Reviewer #2 (Public Review):

Differentiation pathways for parasitic organisms are of considerable importance, as they are relevant to understanding transmission, mechanisms of host specificity as well as, in some cases, offering possible routes to control measures. The transition between mammalian host and insect vector for African trypanosomes has been widely addressed due to accessibility and tractability. However, one view has been dominant, despite, as the authors suggest, considerable counter evidence. The present work posits an alternate pathway, questioning the role of the so called stumpy stage. This is of considerable importance to the immediate field and possibly wider.

The major strengths here are in the use of a good model, and a high number of individual infections. The weaknesses include some assumptions with which I have issue, and given that this work is seeking to overturn a dogma, which also has assumptions, one needs to tread very carefully, to avoid falling into an unscholarly dispute. The major things are for me the assumption that PAD-1 cells are stumpy - almost anything seems to be able to activate PAD-1 and the lack of any quantitative data are concerning. This is difficult really and Matthews also says that PAD-1 does not equal stumpy and morphology is also important. Further, simple expression of EP procyclin is not sufficient for designation as pr cyclic, and the salivary gland cells are assumed metacyclic without demonstration of VSG expression for example. While I accept that these interpretations are reasonable, this is an assumption and in all three cases leads me to feel a little underwhelmed. Perhaps most concerning are the lack of statistical calculations as well as any attempt at further analysis beyond counting. The result is very much phenomenology and lacks any mechanistic insight.

Reviewer #2 (Public Review):

Analyzing EM data from the Drosophila larva, Hueckesfeld et al. investigate and describe the synaptic connectivity of sensory neurons and interneurons that provide input into the neuroendocrine system in fly larvae. The output of neuroendocrine neurons projecting to the ring gland is mostly non-synaptic and identified by receptor expression analysis. Using a modelling approach, they provide a more detailed analysis on newly discovered CO2-responsive cells and their downstream network and also other possible processing pathways from sensory to endocrine neurons. To test some of their model predictions, they analyze the response of predicted CO2-downstream neurons to CO2 exposure.

Strengths of the paper:

The authors did a great job in visualizing the complex connectivity between sensory inputs, interneurons, and endocrine neurons. Neuroendocrine neuron outputs, which are mostly non-synaptic, have been detected by identification of vesicle release regions. The authors went beyond the analysis of EM data and collected a lot of new data to confirm non-synaptic connectivity between neuroendocrine neurons and their downstream targets by performing antibody stainings and trans-tango experiments. This information will be highly valuable to the field.

Sensory inputs in the larvae have been attributed according to previous publications, but the authors also describe a new CO2 sensing function of tracheal TD neurons. Description of this new sensory function is also a valuable addition to the Drosophila field.

The authors used a modelling approach to describe and detect specific processing pathways, for example from a certain sensory modality, or to a specific endocrine neuron. This manuscript underlines that the use of a (simple) computational model framework to understand network motifs within an EM dataset is very powerful. Also, they can confirm that predicted CO2 downstream neurons indeed respond to CO2 in a certain way.

The authors discuss potential functional implications for faster and slower processing pathways (connections over interneurons or direct). Indeed there might be situations where the larva needs to respond in flexible ways that are however also easily reversable (fast pathways), but there might be also other situations where the larva needs to integrate more sensory evidence and which might induce non-reversible behaviors, such as pupation (slow pathways). I think this discussion suggests an interesting concept of the impact/cost of adaptive behavioral changes and the different timescales they can occur.

Weaknesses of the paper:

Data wise, this manuscript is a very descriptive study. The authors visualize the complex and diverse possible processing pathways; however, the function of the circuit remains unknown. To really understand the functional properties behind this complex architecture will require studies focused on single sensory modalities, single pathways and/or single peptidergic classes all in the context of a certain behavioral framework.

The authors try to provide a complete overview over the connectivity within the neuroendocrine system pathways. However, the authors should discuss that the connectivity data from the one EM dataset that they analyzed might be changing across individuals and development. Especially the vesicle release sites might be more variable across individual larvae than synaptic connections. Neuropeptide receptor expression might also change over development.

The authors investigate the TD CO2 sensing pathway in more detail. They show that the sensory neurons and the predicted downstream neurons respond to CO2. This shows that the neural connectivity might serve a functional purpose. There is however another type of sensory neurons that respond to CO2 in the larva (Gr21a receptor neurons- Faucher et al., 2006), which are required for an avoidance response to the stimulus. The authors should discuss and maybe analyze the EM data for possible circuit convergence between the two different CO2 sensory input neurons.

The authors discuss the CO2 response in the context of a stress response. However, the natural environment of larvae, rotten fruits, also emit CO2 as a by-product. Thus, sensing CO2 which converges together with information from Fructose/Glucose sensors might be used for finding or evaluating food sources.

Reviewer #2 (Public Review):

KSR1 functions as a critical rheostat to fine-tune MAPK signalling, and identifying modes by which its over-expression promotes tumor progression is clinically important and potentially druggable. Ras is highly mutated in CRC and unfortunately inhibitors of Ras have been challenging to develop. However, small molecules which stabilize an inactive form of the KSR are actively being developed in an attempt to repress RAS signaling. Thus, this study, which seeks to identify how KSR1 promotes oncogenic mRNA translation, is potentially highly clinically relevant, as it may identify novel druggable targets.

In this manuscript the authors performed polysome profiling in colorectal cancer (CRC) cells and proposed that KSR1 and ERK regulate the translation of EPSTI1 mRNA. They go on to characterize the phenotypes associated with knock-down or knock-out of KSR1 in CRC, and show that their defects in invasion, anchorage-independent growth and switch to a less EMT-like phenotype are all EPSTI1-dependent.

The authors succeeded in providing ample in vitro data that KSR1 and EPSTI1 are potential therapeutic targets in CRC. However, the data demonstrating that KSR1 and ERK regulate EPSTI1 mRNA translation is tenuous. Although the authors state that "EPSTI1 is necessary and sufficient for EMT in CRC cells", the data presented are consistent with a more restrained conclusion of a partial-EMT and not EMT per se. Finally, without an in vivo model it is difficult to glean novel insight into the mechanism by which KSR1 and/or EPSTI1 control the invasive and metastatic behaviour of cells.

Reviewer #2 (Public Review):

Cell fate transitions (such as adenocarcinoma converting to small cell neuroendocrine fate) are an increasing phenomenon observed during therapeutic resistance in lung cancer, prostate cancer, and possibly other cancer types. It is important to understand these mechanisms if we ultimately seek to tailor treatment to a patient's disease and/or to control the pathways that lead to treatment resistance. However, the mechanisms that underly these cell fate changes are not well understood. It has been previously observed (Calbo et al, Cancer Cell, 2011) that activated mutant Kras (commonly associated with adenocarcinoma fate) can promote a non-neuroendocrine fate in SCLC, but the mechanisms are unknown.

