more progenitor cells compared to the Drosophila lineages. The authors argue that the higher number of dividing progenitor cells supports the earlier development of a functional Cx in Tribolium.

While the manuscript clearly shows that type-II NB lineages similar to Drosophila exist in Tribolium, it does not establish a direct link between the characteristics of these lineages and a functional larval Cx in Tribolium, i.e., it does not identify the cause of the heterochronic development of the Cx in these insects. However, the detailed study lays the foundation for lineage tracing and gene function experiments that will elucidate if the higher number of Tribolium type-II NB lineage progenitors, the additional lineage and the timing of developmental progression of the progenitors can indeed be linked with the earlier function of the Cx and/or if other components are required for establishing the functional larval neural circuits in Tribolium such as e.g. larval born neurons as is the case in Drosophila.

Reviewer #3 (Public review):

Summary:

In this paper, Rethemeier et al capitalize on their previous observation that the beetle central complex develops heterochronically compared to the fly and try to identify the developmental origin of this difference. For this reason, they use a fez enhancer trap line that they generated to study the neuronal stem cells (INPs) that give rise to the central complex. Using this line and staining against Drosophila type-II neuroblast markers, they elegantly dissect the number of developmental progression of the beetle type II neuroblasts. They show that the NBs, INPs, and GMCs have a conserved marker progression by comparing to Drosophila marker genes, although the expression of some of the lineage markers (otd, six3, and six4) is slightly different. Finally, they show that the beetle type II neuroblasts lineages are likely longer than the equivalent ones in Drosophila and argue that this might be the underlying reason for the observed heterochrony.

Strengths:

- Very interesting study system that compares a conserved structure that, however, develops in a heterochronic manner.<br /> - Identification of a conserved molecular signature of type-II neuroblasts between beetles and flies. At the same time, identification of transcription factors expression differences in the neuroblasts, as well as identification of an extra neuroblast.<br /> - Nice detailed experiments to describe the expression of conserved and divergent marker genes, including some lineaging looking into co-expression of progenitor (fez) and neuronal (skh) markers.

Weaknesses:

- The link between size and number of neuroblast lineages and the earlier central complex development in beetles is not examined.

Reviewer #2 (Public review):

Summary:

In the work by Scerbo et al, the authors aim to better understand the open question of what factors constrain cells that are genetically predisposed to form cancer (e.g. those with a potentially cancer-causing mutation like activated Ras) to only infrequently undergo this malignant transformation, with a focus on the influence of embryonic or pluripotency factors (e.g. VENTX/NANOG). Using genetically defined zebrafish models, the authors can inducibly express the KRASG12V oncogene using a combination of Cre/Lox transgenes further controlled by optogenetically inducible Cre-activated (CreER fusion that becomes active with light-induced uncaging of a tamoxifen-analogue in a targeted region of the zebrafish embryo). They further show that transient expression and activation of a pluripotency factor (e.g. Ventx fused to a GR receptor that is activated with addition of dexamethasone) must occur in the model in order for overgrowth of cells to occur. This paper describes a genetically tractable and modifiable system for studying the requirements for inducing cellular hyperplasia in a whole organism by combining overexpression of canonical genetic drivers of cancer (like Ras) with epigenetic modifiers (like specific transcription factors), which could be used to study an array of combinations and temporal relationships of these cancer drivers/modifiers.

Strengths:

The combination of Cre/lox inducible gene expression with potentially localized optogenetic induction (CreER and uncaging of tamoxifen analogues) of recombination as well as inducible activation of a transcription factor expressed via mRNA injection (GR-fusion to the TF and dex induction) offers a flexible system for manipulating cell growth, identity, and transcriptional programs. With this system, the authors establish that Ras activation and at least transient Ventx overexpression are together required to induce a hyperproliferative phenotype in zebrafish tissues.

The ability to live image embryos over the course of days with inducible fluorophores indicating recombination events and transgene overexpression offers a tractable in vivo system for studying hyperplastic cells in the context of a whole organism.

The transplant experiments demonstrate the ability of the induced hyperplastic cells to grow upon transfer to new host.

Weaknesses:

There is minimal quantitation of key aspects of the system, most critically in the efficiency of activation of the Ras-TFP fusion (Fig 1) in, purportedly, a single cell. The authors note "On average the oncogene is then activated in a single cell, identified within ~1h by the blue fluorescence of its nuclear marker) but no additional quantitative information is provided. For a system that is aimed at "a statistically relevant single-cell<br /> tracking and characterization of the early stages of tumorigenesis", such information seems essential.

The authors indicate that a single cell is "initiated" (Fig 2) using the laser optogenetic technique, but without definitive genetic lineage tracing, it is not possible to conclude that cells expressing TFP distant from the target site near the ear are daughter cells of the claimed single "initiated" cell. A plausible alternative explanation is 1) that the optogenetic targeting is more diffuse (i.e. some of the light of the appropriate wavelength hits other cells nearby due to reflection/diffraction), so these adjacent cells are additional independent "initiated" cells or 2) that the uncaged tamoxifen analogue can diffuse to nearby cells and allow for CreER activation and recombination. In Fig 2B, the claim is made that "the activated cell has divided, giving rise to two cells" - unless continuously imaged or genetically traced, this is unproven. In addition, it appears that Figures S3 and S4 are showing that hyperplasica can arise in many different tissues (including intestine, pancreas, and liver, S4C) with broad Ras + Ventx activation (while unclear from the text, it appears these embryos were broadly activated and were not "single cell activated using the set-up in Fig 1E? This should be clarified in the manuscript). In Fig S7 where single cell activation and potential metastasis is discussed, similar gut tissues have TFP+ cells that are called metastatic, but this seems consistent with the possibility that multiple independent sites of initiation are occurring even when focal activation is attempted.

Although the hyperplastic cells are transplantable (Fig 4), the use of the term "cells of origin of cancer" or metastatic cells should be viewed with care in the experiments showing TFP+ cells (Fig 1, 2, 3) in embryos with targeted activation for the reasons noted above.

Comments on latest version:

The authors have clarified and strengthened a number of important conclusions/claims.

In Figure 4, the requirement for both kRas and VentX activation for successful transplant and survival of transplanted activated cells does indeed support the need for both MAPK activation and the reprogramming factor. A limitation remains that, as in a tail vein injection in a mouse model, this may be a better measure of the ability of disbursed cells to survive in the embryo, and not "native" metastatic behavior as cells may just lodge in ectopic sites, and survive, but not exhibit complete metastatic potential. Still, these are interesting and important results about the combination effects of an oncogene and a reprogramming factor.

Further, the addition of Fig 2A and additional explanation in the text on the specificity of the light-induced activation of the Ras and/or VentX supports that transgene induction is indeed limited to one or a few cells. We agree that visual tracking of daughter cells over days is technically challenging and will be a revealing and exciting potential addition in the future.

Reviewer #3 (Public review):

Summary:

This study employs an optogenetics approach aimed at activating oncogene (KRASG12V) expression in a single somatic cell, with a focus on following the progression of activated cell to examine tumourigenesis probabilities under altered tissue environments. The research explores the role of stemness factors (VENTX/NANOG/OCT4) in facilitating oncogenic RAS (KRASG12V)-driven malignant transformations. Although the evidence provided is incomplete, the authors propose an important mechanism whereby reactivation of re-programming factors correlates with the increased likelihood of a mutant cell undergoing malignant transformation.

Strengths:

· Innovative Use of Optogenetics: The application of optogenetics for precise activation of KRAS in a single cell is valuable to the field of cancer biology, offering an opportunity to uncover insight into cellular responses to oncogenic mutations.<br /> · Important Observations: The findings concerning stemness factors' role in promoting oncogenic transformation are important, contributing data to the field of cancer biology.

Weaknesses:

Lack of Methodological Clarity: The manuscript lacks detailed descriptions of methodologies, making it difficult to fully evaluate the experimental design and reproducibility, rendering incomplete evidence to support the conclusion. Improving methodological transparency and data presentation will crucially strengthen the paper's contributions to understanding the complex processes of tumorigenesis.

Sub-optimal Data Presentation and Quality:<br /> The resolution of images through-out the manuscript are too low. Images presented in Figure 2 and Figure 4 are of very low resolution. It is very hard to distinguish individual cells and in which tissue they might reside.<br /> Lack of quantitative data and control condition data obtained from images of higher magnification limits the ability to robustly support the conclusions.

Here are some details:<br /> · Tissue specificity of the cells express KRASG12V oncogene: In this study, the ubiquitin promoter was used to drive oncogenic KRASG12V expression. Despite this, the authors claim to activate KRAS in a single brain cell based on their localized photo-activation strategy. However, upon reviewing the methods section, the description was provided that 'Localized uncaging was performed by illumination for 7 minutes on a Nikon Ti microscope equipped with a light source peaking at 405 nm, Figure 1. The size of the uncaging region was controlled by an iris that defines a circular illumination with a diameter of approximately 80 μm.' It is surprising that an epi-fluorescent microscope with an illumination diameter of around 80μm can induce activation in a single brain cell beneath skin tissue. Additionally, given that the half-life for mTFP maturation is around 60 minutes, it is likely that more cells from a variety of different lineages could be activated, but the fluorescence would not be visible until more than 1-hour post-illumination. Authors might want to provide more evidence to support their claim on the single cell KRAS activation.<br /> · Stability of cCYC: The manuscript does not provide information on the half-life and stability of cCYC. Understanding these properties is crucial for evaluating the system's reliability and the likelihood of leakiness, which could significantly influence the study's outcomes.<br /> · Metastatic Dissemination claim: Typically, metastatic cancer cells migrate to and proliferate within specific niches that are conducive to outgrowth, such as the caudal hematopoietic tissue (CHT) or liver. In Figure 3 A, an image showing the presence of mTFP expressing cells in both the head and tail regions of the larva, with additional positive dots located at the fin fold. This is interpreted as "metastasis" by the authors. However, the absence of supportive cellular compartment within the fin-fold tissue makes the presence of mTFP-positive metastatic cells there particularly puzzling. This distribution raises concerns about the spatial specificity of the optogenetic activation protocol.<br /> The unexpected locations of these signals suggest potential ectopic activation of the KRAS oncogene, which could be occurring alongside or instead of targeted activation. This issue is critical as it could affect the interpretation of whether the observed mTFP signal expansion over time is due to actual cell proliferation and infiltration, or merely a result of ectopic RAS transgene activation.<br /> · Image Resolution Concerns: The cells depicted in Figure 3C β, which appear to be near the surface of the yolk sac and not within the digestive system as suggested in the MS, underscore the necessity for higher-resolution imaging. Without clearer images, it is challenging to ascertain the exact locations and states of these cells, thus complicating the assessment of experimental results.<br /> · The cell transplantation experiment is lacking protocol details: The manuscript does not adequately describe the experimental protocols used for cell transplantation, particularly concerning the origin and selection of cells used for injection into individual larvae. This omission makes it difficult to evaluate the reliability and reproducibility of the results. Such as the source of transplanted cells:<br /> • If the cells are derived from hyperplastic growths in larvae where RAS and VX (presumably VENTX) were locally activated, the manuscript fails to mention any use of fluorescence-activated cell sorting (FACS) to enrich mTFP-positive cells. Such a method would be crucial for ensuring the specificity of the cells being studied and the validity of the results.<br /> • If the cells are obtained from whole larvae with induced RAS + VX expression, it is notable and somewhat surprising that the larvae survived up to six days post-induction (6dpi) before cells were harvested for transplantation. This survival rate and the subsequent ability to obtain single cell suspensions raise questions about the heterogeneity of the RAS + VX expressing cells that transplanted.<br /> · Unclear Experimental Conditions in Figure S3B: The images in Figure S3B lack crucial details about the experimental conditions. It is not specified whether the activation of KRAS was targeted to specific cells or involved whole-body exposure. This information is essential for interpreting the scope and implications of the results accurately.<br /> · Contrasting Data in Figure S3C compared to literatures: The graph in Figure S3C indicates that KRAS or KRAS + DEX induction did not result in any form of hyperplastic growth. This observation starkly contrasts with previous literature where oncogenic KRAS expression in zebrafish led to significant hyper-proliferation and abnormal growth, as evidenced by studies such as those published in and Neoplasia (2018), DOI: 10.1016/j.neo.2018.10.002; Molecular Cancer (2015), DOI: 10.1186/s12943-015-0288-2; Disease Models & Mechanisms (2014) DOI: 10.1242/dmm.007831. The lack of expected hyperplasia raises questions about the experimental setup or the specific conditions under which KRAS was expressed. The authors should provide detailed descriptions of the conditions under which the experiments were conducted in Figure S3B and clarifying the reasons for the discrepancies observed in Figure S3C are crucial. The authors should discuss potential reasons for the deviation from previous reports.<br /> Further comments:<br /> Throughout the study, KRAS-activated cell expansion and metastasis are two key phenotypes discussed that Ventx is promoting. However, the authors did not perform any experiments to directly show that KRAS+ cells proliferate only in Ventx-activated conditions. The authors also did not show any morphological features or time-lapse videos demonstrating that KRAS+ cells are motile, even though zebrafish is an excellent model for in vivo live imaging. This seems to be a missed opportunity for providing convincing evidence to support the authors' conclusions.<br /> There were minimal experimental details provided for the qPCR data presented in the supplementary figures S5 and S6, therefore, it is hard to evaluate results obtained.

Reviewer #1 (Public review):

When different groups (populations, species) are presented with similar environmental pressures, how similar are the ultimate targets (genes, pathways)? This study sought to illuminate this broader question via experimental evolution in D. simulans and quantifying gene-expression changes, specifically in the context of standing genetic variation (and not de novo mutation). Ultimately, the authors showed pleiotropy and standing-genetic variation play a significant role in the "predictability" of evolution.

The results of this manuscript look at the interplay between pleiotropy, standing genetic variation and parallelism (i.e. predictability of evolution) in gene expression. Ultimately, their results suggest that (a) pleiotropic genes typically have a smaller range in variation/expression, and (b) adaptation to similar environments tends to favor changes in pleiotropic genes, which leads to parallelism in mechanisms (though not dramatically). However, it is still uncertain how much parallelism is directly due to pleiotropy, instead of a complex interplay between them and ancestral variation.

Reviewer #2 (Public review):

Summary:

Lai and collaborators use a previously published RNAseq dataset derived from an experimental evolution set up to compare the pleiotropic properties of genes which expression evolved in response to fluctuating temperature for over 100 generations. The authors correlate gene pleiotropy with the degree of parallelisms in the experimental evolution set up to ask: are genes that evolved in multiple replicates more or less pleiotropic?

They find that, maybe counter to expectation, highly pleiotropic genes show more replicated evolution. And such effect seems to be driven by direct effects (which the authors can only speculate on) and indirect effect through low variance in pleiotropic genes (which the authors indirectly link to genetic variation underlying gene expression variance).

Weaknesses:

The results offer new insights into the evolution of gene expression and into the parameters that constrain such evolution, i.e., pleiotropy. Although the conclusions are supported by the data, I find the interpretation of the results a little bit complicated.

Major comment:

The major point I ask the authors to address is whether the connection between polygenic adaptation and parallelism can indeed be used to interpret gene expression parallelism. If the answer is not, please rephrase the introduction and discussion, if the answer is yes, please make it explicit in the text why it is so.

The authors argument: parallelism in gene expression is the same as parallelism in SNP allele frequency (AFC) (see L389-383 here they don't mention that this explanation is derived from SNP parallelism and not trait parallelism, and see Fig1 b). In previous publications the authors have explained the low level of AFC parallelism using a polygenic argument. Polygenic traits can reach a new trait optimum via multiple SNPs and therefore although the trait is parallel across replicates, the SNPs are not necessarily so.

In the current paper, they seem to be exchanging SNP AFC by gene expression, and to me, those are two levels that cannot be interchanged. Gene expression is a trait, not a SNP, and therefore the fact that a gene expression doesn't replicate cannot be explained by polygenic basis, because again the trait is gene expression itself. And, actually the results of the simulations show that high polygenicity = less trait parallelism (Fig4).

Now, if the authors focus on high parallel genes (present in e.g. 7 or more replicates) and they show that the eQTLs for those genes are many (highly polygenic) and the AFC of those eQTL are not parallel, then I would agree with the interpretation. But, given that here they just assess gene expression and not eQTL AFC, I do not think they can use the 'highly polygenic = low parallelism' explanation.

The interpretation of the results to me, should be limited to: genes with low variance and high pleiotropy tend to be more parallel, and the explanation might be synergistic pleiotropy.

Comments on revisions: The authors didn't really address any of the comments made by any of the reviewers - basically nothing was changed in the main text. Therefore, I leave my original review unchanged.

Reviewer #3 (Public review):

The authors aim to understand how gene pleiotropy affects parallel evolutionary changes among independent replicates of adaptation to a new hot environment of a set of experimental lines of Drosophila simulans using experimental evolution. The flies were RNAsequenced after more than 100 generations of lab adaptation and the changes in average gene expression were obtained relative to ancestral expression levels from reconstructed ancestral lines. Parallelism of gene expression change among lines is evaluated as variance in differential gene expression among lines relative to error variance. Similarly, the authors ask how the standing variation in gene expression estimated from a handful of flies from a reconstructed outbred line affects parallelism. The main findings are that parallelism in gene expression responses is positively associated with pleiotropy and negatively associated with expression variation. Those results are in contradiction with theoretical predictions and empirical findings. To explain those seemingly contradictory results the authors invoke the role of synergistic pleiotropy and correlated selection, although they do not attempt to measure either.

Strengths:

The study uses highly replicated outbred laboratory lines of Drosophila simulans evolved in the lab under constant hot regime for over 100 generations. This allows for robust comparisons of evolutionary responses among lines.

The manuscript is well written and the hypotheses are clearly delineated at the onset.

The authors have run a causal analysis to understand the causal dependencies between pleiotropy and expression variation on parallelism.

The use of whole-body RNA extraction to study gene expression variation is well justified.

Weaknesses:

The accuracy of the estimate of ancestral phenotypic variation in gene expression is likely low because estimated from a small sample of 20 males from a reconstructed outbred line. It might not constitute a robust estimate of the genetic variation of the evolved lines under study.

There are no estimates of the standing genetic variation of expression levels of the genes under study, only estimates of their phenotypic variation. I wished the authors had been clear about that limitation and had refrained from equating phenotypic variation in expression level with standing genetic variation.

Moreover, since the phenotype studied is gene expression, its genetic basis extends beyond expressed sequences. The phenotypic variation of a gene's expression may thus likely misrepresent the genetic variation available for its evolution. The authors do not present evidence that sequence variation correlates with expression variation.

The authors have not attempted to estimate synergistic pleiotropy among genes, nor how selection acts on gene expression modules. It makes their conclusion regarding the role of synergistic pleiotropy rather speculative.

Reviewer #1 (Public review):

Summary

The authors conducted a study on one of the fundamental research topics in neuroscience: neural mechanisms of credit assignment. Building on the original studies of Walton and his colleagues and subsequent studies on the same topic, the authors extended the research into the delayed credit assignment problem with clever task design, which compared the non-delayed (direct) and delayed (indirect) credit assignment processes. Their primary goal was to elucidate the neural basis of these processes in humans, advancing our understanding beyond previous studies.

Major Strengths and Considerations

Strengths:

(1) Innovative task design distinguishing between direct and indirect credit assignment.<br /> (2) Use of sophisticated multivariate pattern analysis to identify neural correlates of pending representations.<br /> (3) Well-executed study with clear presentation of results.<br /> (4) Extension of previous research to human subjects, providing valuable comparative insights.

Considerations for Future Research:

(1) The task design, while clear and effective, might be further developed to capture more real-world complexity in credit assignment.<br /> (2) There's potential for deeper exploration of the role of task structure understanding in credit assignment processes.<br /> (3) The interpretation of lateral orbitofrontal cortex (lOFC) involvement could be expanded to consider its role in both credit assignment and task structure representation.

Achievement of Aims and Support of Conclusions

The authors successfully achieved their aim of investigating direct and indirect credit assignment processes in humans. Their results provide valuable insights into the neural representations involved in these processes. The study's conclusions are generally well-supported by the data, particularly in identifying neural correlates of pending representations crucial for delayed credit assignment.

Impact on the Field and Utility of Methods

This study makes a significant contribution to the field of credit assignment research by bridging animal and human studies. The methods, particularly the multivariate pattern analysis approach, provide a robust template for future investigations in this area. The data generated offers valuable insights for researchers comparing human and animal models of credit assignment, as well as those studying the neural basis of decision-making and learning.

The study's focus on the lOFC and its role in credit assignment adds to our understanding of this brain region's function

Additional Context and Future Directions

(1) Temporal ambiguity in credit assignment: While the current design provides clear task conditions, future studies could explore more ambiguous scenarios to further reflect real-world complexity.

(2) Role of task structure understanding: The difference in task comprehension between human subjects in this study and animal subjects in previous studies offers an interesting point of comparison.

(3) The authors used a sophisticated method of multivariate pattern analysis to find the neural correlate of the pending representation of the previous choice, which will be used for credit assignment process in the later trials. The authors tend to use expressions that these representations are maintained throughout this intervening period. However the analysis period is specifically at the feedback period, which is irrelevant for the credit assignment of the immediately preceding choice. This task period can interfere with the interference of ongoing credit assignment process. Thus, rather than the passive process of maintaining the information of the previous choice, the activity of this specific period can mean the active process of protecting the information from interfering and irrelevant information. It would be great if the authors could comment on this important interpretational issue.

(4) Broader neural involvement: While the focus on specific regions of interest (ROIs) provided clear results, future studies could benefit from a whole-brain analysis approach to provide a more comprehensive understanding of the neural networks involved in credit assignment.

Comments after the revision:

The authors have adequately addressed the majority of concerns raised in my previous review. The manuscript has demonstrably improved as a result of these revisions and represents a valuable contribution to the literature on credit assignment.

However, some limitations persist that, while not readily resolvable within the scope of the current study, warrant attention. Specifically, the investigation focuses primarily on the temporal dimension of credit assignment. In real-world scenarios, the complexity of credit assignment extends beyond temporal distance to encompass the inherent ambiguity of causal attribution arising from the presence of multiple potential causal events. Resolving this ambiguity necessitates a form of structural understanding of the environment, a capacity presumably possessed by humans and animals. While the experimental design of this study provides explicit cues regarding the structure of the environment, deciphering such structure in natural settings is a crucial component of the credit assignment process.<br /> Future research should prioritize the investigation of credit assignment within more ecologically valid contexts, focusing on the role of structural understanding in navigating the causal ambiguity inherent in real-world environments. Addressing this aspect will be crucial for developing a more complete and nuanced understanding of credit assignment mechanisms.

In addition, the newly added whole-brain searchlight decoding analysis provides an important nuance regarding the neural substrates of credit assignment (Figure S7). The results reveal not only activity in the lateral orbitofrontal cortex (lOFC), but also, and more robustly, in the medial orbitofrontal cortex/ventromedial prefrontal cortex (mOFC/vmPFC) specifically during the "indirect transition condition" and not the "direct transition condition." This finding suggests a potentially more significant role for mOFC/vmPFC in processing complex, non-immediate credit assignment scenarios. This nuance should be explicitly noted to appreciate the complexity of the neural mechanisms at play.