Predominantly using three human small cell lung cancer (SCLC) cell lines, Inoue and colleagues use genetic and pharmacological approaches to focus on potential mechanisms by which Egfr/Kras/Mapk signaling can repress neuroendocrine fate. They make a number of interesting observations that extend our understanding of neuroendocrine cell fate regulation including:

1) Kras-induced NE suppression appears to depend mostly on ERK2, and not ERK1 or PI3K signaling.

2) Kras activation induces chromatin changes including increased H3K27Ac in 2/3 cell lines; increased H3K27Ac in response to HDAC inhibition is associated with NE suppression. Pharmacological inhibition of CBP/p300 (a HAT that promotes H3K27Ac) reduces H3K27Ac and restores NE suppression. Altogether, these findings are consistent with the notion that SCLC cannot tolerate high levels of H3K27Ac.

3) Kras induces the MSK/RSK pathway consistently in cell lines but appears to be functionally-relevant to NE fate only in H82 cells.

4) Kras activation induces chromatin occupancy at ERG and ETS family transcription factor (Etv1, 4, 5) binding sites in 2/3 cell lines, and induces ETV4 (2/3 lines) and ETV5 protein levels (3/3 lines). ETV1 and ETV5 overexpression are sufficient to inhibit NE fate markers in context-dependent manner. Ets family induction appears to occur in a CIC-independent manner.

In addition, some interesting negative data is presented, for example, SOX9 is induced upon Kras activation in 3/3 cell lines but it was not functionally relevant for NE suppression; Notch1, Notch2, and HES1 (known NE fate suppressors) are induced by Kras activation in a cell context-specific manner, but they did not appear functionally-relevant to NE suppression based on HES1 knockout and a pharmacological inhibitor of Notch signaling; Rb1 loss was not sufficient to promote NE fate in EGFR/p53 mutant cell lines, despite its known association with adeno-to-SCLC conversion. Overall, the conclusions in the manuscript are well justified. These findings will be of interest to those especially in lung and prostate cancer studying cell fate conversions in the context of EGFR and AR inhibitor resistance, respectively. These observations will be built upon by these fields.

Weaknesses:

1) One recurring issue in the manuscript is that the observations are often not consistent across the three cell lines and are context-specific effects, and the potential reasons could be explained better. The cell lines chosen unfortunately (but interestingly) represent some of the major cell states of SCLC. H2107 represents the ASCL1+ NE-high subset of SCLC (and has some MYCL). H82 and H524 represent the C-Myc (MYC)-high subset of SCLC, with H82 having a MYC amplification, and both representing the NEUROD1 subtype (which tend to be associated with more MYC). Assessment of NE score using a common approach in the field (Zhang et al, TLCR) shows that H82 cells are already considerably NE-low, with H524 as NE-intermediate/high, and H2017 as NE-high. So, this may be related to why H82 seemed to be the most permissive cell line to change NE fate in multiple assays.

In addition, H2107 and H524 appear to have EP300 mutations, which may contribute to their NE-high nature and contribute to the refractory response to A485 treatment based on the author's model. It's known that MYCL and MYC-driven cell lines differ in numerous aspects from transcriptional signatures, super enhancer usage, metabolic regulation, therapeutic response, etc. This information could be mentioned in the results and discussed when mentioned as a factor near line 540.

2) Related to Figure 4, the authors show that p300 pharmacological inhibition can restore NE fate in presence of Kras. Given that drugs can have off-target effects, it would be helpful to know if genetic knockdown/knockout of p300 phenocopies these effects. Given that CREBBP (CBP) or EP300 (p300) mutations are common in SCLC, it is also relevant whether any of these cell lines have CREBBP (CBP) or EP300 (p300) mutations. It appears H2107 and H524 may have EP300 mutations, and it would be good to know whether the authors have tried to restore EP300 function.

Reviewer #2 (Public Review):

The latest manuscript of Loring and coworkers solves a number of important problems of SARM1 structure and function at once, namely why the purified enzyme has little activity, what size is the active multimer, whether it produces cADPR on the way to ADPR, and how this enzyme may overcome autoinhibition by NAD+ in vivo. In work that is technically sound, the authors describe a phase transition that can be induced by macroviscogens and by citrate in which we are able to see cryoEM images of activated multimers and the induction of SARM1 activity in worms by citrate. Working with concentrated enzyme, the authors are further able to characterize SARM1 activity in detail and clearly show which cations are most inhibitory and that ADPR and not cADPR is the primary product of the reaction.

There is clearly a lot of regulation in the system with NAD+ inhibiting and NMN activating this enzyme and NMNAT, which controls conversion of NMN to NAD+ being localized to the outer Golgi membrane. Golgi and mitochondria are both moved along axons in processes that are totally dependent on cellular energetics. Given the broad contributions that are made by this work, I would not mind if the authors considered whether citrate, either from stressed mitochondria or from inhibition of the cytosolic enzyme ATP-citrate lyase, might be produced at high enough concentration to push SARM1 into the phase transition described herein.

Reviewer #2:

The authors address the vortex formation of bacteria in circular confinements with a particular focus on the difference of swarming vs. swimming (planktonic) motility of individuals. In the field of active matter, this critical distinction has rarely been studied so far but it is oftentimes ignored in modeling studies. Chen et al. show that qualitatively different patterns emerge for swarming and swimming bacteria. I do therefore believe that the work could have substantial influence on future studies devoted to bacterial pattern formation.

I have two main concerns detailed in the following.

1) A central finding of the present study is that the number of vortices/swirls as a function of the well diameter differs for swarming vs. swimming bacteria. The authors argue and show experimentally (Fig. 2) that the behavior is identical for small and large diameters. For intermediate values, however, they report that a single swirl is observed for swarming bacteria whereas swimming bacteria show multiple swirls.

The fact that the behavior is identical for large wells suggests that the bulk behavior is identical. This is also confirmed by Fig. 2E which shows that the spatial correlation function of the velocity is identical in large wells. To me, that suggests that the boundary conditions play a central role for understanding how the observed phenomenology emerges. [Indeed, it was shown in the past that the interaction of bacteria with boundaries crucially determines the formation of swirls in confinement (Lushi, Wieland & Goldstein PNAS 111 9733 (2014). The authors of this work assume reflecting boundary conditions, which -- to my knowledge -- contradicts the finding of Lushi et al.]. The authors, however, explain the difference of the observed patterns within their modeling study in a different way, namely by a different strength of the (anti-)alignment interactions. Changing the interaction at the level of individual cells will, however, change the bulk behavior too. Accordingly, the numerically observed bulk behavior (Fig. 5B ) is very different in both cases (at a qualitative level). It is difficult to judge the difference in detail because the correlation function was not calculated for the simulations.

In short:

The model (Fig. 5A) reproduces the experimental results partially (Fig. 2C), but the modeling analogue to Fig. 2E is missing. The line of arguments seems to me not to be entirely consistent.