Reviewer #2 (Public review):

Summary:

The present manuscript addresses a longstanding challenge in neuroscience: how the brain assigns credit for delayed outcomes, especially in real-world learning scenarios where decisions and outcomes are separated by time. The authors focus on the lateral orbitofrontal cortex and hippocampus, key regions involved in contingent learning. By integrating fMRI data and behavioral tasks, the authors examined how neural circuits maintain a causal link between past decisions and delayed outcomes. Their findings offer insights into mechanisms that could have critical implications for understanding human decision-making.

Strengths:

- The experimental designs were extremely well thought-out. The authors successfully coupled behavioral data and neural measures (through fMRI) to explore the neural mechanisms of contingent learning. This integration adds robustness to the findings and strengthens their relevance.<br /> - The emphasis on the interaction between the lateral orbitofrontal cortex (lOFC) and hippocampus (HC) in this study is very well-targeted. The reported findings regarding their dynamic interactions provide valuable insights into contingent learning in humans.<br /> - The use of advanced modeling framework and analytical techniques allowed the authors to uncover new mechanistic insights regarding a complex case of decision-making process. The methods developed will also benefit analyses of future neuroimaging data on a range of decision-making tasks as well.

Weaknesses:

- Given the limited temporal resolution of fMRI and that the measured signal is an indirect measure of neural activity, it is unclear the extent to which the reported causality reflects the true relationship/interactions between neurons in different regions. That said, I believe this concern is minimized by a series of well-thought-out and robust analyses which consistently point to compelling results.

Comments on revisions:

Thank you for your thorough point-by-point responses to my comments and questions. After carefully reviewing the responses and additional analyses/results provided, I do not have further comments. Importantly, I believe the authors have done a great job addressing inevitable limitations that are inherent to fMRI signals. The thoughtful analyses used in the study combined with the timely questions the manuscript is able to address make the study an important contribution to the field.

Reviewer #3 (Public review):

The authors apply multivoxel decoding analyses from fMRI during reward feedback about the cues previously chosen that led to that feedback. They compare two versions of the task - one in which the feedback is provided about the current trial, and one in which the feedback is provided about the previous trial. Reward probability changes slowly over time, so subjects need to identify which cues are leading to reward at a given time. They find that evidence for recall of the cue in lateral orbitofrontal cortex (lOFC) and hippocampus (HC). They also find that in the second condition, where feedback is for the one-back trial, this representation is mediated by the lateral frontal pole (FPl).

Overall, the analyses are clean and elegant and seem to be complete. I have only a few comments, all of which can be public.

(1) They do find (not surprisingly) that the one-back task is harder. It would be good to ensure that the reason that they had more trouble detecting direct HC & lOFC effects on the harder task was not because the task is harder and thus that there are more learning failures on the harder one-back task. (I suspect their explanation that it is mediated by FPl is likely to be correct. But it would be nice to do some subsampling of the zero-back task [matched to the success rate of the one-back task] to ensure that they still see the direct HC and lOFC there.)

(2) The evidence that they present in the main text (Figure 3) that the HC and lOFC are mediated by FPl is a correlation. I found the evidence presented in Supplemental Figure 7 to be much more convincing. As I understand it, what they are showing in SF7 is that when FPl decodes the cue, then (and only then) HC and lOFC decode the cue. If my understanding is correct, then this is a much cleaner explanation for what is going on than the secondary correlation analysis. If my understanding here is incorrect, then they should provide a better explanation of what is going on so as to not confuse the reader.

(3) I like the idea of "credit spreading" across trials (Figure 1E). I think that credit spreading in each direction (into the past [lower left] and into the future [upper right]) is not equivalent. This can be seen in Figure 1D, where the two tasks show credit spreading differently. I think a lot more could be studied here. Does credit spreading in each of these directions decode in interesting ways in different places in the brain?

Comments on revisions:

After revision, I have no additional comments.

Reviewer #2 (Public review):

This manuscript determines how PA28g, a proteasome regulator that is overexpressed in tumors, and C1QBP, a mitochondrial protein for maintaining oxidative phosphorylation that plays a role in tumor progression, interact in tumor cells to promote their growth, migration and invasion. Evidence for the interaction and its impact on mitochondrial form and function was provided although it is not particularly strong.

The revised manuscript corrected mislabeled data in figures and provides more details in figure legends. Misleading sentences and typos were corrected. However, key experiments that were suggested in previous reviews were not done, such as making point mutations to disrupt the protein interactions and assess the consequence on protein stability and function. Results from these experiments are critical to determine whether the major conclusions are fully supported by the data.

The second revision of the manuscript included the proximity ligation data to support the PA28g-C1QBP interaction in cells. However, the method and data were not described in sufficient detail for readers to understand. The revision also includes the structural models of the PA28g-C1QBP complex predicted by AlphaFold. However, the method and data were not described with details for readers to understand how this structural modeling was done, what is the quality of the resulting models, and the physical nature of the protein-protein interaction such as what kind of the non-covalent interactions exist in the interface of the protein complexes. Furthermore, while the interactions mediated by the protein fragments were tested by pull-down experiments, the interactions mediated by the three residues were not tested by mutagenesis and pull-down experiments. In summary, the revision was improved, but further improvement is needed

Reviewer #1 (Public review):

Summary:

Barlow and coauthors utilized the high-parameter imaging platform of CODEX to characterize the cellular composition of immune cells in situ from tissues obtained from organ donors with type 1 diabetes, subjects presented with autoantibodies who are at elevated risk, or non-diabetic organ donor controls. The panels used in this important study were based up prior publications using this technology, as well a priori and domain specific knowledge of the field by the investigators. Thus, there was some bias in the markers selected for analysis. The authors acknowledge that these types of experiments may be complemented moving forward with the inclusion of unbiased tissue analysis platforms that are emerging that can conduct a more comprehensive analysis of pathological signatures employing emerging technologies for both high-parameter protein imaging and spatial transcriptomics.

Strengths:

In terms of major findings, the authors provide important confirmatory observations regarding a number of autoimmune-associated signatures reported previously. The high parameter staining now increases the resolution for linking these features with specific cellular subsets using machine learning algorithms. These signatures include a robust signature indicative of IFN-driven responses that would be expected to induce a cytotoxic T cell mediated immune response within the pancreas. Notable findings include the upregulation of indolamine 2,3-dioxygenase-1 in the islet microvasculature. Furthermore, the authors provide key insights as to the cell:cell interactions within organ donors, again supporting a previously reported interaction between presumably autoreactive T and B cells.

Weaknesses:

These studies also highlight a number of molecular pathways that will require additional validation studies to more completely understand whether they are potentially causal for pathology, or rather, epiphenomenon associated with increased innate inflammation within the pancreas of T1D subjects. Given the limitations noted above, the study does present a rich and integrated dataset for analysis of enriched immune markers that can be segmented and annotated within distinct cellular networks. This enabled the authors to analyze distinct cellular subsets and phenotypes in situ, including within islets that peri-islet infiltration and/or intra-islet insulitis.

Despite the many technical challenges and unique organ donor cohort utilized, the data are still limited in terms of subject numbers - a challenge in a disease characterized by extensive heterogeneity in terms of age of onset and clinical and histopathological presentation. Therefore, these studies cannot adequately account for all of the potential covariates that may drive variability and alterations in the histopathologies observed (such as age of onset, background genetics, and organ donor conditions). In this study, the manuscript and figures could be improved in terms of clarifying how variable the observed signatures were across each individual donor, with the clear notion that non-diabetic donors will present with some similar challenges and variability.

Reviewer #2 (Public review):

Summary:

The authors aimed to characterize the cellular phenotype and spatial relationship of cell types infiltrating the islets of Langerhans in human T1D using CODEX, a multiplexed examination of cellular markers

Strengths:

Major strengths of this study are the use of pancreas tissue from well-characterized tissue donors, the use of CODEX, a state-of-the-art detection technique of extensive characterization and spatial characterization of cell types and cellular interactions. The authors have achieved their aims with the identification of the heterogeneity of the CD8+ T cell populations in insulitis, the identification of a vasculature phenotype and other markers that may mark insulitis-prone islets, and characterization of tertiary lymphoid structures in the acinar tissue of the pancreas. These findings are very likely to have a positive impact on our understanding (conceptual advance) of the cellular factors involved in T1D pathogenesis which the field requires to make progress in therapeutics.

Weaknesses:

A major limitation of the study is the cohort size, which the authors directly state. However, this study provides avenues of inquiry for researchers to gain further understanding of the pathological process in human T1D.

Comments on revisions:

The authors have responded well to the 3 critiques. They have addressed my specific comments in their revised text.<br /> I have no further comments.

Reviewer #3 (Public review):

Summary:

The authors applied an innovative approach (CO-Detection by indEXing - CODEX) together with sophisticated computational analyses to image pancreas tissues from rare organ donors with type 1 diabetes. They aimed to assess key features of inflammation in both islet and extra-islet tissue areas; they report that the extra-islet space of lobules with extensive islet infiltration differs from the extra-islet space of less infiltrated areas within the same tissue section. The study also identifies four sub-states of inflamed islets characterized by the activation profiles of CD8+T cells enriched in islets relative to the surrounding tissue. Lymphoid structures are identified in the pancreas tissue away from islets, and these were enriched in CD45RA+ T cells - a population also enriched in one of the inflamed islet sub-states. Together, these data help define the coordination between islets and the extra-islet pancreas in the pathogenesis of human T1D.

Strengths:

The analysis of tissue from well-characterized organ donors, provided by the Network for the Pancreatic Organ Donor with Diabetes, adds strength to the validity of the findings.

By using their innovative imaging/computation approaches, key known features of islet autoimmunity were confirmed, providing validation of the methodology.

The detection of IDO+ vasculature in inflamed islets - but not in normal islets or islets that have lost insulin-expression links this expression to the islet inflammation, and it is a novel observation. IDO expression in the vasculature may be induced by inflammation and may lost as disease progresses, and it may provide a potential therapeutic avenue.

The high-dimensional spatial phenotyping of CD8+T cells in T1D islets confirmed that most T cells were antigen experienced. Some additional subsets were noted: a small population of T cells expressing CD45RA and CD69, possibly naive or TEMRA cells, and cells expressing Lag-3, Granzyme-B, and ICOS.

While much attention has been devoted to the study of the insulitis lesion in T1D, our current knowledge is quite limited; the description of four sub-clusters characterized by the<br /> activation profile of the islet-infiltrating CD8+T cells is novel. Their presence in all T1D donors, indicates that the disease process is asynchronous and is not at the same stage across all islets. Although this concept is not novel, this appears to be the most advanced characterization of insulitis stages.

When examining together both the exocrine and islet areas, which is rarely done, authors report that pancreatic lobules affected by insulitis are characterized by distinct tissue markers. Their data support the concept that disease progression may require crosstalk between cells in the islet and extra-islet compartments. Lobules enriched in β-cell-depleted islets were also enriched in nerves, vasculature, and Granzyme-B+/CD3- cells, which may be natural killer cells.

Lastly, authors report that immature tertiary lymphoid structures (TLS) exist both near and away from islets, where CD45RA+ CD8+T cells aggregate, and also observed an inflamed islet-subcluster characterized by an abundance of CD45RA+/CD8+ T cells. These TLS may represent a point of entry for T cells and this study further supports their role in islet autoimmunity.

Weaknesses:

As the author themselves acknowledge, the major limitation is that the number of donors examined is limited as those satisfying study criteria are rare. Thus, it is not possible to examine disease heterogeneity, and the impact of age at diagnosis. Of 8 T1D donors examined, 4 would be considered newly diagnosed (less than 3 months from onset) and 4 had longer disease durations (2, 2, 5 and 6 years). It was unclear if disease duration impacted the results in this small cohort. In the introduction, the authors discuss that most of the pancreata from nPOD donors with T1D lack insulitis. This is correct, yet it is a function of time from diagnosis. Donors with shorter duration will be more likely to have insulitis. A related point is that the proportion of islets with insulitis is low even near diagnosis, Finally, only one donor was examined that while not diagnosed with T1D, was likely in the preclinical disease stage and had autoantibodies and insulitis. This is a critically important disease stage where the methodology developed by the investigators could be applied in future efforts.

While this was not the focus of this investigation, it appears that the approach was very much immune-focused and there could be value in examining islet cells in greater depth using the methodology the authors developed.

Additional comments

Overall, the authors were able to study pancreas tissues from T1D donors and perform sophisticated imaging and computational analysis that reproduce and importantly extend our understanding of inflammation in T1D. Despite the limitations associated with the small sample size, the results appear robust, and the claims are well supported.

The study expands the conceptual framework of inflammation and islet autoimmunity, especially by the definition of different clusters (stages) of insulitis and by the characterization of immune cells in and outside the islets.

Comments on revisions:

I have not felt the need to update the initial review.

However, I note that the paragraph describing the nPOD repository (lines 154-158) can be misinterpreted that insulitis is infrequent in T1D (17 of 200 donors had it) without the clarification that insulitis is present around the time of diagnosis in most patients and it subsides over time. Thus, authors are urged to clarify that the presence of insulitis and its severity are impacted by the disease stage and disease duration.

The last sentence of this paragraph, lines 164-165, although linked to the previous sentence about the cause of death in the donors, may be misconstrued in the context of this paragraph, and it is unclear what data support this statement. Please delete this sentence.

Reviewer #3 (Public review):

Summary:

The authors have thoroughly addressed all my concerns. The revised version of the current manuscript is solid now. It's very interesting that there is bi-potential ability of human CD29/CD56+ myogenic progenitors. The current study substantiates the medical translational potential for human CD29/CD56+ myogenic progenitors in promoting tendon regeneration.

Strengths:

CD29+/CD56+ stem/progenitor cells were transplanted into immunodeficient mice with a tendon injury, and human cells expressing tenogenic markers contributed to the repair of the injured tendon. Furthermore, the authors also show better tendon biomechanical properties and plantarflexion force after transplantation.

Weaknesses:

None. The authors have thoroughly addressed all my concerns.

Reviewer #1 (Public review):

The fundamental claim of the manuscript is that rRNA genes experience substitutions much too quickly, given that they are a multi-copy gene system. As clarified by the authors in their response, and as I think is relatively clear in the manuscript, they are collapsing all copies of the rRNA array down. They first quantify polymorphism (in this expanded definition, where polymorphism means variable at a given site across any copy). The authors find elevated levels of heterozygosity in rRNA genes compared to single copy genes, which isn't surprising, given that there is a substantially higher target size; that being said, the increase in polymorphism is smaller than the increase in target size. They then look at substitutions between mouse species and also between human and chimp, and argue that the substitution rate is too fast compared to single copy genes in many cases.

[Editors' note: we invite readers to consult the review in full from the previous version of the submission: https://doi.org/10.7554/eLife.99992.2.sa1]

Reviewer #2 (Public review):

This revision has further improved the clarity of the paper, better articulating assumptions of the model and data analysis. I particularly appreciate the authors' thorough response to eLife assessment. However, the authors did not provide point-by-point response to the specific comments I had from last round of review and didn't revise the manuscript accordingly, so my major concerns remain.

At conceptual level, my biggest concern with the model is the lack of constraint on V*(K), which makes the null neutral model too "liberal". On the one hand, the number of descendants of each gene copy must be non-negative; on the other hand, even homogenizing process within an individual is extremely strong, it cannot "spread" gene copies across individuals, so the maximum number of descendants of one gene copy cannot exceed the number of offspring that individual has times C. For these reasons, I believe there must be a theoretical upper bound of the value of V*(K), and the actual V*(K) is likely much smaller under realistic strength of the homogenizing process. When I asked about modeling of the underlying homogenizing process, I did not mean the authors need to include specific molecular process in the model; instead, I am asking the authors to provide some realistic scenarios that can give rise to very large V*(K) values. As a result of the very "liberal" neutral model, although I do agree that rejection of null provides stronger evidence for selection in human, it is unclear whether there is no evidence of selection in mouse. Please see below for my specific comments regarding the definition and assumptions of V*(K) (copied from last review).

Regarding the data analysis, although I understand the authors' methodology and rationale behind, I am not convinced that high sequence similarity between rDNA copies guarantees no biases in alignment and variant calling. Furthermore, given divergence between species, I am particularly concerned about the practice of aligning reads of different species to human and mus musculus reference sequences. A separate issue is the calculation of divergence level. Instead of using Fst>0.8 as the criterion of calling fixed sites, the authors could calculate the pairwise average divergence between a random copy from one species and a random copy from another species. Mathematically, this could be calculated as p1(1-p2)+p2(1-p1). The observation that the estimated substitution rates for rDNA with and without CpG sites are so close seems to be an indication of technical error. Please also see below for my specific questions about data analysis (copied from last round of review).

Specific comments from last round of review:

Questions regarding V*(K)<br /> (1) Another key parameter V*(K) was still not defined within the paper. In response 9, the authors explained that V*(K) refers to "the number of progeny to whom the gene copy of interest is transmitted (K) over a specific time interval". However, the meaning of "progeny" remains unclear. Are the authors referring to the descendent copies of a gene copy, or the offspring individuals (i.e., the living organisms)? For example, if a variant spreads horizontally through homogenizing processes and transmits vertically to multiple offspring individuals, the number of descent gene copies could differ substantially from the number of descendent individuals to whom a gene copy is transmitted to. This distinction needs to be clarified and clearly stated in the paper.

(2) The authors state that V*(K)>=1 for rDNA genes because of the homogenizing processes (lines 139-141) without providing justification. It is unclear, at least to me, whether homogenizing processes are expected increase or decrease the variance in "reproductive success" across gene copies. Moreover, the authors claim that V*(K) "can potentially reach values in the hundreds and may even exceed C, resulting in C*=C/V*(K)<1" (Response 7). This claim is unlikely to be true, as the minimum value of K is bounded by zero and E(K) is assumed to be 1. Even in the extreme case that 1% gene copies leave large numbers of descends while the others leave none, V*(K) would still be less than 100. Such extreme case seems highly improbable, given realistic rates of the homogenizing processes.

(3) Regardless of how the authors define V*(K), it is not immediately clear why Equation 1 (N*=NC/V*(K)) holds. Both sides of the equation have their independent meanings, so the authors need to provide a step-by-step derivation demonstrating that they are equal. Only by doing this will the implicit underlying assumptions become clearer. I also strongly recommend that the authors conduct forward-in-time simulations with fixed N, C, V*(K) (however they define it) and μ to confirm that the right side of Equation 1 actually predicts the N* as calculated from the polymorphism level using the equation in line 165.

Questions about Ne* for multi-copy system

(1) While Ne is clearly defined in the standard single-copy gene model as the reciprocal of genetic drift (i.e., the decay in heterozygosity), its meaning for multiple-copy genes is unclear. Based on the context, it appears that the authors define Ne as the parameter that fits the population polymorphism level (Hs) using the equation in line 165. This definition is reasonable, but it should be explicitly clarified in the text."

(2) Without providing justification, the authors assumed that a certain number N* exists for rRNA such that it fits both the polymorphism level (line 156) in recent timescales and divergence level in longer timescales (i.e., in the comparison between Tf and Td). However, if N, C or any other relevant parameters have varied substantially throughout evolution, N* is expected to vary with time, and the same value may not fit both polymorphism and divergence data simultaneously.

Questions about data analysis

(1) A significant issue with aligning reads to a single reference genome is reference bias, referring to the phenomenon that reads carrying the reference alleles tend to align more easily than those with one or more non-reference alleles, thus creating a bias in genotype calling or variant allele frequency quantification. As a result, there may be an underrepresentation of non-reference alleles in called variants or an underestimate of non-reference allele frequency, particularly in regions with high genetic diversity. Simply focusing on bi-allelic SNVs is insufficient to minimize reference bias. Given the fourfold increase in diversity within rDNA, the authors must either provide evidence that reference bias is not a significant concern or adopt graph-based reference genomes or more sophisticated alignment algorithms to address this issue.

(2) The potential for reference bias also renders the analysis of divergence sites unreliable, as aligning reads from one species (e.g. chimpanzee) to the reference of another species (e.g., human) is likely to introduce biases in variant calling between the two. One commonly adopted approach to address this imbalance is to align reads from both species to a third reference genome that is expected to be equidistantly related to both.

(3) Although it is somewhat reassuring that the estimated divergence rate of rDNA between human and macaque is comparable to that of the rest of the genome, there still remains concern of a under-estimation of divergence in rDNA regions due to reference bias issue. Note that while the "third genome" approach reduces imbalance between two genomes in comparison, it may still under-estimate overall divergence level due to under-calling of non-reference variants.<br /> (4) In response to my question about the similarity in rDNA substitution rates estimated with or without CpG sites, the authors suggest that this "may be due to strong homogenizing forces, which can rapidly fix or eliminate variants" (response17). However, this explanation is insufficient, because the observed substitution rate depends on the mutation rate multiplied by the fixation probability, and accelerated fixation or loss does not alter either. Unless the authors can provide more convincing explanation, technical errors in calling of fixed sites still remain a concern.

Minor points:

Line 157: The statement "where μ is the mutation rate of the entire gene" must be wrong, as the heterozygosity calculated with such μ would correspond to the chance of seeing two different haplotypes at gene level, which is incompatible with the empirical calculation specified in Equation 2. Instead, μ must represent the mutation rate per site averaged over the entire gene.

In response 22, the authors explained that the allele frequency spectrum shown in Fig 3 is folded, because the ancestral allele was not determined. However, this is inconsistent with x-axis Fig 3 ranging between 0 and 1. I suspect the x-axis represents the frequency of the alternative (i.e., non-reference) allele. If so, the reported correlation is inflated, as the reference allele is somewhat random, and a variant at joint ALT allele frequencies of (0.9, 0.9) is no different from a variant at (0.1, 0.1). The proper way of calculate this correlation is to first determine the minor allele frequency across individuals and then calculate the correlation between minor allele frequencies.

Similarly, in response 14, it is unclear what the x-axis represents. Is it the ALT allele frequency or derived allele frequency? If the former, why are only variants with AF>0.8 defined as fixed variants, while those with AF<0.2 excluded? If it is the latter, please describe how ancestral state is determined.

Reviewer #1 (Public review):

The revision by Ruan et al clarifies several aspects of the original manuscript that were difficult to understand, and I think it presents some useful and interesting ideas. I understand that the authors are distinguishing their model from the standard Wright-Fisher model in that the population size is not imposed externally, but is instead a consequence of the stochastic reproduction scheme. Here, the authors chose a branching process but in principle any Markov chain can probably be used. Within this framework, the authors are particularly interested in cases where the variance in reproductive success changes through time, as explored by the DDH model, for example. They argue with some experimental results that there is a reason to believe that the variance in reproductive success does change over time.

One of the key aspects of the original manuscript that I want to engage with is the DDH model. As the authors point out, their equations 5 and 6 are assumptions, and not derived from any principles. In essence, the authors are positing that that the variance in reproductive success, given by 6, changes as a function of the current population size. There is nothing "inherent" to a negative binomial branching mechanism that results in this: in fact, the the variance in offspring number could in principle be the same for all time. As relates to models that exist in the literature, I believe that this is the key difference: unlike Cannings models, the authors allow for a changing variance in reproduction through time.

This is, of course, an interesting thing to consider, and I think that the situation the authors point out, in which drift is lower at small population sizes and larger at large population sizes, is not appreciated in the literature. However, I am not so sure that there is anything that needs to be resolved in Paradox 1. A very strong prediction of that model is that Ne and N could be inversely related, as shown by the blue line in Fig 3b. This suggests that you could see something very strange if you, for example, infer a population size history using a Wright-Fisher framework, because you would infer a population *decline* when there is in fact a population *expansion*. However, as far as I know there are very few "surprising population declines" found in empirical data. An obvious case where we know there is very rapid population growth is human populations; I don't think I've ever seen an inference of recent human demographic history from genetic data that suggests anything other than a massive population expansion. While I appreciate the authors empirical data supporting their claim of Paradox 1 (more on the empirical data later), it's not clear to me that there's a "paradox" in the literature that needs explaining so much as this is a "words of caution about interpreting inferred effective population sizes". To be clear, I think those words of caution are important, and I had never considered that you might be so fundamentally misled as to infer decline when there is growth, but calling it a "paradox" seems to suggest that this is an outstanding problem in the literature, when in fact I think the authors are raising a *new* and important problem. Perhaps an interesting thing for the authors to do to raise the salience of this point would be to perform simulations under this model and then infer effective population sizes using e.g. dadi or psmc and show that you could identify a situation in which the true history is one of growth, but the best fit would be one of decline

The authors also highlight that their approach reflects a case where the population size is determined by the population dynamics themselves, as opposed to being imposed externally as is typical in Cannings models. I agree with the authors that this aspect of population regulation is understudied. Nonetheless, several manuscripts have dealt with the case of population genetic dynamics in populations of stochastically fluctuating size. For example, Kaj and Krone (2003) show that under pretty general conditions you get something very much like a standard coalescent; for example, combining their theorem 1 with their arguments on page 36 and 37, they find that exchangeable populations with stochastic population dynamics where the variance does not change with time still converge to exactly the coalescent you would expect from Cannings models. This is strongly suggestive that the authors key result isn't about stochastic population dynamics per se, but instead related to arguing that variance in reproductive success could change through time. In fact, I believe that the result of Kaj and Krone (2003) is substantially more general than the models considered in this manuscript. That being said, I believe that the authors of this manuscript do a much better job of making the implications for evolutionary processes clear than Kaj and Krone, which is important---it's very difficult to understand from Kaj and Krone the conditions under which effective population sizes will be substantially impacted by stochastic population dynamics.

I also find the authors exposition on Paradox 3 to be somewhat strange. First of all, I'm not sure there's a paradox there at all? The authors claim that the lack of dependence of the fixation probability on Ne is a paradox, but this is ultimately not surprising---fixation of a positively selected allele depends mostly on escaping the boundary layer, which doesn't really depend on the population size (see Gillespie's book "The Causes of Molecular Evolution" for great exposition on boundary layer effects). Moreover, the authors *use a Cannings-style argument* to get gain a good approximation of how the fixation probability changes when there is non-Poisson reproduction. So it's not clear that the WFH model is really doing a lot of work here. I suppose they raise the interesting point that the particularly simple form of p(fix) = 2s is due to the assumption that variance in offspring is equal to 1.

In addition, I raised some concerns about the analysis of empirical results on reproductive variance in my original review, and I don't believe that the authors responded to it at all. I'm not super worried about that analysis, but I think that the authors should probably respond to me.

Overall, I feel like I now have a better understanding of this manuscript. However, I think it still presents its results too strongly: Paradox 1 contains important words of caution that reflect what I am confident is an under appreciated possibility, and Paradox 3 is, as far as I'm concerned, not a paradox at all. I have not addressed Paradox 2 very much because I think that another reviewer had solid and interesting comments on that front and I am leaving it to them. That being said, I do think Paradox 2 actually presents a deep problem in the literature and that the authors' argument may actually represent a path toward a solution.

This manuscript can be a useful contribution to the literature, but as it's presented at the moment, I think most of it is worded too strongly and it continues to not engage appropriately with the literature. Theoretical advances are undoubtedly important, and I think the manuscript presents some interesting things to think about, but ultimately needs to be better situated and several of the claims strongly toned down.

References:<br /> Kaj, I., & Krone, S. M. (2003). The coalescent process in a population with stochastically varying size. Journal of Applied Probability, 40(1), 33-48.

Reviewer #2 (Public review):

Summary:

This theoretical paper examines genetic drift in scenarios deviating from the standard Wright-Fisher model. The authors discuss Haldane's branching process model, highlighting that the variance in reproductive success equates to genetic drift. By integrating the Wright-Fisher model with the Haldane model, the authors derive theoretical results that resolve paradoxes related to effective population size.

Strengths:

The most significant and compelling result from this paper is perhaps that the probability of fixing a new beneficial mutation is 2s/V(K). This is an intriguing and potentially generalizable discovery that could be applied to many different study systems.

The authors also made a lot of effort to connect theory with various real-world examples, such as genetic diversity in sex chromosomes and reproductive variance across different species.

Comments on previous revisions:

The author has addressed some of the concerns in my review, and I think the revised manuscript is more clear. I like the discussion about the caveats of the WFH model.

I hope the authors could also discuss the conditions needed for V(K)/Ne to be a reasonable approximation. It is currently unclear how the framework should be adopted in general.

The idea about estimating male-female V(K) ratios from population genetic data is interesting. Unfortunately, the results fell short. The accuracy of their estimators (derived using approximation Ne/V(K) approximation, and certain choice of theta, and then theta estimated with Watterson's estimator) should be tested with simulated results before applying to real data. The reliability of their estimator and their results from real data are unclear.

Arguments made in this paper sometimes lack precision (perhaps the authors want to emphasize intuition, but it seems more confusing than otherwise). For example: The authors stated that "This independence from N seems intuitively obvious: when an advantageous mutation increases to say, 100 copies in determining a population (depending mainly on s), its fixation would be almost certain, regardless of N.". Assuming large Ne, and with approximation, one could assume the probability of loss is e^(-2sn), but the writing about "100 copies" and "almost certain" is very imprecise, in fact, a mutation with s=0.001 segregating at 100 copies in a large Ne population is most probably lost. Whereas in a small population, it will be fixed. Yet the following sentence states "regardless of N. This may be a most direct argument against equating genetic drift, certainly no less important than 1/ N . with N, or Ne (which is supposed to be a function of N's)." I find this new paragraph misleading.

Some of the statements/wordings in this paper still seem too strong to me.

Comments on revisions:

The authors toned down. I am a bit confused because I do not seem to find any point-to-point response to my review.

Reviewer #3 (Public review):

Summary:

Ruan and colleagues consider a branching process model (in their terminology the "Haldane model") and the most basic Wright-Fisher model. They convincingly show that offspring distributions are usually non-Poissonian (as opposed to what's assumed in the Wright-Fisher model), and can depend on short-term ecological dynamics (e.g., variance in offspring number may be smaller during exponential growth). The authors discuss branching processes and the Wright-Fisher model in the context of 3 "paradoxes" --- 1) how Ne depends on N might depend on population dynamics; 2) how Ne is different on the X chromosome, the Y chromosome, and the autosomes, and these differences do match the expectations base on simple counts of the number of chromosomes in the populations; 3) how genetic drift interacts with selection. The authors provide some theoretical explanations for the role of variance in the offspring distribution in each of these three paradoxes. They also perform some experiments to directly measure the variance in offspring number, as well as perform some analyses of published data.

Strengths:

- The theoretical results are well-described and easy to follow.<br /> - The analyses of different variances in offspring number (both experimentally and analyzing public data) are convincing that non-Poissonian offspring distributions are the norm.<br /> - The point that this variance can change as the population size (or population dynamics) change is also very interesting and important to keep in mind.<br /> - I enjoyed the Density-Dependent Haldane model. It was a nice example of the decoupling of census size and effective size.<br /> - Equation (10) is a nice result

Comments on revisions:

I appreciate the effort that the authors have put into the revision, but I still find the framing to be a bit confusing -- these apparent paradoxes only appear in the most basic version of Wright-Fisher models, and so framing the paper as the solution to these paradoxes overlooks much previous work. Saying that existing work discussing exactly these phenomena is "beyond the scope of this study", without citing or interacting in any way with that work is unscholarly. I agree with the authors that the apparent paradoxes that they consider and interesting, and by thinking about branching processes, the apparent paradoxes appear to be less paradoxical, but without contextualizing this work in the substantial Wright-Fisher literature (e.g., Cannings Exchangeable Models and the work of Möhle) it misrepresents the state of the field and the contributions of this paper.

Reviewer #1 (Public review):

Summary:

In this manuscript, Janssens et al. addressed the challenge of mapping the location of transcriptionally unique cell types identified by single nuclei sequencing (snRNA-seq) data available through the Fly Cell Atlas. They identified 100 transcripts for head samples and 50 transcripts for fly body samples allowing identification of every unique cell type discovered through the Fly Cell Atlas. To map all of these cell types, the authors divided the fly body into head and body samples and used the Molecular Cartography (Resolve Biosciences) method to visualize these transcripts. This approach allowed them to build spatial tissue atlases of the fly head and body, to identify the location of previously unknown cell types and the subcellular localization of different transcripts. By combining snRNA-seq data from the Fly Cell Atlas with their spatially resolved transcriptomics (SRT) data, they demonstrated an automated cell type annotation strategy to identify uncharacterized clusters and infer their location in the fly body. This manuscript constitutes a proof-of-principle study to map the location of the cells identified by ever-growing single-cell transcriptomics datasets generated by others.

Strengths:

The authors used the Molecular Cartography (Resolve Biosciences) method to visualize 100 transcripts for head samples and 50 transcripts for fly body samples in high resolution. This method achieves high resolution by multiplexing a large number of transcript visualization steps and allows the authors to map the location of unique cell types identified by the Fly Cell Atlas.

Weaknesses:

Combining single-nuclei sequencing (snRNA-seq) data with spatially resolved transcriptomics (SRT) data is challenging, and the methods used by the authors in this study cannot reliably distinguish between cells, especially in brain regions where the processes of different neurons are clustered, such as neuropils. This means that a grid that the authors mark as a unique cell may actually be composed of processes from multiple cells.

Comments on revisions:

I believe the authors have improved the manuscript by addressing all the concerns and incorporating the suggestions raised by the reviewers. I have no further concerns or suggestions.

Reviewer #1 (Public review):

Summary:

The significance of Notch in liver cancer has been inconsistently described to date. The authors conduct a PDX screen using JAG1 ab and identify 2 sensitive tumor models. Further characterization with bulk RNA seq, scRNA seq, and ATAC seq of these tumors was performed.

Strengths:

The reliance on an extensive panel of PDXs makes this study more definitive than prior studies.

Gene expression analyses seem robust.

Identification of a JAG1-dependent signature associated with hepatocyte differentiation is interesting.

Weaknesses:

The introduction is rather lengthy and not entirely accurate. HCC is a single cancer type/histology. There may be variants of histology (allusion to "mixed-lineage" is inaccurate as combined HCC-CCa are not conventionally considered HCC and are not treated as HCC in clinical practice as they are even excluded from HCC trials), but any cancer type can have differences in differentiation. Just state there are multiple molecular subtypes of this disease.

There is minimal data on the PDXs, despite this being highlighted throughout the text. Clinical and possibly some molecular characterization of these cancers should be provided. It is also odd that the authors include only 35 HCC and then a varied sort of cancer histologies, which is peculiar given their prior statements regarding the heterogeneity of HCC.

"super-responder" is not a meaningful term, I would eliminate this use as it has no clinical or scientific convention that I am aware of.

The "expansion" of the PDX screen is poorly described. Why weren't these PDXs included in the first screen? This is quite odd as the responses in the initial screen were underwhelming. What was the denominator number of all PDXs that were assessed for JAG1 and NOTCH2 expression? This is important as it clarifies how relevant JAG1 inhibition would be to an unselected HCC population.

Was there some kind of determination of the optimal dose or dose dependency for the JAG1 ab? The original description of the JAG1 ab was in mouse lungs, not malignant or liver cells. In addition, supplementary Figure 2D is missing. There needs to be data provided on the specificity of the human-specific JAG1 ab and the anti-NOTCH2 ab. I'm not familiar with these ab, and if they are not publicly accessible reagents, more transparency on this is needed. In addition, given the reliance of the entire paper on these antibodies, I would recommend orthogonal approaches (either chemical or genetic) to confirm the sensitivity and insensitivity of select PDXs to Notch inhibition.

scRNA-seq data seems to add little to the paper and there is no follow-up of the findings. Are the low-expressing JAG1 cells eventually enriched in treated tumors contributing to disease recurrence?

The discussion should be tempered. The finding of only 2 PDXs that are sensitive out of 45+ tumors treated or selected for indicates that JAG1/NOTCH2 inhibition is likely only effective in rare HCC.

Reviewer #2 (Public review):

Summary:

The authors used a large panel of hepatocellular carcinoma patient-derived xenograft models to test the hypothesis that the developmental dependence of the liver on Jagged1-Notch2 signaling is retained in at least a subset of hepatocellular carcinomas. This led to the identification of two models that were extraordinarily sensitive to well-characterized, specific inhibitory antibodies against Jagged1 or Notch2. Based on additional analyses in these in vivo models, the authors provide compelling evidence that the response is due to the inhibition of human Notch2 and human Jagged1 on tumor cells and that this inhibition leads to a change in gene expression from a progenitor-like state to a hepatocyte-like state accompanied by cell cycle arrest. This change in cell state is associated with up-regulation of HNF4a and CEBPB and increased accessibility of predicted HNF4a and CEBPB genomic binding sites, accompanied by loss of accessibility to sequences predicted to bind TFs linked to multipotent liver progenitors. The authors put forth a plausible model in which inhibition of Notch2 downregulates transcriptional repressors of the Hairy/Enhancer of Split family, leading to increased expression of CEBPB and changes in gene expression that drive hepatocyte differentiation.

Strengths:

The strengths of the paper include the breadth of the preclinical screen in PDX models (which may be of an unprecedented size as preclinical trials go), the high quality of the well-characterized antibodies used as therapeutics and as biological perturbagens, the quality of the data and data analysis, and the authors balanced discussion of the strengths and weaknesses of their findings.

Weaknesses:

The principal weakness is the inability to clearly demonstrate the "translatability" of the PDX findings to primary human hepatocellular carcinoma.

Additional Comments:

Hepatocellular carcinoma is increasing in frequency and is difficult to treat; cure is only possible through early diagnosis and surgery, often in the form of liver transplantation. It is also a common cancer, and so even if only 5% of tumors (a value based on the frequency of super-responders in this preclinical trial) fall into the Jagged1-Notch2 group defined by Seidel et al., the development of an effective therapy for this subgroup would be a very important advance. The chief limitation of their work is that it stops short of identifying primary human hepatocellular carcinomas that correspond to the super-responder PDX models. It can be hoped that their intriguing observations will spur work aimed at filling this gap

There are several other loose ends. An unusual feature of this model is that both Jagged 1 and Notch2 are expressed in the same cells, and even in the same individual cells. In developmental systems, the expression of ligands and receptors in the same cell generally produces receptor inhibition rather than activation, a phenomenon described as cis inhibition. Their super-responder tumor models appear to break this rule, and how and why this is so remains to be understood. A follow-up question is what explains the observed heterogeneity in tumor cells, both at the level of Notch2 activation and scRNAseq clustering, and whether these different cell states are static or interchangeable.

Another unanswered issue pertains to the nature of the tumor response to Notch signaling blockade, which appears to be mainly cell cycle arrest. There are a number of human tumors with cell autonomous Notch signaling due to gain of function Notch receptor mutations that also respond to Notch blockade with cell cycle arrest, such as T cell acute lymphoblastic leukemia (T-ALL). In general, clinical trials of pan-Notch inhibitors such as gamma-secretase inhibitors have been disappointing in such tumors, perhaps reflecting a limitation of treatments with significant toxicity that do not kill tumor cells directly. It could be argued that this limitation will be mitigated by the apparently excellent safety profile of Notch2 blocking antibody, which perhaps could be administered for a sustained period, akin to the use of tyrosine kinase inhibitors in chronic myeloid leukemia---but this remains to be determined.

A minor comment is reserved for the statement in the discussion that "In chronic myelomonocytic leukemia, which results from an inactivating mutation in the y-secretase complex component nicastrin, Notch signaling has a tumor suppressive function, that is mediated through direct repression of CEBPA and PU.1 by HES1 (Klinakis et al., 2011)". Thousands of cases of CMML and related myeloid tumors have been subjected to whole exome and even whole genome sequencing without the identification of Notch signaling pathway mutations. Thus, an important tumor suppressive role for Notch-mediated through HES1 in myeloid tumors is not proven.

Reviewer #3 (Public review):

Summary:

Notch is active in HCC, but generally not mutated. The authors use a JAG1-selective blocking antibody in a large panel of liver cancer patient-derived xenograft models. They find JAG-dependent HCCs, and these are aggressive and proliferative. Notch inhibition induces cycle arrest and promotes hepatocyte differentiation, through upregulation of CEBPA expression and activation of existing HNF4A, mimicking normal developmental programs.

The authors use aJ1.b70, a potent and selective therapeutic antibody that inhibits JAG1 against PDX models. They tested over 40 PDX models and found a handful of super-responders to single-agent inhibition. In LIV78 and Li1035 cancer cells, NOTCH2 was expressed and required, in contrast to NOTCH1. RNA-seq showed that the responsive HCCs resembled the S2 transcriptional class of HCCs, which were enriched for Notch-dependent models. They conclude that these dependent tumors have transcriptomes that resemble a hybrid progenitor cell expressing FGF9 and GAS7. Inhibition was able to induce hepatocyte differentiation away from a NOTCH-driven progenitor program. scRNA-seq analysis showed a large population of NOTCH-JAG expressing cells but also showed that there are cells that did not. Not surprisingly, NOTCH2 inhibition leads to increased CEBPA and HNF4A transcriptional activity, which are standard TFs in hepatocytes.

Strengths:

The paper provides useful information about the frequency of HCCs and CCA that respond to NOTCH inhibition and could allow us to anticipate the super-responder rate if these antibodies were actually used in the clinic. The inhibitor tools are highly specific, and provide useful information about NOTCH activities in liver cancers. The large number of PDXs and the careful transcriptomic analyses were positives about the study.

Weaknesses:

The paper is mostly descriptive.

Reviewer #1 (Public review):

Summary:

This article investigates the phenotype of macrophages with a pathogenic role in arthritis, particularly focusing on arthritis induced by immune checkpoint inhibitor (ICI) therapy.

Building on prior data from monocyte-macrophage coculture with fibroblasts, the authors hypothesized a unique role for the combined actions of prostaglandin PGE2 and TNF. The authors studied this combined state using an in vitro model with macrophages derived from monocytes of healthy donors. They complemented this with single-cell transcriptomic and epigenetic data from patients with ICI-RA, specifically, macrophages sorted out of synovial fluid and tissue samples. The study addressed critical questions regarding the regulation of PGE2 and TNF: Are their actions co-regulated or antagonistic? How do they interact with IFN-γ in shaping macrophage responses?

This study is the first to specifically investigate a macrophage subset responsive to the PGE2 and TNF combination in the context of ICI-RA, describes a new and easily reproducible in vitro model, and studies the role of IFNgamma regulation of this particular Mф subset.

Strengths:

Methodological quality: The authors employed a robust combination of approaches, including validation of bulk RNA-seq findings through complementary methods. The methods description is excellent and allows for reproducible research. Importantly, the authors compared their in vitro model with ex vivo single-cell data, demonstrating that their model accurately reflects the molecular mechanisms driving the pathogenicity of this macrophage subset.

Weaknesses:

Introduction: The introduction lacks a paragraph providing an overview of ICI-induced arthritis pathogenesis and a comparison with other types of arthritis. Including this would help contextualize the study for a broader audience.

Results Section: At the beginning of the results section, the experimental setup should be described in greater detail to make an easier transition into the results for the reader, rather than relying just on references to Figure 1 captions.

There is insufficient comparison between single-cell RNA-seq data from ICI-induced arthritis and previously published single-cell RA datasets. Such a comparison may include DEGs and GSEA, pathway analysis comparison for similar subsets of cells. Ideally, an integration with previous datasets with RA-tissue-derived primary monocytes would allow for a direct comparison of subsets and their transcriptomic features.

While it's understandable that arthritis samples are limited in numbers and myeloid cell numbers, it would still be interesting to see the results of PGE2+TNF in vitro stimulation on the primary RA or ICI-RA macrophages. It would be valuable to see RNA-Seq signatures of patient cell reactivation in comparison to primary stimulation of healthy donor-derived monocytes.

Discussion: Prior single-cell studies of RA and RA macrophage subpopulations from 2019, 2020, 2023 publications deserve more discussion. A thorough comparison with these datasets would place the study in a broader scientific context.<br /> Creating an integrated RA myeloid cell atlas that combines ICI-RA data into the RA landscape would be ideal to add value to the field.<br /> As one of the next research goals, TNF blockade data in RA and ICI-RA patients would be interesting to add to such an integrated atlas. Combining responders and non-responders to TNF blockade would help to understand patient stratification with the myeloid pathogenic phenotypes. It would be great to read the authors' opinion on this in the Discussion section.

Conclusion: The authors demonstrated that while PGE2 maintains the inflammatory profile of macrophages, it also induces a distinct phenotype in simultaneous PGE2 and TNF treatment. The study of this specific subset in single-cell data from ICI-RA patients sheds light on the pathogenic mechanisms underlying this condition, however, how it compares with conventional RA is not clear from the manuscript.<br /> Given the substantial incidence of ICI-induced autoimmune arthritis, understanding the unique macrophage subsets involved for future targeting them therapeutically is an important challenge. The findings are significant for immunologists, cancer researchers, and specialists in autoimmune diseases, making the study relevant to a broad scientific audience.

Reviewer #2 (Public review):

Summary/Significance of the findings:

The authors have done a great job by extensively carrying out transcriptomic and epigenomic analyses in the primary human/mouse monocytes/macrophages to investigate TNF-PGE2 (TP) crosstalk and their regulation by IFN-γ in the Rheumatoid arthritis (RA) synovial macrophages. They proposed that TP induces inflammatory genes via a novel regulatory axis whereby IFN-γ and PGE2 oppose each other to determine the balance between two distinct TNF-induced inflammatory gene expression programs relevant to RA and ICI-arthritis.

Strengths:

The authors have done a great job on RT-qPCR analysis of gene expression in primary human monocytes stimulated with TNF and showing the selective agonists of PGE2 receptors EP2 and EP4 22 that signal predominantly via cAMP. They have beautifully shown IFN-γ opposes the effects of PGE2 on TNF-induced gene expression. They found that TP signature genes are activated by cooperation of PGE2-induced AP-1, CEBP, and NR4A with TNF-induced NF-κB activity. On the other hand, they found that IFN-γ suppressed induction of AP-1, CEBP, and NR4A activity to ablate induction of IL-1, Notch, and neutrophil chemokine genes but promoted expression of distinct inflammatory genes such as TNF and T cell chemokines like CXCL10 indicating that TP induces inflammatory genes via IFN-γ in the RA and ICI-arthritis.

Weaknesses:

(1) The authors carried out most of the assays in the monocytes/macrophages. How do APC-cells like Dendritic cells behave with respect to this TP treatment similar dosing?

(2) The authors studied 3h and 24h post-treatment transcriptomic and epigenomic. What happens to TP induce inflammatory genes post-treatment 12h, 36h, 48h, 72h. It is critical to see the upregulated/downregulated genes get normalised or stay the same throughout the innate immune response.

(3) The authors showed IL1-axis in response to the TP-treatment. Do other cytokine axes get modulated? If yes, then how do they cooperate to reduce/induce inflammatory responses along this proposed axis?