2) Inferring the interactions of active particles from observations of the emergent patterns is a highly non-trivial task. In view of this I am not entirely convinced by the arguments put forward by the authors that "more substantial cell-cell cohesive interaction[s]" are the reason why the swirling patterns formed by swarming/swimming bacteria differ. In this context, I want to raise the attention of the authors to Ref. [Peruani, Deutsch & Bär: Phys. Rev. E 74 030904(R) 2006]. In this work, a clustering transition of self-propelled rods was described. "Rafts", referred to as clusters by Peruani et al., are observed as the aspect ratio of rods is increased. Notably, a kinetic transition towards clustering can emerge even in the absence of any attractive interactions. In short, the observation that cells move in parallel (polar clusters) next to each other does not allow to conclude that cohesive interactions are present. The movies S3 and S4 provided by the authors show that the particle shape of swarming and swimming particles is clearly different. In particular, the elongated swarming bacteria show pronounced clusters (Movie S3) whereas the shorter planktonic cells (Movie S4) do not. The difference in aspect ratio does indeed suggest that swarming and swimming bacteria differ in their alignment interaction. However, this contradicts the observation that spatial correlations in large wells are indistinguishable (see comment 1 and Fig. 2E). Side remark: in the main text, the authors argue that changes of the aspect ratio are not the reason for an increased alignment interaction, however, in the discussion section cell morphology changes (e.g. cell elongation and hyper-flagellation) are mentioned as an indicator that swarming is a different phenotype from swimming.

In summary, I believe that the connection of experimental observations and modeling are not entirely convincing.

Reviewer #2 (Public Review):

This manuscript establishes a novel rodent model for prenatal methadone exposure and characterizes various aspects of neurodevelopment in the offspring. Given the global opioid crisis and the rampant rise of drug use by pregnant mothers and incidence of neonatal abstinence/opioid withdrawal syndrome, there is a critical need to determine potential outcomes for children born with this condition. In their model, the investigators use mice that are already taking oxycodone and switched to methadone treatment prior to becoming pregnant, which is a major translational advantage compared to other models where opioid dosing does not start until sometime mid-gestation. The experimental design also included a wide variety of measurable endpoints, including physical development, sensorimotor behavioral tasks, vocalizations, brain imaging, circuit electrophysiology, and histology; this comprehensive approach allows for synthesis of the results that has traditionally been difficult to find in this field, given the vast differences in species, dosing paradigms, etc. Sex differences were also considered, which is especially important given what is known about varying rates of NOWS between males and females. The text is very well-written, including detailed descriptions of statistical analysis.

Despite overall enthusiasm for the study and its findings, there are some concerns regarding the brain volume analyses as well as potential stress confounds with the experimental design. The analysis of structural differences measured by volumetric MRI showed that there were no appreciable differences across grey matter structures with PME (Supp. Fig. 9). This was surprising, given that regional decreases in brain volume are a consistent finding with prenatal drug-exposed offspring (Yuan et al., 2014 [DOI 10.1038/jp.2014.111]; Sirnes et al., 2017 [DOI 10.1016/j.earlhumdev.2017.01.009]; Nygaard et al., 2018 [DOI 10.1016/j.ntt.2018.04.004]). Traditionally, these deficits tend to be more true for white matter than grey, though the authors do not indicate whether this was investigated.

The opioid dosing protocol required twice-daily subcutaneous injections for at least 3 weeks (possibly longer, but it was difficult to determine from the text when exactly the treatments were halted). The effects of maternal/prenatal stress, even in the vehicles, cannot be discounted. The authors rightly noted this caveat in the Discussion, but it remains a critical concern in this otherwise well-designed study.

Reviewer #2:

In this study, the authors perform an impressive field phenotyping experiment on three grafted grapevines all with a common scion cultivar 'Chambourcin' alongside an ungrafted control to assess the associations between rootstock and leaf traits. The traits collected include ionomics, metabolomics, transcriptomics, leaf morphology and physiology. In addition, the authors collect these samples at three phenological stages to incorporate seasonal variation. The authors apply a combination of classification and machine learning methods to test whether features within each phenotypic measurement are predictive of genotype. In some cases, such as the ionomics data, certain ions are predictive of rootstock genotype but only at certain seasonal time points. The datasets presented here are extensive and will be of value to the horticulture field since grafting is such a common technique used in cultivating many crops. Considering the scale of this experiment, the manuscript is at times disconnected, in large part because each dataset is analyzed independently without any integration across phenotypes. The results presented do highlight more of an effect of phenology rather than rootstock on the phenotypes measured.

Major comments:

1) It would be very helpful to have a diagram with the layout in the field and the sampling strategy or a more detailed explanation. This would help to associate which phenotypic data was collected at the same time and on the same plants. For example, it would expand on what is mentioned on line 348 "row 8 sampled early in the day". It would help to know what time of day the samples in each row were collected. Additionally, how do the different irrigation treatments factor into the sampling? A better introduction of the experimental design is needed at the start of the results section along with a description of the genotypes and why they were selected.

2) I understand why running a PCA before the LDA can help reduce the dimensionality of the space to be able to invert the covariance matrix (if that was the motivation?) but is this because there were issues with running LDA alone? I wonder if you've lost important discriminating information between the classes by doing this. Was the LDA run on the datasets first prior to the PCA? This may uncover additional classification that was eliminated by the PCA.

3) For the Random Forest analysis, the authors might consider using k-fold cross validation rather than partitioning the dataset, this is especially beneficial when working with smaller datasets and might improve the predictions. Could all the importance scores be reported rather than just the couple mentioned in the text (line 296).

4) In reference to Figure 1B and C, it would be helpful to indicate on the plots which comparisons are significant based on their model tests. The full test results are presumably in the excel spreadsheet referred to in the reporting form although it was not found with the manuscript materials.

5) Throughout the text there is very little mention of the various grafted genotypes and what is known about the lines. The authors should consider introducing these genotypes and why they were selected for the grafting experiment. What is different among these lines? There is very little discussion of the comparisons between genotypes and what phenotypes are significantly different between the lines and what the implications are for the plant as a whole.

6) Line 287 refers to a post-hoc analysis of the ions, do the ions showing significant variation explained by rootstock and phenology match the ions identified in the ML as important classifiers?

7) For such a large metabolomic dataset, it is surprising that the authors do not present any identification of the metabolites highlighted. The identification of the metabolite features that were found to influence the rootstock main effect would be of interest and might reveal interesting biology. How did these metabolites differ between genotypes? On line 501 in the discussion there is mention of flavanols and stilbenes yet these weren't highlighted in the results section.

8) What is the reasoning for not simply applying a linear modeling approach such as limma on the gene expression data first instead of only applying it to the PCs in order to identify differentially expressed genes between the genotypes? If phenological stage is the strongest effect, what if you run the analysis within each stage to look specifically at the differential responses between grafted lines at each stage? The analysis of the gene expression data, similar to the metabolomics data, seems to be missing an opportunity to uncover underlying biological mechanisms contributing to any genotype effects of grafting, a stated goal of the study. What genes are differentially expressed and do they relate to the metabolomic or ionomic data?