Overall, the data looks good and acceptable but I need to confirm the above-mentioned criticisms.

Reviewer #2 (Public review):

Summary:

The current article presents a new type of analytical approach to the sequential organisation of whale song units.

Strengths:

The detailed description of the internal temporal structure of whale songs is something that has been thus far lacking.

Weaknesses:

The conceptual and terminological bases of the paper are problematical and hamper comparison with other taxa, including humans. According to signal theory, codas are indexical rather than symbolic. They signal an individual's group identity. Borrowing from humans and linguistics, coda inter-group variation represents a case of accents - phonologically different varieties of the same call - not dialects, confirming they are an index. This raises serious doubt about whether alleged "symbolism" and similarity between whale and human vocal behaviour is factual. The same applies to the difference between ICIs (inter-click interval) and IOIs (inter-onset interval). If the two are equivalent, variation in click duration needs to be shown so small that can be considered negligible. This raises serious doubt about whether the alleged variation in whale codas is indeed rhythmic in nature and prevents future efforts for comparison with the vocal capacities of other species. The scope and relevance of this paper for the broader field is limited.

Reviewer #1 (Public review):

Summary:

Lejeune et al. demonstrated sex-dependent differences in the susceptibility to MRSA infection. The authors demonstrated the role of the microbiota and sex hormones as potential determinants of susceptibility. Moreover, the authors showed that Th17 cells and neutrophils contribute to the sex hormone-dependent protection in female mice.

Strengths:

The role of microbiota was examined in various models (germ-free, co-housing, microbiota transplantation). The identification of responsible immune cells was achieved using several genetic knockouts and cell-specific depletion models. The involvement of sex hormones was clarified using ovariectomy and the FCG model.

Weaknesses:

The specific microbial species/strains responsible for the protection, as well as the mechanisms by which these bacteria regulate sex hormone-mediated protection, remain unclear. However, this does not diminish the conceptual significance of the study.

Comments on revisions:

The authors have adequately addressed my previous concerns, and the revised manuscript shows significant improvement.

Reviewer #3 (Public review):

Summary:

Using a mouse model of Staphylococcus aureus gut colonization Lejeune et al demonstrate that the microbiome, immune system, and sex are important contributing factors for whether this important human pathogen persists in the gut. The work begins by describing differential gut clearance of S. aureus in female B6 mice bred at NYU compared to those from Jackson Laboratories (JAX). NYU female mice cleared S. aureus from the gut but NYU male mice and mice of both sexes from JAX exhibited persistent gut colonization. Further experimentation demonstrated that differences between staphylococcal gut clearance in NYU and JAX female mice were attributed to the microbiome. However, NYU male and female mice harbor similar microbiomes, supporting the conclusion that the microbiome cannot account for the observed sex-dependent clearance of S. aureus gut colonization. To identify factors responsible for female clearance of S. aureus, the authors performed RNAseq on intestinal epithelia cells and cells enriched within the lamina propria. This analysis revealed sex-dependent transcriptional responses in both tissues. Genes associated with immune cell function and migration were distinctly expressed between the sexes. To determine which immune cell types contribute to S. aureus clearance Lejeune et al employed genetic and antibody-mediated immune cell depletion. This experiment demonstrated that CD4+ IL17+ cells and neutrophils promote elimination of S. aureus from the gut. Subsequent experiments, including the use of the 'four core genotype model' were conducted to discern between the roles of sex chromosomes and sex hormones. This work demonstrated that sex-chromosome linked genes are not responsible for clearance, increasing the likelihood that hormones play a dominant role in controlling S. aureus gut colonization.

Strengths:

A strength of the work is the rigorous experimental design. Appropriate controls were executed and, in most cases, multiple approaches were conducted to strengthen the authors' conclusions. The conclusions are supported by the data.<br /> The following suggestions are offered to improve an already strong piece of scholarship.

Weaknesses:

The correlation between female sex hormones and elimination of S. aureus from the gut could be further validated by quantifying sex hormones produced in the four core genotype mice in response to colonization. Additionally, and this may not be feasible, but according to the proposed model administering female sex hormones to male mice should decrease colonization. Finally, knowing whether the quantity of IL-17a CD4+ cells change in the OVX mice has the potential to discern whether the abundance/migration of the cells or their activation is promoted by female sex hormones.

In the Discussion the authors highlight previous work establishing a link between immune cells and sex hormone receptors, but whether the estrogen (and progesterone) receptor is differentially expressed in response to S. aureus colonization could be assessed in the RNAseq dataset. Differential expression of known X and Y chromosome linked genes were discussed but specific sex hormones or sex hormone receptors, like the estrogen receptor were not. This potential result could be highlighted.

Comments on revisions:

The authors have adequately addressed my comments. I have only one minor adjustment: the Esr1 mice should be included the Materials and Methods.

Reviewer #1 (Public review):

Summary:

The manuscript by Cao et al. examines an important but understudied question of how chronic exposure to heat drives changes in affective and social behaviors. It has long been known that temperature can be a potent driver of behaviors and can lead to anxiety and aggression. However, the neural circuitry that mediates these changes is not known. Cao et al. take on this question by integrating optical tools of systems neuroscience to record and manipulate bulk activity in neural circuits, in combination with a creative battery of behavior assays. They demonstrate that chronic daily exposure to heat leads to changes in anxiety, locomotion, social approach, and aggression. They identify a circuit from preoptic area (POA) to posterior paraventricular thalamus (pPVT) in mediating these behavior changes. The POA-PVT circuit increases activity during heat exposure. Further, manipulation of this circuit can drive affective and social behavioral phenotypes even in the absence of heat exposure. Moreover, silencing this circuit during heat exposure prevents the development of negative phenotypes. Overall the manuscript makes an important contribution to the understudied area of how ambient temperature shapes motivated behaviors.

Strengths

The use of state-of-the-art systems neuroscience tools (in vivo optogenetics and fiber photometry, slice electrophysiology), chronic temperature-controlled experiments, and a rigorous battery of behavioral assays to determine affective phenotypes. The optogenetic gain of function of affective phenotypes in the absence of heat, and loss of function in the presence of heat are very convincing manipulation data. Overall a significant contribution to the circuit-level instantiation of temperature induced changes in motivated behavior, and creative experiments.

Weaknesses

The authors have fully addressed all of my questions and concerns, with the exception of one comment. They mention that they did carry out measurements of core body temperature as a control during optogenetic experiments and did not see any effects. However, I could only find this reported in the text but could not find the data in the main or supplementary figures.

Reviewer #2 (Public review):

Summary:

The study by Cao et al. highlights an interesting and important aspect of heat- and thermal biology: the effect of repetitive, long-term heat exposure and its impact on brain function.<br /> Even though peripheral, sensory temperature sensors and afferent neuronal pathways conveying acute temperature information to the CNS have been well established, it is largely unknown how persistent, long-term temperature stimuli interact with and shape CNS function, and how these thermally-induced CNS alterations modulate efferent pathways to change physiology and behavior. This study is therefore not only novel but, given global warming, also timely.

The authors provide compelling evidence that neurons of the paraventricular thalamus change plastically over three weeks of episodic heat stimulation and they convincingly show that these changes affect behavioral outputs such as social interactions, and anxiety related behaviors.

Strengths:

• It is impressive that the assessed behaviors can be (i) recruited by optogenetic fiber activation and (ii) inhibited by optogenetic fiber inhibition when mice are exposed to heat. Technically, when/how long is the fiber inhibition performed? It says in the text "3 min on and 3 min off". Is this only during the 20 minutes heat stimulation or also at other times?<br /> • It is interesting that the frequency of activity in pPVT neurons, as assessed by fiber photometry, stays increased after long-term heat exposure (day 22) when mice are back at normal room temperature. This appears similar to a previous study that found long-term heat exposure to transform POA neurons plastically to become tonically active (https://www.biorxiv.org/content/10.1101/2024.08.06.606929v1 ). Interestingly, the POA neurons that become tonically active by persistent heat exposure described in the above study are largely excitatory and thus these could drive the activity of the pPVT neurons analyzed in this study.<br /> How can it be reconciled that the majority of the inputs from the POA are found to be largely inhibitory (Fig. 2H)? Is it possible that this result stems from the fact that non-selective POA-to-pPVT projections are labelled by the approach used in this study and not only those pathways activated by heat? These points would be nice to discuss.<br /> • It is very interesting that no LTP can be induced after chronic heat exposure (Fig. K-M); the authors suggest that "the pathway in these mice were already saturated" (line 375). Could this hypothesis be tested in slices by employing a protocol to extinguish pre-existing (chronic heat exposure-induced) LTP? This would provide further strength to the findings/suggestion that an important synaptic plasticity mechanism is at play that conveys behavioral changes upon chronic heat stimulation.<br /> • It is interesting that long-term heat does not increase parameters associated with depression (Fig. 1N-Q), how is it with acute heat stress, are those depression parameters increased acutely? It would be interesting to learn if "depression indicators" increase acutely but then adapt (as a consequence of heat acclimation) or if they are not changed at all and are also low during acute heat exposure.

Reviewer #3 (Public review):

In this study, Cao et al. explore the neural mechanisms by which chronic heat exposure induces negative valence and hyperarousal in mice, focusing on the role of the posterior paraventricular nucleus (pPVT) neurons that receive projections from the preoptic area (POA). The authors show that chronic heat exposure leads to heightened activity of the POA projection-receiving pPVT neurons, potentially contributing to behavioral changes such as increased anxiety level and reduced sociability, along with heightened startle responses. In addition, using electrophysiological methods, the authors suggest that increased membrane excitability of pPVT neurons may underlie these behavioral changes. The use of a variety of behavioral assays enhances the robustness of their claim. Moreover, while previous research on thermoregulation has predominantly focused on physiological responses to thermal stress, this study adds a unique and valuable perspective by exploring how thermal stress impacts affective states and behaviors, thereby broadening the field of thermoregulation.

While the manuscript has been revised and some efforts have been made to address the reviewers' concerns, the majority of the issues raised remain insufficiently resolved. Therefore, the reviewer has highlighted key major points that the authors should address to strengthen the manuscript's conclusions.

Major points<br /> The manuscript highlights the increased activity in pPVT neurons receiving projections from the POA (Figure 3) and shows that these neurons are necessary for heat-induced behavioral changes (Figures 4N-W). However, it remains unclear whether the POA-to-pPVT projection itself plays a critical role. Since pPVT recipient neurons can receive inputs from various brain regions, the role of the POA input in driving these effects needs to be validated more explicitly.<br /> (1) To establish this, the authors should conduct experiments directly inhibiting the POA-to-pPVT projection and demonstrate whether the increased activity in pPVT neurons due to chronic heat exposure is abolished when the POA is blocked.<br /> (2) Alternatively, the authors could use anterograde labeling from the POA and specifically target recipient neurons in the pPVT to confirm that the observed excitatory inputs originate from the POA (related to Figure 6).<br /> (3) If these experiments are not feasible, the authors should consider toning down the emphasis on the POA's role throughout the manuscript and discussing this limitation explicitly. The term "POA recipient pPVT neurons" should be used consistently to avoid misleading implications that the POA-to-pPVT excitatory projection is definitively established as the key pathway.<br /> a) For example, in lines 368-369, the phrase "The increase in presynaptic excitability of the POA to pPVT excitatory pathway" represents a logical jump, as the data only support the "differential increase in presynaptic excitability of the excitatory pathway" (as described in lines 358-359) without specifically confirming the POA-to-pPVT pathway.<br /> b) Similarly, in lines 442-446, the statement "the role of excitatory projections from POA to pPVT in chronic heat exposure-induced emotional changes" should be revised to "the role of excitatory projection recipient pPVT in chronic heat~," as the data do not provide direct evidence that heat-responsive POA neurons projecting to pPVT mediate these effects. Such revisions would improve clarity and ensure that the conclusions remain aligned with the presented data.

Joint Public Review:

Satoshi Yamashita et al., investigate the physical mechanisms driving tissue bending using the cellular Potts Model, starting from a planar cellular monolayer. They argue that apical length-independent tension control alone cannot explain bending phenomena in the cellular Potts Model, contrasting with previous works, particularly Vertex Models. They conclude that an apical elastic term, with zero rest value (due to endocytosis/exocytosis), is necessary to achieve apical constriction and that tissue bending can be enhanced by adding a supracellular myosin cable. Additionally, a very high apical elastic constant promotes planar tissue configurations, opposing bending.

Strengths:

- The finding of the required mechanisms for tissue bending in the cellular Potts Model provides a natural alternative for studying bending processes in situations with highly curved cells.

- Despite viewing cellular delamination as an undesired outcome in this particular manuscript, the model's capability to naturally allow T1 events might prove useful for studying cell mechanics during out-of-plane extrusion.

[Editors' note: The previous reviews have not been updated, as the changes to the manuscript were restricted to refining the text. The authors addressed all of the minor points raised by the reviewers. Some of the major points such as the lack of a summary quantification still stand. The previous reviews are here: https://doi.org/10.7554/eLife.93496.2.sa1]

Reviewer #1 (Public review):

Summary:

Dopamine neurons contribute to motivated and motor behaviors in many ways, and ample recent evidence has suggested that distinct dopamine neuron subclasses support discrete behavioral and circuit functions. Prior studies have subdivided dopamine neurons by spatial localization, gene expression patterns, and physiological properties. However, many of these studies were bound by previous technical limitations that made comprehensive subclassification efforts difficult or impossible. The main goal of this manuscript was to characterize and further define dopamine neuron heterogeneity in the ventral midbrain. The study uses cutting-edge single nucleus RNA-seq (on the 10X Genomics platform) and spatial transcriptomics (on the MERFISH platform) to define dopamine neuron heterogeneity with unprecedented resolution. The result is a convincing and comprehensive subclassification of dopamine neurons into three main families, each with major branches and subtypes. In addition, the study reports comparisons between wild type mice and mice that harbor a G2019S mutation in the Lrrk2 gene, which models a common cause of autosomally dominant Parkinson's Disease in humans. These results, while less robust due to the nature of the group comparisons, nevertheless identify vulnerability within specific dopamine neuron subpopulations. This vulnerability may contribute unique risk to dopamine neuron loss in the context of Parkinson's disease. Overall, the study is careful and rigorous and provides a critical resource for the rapidly evolving knowledge of dopamine neuron subtypes.

Strengths:

-The creation of a public-facing app where the snRNA-seq data can be investigated by anyone is a major strength.<br /> -The manuscript includes careful comparisons to prior datasets that have sought to explore dopamine neuron heterogeneity. The result is a useful synthesis of new findings with previously published work, which is helpful for moving the field forward in this area.<br /> -The integration of snRNA-seq with MERFISH results is particularly strong, and enables insight not only into subclassification, but also into how this relates to spatial localization. The careful neuroanatomy reveals important distinctions between Sox6, Calb1, and Gad2 positive dopamine neuron families, with some degree of spatial overlap.

Reviewer #2 (Public review):

Gaertner and colleagues present a study examining the transcriptomic diversity and spatial location of dopaminergic neurons from mice and examine the changes in gene expression resulting from knock in of the Parkinson's LRRK G2019S risk variant. Overall, I found the manuscript presented their study very clearly, well written with very clear figures for the most part. I am not an expert on mouse neuroanatomy but found their classification reasonably well justified and spatial orientation of dopaminergic neurons within the mouse brain informative and clear. While trends were clear and well presented, the apparent spatial heterogeneity suggests that knowledge of the functional connections and roles of these neurons will be required to better interpret the results presented but nonetheless their findings exposed significant detail that is required for further understanding.

The study of the transcriptional effects of the LRRK2 KI was also informative and clearly framed in terms of a focused analyses on the effects of the KI only on dopaminergic neurons.

I thank the authors for addressing my previous concerns and comments, and feel they have done so well. I agree that as GSEA only includes ranked genes from the specific study, the gene set is already limited to the relevant background.

Reviewer #2 (Public review):

The strengths of this paper are clear: The authors are asking a novel question about geometric representation that would be relevant to a broad audience. Their question has a clear grounding in pre-existing mathematical concepts, that have been only minimally explored in cognitive science. Moreover, the data themselves are quite striking, such that my only concern would be that the data seem almost too perfect. It is hard to know what to make of that, however. From one perspective, this is even more reason the results should be published. Yet I am of the (perhaps unorthodox) opinion that reviewers should voice these gut reactions, even if it does not influence the evaluation otherwise. I have a few additional comments:

(1) The authors have now explained their theoretical position in a much more thorough and accessible way. I applaud them for that.

(2) Although I continue to believe that the manipulation in Experiment 1 is imperfect, I am convinced by the authors that the subsequent evidence is more convincing, and thus that the merit of this work lies mostly in those data.

If these results are robust, I believe the authors have discovered something of great value. While this paper stops short of providing definitive evidence in support of the Erlangen program (just as most work in vision science has stopped short of providing definitive evidence in support of its favored view), the data are sufficiently novel and provocative that these theories are worth entertaining further.

Reviewer #1 (Public review):

Summary:

This study examined the changes in ATL GABA levels induced by cTBS and its relationship with BOLD signal changes and performance in a semantic task. The findings suggest that the increase in ATL GABA levels induced by cTBS is associated with a decrease in BOLD signal. The relationship between ATL GABA levels and semantic task performance is nonlinear, and more specifically, the authors propose that the relationship is an inverted U-shaped relationship.

Strengths:

The findings of the research regarding the increase of GABA and decrease of BOLD caused by cTBS, as well as the correlation between the two, appear to be reliable. This should be valuable for understanding the biological effects of cTBS.

Weakness:

I am pleased to see the authors' feedback on my previous questions and suggestions, and I believe the additional data analysis they have added is helpful. Here are my reserved concerns and newly discovered issues.

(1) Regarding the Inverted U-Shaped Curve In the revised manuscript, the authors have accepted some of my suggestions and conducted further analysis, which is now presented in Figure 3B. These results provide partial support for the authors' hypothesis. However, I still believe that the data from this study hardly convincingly support an inverted U-shaped distribution relationship.<br /> The authors stated in their response, "it is challenging to determine the optimal level of ATL GABA," but I think this is achievable. From Figures 4C and 4D, the ATL GABA levels corresponding to the peak of the inverted U-shaped curve fall between 85 and 90. In my understanding, this can be considered as the optimal level of ATL GABA estimated based on the existing data and the inverted U-shaped curve relationship. However, in the latter half of the inverted U-shaped curve, there are quite few data points, and such a small number of data points hardly provides reliable support for the quantitative relationship in the latter half of the curve. I suggest that the authors should at least explicitly acknowledge this and be cautious in drawing conclusions. I also suggest that the authors consider fitting the data with more types of non-linear relationships, such as a ceiling effect (a combination of a slope and a horizontal line), or a logarithmic curve.

(2) In Figure 2F, the authors demonstrated a strong practice effect in this study, which to some extent offsets the decrease in behavioral performance caused by cTBS. Therefore, I recommend that the authors give sufficient consideration to the practice effect in the data analysis.<br /> One issue is the impact of the practice effect on the classification of responders and non-responders. Currently, most participants are classified as non-responders, suggesting that the majority of the population may not respond to the cTBS used in this study. This greatly challenges the generalizability of the experimental conclusions. However, the emergence of so many non-responders is likely due to the prominent practice effect, which offsets part of the experimental effect. If the practice effect is excluded, the number of responders may increase. The authors might estimate the practice effect based on the vertex simulation condition and reclassify participants after excluding the influence of the practice effect.<br /> Another issue is that considering the significant practice effect, the analysis in Figure 4D, which mixes pre- and post-test data, may not be reliable.

(3) The analysis in Figure 3A has a double dipping issue. Suppose we generate 100 pairs of random numbers as pre- and post-test scores, and then group the data based on whether the scores decrease or increase; the pre-test scores of the group with decreased scores will have a very high probability of being higher than those of the group with increased scores. Therefore, the findings in Figure 3A seem to be meaningless.

(4) The authors use IE as a behavioral measure in some analyses and use accuracy in others. I recommend that the authors adopt a consistent behavioral measure.

Reviewer #2 (Public review):

Summary:

The authors combined inhibitory neurostimulation (continuous theta-burst stimulation, cTBS) with subsequent MRI measurements to investigate the impact of inhibition of the left anterior temporal lobe (ATL) on task-related activity and performance during a semantic task and link stimulation-induced changes to the neurochemical level by including MR spectroscopy (MRS). cTBS effects in the ATL were compared with a control site in the vertex. The authors found that relative to stimulation of the vertex, cTBS significantly increased the local GABA concentration in the ATL. cTBS also decreased task-related semantic activity in the ATL and potentially delayed semantic task performance by hindering a practice effect from pre to post. Finally, pooled data with their previous MRS study suggest an inverted u-shape between GABA concentration and behavioral performance. These results help to better understand the neuromodulatory effects of non-invasive brain stimulation on task performance.

Strengths:

Multimodal assessment of neurostimulation effects on the behavioral, neurochemical, and neural levels. In particular, the link between GABA modulation and behavior is timely and potentially interesting.

Weaknesses:

The analyses are not sound. Some of the effects are very weak and not all conclusions are supported by the data since some of the comparisons are not justified. There is some redundancy with a previous paper by the same authors, so the novelty and contribution to the field are overall limited. A network approach might help here.

Reviewer #3 (Public review):

Summary:

The authors used cTBS TMS, magnetic resonance spectroscopy (MRS), and functional magnetic resonance imaging (fMRI) as the main methods of investigation. Their data show that cTBS modulates GABA concentration and task-dependent BOLD in the ATL, whereby greater GABA increase following ATL cTBS showed greater reductions in BOLD changes in ATL. This effect was also reflected in the performance of the behavioural task response times, which did not subsume to practice effects after AL cTBS as opposed to the associated control site and control task. This is in line with their first hypothesis. The data further indicates that regional GABA concentrations in the ATL play a crucial role in semantic memory because individuals with higher (but not excessive) GABA concentrations in the ATLs performed better on the semantic task. This is in line with their second prediction. Finally, the authors conducted additional analyses to explore the mechanistic link between ATL inhibitory GABAergic action and semantic task performance. They show that this link is best captured by an inverted U-shaped function as a result of a quadratic linear regression model. Fitting this model to their data indicates that increasing GABA levels led to better task performance as long as they were not excessively low or excessively high. This was first tested as a relationship between GABA levels in the ATL and semantic task performance; then the same analyses were performed on the pre and post-cTBS TMS stimulation data, showing the same pattern. These results are in line with the conclusions of the authors.

Comments on revisions:

The authors have comprehensively addressed my comments from the first round of review, and I consider most of their answers and the steps they have taken satisfactorily. Their insights prompted me to reflect further on my own knowledge and thinking regarding the ATL function.

I do, however, have an additional and hopefully constructive comment regarding the point made about the study focusing on the left instead of bilateral ATL. I appreciate the methodological complexities and the pragmatic reasons underlying this decision. Nevertheless, briefly incorporating the justification for this decision into the manuscript would have been beneficial for clarity and completeness. The presented argument follows an interesting logic; however, despite strong previous evidence supporting it, the approach remains based on an assumption. Given that the authors now provide the group-level fMRI results captured more comprehensively in Supplementary Figure 2, where the bilateral pattern of fMRI activation can be observed in the current data, the authors could have strengthened their argument by asserting that the activation related to the given semantic association task in this data was bilateral. This would imply that the TMS effects and associated changes in GABA should be similar for both sites. Furthermore, it is worth noting the approach taken by Pobric et al. (2007, PNAS), who stimulated a site located 10 mm posterior to the tip of the left temporal pole along the middle temporal gyrus (MTG) and not the bilateral ATL.

Reviewer #1 (Public review):

Summary:

This study explores the immune microenvironment of the placenta in preeclampsia (PE), which is often accompanied by gestational diabetes mellitus (GDM). Using CyTOF, they found that placentas from PE cases showed increased frequencies of memory-like Th17 cells, memory-like CD8⁺ T cells, and pro-inflammatory macrophages, alongside decreased levels of anti-inflammatory macrophages and granulocyte myeloid-derived suppressor cells (gMDSCs) compared to normal pregnancies. Further analysis revealed a positive correlation between pro-inflammatory macrophages and the expanded T cell populations, and a negative correlation with gMDSCs. Single-cell RNA sequencing provided mechanistic insights: transferring a specific subset of pro-inflammatory macrophages (F4/80⁺CD206⁻ with a distinct gene expression profile) from the uterus of PE mice to normal pregnant mice induced the formation of pathogenic memory-like Th17 cells via the IGF1-IGF1R pathway. This cellular interplay not only contributed to the development but also to the recurrence of PE. Additionally, these macrophages promoted the production of memory-like CD8⁺ T cells while inhibiting gMDSCs at the maternal-fetal interface, culminating in PE-like symptoms in mice. In conclusion, the study identifies a PE-specific immune cell network regulated by pro-inflammatory macrophages, offering new insights into the pathogenesis of preeclampsia.

Strengths:

Utilization of both human placental samples and multiple mouse models to explore the mechanisms linking inflammatory macrophages and T cells to preeclampsia (PE).<br /> Incorporation of cutting-edge and complementary techniques such as CyTOF, scRNA-seq, bulk RNA-seq, and flow cytometry.

Identification of specific immune cell populations and their roles in PE.<br /> Demonstration of the adverse effects of pro-inflammatory macrophages and T cells on pregnancy outcomes through in vivo manipulations.

Comments on revised version:

Several weaknesses were addressed during revision by conducting additional experiments, clarifying the manuscript's text, and incorporating new data that was not initially included.

Reviewer #2 (Public review):

Summary:

Fei, Lu, Shi, et al. present a thorough evaluation of the immune cell landscape in pre-eclamptic human placentas by single-cell multi-omics methodologies compared to normal control placentas. Based on their findings of elevated frequencies of inflammatory macrophages and memory-like Th17 cells, they employ adoptive cell transfer mouse models to interrogate the coordination and function of these cell types in pre-eclampsia immunopathology. They demonstrate the putative role of the IGF1-IGF1R axis as the key pathway by which inflammatory macrophages in the placenta skew CD4+ T cells towards an inflammatory IL-17A-secreting phenotype that may drive tissue damage, vascular dysfunction, and elevated blood pressure in pre-eclampsia, leaving researchers with potential translational opportunities to pursue this pathway in this indication.

They present a major advance to the field in their profiling of human placental immune cells from pre-eclampsia patients where most extant single-cell atlases focus on term versus preterm placenta, or largely examine trophoblast biology with a much rarer subset of immune cells. While the authors present vast amounts of data at both the protein and RNA transcript level, we, the reviewers, feel this manuscript is still in need of much more clarity in its main messaging, and more discretion in including only key data that supports this main message most effectively.

Strengths:

(1) This study combines human and mouse analyses and allows for some amount of mechanistic insight into the role of pro-inflammatory and anti-inflammatory macrophages in the pathogenesis of pre-eclampsia (PE), and their interaction with Th17 cells.

(2) Importantly, they do this using matched cohorts across normal pregnancy and common PE comorbidities like gestation diabetes (GDM).

(3) The authors have developed clear translational opportunities from these "big data" studies by moving to pursue potential IGF1-based interventions.

[Editors' note: the authors have provided responses to the previously identified weaknesses]

Reviewer #1 (Public review):

Summary:

The authors investigated the elasticity of controllability by developing a task that manipulates the probability of achieving a goal with a baseline investment (which they refer to as inelastic controllability) and the probability that additional investment would increase the probability of achieving a goal (which they refer to as elastic controllability). They found that a computational model representing the controllability and elasticity of the environment accounted better for the data than a model representing only the controllability. They also found that prior biases about the controllability and elasticity of the environment were associated with a composite psychopathology score. The authors conclude that elasticity inference and bias guide resource allocation.

Strengths:

This research takes a novel theoretical and methodological approach to understanding how people estimate the level of control they have over their environment, and how they adjust their actions accordingly. The task is innovative and both it and the findings are well-described (with excellent visuals). They also offer thorough validation for the particular model they develop. The research has the potential to theoretically inform the understanding of control across domains, which is a topic of great importance.

Weaknesses:

An overarching concern is that this paper is framed as addressing resource investments across domains that include time, money, and effort, and the introductory examples focus heavily on effort-based resources (e.g., exercising, studying, practicing). The experiments, though, focus entirely on the equivalent of monetary resources - participants make discrete actions based on the number of points they want to use on a given turn. While the same ideas might generalize to decisions about other kinds of resources (e.g., if participants were having to invest the effort to reach a goal), this seems like the kind of speculation that would be better reserved for the Discussion section rather than using effort investment as a means of introducing a new concept (elasticity of control) that the paper will go on to test.

Setting aside the framing of the core concepts, my understanding of the task is that it effectively captures people's estimates of the likelihood of achieving their goal (Pr(success)) conditional on a given investment of resources. The ground truth across the different environments varies such that this function is sometimes flat (low controllability), sometimes increases linearly (elastic controllability), and sometimes increases as a step function (inelastic controllability). If this is accurate, then it raises two questions.

First, on the modeling front, I wonder if a suitable alternative to the current model would be to assume that the participants are simply considering different continuous functions like these and, within a Bayesian framework, evaluating the probabilistic evidence for each function based on each trial's outcome. This would give participants an estimate of the marginal increase in Pr(success) for each ticket, and they could then weigh the expected value of that ticket choice (Pr(success)*150 points) against the marginal increase in point cost for each ticket. This should yield similar predictions for optimal performance (e.g., opt-out for lower controllability environments, i.e., flatter functions), and the continuous nature of this form of function approximation also has the benefit of enabling tests of generalization to predict changes in behavior if there was, for instance, changes in available tickets for purchase (e.g., up to 4 or 5) or changes in ticket prices. Such a model would of course also maintain a critical role for priors based on one's experience within the task as well as over longer timescales, and could be meaningfully interpreted as such (e.g., priors related to the likelihood of success/failure and whether one's actions influence these). It could also potentially reduce the complexity of the model by replacing controllability-specific parameters with multiple candidate functions (presumably learned through past experience, and/or tuned by experience in this task environment), each of which is being updated simultaneously.

Second, if the reframing above is apt (regardless of the best model for implementing it), it seems like the taxonomy being offered by the authors risks a form of "jangle fallacy," in particular by positing distinct constructs (controllability and elasticity) for processes that ultimately comprise aspects of the same process (estimation of the relationship between investment and outcome likelihood). Which of these two frames is used doesn't bear on the rigor of the approach or the strength of the findings, but it does bear on how readers will digest and draw inferences from this work. It is ultimately up to the authors which of these they choose to favor, but I think the paper would benefit from some discussion of a common-process alternative, at least to prevent too strong of inferences about separate processes/modes that may not exist. I personally think the approach and findings in this paper would also be easier to digest under a common-construct approach rather than forcing new terminology but, again, I defer to the authors on this.

Reviewer #2 (Public review):

Summary:

In this paper, the authors test whether controllability beliefs and associated actions/resource allocation are modulated by things like time, effort, and monetary costs (what they call "elastic" as opposed to "inelastic" controllability). Using a novel behavioral task and computational modeling, they find that participants do indeed modulate their resources depending on whether they are in an "elastic," "inelastic," or "low controllability" environment. The authors also find evidence that psychopathology is related to specific biases in controllability.

Strengths:

This research investigates how people might value different factors that contribute to controllability in a creative and thorough way. The authors use computational modeling to try to dissociate "elasticity" from "overall controllability," and find some differential associations with psychopathology. This was a convincing justification for using modeling above and beyond behavioral output and yielded interesting results. Interestingly, the authors conclude that these findings suggest that biased elasticity could distort agency beliefs via maladaptive resource allocation. Overall, this paper reveals some important findings about how people consider components of controllability.

Weaknesses:

The primary weakness of this research is that it is not entirely clear what is meant by "elastic" and "inelastic" and how these constructs differ from existing considerations of various factors/calculations that contribute to perceptions of and decisions about controllability. I think this weakness is primarily an issue of framing, where it's not clear whether elasticity is, in fact, theoretically dissociable from controllability. Instead, it seems that the elements that make up "elasticity" are simply some of the many calculations that contribute to controllability. In other words, an "elastic" environment is inherently more controllable than an "inelastic" one, since both environments might have the same level of predictability, but in an "elastic" environment, one can also partake in additional actions to have additional control over achieving the goal (i.e., expend effort, money, time).

Reviewer #3 (Public review):

A bias in how people infer the amount of control they have over their environment is widely believed to be a key component of several mental illnesses including depression, anxiety, and addiction. Accordingly, this bias has been a major focus in computational models of those disorders. However, all of these models treat control as a unidimensional property, roughly, how strongly outcomes depend on action. This paper proposes---correctly, I think---that the intuitive notion of "control" captures multiple dimensions in the relationship between action and outcome is multi-dimensional. In particular, the authors propose that the degree to which outcome depends on how much *effort* we exert, calling this dimension the "elasticity of control". They additionally propose that this dimension (rather than the more holistic notion of controllability) may be specifically impaired in certain types of psychopathology. This idea thus has the potential to change how we think about mental disorders in a substantial way, and could even help us better understand how healthy people navigate challenging decision-making problems.

Unfortunately, my view is that neither the theoretical nor empirical aspects of the paper really deliver on that promise. In particular, most (perhaps all) of the interesting claims in the paper have weak empirical support.

Starting with theory, the elasticity idea does not truly "extend" the standard control model in the way the authors suggest. The reason is that effort is simply one dimension of action. Thus, the proposed model ultimately grounds out in how strongly our outcomes depend on our actions (as in the standard model). Contrary to the authors' claims, the elasticity of control is still a fixed property of the environment. Consistent with this, the computational model proposed here is a learning model of this fixed environmental property. The idea is still valuable, however, because it identifies a key dimension of action (namely, effort) that is particularly relevant to the notion of perceived control. Expressing the elasticity idea in this way might support a more general theoretical formulation of the idea that could be applied in other contexts. See Huys & Dayan (2009), Zorowitz, Momennejad, & Daw (2018), and Gagne & Dayan (2022) for examples of generalizable formulations of perceived control.

Turning to experiment, the authors make two key claims: (1) people infer the elasticity of control, and (2) individual differences in how people make this inference are importantly related to psychopathology.

Starting with claim 1, there are three sub-claims here; implicitly, the authors make all three. (1A) People's behavior is sensitive to differences in elasticity, (1B) people actually represent/track something like elasticity, and (1C) people do so naturally as they go about their daily lives. The results clearly support 1A. However, 1B and 1C are not supported.

Starting with 1B, the experiment cannot support the claim that people represent or track elasticity because the effort is the only dimension over which participants can engage in any meaningful decision-making (the other dimension, selecting which destination to visit, simply amounts to selecting the location where you were just told the treasure lies). Thus, any adaptive behavior will necessarily come out in a sensitivity to how outcomes depend on effort. More concretely, any model that captures the fact that you are more likely to succeed in two attempts than one will produce the observed behavior. The null models do not make this basic assumption and thus do not provide a useful comparison.

For 1C, the claim that people infer elasticity outside of the experimental task cannot be supported because the authors explicitly tell people about the two notions of control as part of the training phase: "To reinforce participants' understanding of how elasticity and controllability were manifested in each planet, [participants] were informed of the planet type they had visited after every 15 trips." (line 384).

Finally, I turn to claim 2, that individual differences in how people infer elasticity are importantly related to psychopathology. There is much to say about the decision to treat psychopathology as a unidimensional construct. However, I will keep it concrete and simply note that CCA (by design) obscures the relationship between any two variables. Thus, as suggestive as Figure 6B is, we cannot conclude that there is a strong relationship between Sense of Agency and the elasticity bias---this result is consistent with any possible relationship (even a negative one). The fact that the direct relationship between these two variables is not shown or reported leads me to infer that they do not have a significant or strong relationship in the data.

There is also a feature of the task that limits our ability to draw strong conclusions about individual differences in elasticity inference. As the authors clearly acknowledge, the task was designed "to be especially sensitive to overestimation of elasticity" (line 287). A straightforward consequence of this is that the resulting *empirical* estimate of estimation bias (i.e., the gamma_elasticity parameter) is itself biased. This immediately undermines any claim that references the directionality of the elasticity bias (e.g. in the abstract). Concretely, an undirected deficit such as slower learning of elasticity would appear as a directed overestimation bias.

When we further consider that elasticity inference is the only meaningful learning/decision-making problem in the task (argued above), the situation becomes much worse. Many general deficits in learning or decision-making would be captured by the elasticity bias parameter. Thus, a conservative interpretation of the results is simply that psychopathology is associated with impaired learning and decision-making.

Minor comments:

Showing that a model parameter correlates with the data it was fit to does not provide any new information, and cannot support claims like "a prior assumption that control is likely available was reflected in a futile investment of resources in uncontrollable environments." To make that claim, one must collect independent measures of the assumption and the investment.

Did participants always make two attempts when purchasing tickets? This seems to violate the intuitive model, in which you would sometimes succeed on the first jump. If so, why was this choice made? Relatedly, it is not clear to me after a close reading how the outcome of each trial was actually determined.

It should be noted that the model is heuristically defined and does not reflect Bayesian updating. In particular, it overestimates control by not using losses with less than 3 tickets (intuitively, the inference here depends on your beliefs about elasticity). I wonder if the forced three-ticket trials in the task might be historically related to this modeling choice.

Reviewer #1 (Public review):

Summary:

This study identified three independent components of glucose dynamics-"value," "variability," and "autocorrelation", and reported important findings indicating that they play an important role in predicting coronary plaque vulnerability. Although the generalizability of the results needs further investigation due to the limited sample size and validation cohort limitations, this study makes several notable contributions: validation of autocorrelation as a new clinical indicator, theoretical support through mathematical modeling, and development of a web application for practical implementation. These contributions are likely to attract broad interest from researchers in both diabetology and cardiology and may suggest the potential for a new approach to glucose monitoring that goes beyond conventional glycemic control indicators in clinical practice.

Strengths:

The most notable strength of this study is the identification of three independent elements in glycemic dynamics: value, variability, and autocorrelation. In particular, the metric of autocorrelation, which has not been captured by conventional glycemic control indices, may bring a new perspective for understanding glycemic dynamics. In terms of methodological aspects, the study uses an analytical approach combining various statistical methods such as factor analysis, LASSO, and PLS regression, and enhances the reliability of results through theoretical validation using mathematical models and validation in other cohorts. In addition, the practical aspect of the research results, such as the development of a Web application, is also an important contribution to clinical implementation.

Weaknesses:

The most significant weakness of this study is the relatively small sample size of 53 study subjects. This sample size limitation leads to a lack of statistical power, especially in subgroup analyses, and to limitations in the assessment of rare events. In terms of validation, several challenges exist, including geographical and ethnic biases in the validation cohorts, lack of long-term follow-up data, and insufficient validation across different clinical settings. In terms of data representativeness, limiting factors include the inclusion of only subjects with well-controlled serum cholesterol and blood pressure and the use of only short-term measurement data. In terms of elucidation of physical mechanisms, the study is not sufficient to elucidate the mechanisms linking autocorrelation and clinical outcomes or to verify them at the cellular or molecular level.

Reviewer #2 (Public review):

Summary:

Sugimoto et al. explore the relationship between glucose dynamics - specifically value, variability, and autocorrelation - and coronary plaque vulnerability in patients with varying glucose tolerance levels. The study identifies three independent predictive factors for %NC and emphasizes the use of continuous glucose monitoring (CGM)-derived indices for coronary artery disease (CAD) risk assessment. By employing robust statistical methods and validating findings across datasets from Japan, America, and China, the authors highlight the limitations of conventional markers while proposing CGM as a novel approach for risk prediction. The study has the potential to reshape CAD risk assessment by emphasizing CGM-derived indices, aligning well with personalized medicine trends.

Strengths:

(1) The introduction of autocorrelation as a predictive factor for plaque vulnerability adds a novel dimension to glucose dynamic analysis.

(2) Inclusion of datasets from diverse regions enhances generalizability.

(3) The use of a well-characterized cohort with controlled cholesterol and blood pressure levels strengthens the findings.

(4) The focus on CGM-derived indices aligns with personalized medicine trends, showcasing the potential for CAD risk stratification.

Weaknesses:

(1) The link between autocorrelation and plaque vulnerability remains speculative without a proposed biological explanation.

(2) The relatively small sample size (n=270) limits statistical power, especially when stratified by glucose tolerance levels.

(3) Strict participant selection criteria may reduce applicability to broader populations.

(4) CGM-derived indices like AC_Var and ADRR may be too complex for routine clinical use without simplified models or guidelines.

(5) The study does not compare CGM-derived indices to existing advanced CAD risk models, limiting the ability to assess their true predictive superiority.

(6) Varying CGM sampling intervals (5-minute vs. 15-minute) were not thoroughly analyzed for impact on results.

Reviewer #3 (Public review):

Summary:

This is a retrospective analysis of 53 individuals over 26 features (12 clinical phenotypes, 12 CGM features, and 2 autocorrelation features) to examine which features were most informative in predicting percent necrotic core (%NC) as a parameter for coronary plaque vulnerability. Multiple regression analysis demonstrated a better ability to predict %NC from 3 selected CGM-derived features than 3 selected clinical phenotypes. LASSO regularization and partial least squares (PLS) with VIP scores were used to identify 4 CGM features that most contribute to the precision of %NC. Using factor analysis they identify 3 components that have CGM-related features: value (relating to the value of blood glucose), variability (relating to glucose variability), and autocorrelation (composed of the two autocorrelation features). These three groupings appeared in the 3 validation cohorts and when performing hierarchical clustering. To demonstrate how these three features change, a simulation was created to allow the user to examine these features under different conditions.

Review:

The goal of this study was to identify CGM features that relate to %NC. Through multiple feature selection methods, they arrive at 3 components: value, variability, and autocorrelation. While the feature list is highly correlated, the authors take steps to ensure feature selection is robust. There is a lack of clarity of what each component (value, variability, and autocorrelation) includes as while similar CGM indices fall within each component, there appear to be some indices that appear as relevant to value in one dataset and to variability in the validation. We are sceptical about statements of significance without documentation of p-values. While hesitations remain, the ability of these authors to find groupings of these many CGM metrics in relation to %NC is of interest. The believability of the associations is impeded by an obtuse presentation of the results with core data (i.e. correlation plots between CGM metrics and %NC) buried in the supplement while main figures contain plots of numerical estimates from models which would be more usefully presented in supplementary tables. Given the small sample size in the primary analysis, there is a lot of modeling done with parameters estimated where simpler measures would serve and be more convincing as they require less data manipulation. A major example of this is that the pairwise correlation/covariance between CGM_mean, CGM_std, and AC_var is not shown and would be much more compelling in the claim that these are independent factors. Lack of methodological detail is another challenge. For example, the time period of CGM metrics or CGM placement in the primary study in relation to the IVUS-derived measurements of coronary plaques is unclear. Are they temporally distant or proximal/ concurrent with the PCI? A patient undergoing PCI for coronary intervention would be expected to have physiological and iatrogenic glycemic disturbances that do not reflect their baseline state. This is not considered or discussed. The attempts at validation in external cohorts, Japanese, American, and Chinese are very poorly detailed. We could only find even an attempt to examine cardiovascular parameters in the Chinese data set but the outcome variables are unspecified with regard to what macrovascular events are included, their temporal relation to the CGM metrics, etc. Notably macrovascular event diagnoses are very different from the coronary plaque necrosis quantification. This could be a source of strength in the findings if carefully investigated and detailed but due to the lack of detail seems like an apples-to-oranges comparison. Finally, the simulations at the end are not relevant to the main claims of the paper and we would recommend removing them for the coherence of this manuscript.

Reviewer #1 (Public review):

Summary:

This study represents an incremental step toward mitochondrial DNA editing but raises several concerns regarding its impact and broader applicability. The reported in vitro editing efficiency of 17% in mitotic cells, with non-specific editing across multiple A:T sites, offers limited improvement over prior technologies like DdCBE. Editing efficiency for the Mt-Atp6 gene was even lower (~4%), rendering it unlikely to produce functional changes relevant to mitochondrial function or bioenergetics.

While the modified TadA8e(V28R) mutant alleviated toxicity and enabled sufficient AAV production for in vivo experiments, the low in vivo editing efficiency (~4%) after 4 weeks was disappointing and unlikely to be biologically meaningful. Furthermore, the use of P1 postnatal tissues, which are still developing, raises questions about their suitability as models for postmitotic tissues, especially since the brain - a key organ affected by mitochondrial diseases - was excluded from the analysis.

Despite demonstrating feasibility for mitochondrial adenine base editing, the study highlights significant limitations, underscoring the need for further optimization. The reviewer also suggests adopting clearer terminology, such as "pathological variant" instead of "mutation," to enhance precision.

Strengths:

The study demonstrates the feasibility of adenine base editing in mitochondrial DNA, marking a step forward in expanding mitochondrial genome engineering capabilities. A notable strength is the development of a modified TadA8e(V28R) mutant, which successfully mitigated toxicity and enabled sufficient AAV production for in vivo experiments. This technical advancement addresses a key challenge in mitochondrial gene editing and provides a foundation for improving delivery methods and reducing off-target effects.

Additionally, the study highlights the potential for targeted mitochondrial DNA modifications using optimized TALEs, achieving A:T to G:C conversions in multiple genes. While the in vitro editing efficiency remains modest, the approach represents an important proof-of-concept for potentially advancing mitochondrial editing technologies, particularly in the context of addressing pathological variants.

Weaknesses:

The major weaknesses of the study center around its low editing efficiency, both in vitro and in vivo. In vitro editing achieved only 17% efficiency in mitotic cells, while the efficiency for the Mt-Atp6 gene was even lower, around 4%. This level of editing is unlikely to produce meaningful functional or biological changes, particularly in cells with pathological mtDNA variants. Similarly, in vivo, editing efficiency after a 4-week exposure period remained at approximately 4%, which is insufficient to support claims of effective mitochondrial genome editing. Another significant limitation is the lack of editing specificity, as observed changes occurred at multiple A:T sites within and across the editing window rather than being confined to a single position, raising concerns about precision and off-target effects.

The use of P1 postnatal mouse tissues also raises questions about the relevance of the model, as these tissues are still undergoing development and may not truly reflect postmitotic states. This casts doubt on whether the findings are transferable to mature tissues, such as the adult brain, which is frequently affected by mitochondrial diseases. Furthermore, the exclusion of brain tissue from the analysis limits the study's applicability to neurological disorders, a key area of mitochondrial disease research. The rationale for excluding brain tissue is not addressed, leaving an important gap in the study's scope.

The findings also lack novelty, as the reported low efficiency and lack of specificity are consistent with previous studies, making it unclear whether this work represents a significant advancement over existing technologies.