9) In the methods, there are three irrigation treatments described yet this is not mentioned in the results section. While it seems as though rainfall mitigated much of the irrigation effect there does appear to be differences in water availability to the vines as described in the provided github page. Were various irrigation treatment sets sampled for all phenotypes? Or were the ionomics, metabolomics and transcriptome analysis done on the same irrigation treatments? If not, was this effect considered in the analysis? This is yet another variable that would greatly influence the response and should be considering when assessing the effects of grafting. Further detail about the sampling and conditions is needed to clarify.

10) In figure 1 there is information about leaf age. For the metabolomics a mature leaf was sampled, transcriptomics the youngest leaf, and physiology it is not specified. Could you clarify the leaves that were sampled and how they relate across phenotypes. This is an important point to mention given the differences observed for the ionomics data.

11) In reference to the vine physiology, were these all collected from the same irrigation treatment? Was the sampling of each genotype spread out over the 3h window to account for time of day variation? It would be helpful to have the significant comparisons indicated in the figure. What are the letters referring to on lines 402-403 with the p. values? This section would be greatly improved by additional clarity in the text.

12) Given the focus on grafting, the analysis presented in Figure 6 does not seem to contribute to this objective. Could this be expanded on to look within and across genotypes to see if different phenotypes covary and to compare the dimensions of variation across genotypes rather than combining them all together? This would complement the previous analyses and hopefully reveal the differences that were highlighted in the earlier sections.

13) The results section is very disjointed and the datasets are presented almost as completely separate studies. To improve clarity in the results section, the authors might consider expanding on the findings of the LDA and ML analysis for each phenotype and connecting them together.

Reviewer #2 (Public Review):

In this manuscript, the authors generated transgenic zebrafish reporter lines that allow observation of cytoplasmic lipid droplets in vivo. They knocked in GFP or RFP in the endogenous loci of perilipin 2 and 3, and showed that the reporter genes exhibited similar temporal and spatial expression in the intestine in response to acute high-fat feeding as the endogenous perilipin 2 and 3 transcripts. They also characterized the reporter gene expression in the liver, adipocytes, and around neuromasts. These tools open up new opportunities to study lipid droplets dynamics in live zebrafish that is not feasible in mouse models. Overall the manuscript is well written. The authors have discussed in details the strength and caveats of these reporters. The weakness is the descriptive nature of the study - many interesting observations but no mechanistic study. I have the additional comments:

1) It is curious that in plin2 and plin3 reporter fish, the fluorescent tags were inserted at the 5' and 3' of the open reading frame, respectively. The authors did not provide any explanation. Does the location where the fluorescent tag is inserted affect the expression of the reporter genes?

2) GFP and TagRFP-T are not fast folding fluorescent proteins and are very stable, which may not be the best options for studying the formation and degradation of lipid droplets. How the fluorescent tags affect the stability and clearance of the protein should be carefully characterized.

3) Was there any indel being introduced by TALENs in these knockin fish? Is there off target effects of the TALENs?

4) The authors also generated transgenic fish overexpressing human PLIN2 and PLIN3 fluorescent fusion proteins. Is the subcellular localization of these fusion proteins similar to the zebrafish knockin under nofed and fed conditions? In other words, do human PLIN2 and PLIN3 proteins behave similarly as the zebrafish orthologs?

Reviewer #2 (Public Review):

The authors eloquently showed that IL-33 was produced from stromal cells following Toxoplasma infection and that the absence of IL-33 signaling resulted in increased parasitemia. In agreement with this observation, they found that exogenous IL-33 reduced parasite load and increased the recruitment of inflammatory monocytes that are critical for resistance. The manuscript is well written and data presented here supports the major findings of this work.

Reviewer #2 (Public Review):

Overall this is a solid and technically sound manuscript, and I have only two relatively minor suggestions for improvement:

1) Tetramer versus dimer

The particles that were analyzed by cryoEM were composed of four THO-Sub2 protomers, yet the authors argue that a dimer is the functional unit. Why? The tetramer versus dimer organization needs to be better discussed, also in light of the observation that the human complex can also form a tetramer.

2) Sub2 activation mechanism

The authors should more carefully discuss how THO 'activates' Sub2 (and how the 'semi-open state' leads to activation) and indicate the RNA binding surface of Sub2 in their model.

Reviewer #2 (Public Review):

This manuscript will be of interest to a broad audience of immunologists especially those studying host-pathogen interactions, mucosal immunology, innate immunity and interferons. The study reveals a novel role for neutrophils in the regulation of pathological inflammation during viral infection of the genital mucosa. The main conclusions are well supported by a combination of precise technical approaches including neutrophil-specific gene targeting and antibody-mediated inhibition of selected pathways.

In this study by Lebratti, et al the authors examined the impact of neutrophil depletion on disease progression, inflammation and viral control during a genital infection with HSV-2. They find that removal of neutrophils prior to HSV-2 infection resulted in ameliorated disease as assessed by inflammatory score measurements. Importantly, they show that neutrophil depletion had no significant impact on viral burden nor did it affect the recruitment of other immune cells thus suggesting that the observed improvement on inflammation was a direct effect of neutrophils. The role of neutrophils in promoting inflammation appears to be specific to HSV-2 since the authors show that HSV-1 infection resulted in comparable numbers of neutrophils being recruited to the vagina yet HSV-1 infection was less inflammatory. This observation thus suggests that there might be functional differences in neutrophils in the context of HSV-2 versus HSV-1 infection that could underlie the distinct inflammatory outcomes observed in each infection. In ordered to uncover potential mechanisms by which neutrophils affect inflammation the authors examined the contributions of classical neutrophil effector functions such as NETosis (by studying neutrophil-specific PAD4 deficient mice), reactive oxygen species (using mice global defect in NADH oxidase function) and cytokine/phagocytosis (by studying neutrophil-specific STIM-1/STIM-2 deficient mice). The data shown convincingly ruled out a contribution by the neutrophil factors examined. The authors thus performed an unbiased single cell transcriptomic analysis of vaginal tissue during HSV-1 and HSV-2 infection in search for potentially novel factors that differentially regulate inflammation in these two infections. tSNE analysis of the data revealed the presence of three distinct clusters of neutrophils in vaginal tissue in mock infected mice, the same three clusters remained after HSV-1 infection but in response to HSV-2 only two of the clusters remained and showed a sustained interferon signature primarily driven by type I interferons (IFNs). In order to directly interrogate the impact of type I IFN on the regulation of inflammation the authors blocked type I IFN signaling (using anti IFNAR antibodies) at early or late times after infection and showed that late (day 4) IFN signaling was promoting inflammation while early (before infection) IFN was required for antiviral defense as expected. Importantly, the authors examined the impact of neutrophil-intrinsic IFN signaling on HSV-2 infection using neutrophil-specific IFNAR1 knockout mice (IFNAR1 CKO). The genetic ablation of IFNAR1 on neutrophils resulted in reduced inflammation in response to HSV-2 infection but no impact on viral titers; findings that are consistent with observations shown for neutrophil-depleted mice. The use of IFNAR1 CKO mice strongly support the importance of type I IFN signaling on neutrophils as direct regulators of neutrophil inflammatory activity in this model. Since type I IFNs induce the expression of multiple genes that could affect neutrophils and inflammation in various ways the authors set out to identify specific downstream effectors responsible for the observed inflammatory phenotype. This search lead them to IL-18 as possible mediator. They showed that IL-18 levels in the vagina during HSV-2 infection were reduced in neutrophil-depleted mice, in mice with "late" IFNAR blockade and in IFNAR1 CKO mice. Furthermore, they showed that antibody-mediated neutralization of IL-18 ameliorated the inflammatory response of HSV-2 infected mice albeit to a lesser extent that what was seen in IFNAR1 CKO. Altogether, the study presents intriguing data to support a new role for neutrophils as regulators of inflammation during viral infection via an IFN-IL-18 axis.