Collectively, these weaknesses underscore the need for further optimization of the approach, improved targeting specificity, and validation in more relevant models to demonstrate therapeutic potential.

Reviewer #2 (Public review):

The authors have demonstrated the use of adenine base editors delivered via adeno-associated viruses to introduce edits in the mitochondrial genome. The manuscript describes the methodology well, and the conclusions are aptly supported by the results. It highlights the potential of these base editors to model mtDNA variations in somatic tissues in animal models.

However, there are a few comments that need to be addressed:

(1) Limitations of the small sample size need to be explained clearly for the results described.

(2) It will be beneficial for the readers if some light is shed on the possible reasons why the efficiencies of adenine base editing are lower than those reported for published cytosine base editors to introduce edits in the mitochondrial DNA.

(3) The conclusion should more explicitly address the limitations and future directions on low editing efficiency and what can be possible optimization steps.

(4) In Figure 1, A-to-G editing for the genes Mt-Cytb, Mt-CoII, and Mt-Atp6 appears to be strand-specific for the different architectures of adenine base editors. Do authors have a possible hypothesis if one of the strands is more favorable to editing depending on where the TadA8 binds or is it random?

Reviewer #1 (Public review):

In all animals, the fertilized egg is transcriptionally silent, and thus early embryonic development relies on maternally deposited factors. A key mode of regulation is translational control to produce the proteins needed by the developing embryo. In zebrafish as well as other animals, distinct ribosomes, those coming from the maternal pool (maternal ribosomes produced in the germ line/oocytes), and those produced from new transcription after genome activation (somatic ribosomes). In zebrafish, the maternal pool consists of a "maternal" rRNA produced from rDNA on chromosome 4, that has previously been shown to be amplified or expressed specifically in the germ line and in oocytes. The observed sex-specific expression of m-rDNA has led to models that it is involved in sex differentiation and/or maternal control of early embryonic development, both as mediators of translation and as a source of raw materials needed to produce new ribosomes. The work to date in the field indicates that maternal and somatic ribosomes are distinct in their expression profiles but whether they have unique, or gene-specific activities awaits determining if somatic rDNA can functionally replace m-rDNA.

In this manuscript, the authors investigated the expression profiles, protein composition, and ability of maternal and somatic ribosome components to interact with one another and their association with polysomes. This study reports sequence differences between maternal and somatic ribosomal components as well as proteomics and structural analysis of ribosome composition in oocytes and early development. This analysis shows that ribosome subunit composition changes over developmental time but did not uncover evidence suggesting maternal or somatic ribosome-specific ribosomal protein paralog use. The key findings of this work are:<br /> (1) Observation of hybrid ribosomes composed of subunits of maternal and somatic origin in the embryo.<br /> (2) Detection of both maternal and somatic ribosomes in polysomes, indicating maternal and somatic ribosomes both support translation in the embryos and may not be functionally unique.<br /> (3) Persistent expression of m-rRNA in germ cells, suggesting m-ribosomes, as the main ribosome type present, are important for translation in germ cells. The question of ribosome heterogeneity and the function of maternal versus somatic rDNA and ribosomes is of great interest to the broader scientific community. Overall, the manuscript is clearly written and the solid data provided support the main ideas and conclusions.

Specific points are detailed below.

(1) In Figure 1D the m-rRNA abundance goes down at 3dpf, then up again while the s-rRNA steadily increases and peaks at 3dpf then drops thereafter. As presented in the graph it is unclear if this up-then-down trend is consistently observed or not. There are bars on the graph for m-rRNA but not for s-rRNA, thus it is unclear how many times this experiment was performed for the s-rRNA or how variable the results were from sample to sample. Beyond this technical point, if the pattern is consistent, this is an interesting observation as it would signal either a shift in rDNA transcription to silence the somatic locus and/or post-transcriptional targeted degradation of the somatic rRNA in germ cells.

(2) Although qualified by the authors to some extent, the conclusion regarding maternal ribosomes and specificity related to the translation of germ line-specific transcripts is potentially confusing or misleading. Since the maternal form appears to be the only or predominant form of ribosomes in the germ cells at this stage, these would be the only ribosomes available for translation in germ cells. So, any RNA being translated in the germ cells, even RNAs that are not specifically expressed in the germline would be "enriched in association with" and translated by the maternal ribosomes in germ cells. Additional supporting evidence would be required to support the conclusion that the maternal ribosomes are specifically dedicated to the translation of germ cell-specific RNAs, like nanos3, rather than just general translation in germ cells. Consistent with a more general role for the maternal ribosomes in translation in germ cells, differential codon use has been previously documented for the RNAs produced in oocytes (aka maternal RNAs) (for example Bazzini et al EMBO 2016; Mishima and Tomari Mol Cell 2016), and tRNA genes were recently reported by Wilson and Postlethwait to reside along with the maternal 5S genes and maternal-specific spliceosome components in the region of chromosome 4 that is differentially activated in oocytes and testis (region 2 coding genes are silenced in the ovary but maternal ribosome-related genes are expressed in the ovary; region 4 contains the maternal 45S gene). Further, some of the authors of this manuscript undergo a shift in tRNA repertoire and a change in iso-decoder expression at the onset of gastrulation (Rappol et al, Nucleic Acids Research 2024). Technical limitations pose challenges to definitively testing the hypothesis, but it would be helpful to place the findings here in the context of the published work.

(3) "An alternate and non-exclusive hypothesis is that the maternal rDNA locus may be involved in PGC fate and sex determination in zebrafish." It would be helpful to further discuss the published evidence supporting this hypothesis. In accord with a potential role for m-rDNA in ovary differentiation, differential methylation of m-rDNA has been previously reported, with high methylation in testis and low methylation in ovaries. Further, several groups have shown that treating fish with broad inhibitors of methyltransferases causes testis-biased differentiation of the gonad. Finally, Moser et al (Philosophical Transactions of the Royal Society B 2024) recently published work in which CRISPR-Cas9 was used to target the 45S m-rDNA promoter and interfere with its expression. The mutants with these promoter mutations developed as fertile males, consistent with a role for m-rDNA in ovary differentiation. A recent paper from Moser et. al. (Philosophical Transactions of the Royal Society B 2024) showing that disrupting the m-rDNA locus leads to male-only development should be discussed. This paper does not exclude the possibility of a maternal role for the ribosomes since only one female was recovered among the 45S-m-rDNA mutants. The expression data in Figure 1D of this manuscript showing that m-rRNA levels go down and then up in PGCs indicates the PGCs are making their own m-rRNA. This observation together with the recovery of fertile males reported in the Moser et al study (Philosophical Transactions of the Royal Society B 2024) doesn't seem to support a requirement for m-rDNA in PGC fate or germ cell-specific translation, at least in testis, since the mutant males produce sperm and are fertile.

(4) Although the rationale for examining rRNAs in adult tumors, cultured zebrafish cell lines, and during fin regeneration is clear based on the published literature showing elevated embryonic rRNAs, this line of investigation doesn't add much to this study and is a bit of a distraction. That said, the observation that in contrast to published work, neither the maternal (early embryo) nor the specific rRNAs examined are unregulated in these contexts is important and warrants communication with the research community.

(5) The numbers of embryos and stages are not consistently stated in the manuscript. For example, in the "Isolation of zebrafish ribosome." and "isolation of monosomes" sections of the methods, the stage and number of embryos used for the IPs are not clearly stated in the methods. These important details should be stated throughout the manuscript so that others can perform future studies in a manner that will facilitate comparisons.

(6) The terminology used for the RiboFLAG experiments is potentially confusing or misleading. Specifically, different terms are used to describe the source of the ribosomes (Figure 5, Figure S7, Figure S8 and in the text). For example, "transmission" is used to describe "maternal transmission" for Mat-RiboFLAG, and "paternal transmission" is used for Som-RiboFLAG, and in Figure 5 and Figure S8 "maternally provided" and "paternally provided" are used. However, these terms may be confusing or unintentionally misleading because transmission and provided refer to two different things. In the case of Mat-RiboFLAG, the terms refer to the maternal Rpl10-FLAG ribosomes, which the progeny receive from their mother independent of whether or not they express the transgene. On the other hand, for Som-RiboFLAG, the terms refer to the transgene rather than the Rpl10-FLAG ribosomes that will be produced by the embryo using the transgene they inherited from their father. Consider instead sticking to "maternal" and "somatic", or alternatively "zygotic expression" and "maternal expression" or "zygotic ribosomes" and "maternal ribosomes".

Reviewer #2 (Public review):

Summary:

The study expands previous knowledge on the dual ribosome system in zebrafish by demonstrating the expression of maternal ribosomes in the primordial germ cells as well as the formation of hybrid ribosomes combining subunits of maternal and somatic ribosomes. Although the distinction between the two types is clear at the rRNA level, this is not paralleled at the protein level. An attempt to associate the expression of germ-line-specific transcripts to maternal ribosomes remains inconclusive. Thus, evidence for the functional specialisation of ribosomes in this system is still lacking.

Strengths:

The experiments are well-conducted and the main conclusions are well-supported.

Weaknesses:

The attempt to take advantage of the system to provide an example of functional ribosome specialisation is justified and the expression of maternal-type ribosomes in the germ line may still be key to understanding the expression of classes of mRNA. However, an alternative possibility related to genome evolution and sex determination is equally relevant.

Assessment following the structure of the manuscript:

Shah et al.: "A dual ribosomal system in zebrafish soma and germline"

The zebrafish dual ribosome system is attractive because it offers a favourable setting to look for ribosome specialization and my impression is that this is exactly what the authors set out to do rather than to try to understand why zebrafish have this unusual setup. If this is correct, the title and the abstract should better reflect the authors' aim and main results. The title suggests to the non-specialist that the dual ribosome system is a novel find which obviously is not the case.

I was a bit confused when reading the introduction. In the first paragraph, it was unclear to me if the degradation of maternal ribosomes is an active process different from normal turnover. I also found the third paragraph slightly out of tune with the discussion section. The dual ribosome setting at the level of ribosomal RNA genes represents an extreme case of sequence heterogeneity and appears to be sporadic in nature in that it only is reported from Plasmodium and zebrafish. The Xenopus example is 5S rRNA (as also mentioned in the discussion section), and the Drosophila example is protein composition, only. If a broader view of ribosome types is intended, there will be more examples, e.g. Trypanosomes that express different stage-dependent ribosomes at the level of rRNA modifications. The occurrence of dual ribosomes in fish should be placed in context with insight from other fish genomes, e.g. Medaka, which has only one type of ribosomes. Also, the duality in zebrafish is not restricted to ribosomes, but also comprises two types of spliceosomes. These observations suggest that the phenomenon should be investigated in the context of genome evolution. This is appropriately brought up in the discussion section, but I believe it would serve the reading of the manuscript if this was made clear from the beginning. With respect to the structural aspects, I am puzzled why one of the few other papers studying this system, Ramachandran et al. RNA 2020 (PMID: 32912962) is not referenced. This paper is focused on ribose methylation of the two types of ribosomal RNA and should be relevant to several aspects of the present study.

The manuscript reports three novel and important findings. First, the maternal-type ribosomes are expressed in PGCs, where they furthermore are shown to translate germ line-specific transcripts, and in the male germ line. Regardless, the authors wisely decide to maintain the classical terminology of maternal and somatic ribosomes. Second, both types of ribosomes are polysome-associated and thus translationally active at 24 hpf when they are found in equal amounts. An elaborate experiment shows that hybrid ribosomes are formed at this stage. Finally, a RIP experiment fails to show selectivity in ribosomal recruitment of a germ line-specific mRNA based on the nanos3 3´-UTR. There are several other results, but these are mainly confirmatory or negative, albeit of good quality and important to communicate.

The part of the study that describes differences in protein composition is a bit difficult to follow, partly because of the complexity of the results, and partly because of the disappointment that no parallel changes in proteins to the clear differences in rRNA were observed. Except for the discussion of eS8 in relation to subunit bridging, it is purely descriptive. There is quite a literature on paralog expression (e.g. in yeast and humans) and perhaps it would be possible to relate to the literature in a way that could provide more meaning to the observations. From the M&M section, it appears that the proteomics data were already published in the Leesch and Lorenzo-Orts et al. paper (Nature 2023). They are here found in Table S1 which is presented in a minimal fashion, from which it is time-consuming to extract meaningful information, e.g. on how stringently the ribosomes were prepared.

The hybrid-ribosome observation is convincing, but additional information on the choice of cycloheximide concentration would be helpful to rule out other interpretations.

The experiment on translation of primordial germ cell-specific transcripts by maternal ribosomes is a key experiment. Unfortunately, the experiment failed to show selectivity compared to somatic ribosomes, and in my reading, the promise in the abstract of "preferential association" is not quite justified. More importantly, this experiment is not exhaustive, and a more elaborate discussion on the limitations of the experiment and other approaches would be helpful.

The discussion section is interesting. Importantly, the authors make the non-specialist aware of the peculiarities of laboratory strains of zebrafish with respect to the lack of sex chromosomes and a possible connection between the rDNA locus and sex determination. This information is critical to include in a journal that has a broad readership. I was unable to follow the argument about the 3´half of 5.8S "to play a role" in ribosome degradation based on Locati et al., 2018 (which is missing from the reference list) and "serve as a target for degradation of maternal ribosomes". Kinetic effects on the degradation pattern of rRNA are frequently observed and difficult to interpret.

Reviewer #3 (Public review):

Summary:

Ribosomes are generally considered homogeneous complexes with no inherent role in regulating translation. However, recent studies have found heterogeneity in the composition of ribosome accessory factors, proteins, and ribosomal RNA. Moreover, there is evidence that district ribosomal isoforms are produced at different developmental stages in Xenopus, Drosophila, and zebrafish. In Drosophila, germline-derived ribosomes have a different protein composition to those produced by somatic cell types. In zebrafish, germline vs. somatic ribosomes have been shown to incorporate distinct rRNA isoforms. However, the functional significance of ribosome heterogeneity is not known.

The manuscript by Shah et al., uses the power of the zebrafish to test the hypothesis that maternal ribosome isoforms have a distinct function relative to ribosome isoforms produced by somatic cells after the maternal-to-zygotic transition (MTZ). They confirm previous findings that all maternal rRNA are derived from the maternal-specific rRNA locus on Chromosome 4. Additionally, proteomic analysis showed that maternal and somatic ribosomes also differ in protein composition. Using ribosome tagging experiments they showed that maternally derived subunits can form functional heteroduplexes (hybrids) with somatic-derived subunits. Finally, they show that maternal-derived ribosomes continue to be expressed in germ cells where they preferentially associate with the maternally derived and germline localized nanos3 mRNA. This suggests a possible role of maternal ribosomes in germ cell-specific translational regulation.

Strengths:

The authors use the experimental power of zebrafish to test the hypothesis that maternal and somatic-derived ribosomes have distinct functions. They use state-of-the art proteomics, molecular modeling, and transgenesis techniques. For the most part, the data presented is clear and supports their conclusions.

Weaknesses:

Using pulldown experiments they show that maternal ribosomes associate with the PGC-enriched nanos3 RNA, suggesting a role for the maternal isoform in germline-specific translation. However, they acknowledge that the level of enrichment is similar to the level of maternal vs. somatic isoforms that localize to PGCs. The nanos3 mRNA is unique in that it is actively degraded in somatic cells shortly after MTZ so is never present in cells that express the somatic isoforms. Therefore, the association of nanos3 with maternal ribosomes shows that these ribosomes can associate with germline-specific RNAs, but does not provide compelling evidence for a maternal isoform-specific role in translational regulation.

Reviewer #1 (Public review):

Summary:

This study investigates the relationship between climate variables and malaria incidence from monthly records, for rainfall, temperature, and a measure of ENSO, in a lowland region of Kenya in East Africa. Wavelet analyses show significant variability at the seasonal scale at the 6-month scale with some variation in its signal over time, and some additional variability at the 12-month scale for some variables. As conducted, the analyses show weak (non-significant) signals at the interannual time scales (longer than seasonal). Cross-wavelet analysis also highlights the 6-month scale and the association of malaria and climate variables at that scale, with some signal at 12 months, reflecting the role of climate in seasonality. Evidence is presented for some small changes in the lags of the response of malaria to the seasonal climate drivers over time.

Strengths:

Although there have been many studies of climate drivers of malaria dynamics in East Africa, these analyses have been largely focused on highlands where these drivers are expected to exhibit the strongest signal of association with disease burden at interannual and longer time scales. It is therefore of interest to take advantage of a relatively long time series of cases to examine the role of climate variables in more endemic malaria in lowlands.

Weaknesses:

(1) Major comments:

The work is not sufficiently placed in the context of what is known about climate variability in East Africa, and the role of climate variables in the temporal variation of malaria cases in this region. This context includes the relationship between large (global/regional) drivers of interannual climate variability such as ENSO (and the Indian Ocean Dipole) and local temporal patterns in rainfall and temperature. There is for example literature on the influence of those drivers and the short and long rains in East Africa. That is, phenomena such as ENSO would influence malaria through those local climate variables. This context should be considered when formulating and interpreting the analyses.

There are conceptual problems with the design of the analyses which can limit the findings on association. It is not surprising that rainfall would exhibit a clear association at seasonal scales. It is nevertheless valuable to confirm this as the authors have done and to examine the faster than 12-month scale, given the typical pattern of two rainfall seasons in this area. However, the results on temperature are less clear. If rainfall is the main limiting factor for the transmission season, the temperature variation that would matter can be during the rainy periods. One would then see an association with temperature only in particular windows of time during the year, when rainfall is sufficient (see for example, Rodo et al. Nat. Commun. 2022, for this finding in a highland region of Ethiopia). For this situation, there would be no clear association with temperature when all months are considered, and one would not find a significant relationship (or a lagged one) between peak times in this climate factor and malaria's seasonal cases. It would be difficult for the wavelet analysis to reveal such an effect. Another consideration is whether to use an ENSO variable that includes seasonality or to use an ENSO index computed as an anomaly, to focus on interannual variability. That is, it is most relevant to consider how ENSO influences time scales of variation longer than seasonal (the multiannual variation in seasonal epidemics) and for this purpose, one would typically rely on an anomaly. This choice would better enable one to see whether there is a role of ENSO at interannual time scales. It would also make sense to analyze with cross-wavelets the effect of ENSO on local climate factors, temperature, and rainfall, and not only on malaria. This would allow us to establish evidence for a chain of causality, from a global driver of interannual variability to local climate variability to malaria incidence.

The multiresolution analysis and associated analysis of lag variations were confusing and difficult to follow as presented: (1) the lags chosen by the multiresolution analysis do not match the phase differences of the cross-wavelet analysis if I followed what was presented. On page 8, phase differences are expressed in months. I do not understand then the following statements on page 9: "The phase differences obtained by the cross-wavelet transforms were turned into lags, allowing us to plot the evolution of the lags over time". The resulting lags in Figure 6 are shorter than the phase differences provided in the text on page 8. (2) The phase difference of the cross-wavelet analyses for malaria and temperature is also too long for this climate factor to explain an effect on the vector and then on the disease. (3) In Table 3, the regression results that are highlighted are those for Land Surface Temperatures (LST) and ENSO, with a weak but significant negative linear correlation, and for LST and bednet coverage, and this is considered part of the lag analysis. The previous text and analyses up to that point do not seem to consider the relationship of ENSO and local climate variables, or that between local climate variables and bednets (which would benefit from some context for the causal pathways this would reflect).

The conclusion in the Abstract: "Our study underlines the importance of considering long-term time scales when assessing malaria dynamics. The presented wavelet approach could be applicable to other infectious diseases" needs to be reformulated. The use of "long-term" time scales for those of ENSO and interannual variability is not consistent with the climate literature, where long-term could be interpreted as decadal and longer. The time scales beyond those of seasonality, especially those of climate variability, have been addressed in many malaria studies. It is not compelling to have the significance of this study be the importance of considering those time scales. This is not new. I recommend focusing on what has been done for lowland malaria and endemic regions (for example, in Laneri et al. PNAS 2015) as there has been less work for those regions than for seasonal epidemic ones of low transmission (e.g. altitude fringes and desert ones, e.g. Laneri et al. PloS Comp. Biol. 2010; Roy et al. Mal. J. 2015). Also, wavelet analyses have been used extensively by now to consider the association of climate variables and infectious diseases at multiple time scales. There is here an additional component of the analysis but the decomposition that underlies the linear regressions is also not that new, as decompositions of time series have been used before in this area. In summary, I recommend a more appropriate and compelling conclusion on what was learned about malaria at this location and what it may tell us about other, similar, locations, but not malaria dynamics everywhere.

The conversion from monthly cases to monthly incidence needs a better explanation of the Methods, rather than a referral to another paper. This is a key aspect of the data. It may be useful to plot the monthly time series of both variables in the Supplement, for comparison.

There is plenty of evidence of the seasonal role of rainfall on malaria's seasonality in many regions. The literature cited here to support this well-known association is quite limited. It would be useful to provide a context that better reflects the literature and some context for the environmental conditions of this lowland region that would explain the dominant role of rainfall on malaria seasonality. Two papers (from 2017 and 2019) are cited in the second paragraph of the introduction as showing that "key climatic factors are rainfall and temperatures". This is a misrepresentation of the field. That these factors matter to malaria in general has been known for a very long time given that the vectors are mosquitoes, and the cited studies are particular ones that examine the mechanistic basis of this link for modeling purposes. Either these papers are presented as examples, with a more accurate description of what they add to the earlier literature or earlier literature should be acknowledged. Also, what has been much less studied is the role of these variables at interannual time scales, as potentially mediating the effects of global drivers in teleconnections.

(2) Minor comments:

In relation to the conceptual issues raised above, it would be valuable to consider whether the negative association with temperature persists if one considers mean temperature during the rainy seasons only, against the total cases in the transmission season each year (as in Rodó et al. 2021). This would allow one to disentangle whether the negative association reflects a robust result or an artifact of an interaction between temperature and rainfall so that the former matters when the latter is permissive for transmission.

The conclusion in the Discussion " This suggests that minor climate variations have a limited impact on malaria incidence at shorter time scales, whereas climatic trends may play a more substantial role in shaping long-term malaria dynamics" is unsubstantiated. There is no clear result in the paper on climatic trends that I can see.

The Abstract writes: "The true impact of climate change...". This paper is not about climate change but about climate seasonality and variability. This text needs to be changed to make it consistent with the content of the paper.

Page 2, Introduction: The statement on Pascual et al. 2008 is not completely accurate. This paper shows an interplay of climate variability and disease dynamics, but not cycles that are completely independent of climate.

Page 2, next sentence: "More recently, such cycles have been attributed to global climate drivers such as ENSO (Cazelles et al., 2023)". This writing is also somewhat unclear. Are you referring to the cycles for the same location in Kenya? Or generically, to the interannual variability of malaria?

There are multiple places in the writing that could be edited.

Reviewer #2 (Public review):

Summary:

The analyses of long-time malaria series to investigate the complex relationship between malaria incidence and climate is hampered by the non-stationarity introduced by both changing control interventions and irregular climate events such as the el nino Southern Oscillation (ENSO).

Strengths:

By applying wavelets the authors were able to investigate the effect of the major climate factors such as rainfall, air and land temperature, and sea surface temperature (as a measure for ENSO) while at the same time taking into account changing bednet coverage. The wavelet approach is both flexible and powerful and was able to demonstrate well that shorter term. seasonal fluctuation in malaria incidence in Western Kenya is driven by rainfall patterns, while providing some evidence for temperature and SST may predict fluctuations at longer timescales.

Weaknesses:

While flexible and able to deal with non-stationarity, the wavelet approach does not really allow investigation of multiple factors at the same time but is limited to uni- and bivariate analyses. This limits the interpretability of the effect of complex climate patterns while also 'adjusting' for the changing control environment. There is also some concern that the choice of the wavelet and transforms used for different analyses (Morelet, Coiflet, maximal overlap discreet transform) may affect the results. The reasons for choosing these particular wavelets and transforms are not always evident.

The attempt to investigate the effect of longer terms / irregular period climate events is laudable. However, why were the analyses restricted to only ENSO (measured as SST)? Other climate factors such as e.g. the Indian Ocean Dipole (i.e. the difference in SST between the western and eastern Indian Ocean) are also known to affect climate and rainfall patterns in Eastern Africa.

Nevertheless, this work is a compelling demonstration of the utility of wavelets for the analyses of (non-stationary) epidemiological time series data.

Reviewer #1 (Public review):

This work derives a general theory of optimal gain modulation in neural populations. It demonstrates that population homeostasis is a consequence of optimal modulation for information maximization with noisy neurons. The developed theory is then applied to the distributed distributional code (DDC) model of the primary visual cortex to demonstrate that homeostatic DDCs can account for stimulus-specific adaptation.

What I consider to be the most important contribution of this work is the unification of efficient information transmission in neural populations with population homeostasis. The former is an established theoretical framework, and the latter is a well-known empirical phenomenon - the relationship between them has never been fully clarified. I consider this work to be an interesting and relevant step in that direction.

The theory proposed in the paper is rigorous and the analysis is thorough. The manuscript begins with a general mathematical setting to identify normative solutions to the problem of information maximization. It then gradually builds towards questions about approximate solutions, neural implementation and plausibility of these solutions, applications of the theory to specific models of neural computation (DDC), and finally comparisons to experimental data in V1. Such a connection of different levels of abstraction is an obvious strength of this work.

Overall I find this contribution interesting and assess it positively. At the same time, I have three major points of criticism, which I believe the authors should address. I list them below, followed by a number of more specific comments and feedback.

Major comments:

(1) Interpretation of key results and relationship between different parts of the manuscript. The manuscript begins with an information-transmission ansatz which is described as "independent of the computational goal" (e.g. p. 17). While information theory indeed is not concerned with what quantity is being encoded (e.g. whether it is sensory periphery or hippocampus), the goal of the studied system is to *transmit* the largest amount of bits about the input in the presence of noise. In my view, this does not make the proposed framework "independent of the computational goal". Furthermore, the derived theory is then applied to a DDC model which proposes a very specific solution to inference problems. The relationship between information transmission and inference is deep and nuanced. Because the writing is very dense, it is quite hard to understand how the information transmission framework developed in the first part applies to the inference problem. How does the neural coding diagram in Figure 3 map onto the inference diagram in Figure 10? How does the problem of information transmission under constraints from the first part of the manuscript become an inference problem with DDCs? I am certain that authors have good answers to these questions - but they should be explained much better.

(2) Clarity of writing for an interdisciplinary audience. I do not believe that in its current form, the manuscript is accessible to a broader, interdisciplinary audience such as eLife readers. The writing is very dense and technical, which I believe unnecessarily obscures the key results of this study.

(3) Positioning within the context of the field and relationship to prior work. While the proposed theory is interesting and timely, the manuscript omits multiple closely related results which in my view should be discussed in relationship to the current work. In particular:

A number of recent studies propose normative criteria for gain modulation in populations:

- Duong, L., Simoncelli, E., Chklovskii, D. and Lipshutz, D., 2024. Adaptive whitening with fast gain modulation and slow synaptic plasticity. Advances in Neural Information Processing Systems<br /> - Tring, E., Dipoppa, M. and Ringach, D.L., 2023. A power law describes the magnitude of adaptation in neural populations of primary visual cortex. Nature Communications, 14(1), p.8366.<br /> - Młynarski, W. and Tkačik, G., 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology<br /> - Haimerl, C., Ruff, D.A., Cohen, M.R., Savin, C. and Simoncelli, E.P., 2023. Targeted V1 co-modulation supports task-adaptive sensory decisions. Nature Communications<br /> - The Ganguli and Simoncelli framework has been extended to a multivariate case and analyzed for a generalized class of error measures:<br /> - Yerxa, T.E., Kee, E., DeWeese, M.R. and Cooper, E.A., 2020. Efficient sensory coding of multidimensional stimuli. PLoS Computational Biology<br /> - Wang, Z., Stocker, A.A. and Lee, D.D., 2016. Efficient neural codes that minimize LP reconstruction error. Neural Computation, 28(12),

More detailed comments and feedback:

(1) I believe that this work offers the possibility to address an important question about novelty responses in the cortex (e.g. Homann et al, 2021 PNAS). Are they encoding novelty per-se, or are they inefficient responses of a not-yet-adapted population? Perhaps it's worth speculating about.

(2) Clustering in populations - typically in efficient coding studies, tuning curve distributions are a consequence of input statistics, constraints, and optimality criteria. Here the authors introduce randomly perturbed curves for each cluster - how to interpret that in light of the efficient coding theory? This links to a more general aspect of this work - it does not specify how to find optimal tuning curves, just how to modulate them (already addressed in the discussion).

(3) Figure 8 - where do Hz come from as physical units? As I understand there are no physical units in simulations.

(4) Inference with DDCs in changing environments. To perform efficient inference in a dynamically changing environment (as considered here), an ideal observer needs some form of posterior-prior updating. Where does that enter here?

(5) Page 6 - "We did this in such a way that, for all ν, the correlation matrices, ρ(ν), were derived from covariance matrices with a 1/n power-law eigenspectrum (i.e., the ranked eigenvalues of the covariance matrix fall off inversely with their rank), in line with the findings of Stringer et al. (2019) in the primary visual cortex." This is a very specific assumption, taken from a study of a specific brain region - how does it relate to the generality of the approach?

Reviewer #2 (Public review):

Summary:

Using the theory of efficient coding, the authors study how neural gains may be adjusted to optimize coding by noisy neural populations while minimizing metabolic costs. The manuscript first presents mathematical results for the general case where the computational goals of the neural population are not specified (the computation is implicit in the assumed tuning curves) and then develops the theory for a specific probabilistic coding scheme. The general theory provides an explanation for firing rate homeostasis at the level of neural clusters with firing rate heterogeneity within clusters, and the specific application further captures stimulus-specific and neuron-specific adaptation in the visual cortex.

The mathematical derivations, simulations, and application to visual cortex data are solid as far as I can tell.

In the current format, the significance is difficult to assess fully: the manuscript is a bit sprawling, in the first half the general theory is lengthy and technical, and then in the second half a few phenomena are addressed without a clear relation between them (rate homeostasis, rate heterogeneity, synaptic homeostasis, V1 adaptation, divisive normalization), requiring several ad-hoc choices and assumptions.

Strengths:

The problem of efficient coding is a long-standing and important one. This manuscript contributes to that field by proposing a theory of efficient coding through gain adjustments, independent of the computational goals of the system. The main result is a normative explanation for firing rate homeostasis at the level of neural clusters (groups of neurons that perform a similar computation) with firing rate heterogeneity within each cluster. Both phenomena are widely observed, and reconciling them under one theory is important.

The mathematical derivations are thorough as far as I can tell. Although the model of neural activity is artificial, the authors make sure to include many aspects of cortical physiology, while also keeping the models quite general.

Section 2.5 derives the conditions in which homeostasis would be near-optimal in the cortex, which appear to be consistent with many empirical observations in V1. This indicates that homeostasis in V1 might be indeed close to the optimal solution to code efficiently in the face of noise.

The application to the data of Benucci et al 2013 is the first to offer a normative explanation of stimulus-specific and neuron-specific adaptation in V1.

Weaknesses:

The novelty and significance of the work are not presented clearly. The relation to other theoretical work, particularly Ganguli and Simoncelli and other efficient coding theories, is explained in the Discussion but perhaps would be better placed in the Introduction, to motivate some of the many choices of the mathematical models used here.

The manuscript is very hard to read as is, it almost feels like this could be two different papers. The first half seems like a standalone document, detailing the general theory with interesting results on homeostasis and optimal coding. The second half, from Section 2.7 on, presents a series of specific applications that appear somewhat disconnected, are not very clearly motivated nor pursued in-depth, and require ad-hoc assumptions.

For instance, it is unclear if the main significant finding is the role of homeostasis in the general theory or the demonstration that homeostatic DDC with Bayes Ratio coding captures V1 adaptation phenomena. It would be helpful to clarify if this is being proposed as a new/better computational model of V1 compared to other existing models.

Early on in the manuscript (Section 2.1), the theory is presented as general in terms of the stimulus dimensionality and brain area, but then it is only demonstrated for orientation coding in V1.

The manuscript relies on a specific response noise model, with arbitrary tuning curves. Using a population model with arbitrary tuning curves and noise covariance matrix, as the basis for a study of coding optimality, is problematic because not all combinations of tuning curves and covariances are achievable by neural circuits (e.g. https://pubmed.ncbi.nlm.nih.gov/27145916/ )

The paper Benucci et al 2013 shows that homeostasis holds for some stimulus distributions, but not others i.e. when the 'adapter' is present too often. This manuscript, like the Benucci paper, discards those datasets. But from a theoretical standpoint, it seems important to consider why that would be the case, and if it can be predicted by the theory proposed here.

Reviewer #1 (Public review):

Summary:

In this study, Bu et al examined the dynamics of TRPV4 channel in cell overcrowding in carcinoma conditions. They investigated how cell crowding (or high cell confluence) triggers a mechano-transduction pathway involving TRPV4 channels in high-grade ductal carcinoma in situ (DCIS) cells that leads to large cell volume reduction (or cell volume plasticity) and pro-invasive phenotype.

In vitro, this pathway is highly selective for highly malignant invasive cell lines derived from a normal breast epithelial cell line (MCF10CA) compared to the parent cell line, but not present in another triple-negative invasive breast epithelial cell line (MDA-MB-231). The authors convincingly showed that enhanced TRPV4 plasmamembrane localization correlates with high-grade DCIS cells in patient tissue samples. Specifically in invasive MCF10DCIS.com cells they showed that overcrowding or over-confluence leads to a decrease in cell volume and intracellular calcium levels. This condition also triggers the trafficking of TRPV4 channels from intracellular stores (nucleus and potentially endosomes), to the plasma membrane (PM). When these over-confluent cells are incubated with a TRPV4 activator, there is an acute and substantial influx of calcium, attesting the fact that there are high number of TRPV4 channels present on the PM. Long-term incubation of these over-confluent cells with the TRPV4 activator results in the internalization of the PM-localized TRPV4 channels.

In contrast, cells plated at lower confluence primarily have TRPV4 channels localized in the nucleus and cytosol. Long-term incubation of these cells at lower confluence with a TRPV4 inhibitor leads to the relocation of TRPV4 channels to the plasma membrane from intracellular stores and a subsequent reduction in cell volume. Similarly, incubation of these cells at low confluence with PEG 3000 (a hyperosmotic agent) promotes the trafficking of TRPV4 channels from intracellular stores to the plasma membrane.

Strengths:

The study is elegantly designed and the findings are novel. Their findings on this mechano-transduction pathway involving TRPV4 channels, calcium homeostasis, cell volume plasticity, motility and invasiveness will have a great impact in the cancer field and potentially applicable to other fields as well. Experiments are well-planned and executed, and the data is convincing. Authors investigated TRVP4 dynamics using multiple different strategies- overcrowding, hyperosmotic stress, pharmacological and genetic means, and showed a good correlation between different phenomena.

Reviewer #2 (Public review):

The metastasis poses a significant challenge in cancer treatment. During the transition from non-invasive cells to invasive metastasis cells, cancer cells usually experience mechanical stress due to a crowded cellular environment. The molecular mechanisms underlying mechanical signaling during this transition remain largely elusive. In this work, the authors utilize an in vitro cell culture system and advanced imaging techniques to investigate how non-invasive and invasive cells respond to cell crowding, respectively.

The results clearly show that pre-malignant cells exhibit a more pronounced reduction in cell volume and are more prone to spreading compared to non-invasive cells. Furthermore, the study identifies that TRPV4, a calcium channel, relocates to the plasma membrane both in vitro and in vivo (patient's samples). Activation and inhibition of TRPV4 channel can modulate the cell volume and cell mobility. These results unveil a novel mechanism of mechanical sensing in cancer cells, potentially offering new avenues for therapeutic intervention targeting cancer metastasis by modulating TRPV4 activity. This is a very comprehensive study, and the data presented in the paper are clear and convincing. The study represents a very important advance in our understanding of the mechanical biology of cancer.

Reviewer #1 (Public review):

Summary:

The study by Jena et al. addresses important questions on the fundamental mechanisms of genetic adaptation, specifically, does adaptation proceed via changes of copy number (gene duplication and amplification "GDA") or by point mutation. While this question has been worked on (for example by Tomanek and Guet) the authors add several important aspects relating to resistance against antibiotics and they clarify the ability of Lon protease to reduce duplication formation (previous work was more indirect).

A key finding Jena et al. present is that point mutations after significant competition displace GDA. A second one is that alternative GDA constantly arise and displace each other (see work on GDA-2 in Figure 3). Finally, the authors found epistasis between resistance allele that was contingent on lon. Together this shows an intricate interplay of lon proteolysis for the evolution and maintenance of antibiotic resistance by gene duplication.

Strengths:

The study has several important strengths: (i) the work on GDA stability and competition of GDA with point mutations is a very promising area of research and the authors contribute new aspects to it, (ii) rigorous experimentation, (iii) very clearly written introduction and discussion sections. To me, the best part of the data is that deletion of lon stimulates GDA, which has not been shown with such clarity until now.

Weaknesses:

Previously raised minor weaknesses and technical questions have been adequately resolved in the revised manuscript. As the experiments and their results are described in great detail the interested reader needs stamina. The details will, however, be informative to the specialist.

Reviewer #3 (Public review):

Summary:

This is an important paper that investigates the relationship between proteolytic stability of an antibiotic target enzyme and the evolution of antibiotic resistance via increased gene copy number. The target of the antibiotic trimethoprim is dihydrofolate reductase (DHFR). In Escherichia coli, DHFR is encoded by folA and the major proteolysis housekeeping protease is Lon (lon). In this manuscript, the authors report the result of the experimental evolution of a lon mutant strain of E. coli in response to sub-inhibitory concentrations of the antibiotic trimethoprim then investigate the relationship between proteolytic stability of DHFR mutants and the evolution of folA gene duplication. After 25 generations of serial passaging in a fixed concentration of trimethoprim, the authors found that folA duplication events were more common during evolution of the lon strain, than the wt strain. However, with continued passaging, some folA duplications were replaced by a single copy of folA containing a trimethoprim resistance-conferring point mutation. Interestingly, evolution of the lon strain in the setting of increasing concentrations of trimethoprim resulted in evolved strains with different levels of DHFR expression. In particular, some strains maintained two copies of a mutant folA that encoded an unstable DHFR. In a lon+ background, this mutant folA did not express well and did not confer trimethoprim resistance. However, in the lon- background, it displayed higher expression and conferred high-level trimethoprim resistance. The authors concluded that maintenance of the gene duplication event (and the absence of Lon) compensated for the proteolytic instability of this mutant DHFR. In summary, they provide evidence that the proteolytic stability of an antibiotic target protein is an important determinant of the evolution of target gene copy number in the setting of antibiotic selection.

Strengths:

The major strength of this paper is identifying an example of antibiotic resistance evolution that illustrates the interplay between the proteolytic stability and copy number of an antibiotic target in the setting of antibiotic selection. The results are rigorous and convincingly support the conclusions. This paper will be of interest to any biologist that studies the evolution of resistance mechanisms or gene duplication.

Weaknesses:

The impact of this finding is somewhat limited given that it is a single example that occurred in a lon strain of E. coli. Although the specific mechanism is unlikely to occur naturally, this study represents an important and convincing proof of the principle that gene duplication can provide increased expression demand for an unstable resistance determinant in the setting of antibiotic selection.

Reviewer #1 (Public review):

Summary:

The authors conducted a human neuroimaging study investigating the role of context in the representation of fear associations when the contingencies between a conditioned stimulus and shock unconditioned stimulus switch between contexts. The novelty of the analysis centered on neural pattern similarity to derive a measure of context and cue stability and generalization across different regions of the brain. Given the complexity and nuance of the results, it is kind of difficult to provide a concise summary. But during fear and reversal, there was cue generalization (between current CS+ cues) in the canonical fear network, and "item stability" for cues that changed their association with the shock in the IFG and precuneus. Reinstatement was quantified as pattern similarity for items or sets of cues from the earlier phases to the test phases, and they found different patterns in the IFG and dmPFC. A similar analytical strategy was applied to contexts.

Strengths:

Overall, I found this to be a novel use of MVPA to study the role of context in the reversal/extinction of human fear conditioning that yielded interesting results. The paper was overall well-written, with a strong introduction and fairly detailed methods and results. The lack of any univariate contrast results from the test phases was used as motivation for the neural pattern similarity approach, which I appreciated as a reader.

Weaknesses:

This is quite a complicated protocol and analysis plan. The authors did a decent job explaining it, given the complexity of the approach and the dense results. But it did take reading it a couple of times to start to understand it. I'm not sure if there is a simpler way to describe the approach though. Just an observation. But perhaps there is a better way to explain the density of the different comparisons between the multiple cues and contexts. It can be difficult to totally avoid jargon in a complex scientific article, but the paper is very jargon-y.

Here are a few more comments and stray observations, in no particular order of importance.

(1) I had a difficult time unpacking lines 419-420: "item stability represents the similarity of the neural representation of an item to other representations of this same item."

(2) The authors use the phrase "representational geometry" several times in the paper without clearly defining what they mean by this.

(3) The abstract is quite dense and will likely be challenging to decipher for those without a specialized knowledge of both the topic (fear conditioning) and the analytical approach. For instance, the goal of the study is clearly articulated in the first few sentences, but then suddenly jumps to a sentence stating "our data show that contingency changes during reversal induce memory traces with distinct representational geometries characterized by stable activity patterns across repetitions..." this would be challenging for a reader to grok without having a clear understanding of the complex analytical approach used in the paper.

(4) Minor: I believe it is STM200 not the STM2000.

(5) Line 146: "...could be particularly fruitful as a means to study the influence of fear reversal or extinction on context representations, which have never been analyzed in previous fear and extinction learning studies." I direct the authors to Hennings et al., 2020, Contextual reinstatement promotes extinction generalization in healthy adults but not PTSD, as an example of using MVPA to decipher reinstatement of the extinction context during test.

(6) This is a methodological/conceptual point, but it appears from Figure 1 that the shock occurs 2.5 seconds after the CS (and context) goes off the screen. This would seem to be more like a trace conditioning procedure than a standard delay fear conditioning procedure. This could be a trivial point, but there have been numerous studies over the last several decades comparing differences between these two forms of fear acquisition, both behaviorally and neurally, including differences in how trace vs delay conditioning is extinguished.

(7) In Figure 4, it would help to see the individual data points derived from the model used to test significance between the different conditions (reinstatement between Acq, reversal, and test-new).

Reviewer #2 (Public review):

Summary:

This is a timely and original study on the geometry of macroscopic (2.5 mm) brain representations of multiple cues and contexts in Pavlovian fear conditioning. The authors report that these representations differ between initial learning, and reversal learning, and remain stable during extinction.

Strengths:

The authors address an important question and use a rigorous experimental methodology.

Weaknesses:

The findings are limited (a) by the chosen spatial resolution (2.5 mm) which is far away from what modern fMRI can achieve, and (b) by the statistical analysis method. While transparently reported, their voxel-wise correction for multiple comparisons rests on a false discovery rate (i.e. 5% of the reported findings should be considered false positives) and there is no correction for the number of hypothesis tests (with an exception in some post hoc tests). Furthermore, there are some minor presentation issues that the authors could address to improve clarity.

Reviewer #1 (Public review):

Summary:

The authors seek to understand the role of different ratios of excitatory to inhibitory (EI) neurons, which in experimental studies of the cerebral cortex have been shown to range from 4 to 9. They do this through a simulation study of sparsely connected networks of excitatory and inhibitory neurons.

Their main finding is that the participation ratio and decoding accuracy increase as the E/I ratio decreases. This suggests higher computational complexity.

This is the start of an interesting computational study. However, there is no analysis to explain the numerical results, although there is a long literature of reduced models for randomly connected neural networks which could potentially be applied here. (For example, it seems that the authors could derive a mean field expression for the expected firing rate and variance - hence CV - which could be used to target points in parameter space (vs. repeated simulation in Figures 1,2).) The paper would be stronger and more impactful if this was attempted.

Strengths:

Some issues I appreciated are:

(1) The use of a publicly available simulator (Brian), which helps reproducibility. I would also request that the authors supply submission or configuration scripts (if applicable, I don't know Brian).

(2) A thorough exploration of the parameter space of interest (shown in Figure 2).

(3) A good motivation for the underlying question: other things being equal, how does the E/I ratio impact computational capacity?

Weaknesses:

(1) Lack of mathematical analysis of the network model

Major issues I recommend that the authors address (not sure whether these are "weaknesses"):

(1) In "Coding capacity in different layers of visual cortex" the authors measure PR values from layers 2/3 and 4 in VISp and find that layer 2/3 has a higher PR than layer 4.

But in Dahmen et al. 2020 (https://doi.org/10.1101/2020.11.02.365072 ), the opposite was found (see Figure 2d of Dahmen et al.): layer 2 had a lower PR than layer 4. Can the authors explain how that difference might arise? i.e. were they analyzing the same data sets? If so why the different results? Could it have to do with the way the authors subsample for the E/I ratio?

From the Methods of that paper: "Visual stimuli were generated using scripts based on PsychoPy and followed one of two stimulus sequences ("brain observatory 1.1" and<br /> "functional connectivity"). We focused on spontaneous neural activity registered while the animal was not performing any task. In each session, the spontaneous activity condition lasted 30 minutes while the animal was in front of a screen of mean grey luminance. We, therefore, analyzed 26 of the original 58 sessions corresponding to the "functional connectivity" subdataset as they included such a period of spontaneous activity. " This suggests to me they may have analyzed recordings with the other stimulus sequence; however, the hypothesis that E/I ratio should modulate dimensionality would not seem to "care" about which stimulus sequence was used.

(2) In Discussion (pg. 20, line 383): "They showed that brain regions closer to sensory input, like the thalamus, have higher dimensionality than those further away, such as<br /> the visual cortex. " How is this consistent with the hypothesis that "higher dimensionality might be linked to more complex cognitive functions"?

(3) What is the probability of connection between different populations? e.g. the probability of there being a synaptic connection between any two E cells? I could not find a statement about this. It should be included in the Methods.

(4) pg. 27, line 540: "Synchronicity within the network" For each cell pair, the authors use the maximum cross-correlation over time lag. I don't think I have seen this before. Can the authors explain why they use this measurement, vs (a) integrated cross-correlation or (b) cross-correlation at some time scale? Also, it seems like this fails to account for neuron pairs for which there is a strong inhibitory correlation.