In aggregate, the data shown support the author's main conclusions, but some of the technical approaches need clarification and in some cases further validation that they are working as intended.

1) The use of anti-Ly6G antibodies (clone 1A8) to target neutrophil depletion in mice has been shown to be more specific than anti-Gr1 antibodies (which targets both monocytes and neutrophils) thus anti-Ly6G antibodies are a good technical choice for the study. Neutrophils are notoriously difficult to deplete efficiently in vivo due at least in part to their rapid regeneration in the bone marrow. In order to sustain depletion, previous reports indicate the need for daily injection of antibodies. In the current study the authors report the use of only one, intra-peritoneal injection (500 mg) of 1A8 antibodies and that this single treatment resulted in diminished neutrophil numbers in the vagina at day 5 after viral infection (Fig 1A). Data shown in figure 2B suggests that there are neutrophils present in the vagina of uninfected mice, that there is a significant increase in their numbers at day 2 and that their numbers remain fairly steady from days 2 to 5 after infection. In order to better understand the impact antibody-mediated depletion in this model the authors should have examined the kinetics of depletion from day 0 through 5 in the vaginal tissue after 1A8 injection as compared to the effect of antibodies in the periphery. These additional data sets would allow for a deeper understanding of neutrophil responses in the vagina as compared to what has been published in other models of infection at other mucosal sites.

2) The authors used antibody-mediated blockade as a means to interrogate the impact of type I IFNs and IL-18 in their model. The kinetics of IFNAR blockade were nicely explained and supported by data shown in supplementary figure 4. IFNAR blockade was done by intra-peritoneal delivery of antibodies at one day before infection or at day 4 after infection. When testing the role of IL-18 the authors delivered the blocking antibody intra-vaginally at 3 days post infection. The authors do not provide a rationale for changing delivery method and timing of antibody administration to target IL-18 relative to IFNAR signaling. Since the model presented argues for an upstream role for IFNAR as inducer of IL-18 it is unclear why the time point used to target IL-18 is before the time used for IFNAR.

3) An open question that remains is the potential mechanism by which IL-18 is acting as effector cytokine of epithelial damage. As acknowledged by the authors the rescue seen in IFNAR1 CKO mice (Fig 5C) is more dramatic that targeting IL-18 (Fig 6D). It is thus very likely that IFNAR signaling on neutrophils is affecting other pathways. It would have been greatly insightful to perform a single cell RNA seq experiment with IFNAR CKO mice as done for WT mice in Fig 3. Such an analysis might would have provided a more thorough understanding of neutrophil-mediated inflammatory pathways that operate outside of classical neutrophil functions.

4) The inflammatory score scale used is nicely described in the methods and it took into consideration external signs of vaginal inflammation by visual observation. It would have been helpful to mention whether the inflammation scoring was done by individuals blinded to the experimental groups.

5) The presence of distinct clusters of neutrophils in the scRNA-seq data analysis is a fascinating observation that might suggest more diversity in neutrophils than what is currently appreciated. In this study, the authors do not provide a list of the genes expressed in each cluster within the data shown in the paper. Although the entire data set is deposited and publicly available, having the gene lists within the paper would have been helpful to provide a deeper understanding of the current study.

Reviewer #2 (Public Review):

This manuscript shows the functional relevance of mNatA catalytic subunit, mNAA10, in mammals' development. Moreover, authors have found a new NatA catalytic subunit in mice, mNAA12, that can compensate mNAA10 inactivation in mice. Interestingly, inactivation of mNAA10 in mice induces some developmental defects similar to those observed in Ogden syndrome (OS) patients including lethality in infants. This study provides several evidences and explains some of the defects observed in OS patients like supernumerary vertebrae and hydrocephaly supporting the relevance of hNAA10 mutations in the development of OS. Moreover, authors have observed in mice some developmental deficiencies not observed previously in OS patients, like supernumerary ribs, that after patient re-examination they have been observed in humans too. Curiously, the results presented in this article show that inactivation of mNatA catalytic subunit does not affects dramatically protein N-terminal acetylation, probably as consequence of mNAA12 paralog function as mNatA catalytic subunit when mNAA10 is not present. Interestingly, gene inactivation supports the biological significance of NAA10 as the main NatA catalytic subunit as mNAA12 inactivation is not associated with any clear phenotype. In spite of being one of the most frequent protein modifications protein N-terminal acetylation has not attracted proper attention, therefore this paper can draw more attention to this important protein modification.

Reviewer #2 (Public Review):

The authors show that SUSD4 is expressed throughout the brain and is abundant in cerebellar dendrites and spines. Mice with deletion of SUSD4 have motor coordination and learning deficits, along with impaired LTD induction. The also attempt to show that GluA2 AMPA subunits are misregulated, but that is not as convincing. They find Nedd1, along with many other proteins in a proteomic screen for SUSD4 interactors, and try to explain the phenotypes through the regulation of GluA2 degradation by Nedd4 through SUSD4. These are potentially interesting findings, but very preliminary at this point. While the electrophysiology is good, the mechanistic studies are incomplete.

Major comments:

In Figure 1 localization images are shown using exogenous protein. Can the authors visualize endogenous protein?

It appears that SUSD4 is expressed in multiple brain regions, even at higher levels than the cerebellum. The authors should provide a good explanation for why deficits in the KO do not affect other functions, and seem to preferentially affect cerebellar functions.

Figure 4: immunofluorescence data are not very convincing.

Figure 5: The use of the word "could" is not supporting a strong conclusion. The authors should demonstrate whether SUSD4 DOES indeed regulate GluA2.

Overall, while the electrophysiology seems fine, the mechanistic studies are preliminary and speculative at this point.