(5) "When stimulated, a time-varying input, μext(t), is applied to 2,000 randomly selected excitatory neurons. " I would guess that computing PR would depend on the overlap of the 500 neurons analyzed and this population. Do the authors check or control for that?

5b) Related: to clarify, are the 500 neurons chosen from the analysis equally likely to be E or I neurons?

Reviewer #2 (Public review):

Summary:

Alizadeh et al. investigate how varying cellular E/I (excitatory/inhibitory) composition impacts coding across cortical layers. They build on findings from a recent study (Huang et al., 2022) that demonstrated a decrease in the fraction of inhibitory neurons from L2/3 to L4. Using a network of excitatory and inhibitory leaky integrate-and-fire neurons, they systematically assess how these anatomical features influence the dimensionality of network activity and coding capacity. Their key finding is that increasing the proportion of inhibitory neurons enhances the dimensionality of activity and improves the encoding of time-varying stimuli.

Strengths:

The authors use a clear methodology and well-established model of network activity that allows them to relate network parameters to the coding properties. They systematically evaluate the impact of the key features of the inhibitory population. Thus, in addition to changing the fraction of inhibitory cells, they control for the inhibitory firing threshold of inhibitory neurons and connection strength between inhibitory and excitatory cells. Furthermore, they show their modeling results are aligned with the analysis of the spiking activity in L2/3 vs. L4 from the Allen Institute data.

Weaknesses:

One general shortcoming of this approach is that it focuses on a small preselected number of network features. For example, it is unclear to what extent the results would be affected by other aspects of the organization of cortical columns, such as subclasses of inhibitory cells (SOM, VIP, PV), specific differences in synapses, realistic population sizes, or even connectivity between layers. Similarly, the models of L2/3 and L4 are constrained based on a limited set of observations, and it has not been demonstrated whether the same findings hold true for V1 recordings analyzed by the authors.

The modeling relies on anatomical data from the barrel cortex, but the decoding comparison is based on V1 data. This raises questions about how anatomical differences between regions may influence the conclusions.

The coding capacity appears inversely correlated with the firing rate, which in this study is largely influenced by the properties of the inhibitory population. It would be important to confirm that the observed changes in coding capacity and participation ratio are not solely driven by firing rate changes.

Reviewer #1 (Public review):

This manuscript presents a pipeline incorporating a deep generative model and peptide property predictors for the de novo design of peptide sequences with dual antimicrobial/antiviral functions. The authors synthesized and experimentally validated three peptides designed by the pipeline, demonstrating antimicrobial and antiviral activities, with one leading peptide exhibiting antimicrobial efficacy in animal models.

Overall, the authors have addressed each major comment through new experiments, particularly by validating 24 peptides, clarifying alignment methods, and demonstrating sequence novelty. These additions have strengthened the manuscript. To further refine the work, it would be helpful to briefly describe any steps taken to mitigate GAN pathologies (such as mode collapse), provide a short rationale for the use of five AVP classifiers and how they complement each other, and clearly present the expanded experimental data (including MIC values and antiviral results) in the main text. Finally, the authors should also compare their approach with recently described deep-learning-enabled antibiotic discovery methods.

Reviewer #2 (Public review):

Summary:

This study marks a noteworthy advance in the targeted design of AMPs, leveraging a pioneering deep learning framework to generate potent bifunctional peptides with specificity against both bacteria and viruses. The introduction of a GAN for generation and a GCN-based AMPredictor for MIC predictions is methodologically robust and a major stride in computational biology. Experimental validation in vitro and in animal models, notably with the highly potent P076 against a multidrug-resistant bacterium and P002's broad-spectrum viral inhibition, underpins the strength of their evidence. The findings are significant, showcasing not just promising therapeutic candidates, but also demonstrating a replicable means to rapidly develop new antimicrobials against the threat of drug-resistant pathogens.

Strengths:

The de novo AMP design framework combines a generative adversarial network (GAN) with an AMP predictor (AMPredictor), which is a novel approach in the field. The integration of deep generative models and graph-encoding activity regressors for discovering bifunctional AMPs is cutting-edge and addresses the need for new antimicrobial agents against drug-resistant pathogens. The in vitro and in vivo experimental validations of the AMPs provide strong evidence to support the computational predictions. The successful inhibition of a spectrum of pathogens in vitro and in animal models gives credibility to the claims. The discovery of effective peptides, such as P076, which demonstrates potent bactericidal activity against multidrug-resistant A. baumannii with low cytotoxicity, is noteworthy. This could have far-reaching implications for addressing antibiotic resistance. The demonstrated activity of the peptides against both bacterial and viral pathogens suggests that the discovered AMPs have a wide therapeutic potential and could be effective against a range of pathogens.

Comments on revisions: I have no further comments on revisions.

Reviewer #3 (Public review):

Summary:

Dong et al. described a deep learning-based framework of antimicrobial (AMP) generator and regressor to design and rank de novo antimicrobial peptides (AMPs). For generated AMPs, they predicted their minimum inhibitory concentration (MIC) using a model that combines the Morgan fingerprint, contact map and ESM language model. For their selected AMPs based on predicted MIC, they also use a combination of antiviral peptide (AVP) prediction models to select AMPs with potential antiviral activity. They experimentally validated 3 candidates for antimicrobial activity against S. aureus, A. baumannii, E. coli, and P. aeruginosa, and their toxicity on mouse blood and three human cell lines. The authors select their most promising AMP (P076) for in vivo experiments in A. baumannii-infected mice. They finally test the antiviral activity of their 3 AMPs against viruses.

Strengths:

- The development of de novo antimicrobial peptides (AMPs) with the novelty of being bifunctional (antimicrobial and antiviral activity).

- Novel, combined approach to AMP activity prediction from their amino acid sequence.

Weaknesses:

- I missed the justification for combined antiviral and antibacterial activities. As the authors responded, less than 10% of the training data has antiviral activity. Therefore, I do not understand how the high percentage of antiviral activities was achieved. Especially reading that the antiviral filtering did not have an influence on the number of antiviral peptides obtained.

- I had difficulty in reading the story because of the use of acronyms without referring to their full name for the first time, and incomplete information annotation in figures and captions.

Joint Public Review:

This is an interesting, timely, and high-quality study on the potential neuroprotective capabilities of C-C chemokine receptor type 5 (CCR5) antagonists in ischemic stroke. The focus is on preclinical investigations.

An outstanding feature is that stroke patient representatives have directly participated in the work. Although this is often called for, it is hardly realized in research practice, so the work goes beyond established standards.

The included studies were assessed regarding the therapeutic impact and their adherence to current quality assurance guidelines such as STAIR and SRRR, another important feature of this work. While overall results were promising, there were some shortcomings regarding guideline adherence.

The paper is very well written and concise yet provides much highly useful information. It also has very good illustrations, and extremely detailed and transparent supplements.

[Editors' note: The authors have responded appropriately to the comments shared by the reviewers. The authors have provided a good academic justification for not needing to update the literature search, as one of the reviewers had suggested.]

Reviewer #1 (Public review):

Summary:

The manuscript entitled "Phosphodiesterase 1A Physically Interacts with YTHDF2 and Reinforces the Progression of Non-Small Cell Lung Cancer" explores the role of PDE1A in promoting NSCLC progression by binding to the m6A reader YTHDF2 and regulating the mRNA stability of several novel target genes, consequently activating the STAT3 pathway and leading to metastasis and drug resistance.

Strengths:

The study addresses a novel mechanism involving PDE1A and YTHDF2 interaction in NSCLC, contributing to our understanding of cancer progression.

Reviewer #2 (Public review):

Summary

This revised manuscript investigates the role and the mechanism by which PDE1 impacts NSCLC progression. They provide evidence to demonstrate that PDE1 binds to m6A reader YTHDF2, in turn, regulating STAT3 signaling pathway through its interaction, promoting metastasis and angiogenesis.

Strength:

The study uncovers a novel PDE1A/YTHDF2/SOCS2/STAT3 pathway in NSCLC progression and the findings provide a potential treatment strategy for NSCLC patients with metastasis.

Weakness:

In discussion, it is stated in the revised version that "the role of YTHDF2 in PDE1A-driven tumor metastasis should be elucidated in future studies", however, given that physical interaction of PDE1A and YTHDF2 plays a critical role in PDE1A-mediated NSCLC metastasis, whether YTHDF2 mimicking the effect of PDE1A in metastasis will strength the manuscript.

Reviewer #1 (Public review):

Summary:

This paper presents a compelling and comprehensive study of decision-making under uncertainty. It addresses a fundamental distinction between belief-based (cognitive neuroscience) formulations of choice behavior with reward-based (behavioral psychology) accounts. Specifically, it asks whether active inference provides a better account of planning and decision making, relative to reinforcement learning. To do this, the authors use a simple but elegant paradigm that includes choices about whether to seek both information and rewards. They then assess the evidence for active inference and reinforcement learning models of choice behavior, respectively. After demonstrating that active inference provides a better explanation of behavioral responses, the neuronal correlates of epistemic and instrumental value (under an optimized active inference model) are characterized using EEG. Significant neuronal correlates of both kinds of value were found in sensor and source space. The source space correlates are then discussed sensibly, in relation to the existing literature on the functional anatomy of perceptual and instrumental decision-making under uncertainty.

Comments on revisions:

Many thanks for attending to my previous comments. I think your manuscript is now easier to read - and your new (Bayesian) analyses are described clearly.

Reviewer #3 (Public review):

Summary:

This paper aims to investigate how the human brain represents different forms of value and uncertainty that participate in active inference within a free-energy framework, in a two-stage decision task involving contextual information sampling, and choices between safe and risky rewards, which promotes shifting between exploration and exploitation. They examine neural correlates by recording EEG and comparing activity in the first vs second half of trials and between trials in which subjects did and did not sample contextual information, and perform a regression with free-energy-related regressors against data "mapped to source space."

Strengths:

This two-stage paradigm is cleverly designed to incorporate several important processes of learning, exploration/exploitation and information sampling that pertain to active inference. Although scalp/brain regions showing sensitivity to the active-inference related quantities do not necessarily suggest what role they play, they are illuminating and useful as candidate regions for further investigation. The aims are ambitious, and the methodologies are impressive. The paper lays out an extensive introduction to the free energy principle and active inference to make the findings accessible to a broad readership.

Weaknesses:

It is worth noting that the high lower-cutoff of 1 Hz in the bandpass filter, included to reduce the impact of EEG noise, would remove from the EEG any sustained, iteratively updated representation that evolves with learning across trials, or choice-related processes that unfold slowly over the course of the 2-second task windows. It is thus possible there are additional processes related to the active inference quantities that are missed here. This is not a flaw as one must always try to balance noise removal against signal removal in filter settings - it is just a caveat. As the authors also note, the regions showing up as correlated with model parameters change depending on source modelling method and correction for multiple comparisons, warranting some caution around the localisation aspect.

Reviewer #2 (Public review):

Summary:

Juvenile hormone (JH) is a pleiotropic terpenoid hormone in insects that mainly regulates their development and reproduction. In particular, its developmental functions are described as the "status quo" action, as its presence in the hemolymph (the insect blood) prevents metamorphosis-initiating effects of ecdysone, another important hormone in insect development, and maintains the juvenile status of insects.

While such canonical functions of JH are known to be mediated by its intracellular receptor complex composed of Met and Tai, there have been multiple reports suggesting the presence of cell membrane receptor(s) for JH, which mediate non-genomic effects of this terpenoid hormone. In particular, the presence of receptor tyrosine kinases (RTKs) that phosphorylate Met/Tai in response to JH and thus indirectly affect the canonical JH signaling pathway has been strongly suggested. Given the importance of JH in insect physiology and the fact that the JH signaling pathway is a major target of insect growth regulators, elucidating the identify and functions of putative JH membrane receptors is of great significance form both basic and applied perspectives.

In the present study, the authors identified candidate receptors for such cell membrane JH receptors, CAD96CA and FGFR1, in the cotton bollworm, Helicoverpa armigera.

Strengths:

Their in vitro analyses are conducted thoroughly using multiple methods, which overall support their claim that these receptors can bind to JH and mediate their non-genomic effects.

Their CRISPR-Cas-mediated mutagenesis in vivo shows that mutation of the two RTKs causes acceleration of pupation, which is consistent with the mutant phenotype of the intracellular JH receptor, Met1. Although this is different from the typical phenotype one would expect from JH signaling deficiency in lepidopteran insects (i.e. precocious metamorphosis), the results overall support their claim that these two RTKs modulate genomic JH effects by phosphorylating the intracellular receptors.

Weaknesses:

Although their loss-of-function analyses suggest that the two RTKs likely have redundant functions in vivo, it is unclear whether they have any different functions in mediating JH functions in different physiological contexts. It also remains unknown whether other endogenous ligands for these RTKs affect canonical, genomic JH signaling in vivo.

Reviewer #1 (Public review):<br /> <br /> Summary:

Juvenile Hormone (JH) plays a key role in insect development and physiology. Although the intracellular receptor for JH was identified long ago, a number of studies have shown that part of JH functions should be fulfilled through binding to an unknown membrane receptor, which was proposed to belong to the RTK family. In this study, the authors screened all RTKs from the H. armigera genome for their ability to mediate responses to JH III treatment both in cultured cells and in developping animals. They also present convincing evidence that CAD96CA and FGFR1 directly bind JH III, and that their role might be conserved in other insect species.

Strengths:

Altogether, the experimental approach is very complete and elegant, providing evidence for the role of CAD96CA and FGFR1 in JH signalling using different techniques and in different contexts. I believe that this work will open new perspectives to study the role of JH and better understand what is the contribution of signalling through membrane receptors for JH-dependent developmental processes.

Weaknesses:

Unfortunately, the revised manuscript does not show significant improvement. While the identification of the receptors is highly convincing, important issues about the biological relevance remain unaddressed.

First, the main point I raised about the first version of this article is that the redundancy and/or specificity of the two receptors should be clarified, even though I understand that it cannot be deeply investigated here. I believe that this point, shared by all reviewers, is highly relevant for the scope of this work. In this revised version, it is still unclear how to reconcile gain and loss-of-function experiments and the different expression profiles of the receptors.

Second, the newly added explanations and pieces of discussion provided about the mild in vivo phenotypes of early pupation upon Cad96ca or Fgfr1 knock-out do not clarify the issue but instead put emphasis on methodological issues. Indeed, it is not clear whether the mild phenotypes reflect the biological role of Cad96ca and Fgfr1, or the redundancy of these two RTKs (and/or others), or some issue with the knock-out strategy (partial efficiency, mosaicism...).

Finally, parts of the updated discussion and the modifications to the figures are confusing.

Reviewer #2 (Public review):

Summary:

Juvenile hormone (JH) is a pleiotropic terpenoid hormone in insects that mainly regulates their development and reproduction. In particular, its developmental functions are described as the "status quo" action, as its presence in the hemolymph (the insect blood) prevents metamorphosis-initiating effects of ecdysone, another important hormone in insect development, and maintains the juvenile status of insects.

While such canonical functions of JH are known to be mediated by its intracellular receptor complex composed of Met and Tai, there have been multiple reports suggesting the presence of cell membrane receptor(s) for JH, which mediate non-genomic effects of this terpenoid hormone. In particular, the presence of receptor tyrosine kinase(s) that phosphorylate Met/Tai in response to JH and thus indirectly affect the canonical JH signaling pathway has been strongly suggested. Given the importance of JH in insect physiology and the fact that the JH signaling pathway is a major target of insect growth regulators, elucidating the identify and functions of putative JH membrane receptors is of great significance from both basic and applied perspectives.

In the present study, the authors identified candidate receptors for such cell membrane JH receptors, CAD96CA and FGFR1, in the cotton bollworm Helicoverpa armigera.

Strengths:

Their in vitro analyses are conducted thoroughly using multiple methods, which overall supports their claim that these receptors can bind to JH and mediate their non-genomic effects.

Weaknesses:

Results of their in vivo experiments, particularly those of their loss-of-function analyses using CRISPR mutants are still preliminary, and the results rather indicate that these membrane receptors do not have any physiologically significant roles in vivo. More specifically, previous studies in lepidopteran species have clearly and repeatedly shown that precocious metamorphosis is the hallmark phenotype for all JH signaling-deficient larvae. In contrast, the present study showed that Cad96ca and Fgfr1 G0 mutants only showed slight acceleration in their pupation timing, which is not a typical phenotype one would expect from JH signaling deficiency. This is inconsistent with their working model provided in Figure 6, which indicates that these cell membrane JH receptors promote the canonical JH signaling by phosphorylating Met/Tai.

If the authors argue that this slight acceleration of pupation is indeed a major JH signaling-deficient phenotype in Helicoverpa, they need to provide more data to support their claim by analyzing CRISPR mutants of other genes involved in JH signaling, such as Jhamt and Met. An alternative explanation is that there is functional redundancy between CAD96CA and FGFR1 in mediating phosphorylation of Met/Tai. This possibility can be tested by analyzing double knockouts of these two receptors.

Currently, the validity of their calcium imaging analysis in Figure 5 is also questionable. When performing calcium imaging in cultured cells, it is critically important to treat all the cells at the end of each experiment with a hormone or other chemical reagents that universally induce calcium increase in each particular cell line. Without such positive control, the validity of calcium imaging data remains unknown, and readers cannot properly evaluate their results.

Reviewer #3 (Public review):

Summary:

In this study, Li et al. identified CAD96CA and FGF1 among 20 receptor tyrosine kinase receptors as mediators of JH signaling. By performing a screen in HaEpi cells with overactivated JH signaling, the authors pinpointed two main RTKs that contribute to the transduction of JH. Using the CRISPR/Cas9 system to generate mutants, the authors confirmed that these RTKs are required for normal JH activation, as precocious pupariation was observed in their absence. Additionally, the authors demonstrated that both CAD96CA and FGF1 exhibit a high affinity for JH, and their activation is necessary for the proper phosphorylation of Tai and Met, transcription factors that promote the transcriptional response. Finally, the authors provided evidence suggesting that the function of CAD96CA and FGF1 as JH receptors is conserved across insects.

Strengths:

The data provided by the authors are convincing and support the main conclusions of the study, providing ample evidence to demonstrate that phosphorylation of the transducers Met and Tai mainly depends on the activity of two RTKs. Additionally, the binding assays conducted by the authors support the function of CAD96CA and FGF1 as membrane receptors of JH. The study's results validate, at least in H. amigera, the predicted existence of membrane receptors for JH.

Weaknesses:

The authors have provided evidences that the Cad96Ca and FGF1 RTK receptors contribute to JH signaling through CRISPR/Cas9, inducing precocious metamorphosis, although not to the same extent as absence of JH. Therefore, it still remains unclear whether these RTKs are completely required for pathway activation or only necessary for high activation levels during the last larval stage.

While the authors have included some additional data, the mechanism by which different RTKs function in transducing JH signaling in a tissue specific manner is still unclear. As the authors note in the discussion, it is possible that other RTKs may also play a role in facilitating the transduction of JH signaling.

Lastly, the study does not yet explain how RTKs with known ligands could also bind JH and contribute to JH signaling activation. Although receptor promiscuity has been suggested as a possible mechanism, future studies could explore whether activation of RTK pathways by their known ligands induces certain levels of JH transducer phosphorylation, which, in the presence of JH, could contribute to full pathway activation without the need for direct JH-RTK binding.

Reviewer #1 (Public review):

Summary:

This work is meant to help create a foundation for future studies of the Central Complex, which is a critical integrative center in the fly brain. The authors present a systematic description of cellular elements, cell type classifications, behavioral evaluations and genetic resources available to the Drosophila neuroscience community.

Strengths:

The work contributes new, useful and systematic technical information in compelling fashion to support future studies of the fly brain. It also continues to set a high and transparent standard by which large-scale resources can be defined and shared.

Weaknesses:

Manuscript revisions by the authors addressed all proposed weaknesses from the original version.

Reviewer #2 (Public review):

Summary:

In this paper, Wolff et al. describe an impressive collection of newly created split-GAL4 lines targeting specific cell types within the central complex (CX) of Drosophila. The CX is an important area in the brain that has been involved in the regulation of many behaviors including navigation and sleep/wake. The authors advocate that to fully understand how the CX functions, cell-specific driver lines need to be created. In that respect, this manuscript will be of very important value to all neuroscientists trying to elucidate complex behaviors using the fly model. In addition, and providing a further very important finding, the authors went on to assess neurotransmitter/neuropeptides and their receptors expression in different cells of the CX. These findings will also be of great interest to many and will help further studies aimed at understanding the CX circuitries. The authors then investigated how different CX cell types influence sleep and wake. While the description of the new lines and their neurochemical identity is excellent, the behavioral screen seems to be unfinished and could have been more matured.

Strengths:

(1) The description of dozens of cell-specific split-GAL4 lines is extremely valuable to the fly community. The strength of the fly system relies on the ability to manipulate specific neurons to investigate their involvement in a specific behavior. Recently, the need to use extremely specific tools has been highlighted by the identification of sleep-promoting neurons located in the VNC of the fly as part of the expression pattern of the most widely used dorsal-Fan Shaped Body (dFB) GAL4 driver. These findings should serve as a warning to every neurobiologist, make sure that your tool is clean. In that respect, the novel lines described in this manuscript are fantastic tools that will help the fly community.<br /> (2) The description of neurotransmitter/neuropeptides expression pattern in the CX is of remarkable importance and will help design experiments aimed at understanding how the CX functions.

Weaknesses:

(1) I find the behavioral (sleep) screen of this manuscript to be incomplete. It appears to me that this part of the paper is not as developed as it could be. The authors have performed neuronal activation using thermogenetic and/or optogenetic approaches. For some cell types, only thermogenetic activation is shown. There is no silencing data and/or assessment of sleep homeostasis or arousal threshold. The authors find that many CX cell types modulate sleep and wake but it's difficult to understand how these findings fit one with the other. It seems that each CX cell type is worthy of its own independent study and paper. I am fully aware that a thorough investigation of every CX neuronal type in sleep and wake regulation is a herculean task. So, altogether I think that this manuscript will pave the way for further studies on the role of CX neurons in sleep regulation.<br /> (2) Linked to point 1, it is possible that the activation protocols used in this study are insufficient for some neuronal types. The authors have used 29{degree sign} for thermogenetic activation (instead of the most widely used 31{degree sign}) and a 2Hz optogenetic activation protocol. The authors should comment on the fact that they may have missed some phenotypes by using these mild activation protocols.<br /> (3) There are multiple spelling errors in the manuscript that need to be addressed.

Comments on revisions:

I am satisfied with the authors response. This paper provides excellent starting points for additional studies into the role of different CX cell types in sleep and wake.

Reviewer #4 (Public review):

Summary:

This is an important study that underscores that reproduction-survival trade-offs are not manifested (contrary to what generally accepted theory predicts) across a range of studies on birds. This has been studied by a meta-analytical approach, gathering data from a set of 46 papers (30 bird species). The overall conclusion is that there are no trade-offs apparent unless experimental manipulations push the natural variability to extreme values. In the wild, the general pattern for within-species variation is that birds with (naturally) larger clutches survive better.

Likely impact:

I think this is an important contribution to a slow shift in how we perceive the importance of trade-offs in ecology and evolution in general. While the current view still is that one individual excelling in one measure of its life history (i.e. receiving benefits) must struggle (i.e. pay costs) in another part. However, a positive correlation between all aspects of life history traits is possible within an individual (such as due to developmental conditions or fitting to a particular environment). Simply, some individuals can perform generally better (be of good quality than others).