Reviewer #2 (Public Review):

In this manuscript, Galbraith et al add to our understanding of COVID19 pathobiology by undertaking a cross-sectional survey of 73 hospitalized COVID19 patients with non-severe disease. They perform very broad multi-omics analysis, including plasma proteomics, cytokine profiling and mass cytometry. The authors propose that disease course can be classified by the titer of anti-CoV2 antibodies, which in turn is associated with distinct changes in circulating proteins, cytokines and immune subsets. Interesting correlations with complement and coagulation factors are noted. These findings suggest an alternative way to map disease progression in COVID19 and have implications for broader studies of COVID19 pathobiology. In particular, it will in interesting to extend this framework to analyze a broader spectrum of COVID19 patients, particularly those with poor outcome.

Reviewer #2 (Public Review):

"Feeding Experimentation Device version 3 (FED3): An open-source device for measuring food intake and operant behavior" describes the third iteration of an open-source automatic feeding device to be used with mice. I have no concerns about this paper and would recommend it as is. The authors have provided an incredible resource for the fields of feeding and reward-related behaviors, and provide all the details needed for assembly and use. Moreover, the data that they have collected using this device constitutes an advance, particularly the circadian rhythms of feeding, as well as the increase in operant responding during the light cycle. This device enables homecage measurement of feeding and training for motivational behavior, enabling most any laboratory to examine feeding behaviors in their experiments.

Reviewer #2 (Public Review):

Although the major activation steps and general mechanistic underpinnings of SOCE have been reported in a flurry of literatures, they are largely descriptive and lack quantitative information. One topic of greatest interest to the CRAC channel field is the structural basis of CC1-CAD/SOAR-mediated STIM1 autoinhibition. Using single-molecule Förster resonance energy transfer (smFRET) and protein crosslinking approaches, Dorp et al provides a binding model for the CC1-CAD interaction. This model explains the role of CC1 in STIM1 activation, and delineates the activation process of STIM1 CT. It also clarifies the controversy on the two varying structures regarding the packing of the CAD/SOAR domain by favoring the X-ray structure over the NMR structure. The conclusions of this paper are mostly well supported by data. The only minor concern is to reconcile some of the conflicting results (regarding the relative positions of some residues used in the crosslinking study, as well as the CC1-alpha 1 helix), made between this study and a recent structural study, i.e., the NMR solution structure of CC1 reported by the Romanin/Muller's groups (PMID: 33106661). Overall, this study covers a timely topic to address a long-standing question in the ORAI-STIM signaling field, i.e., the structural basis of CC1-CAD association that keeps STIM1 largely quiescent in the resting condition. This work, regarded by this reviewer as a "tour-de-force" by meticulously scanning through many key residues within the multiple CC1/CAD helices, certainly warrants immediate publication.

Notable strengths:

1) smFRET is increasingly being used to determine distances, structures, and dynamics of biomolecules. Full length STIM1 and STIM1 C-terminus have been always difficult to obtain crystal structure due to its tendency for aggregation and the existence of large disordered regions. Herein, the authors selected smFRET as the major tool to overcome this hurdle and illuminated the CC1-CAD binding models to provide novel mechanistic insights into STIM1 auto-inhibition mediated by the intramolecular cis CC1-CAD association.

2) The efforts to extend crosslinking of ctSTIM1 to flSTIM1 are particularly commendable, moving one more step closer to the physiological scenario.

Minor weaknesses:

1) The authors proposed a CC1 model displaying "tandem connection of "CC1α1- CC1α2", that shows notable discrepancies with the recent CC1 NMR solution structure (PMID: 33106661). In the latter structure, the three helices are intertwined to form a bundle like structure. An in-depth discussion is certainly needed to clarify the difference. Some possibilities include: (i) Is this due to the artifact of the CC1 NMR structure (done in the presence of helix-stabilizing reagents)? (ii) is this due to the introduction of cysteine residues for the assays? (iii) is this due to absence of the CAD/SOAR part, or other regulatory components, in the solution structure? Repeating one or two key smFRET/crosslinking experiments in the presence of the similar buffer condition as in the NMR study would provide clues to these possibilities.

2) Another concern, very minor though, is regarding cysteine crosslinking flSTIM1 by 0.2 mM diamide. Will the addition of diamide cause undesired activation of STIM1 in the absence of cyclopiazonic acid?

Reviewer #2:

In this paper, Werkhoven and colleagues describe a large-scale effort, using Drosophila, to study variation in behavior among individuals with identical genotypes, and raised in very similar environmental conditions. This addresses the important and basic question of how much behavioral variability exists under such conditions, e.g. due to stochastic processes during development. By looking across many different behaviors, the authors are able also to investigate the nature of this variability. The key conclusion of the paper is that this intragenotypic variability is high dimensional, and cannot be explained by a small set of behavioral syndromes. They find that this observation is robust to the method they use to quantify behavior, and also holds to different degrees in data sets acquired from outbred flies, or files subjected to genetic perturbations of neural activity. Furthermore, they have generated a data set that allows correlation of behavioral biases in individual animals with transcriptomic data. Altogether, this is an impressive study that, beyond its important conclusions, opens up the possibilities for many further explorations in this area, and should be interesting to a broad audience. The experiments are well designed and overall the paper is very nicely written and clear to understand.

Reviewer #2:

Nguyen et al. developed a novel method of transcranial focused ultrasound stimulation and used it to stimulate anesthetized rats while performing extracellular recordings in the hippocampus. They find that the stimulation has different amplitude-dependent effects on putative inhibitory interneurons and excitatory principal cells. This finding is exciting because it suggests that transcranial ultrasound could be used to specifically reduce or increase firing rates in excitatory or inhibitory neurons in a particular part of the brain (resolution in the mm range). In principle, this could also be applied to humans. Simultaneously measured oscillations of the local field potential, particularly (but not exclusively) in the theta band (3-10 Hz) could also be manipulated in a bidirectional manner depending on the stimulation amplitude. Such cortical oscillations have been strongly linked to a wide range of functions including memory, and the potential to manipulate them in an anatomically precise manner is exciting and could even lead to new therapy approaches. Although it is not new that ultrasound can be used to modulate neuronal activity, this paper reaches a new level of precision by demonstrating that bidirectional effects can in principle be limited to one cell class or one frequency band. Thus, it could provide a great alternative to current methods that either provide much less precision (e.g. transcranial magnetic stimulation) or rely on more invasive methods (e.g. deep brain stimulation) or genetics (e.g. optogenetics).

The study is well-designed with stimulation at 3 different amplitudes applied in the same rat, whereby each 3-minute stimulation is compared to a 3-minute sham session where the transducer is 1 cm above the skull. Baseline sessions before each stimulation and sham session did not show any differences, showing no spillover-effects from the previous stimulus. Effects on brain temperature were also measured and shown to be negligible compared to normal variability.

Low intensity stimuli lead to a reduction in firing rates in putative interneurons and a reduction in theta oscillation power, whereas high intensity stimuli lead to an increase in firing rates in putative principal cells, with intermediate intensities having largely no effect.

In principle, these findings could provide novel insights into the mechanisms underlying ultrasound stimulation, but neither of the two discussed main modes of action (mechanical and thermal) appears consistent with the results. Thus, no model could be offered that might give some insight into the underlying mechanisms of ultrasound modulation of neuronal activity. This might be an issue for future work, and if the results were more robust perhaps this would not matter as much. However, the overall size of the effects appears to be too small to be of practical use as a reliable tool for manipulation of neural circuits. Although the authors show statistical significance, some details of the analysis are not fully clear and may need to be further corrected for multiple testing. It remains unclear if perhaps larger or different effects would be achieved when recording through the skin, without anesthesia, in different brain areas, in differently defined subclasses of neurons or with a different stimulation protocol (frequency, duration, amplitude). Thus, although the technique appears promising, more work is needed.

Reviewer #2 (Public Review):

Judd et al. systematically examine the input/output connectivity of discrete excitatory and inhibitory neuronal subpopulations in the cerebellar interposed anterior nucleus (IntA) using conditional AAV and rabies virus mapping strategies. The authors first define distinctions in the output connectivity of excitatory and inhibitory neurons in the IntA nucleus, and describe a surprisingly much wider projection pattern by inhibitory neurons than previously thought. They also characterize distinctions in projection pattern between identifiable subtypes of IntA inhibitory neurons as well as distinctions in morphology of their terminal fields. The authors next explore the input connectivity of excitatory and inhibitory neurons in the IntA nucleus and found that excitatory output neurons receive fewer, but more organized inputs than inhibitory output neurons, and that many output targets provide reciprocal connections with the CN.

In general, the output analysis is strong and there are only a few questions about interpretation of the distinctions of projections by different subtypes of IntA inhibitory neurons. For instance, the distribution of the initial targeting within the cerebellar nuclei, cerebellar cortex and outside the cerebellum was not analyzed in Ntsr1-Cre and Gad1-Cre similar to the analysis performed for the intersectional output analysis. Clarification on whether and how the distinctions in projections could be due to variability in the specificity of the initial targeting or recombination ability of the two mouse Cre-lines is needed to strengthen interpretation of the different projections patterns observed. As for the input analysis using rabies, there were two major issues identified.

First, the use of conditional GFP-labeled G protein and the use of rabies that is also GFP potentially confounds analysis of input cells.

Next, the low number of starter cells is a concern and the identity of starter cells outside the cerebellar nuclei in Ntsr1-Cre and Gad1-Cre is vague and needs to be clarified. This is important for interpretation of whether input structures observed project specifically into the CN or also into the cerebellar cortex, and whether distinctions observed in number of input structures may reflect amount of starter cells in each Cre line.

Reviewer #2 (Public Review):

This manuscript by Sando and Sudhof addresses whether GPCR activity of latrophilin2 and 3 is necessary for the role of these proteins in synapse formation. The key findings are:

— the generation and validation of mutants that lack transmembrane and intracellular domains (but are GPI-anchored instead), the lack only intracellular domains, or that contain all domains but lack GPCR-activity. All mutants work properly in cell aggregation assays and appear to be localized normally when overexpressed in wild type neurons. This also led to the development of an elegant PKA-phosphorylation reporter assay.

— in cultured latrohphilin 3 knockout neurons, latrophilin3 expression restores a decreased synapse density and mini-frequency, but the GPI-anchored, truncated or inactive versions do not restore these parameters.

— in vivo/hippocampal brain slices, latrophilin2 knockout impaired perforant path but not Schaffer collateral transmission onto CA1 neurons, and rescue required latrphilin2 GPCR activity. Conversely, Latrophilin3 knockout impaired Schaffer collateral but not perforant path transmission onto CA1 neurons, and rescue required latrophilin3 GPCR activity.

— finally, monosynaptic tracing confirmed that latrophilin3 knockout reduced inputs onto CA1 starter neurons, and rescue again required GPCR activity.

Altogether, the data are rigorously acquired, the paper is well written, and the finding that GPCR activity is necessary for latrophilins' role is both surprising and important. It is also elegant, as coupling cell-adhesion directly to signal transduction via a single molecule for synapse formation is a compelling way to drive synaptic assemblies. Naturally, the question arises how compartmentalized GPCR-signaling then instructs synapse formation, a topic that will undoubtedly require and attract more research. This is an exciting manuscript that will inspire new research on compartmentalized GPCR signaling at the synapse. Given the central importance of surface trafficking and localization within spines for the conclusions, better description of experimental procedures and quantification, and possibly additional data would clearly strengthen this point.

Reviewer #2:

Epilepsy is often an early sign observed in Alzheimer patients and there are several mechanisms that may contribute to this hyperexcitability. In this study, the authors focused on an important observation suggesting that intracellular Amyloid beta, a protein often found in plaques in the brain, is found early on inside neurons of the hippocampus, the learning and memory center of the brain. Interestingly, when unique early forms of Ab named oligomers were introduced inside neurons, the cells and surrounded circuits became hyperexcitable. This increased excitability was mediated mainly by the release of glutamate on AMPA glutamate receptors. Remarkedly, these excitatory effects were triggered by intracellular amyloid oligomers through a retrograde signal named nitrous oxide. This manuscript suggests that early stages of the disease may comprise significant increases in network excitability that may trigger a cascade of synaptic dysfunction and cognitive deficits such as memory loss.

Here are my comments to strengthen the manuscript. Overall this is a strong study with an interesting take on the role of intracellular amyloid and how it contributes to increased network excitability in AD.

There is an interest to determine the mechanisms responsible for the hyperexcitability often associated with familial and sporadic forms of Alzheimer's disease. Many have focused on possible reduction in inhibitory interneuron function as essential drivers of the increased excitability of the network. Although there exist a large number of investigations determining the effects of extracellular Ab on synaptic transmission, the intracellular effects of Ab and its contribution to disruptions of synaptic transmission remains less well understood. A couple of studies have shown that intracellular application of Ab (Ab42) induces decreases in long-term potentiation and basal synaptic transmission. In this study, the authors have investigated how intracellular Ab oligomers (iAbo) contribute to enhanced excitability in the CA1 region of the hippocampus. To do so, they have intracellularly applied human brain-derived and synthetic Ab oligomers through the patch-pipette in principal neurons recorded in vitro and in vivo.

In this study, the authors show that intracellular application of intracellular Ab oligomers increased the frequency and the amplitude of excitatory currents and spiking in ex vivo hippocampal slices. Effects that were mimicked by human oligomers. The intracellular amyloid mediated effects were through the amplification of AMPAergic spontaneous activity and currents, and, to a lesser extent, spontaneous GABAA mediated currents. Miniature frequency and amplitude of AMPA-mediated EPSCs were also increased and were sensitive to PKC blockers. Interestingly, since intracellular Ab increased the frequency of EPSCs, which is a presynaptic effect, a signaling molecule is likely to be released postsynaptically to modulate presynaptic terminals. The hypothesis that the retrograde signal NO was involved by determining the sensitivity of NOS inhibitor L-NAME. L-NAME reduced the increased iAbo mediated frequency of spontaneous post-synaptic excitatory currents in cultured neurons. The L-NAME compound was shown to reduce the iAbo -mediated No from both the recorded and neighboring neurons providing further evidence that intracellular Ab oligomers triggered NO release and increased glutamate release. Increases in the excitability of CA1 pyramidal cells were also observed in vivo by intracellular application of AB oligomer. Overall, this is a well written study that demonstrates a novel perspective of the effects of intracellular Ab oligomers on CA1 principal neurons and suggests possible mechanisms underlying hyperexcitability.

Novelty:

1) use intracellular oligomers, synthetics and humans

2) Showing that iAb oligo increased post and presynaptic AMPA-mediated EPSCs.

3) The presynaptic increases in EPSCs were mediated by NOS and NO, this could potentially spread widely across the network.

4) spontaneous IPSCs were also increased (through an undetermined mechanism).

5) the iAbo increase in excitation was also observed in vivo.

Questions:

Intracellular Ab produces both an increase in EPSCs and IPSCs. However, in Fig 3, the IPSCs, measures using a charge transfer quantification, did not show a significant change in response to iAbo, in contrast to EPSCs. This spontaneous inhibition here was measured as charge transfer which depends on the amount of charges in time. I wonder why this was not significant since this measurement should have picked up a possible increase in spontaneous IPSCs?

With regard to the inhibition, In the schematic on Fig. 10, I find this incomplete and slightly inaccurate since it shows one terminal releasing both glutamate and GABA with NO increasing both. While this is obviously an oversimplification, it's slightly inaccurate since NO was not directly shown to increase sIPSCs. Were NOS blockers able to disrupt the increase in sIPSCs? Moreover, there are many papers that have shown that PKC can also phosphorylate GABA receptors and increase their conductance. What could be the reason that this was not involved here? This needs to be discussed.

The experiments were done in cultured neurons, in slices and in vivo. It's not always easily discernible in what conditions the experiments were done when reading the manuscript, especially when looking at the figures and figure legends. This should be at least stated in the figure legends. To help the reader, the conditions in which the currents were recorded (GABA and or excitatory receptor blockers, other ion blockers could be indicated in the figure legends to ease the comprehension of how the experiments were done and what was measured). In relation to this, was the sIPSC iAbo-mediated increases also blocked by L-NAME?

In other studies, investigating intracellular application of Ab, such as the Ripoli et al., 2014 paper, showed that iAb produced significant reductions in EPSCs in their hippocampal neurons. What are the differences explaining this? This should be discussed. Similarly, Gulisano et al., 2019, showed that extracellular, but not intracellular oligo Ab had effects on excitability when it was applied extracellularly but not intracellularly. This should also be discussed.

In the introduction, it's mentioned that the nature of hyperexcitability is unknown. I agree that it's incompletely known, but what is known is that there is a large variety of possible causes. For example, changes in GABAergic interneuron function (see Hijazi et Al 2019) is well known to be a contributing factor. There are many studies that have shown possible contributing causes of hyperexcitability, therefore, something IS known, and this should be identified in the introduction.

How do these increases in synaptic transmission by applying pM concentrations of oligomers fit with the data showing that extracellular Ab oligomers of comparable concentrations decrease synaptic transmission through presynaptic reductions in glutamate release? This needs to be put into context and discussed.

Reviewer #2:

The authors are reporting a new approach termed ORACLE to develop locus-specific phage variants, which includes a recombination step, whose efficacy is improved by the overexpression of a dedicated recombinase, followed by an enrichment performed using CRISPR/Cas9. They applied this method to create a mutant library containing 1660 variants of the tip domain of the T7 tail fiber. Performance of each variant was determined by quantifying their abundance before and after selection on three E. coli strains compared to the WT phage. Their findings show that single amino acid changes in the tip of gp17 can have major consequences on phage performance on different hosts. Then they tested whether these variants would be less prone to select phage-resistant using an UTI strain. Finally, they searched for variants that would be more prone to infect one host than another and successfully tested their predictions.

The ORACLE approach is overall novel and has some advantages over existing methods, mainly for generation of mutation libraries of genes. Authors did a nice (even if very lengthy) job of showing how mutants have consequences to structure and function of the tail fiber gene and how that influences performance on different hosts, including combating host resistance.

The authors state that ORACLE overcomes three major hurdles that make it better than existing methods, one of which is "generalizability for virtually any phage", while denouncing other systems for being applicable for highly transformable hosts only. This is highly exaggerated since ORACLE requires transformation of two plasmids (helper and donor) including one with tunable gene expression, which is clearly not possible in many bacteria. Furthermore, the enrichment step requires a strain with a functional CRISPR/Cas9 system, which again is not so obvious in the bacterial world.

The authors disregard bias that can be generated at the "O" step if a variant reproduces better than the wt. They should also mention bias arising from non-viable or severely infection hampered variants, which is briefly mentioned later in the manuscript but should be mentioned earlier, would not pass the accumulation step.

The weakest paragraph is the one dealing with the UTI strain. I have the feeling that this paragraph could simply be deleted without changing the overall story. Approaching resistance, selection, and evolution would require more experiments than the very simplistic lysis curves. The authors did not even show adequately that cells growing after 5-10 hours are either genotypically or phenotypically resistant cells. A more appropriate qualification would be "insensitive" instead of resistant.

Reviewer #2 (Public Review):

In the present manuscript Radaszkiewicz et al. analyze the role of Ring Finger Protein 43 (RNF43) in inhibiting the noncanonical WNT5A pathway. The authors demonstrate that RNF43 can interact with proteins involved in the WNT5A pathway, including ROR1, ROR2, VANGL1 and VANGL2. Specifically, they propose that RNF43 induces: i) VANGL2 ubiquitination and proteasomal degradation and ii) clathrin-dependent internalization of the ROR1 receptor. Considering the role of the WNT5A pathway in melanoma metastasis and resistance to targeted therapy, the authors further explore the role of RNF43 in melanoma invasion and resistance to vemurafenib. The authors ultimately conclude that RNF43 can prevent invasion and resistance to targeted therapy by inhibiting the WNT5A pathway. The data supporting the interaction between RNF43 and proteins involved in the WNT5A pathway are pretty rigorous. However, the study would benefit from additional experiments in the context of RNF43's role in invasion and resistance to targeted therapy in melanoma. Overall, the techniques utilized in the manuscript are appropriate, however additional cell lines and in vivo studies are strongly recommended to strengthen the manuscript.

Reviewer #2 (Public Review):

P2X2 activation depends on both ATP binding and voltage. However, the voltage sensor of P2X2 is not elucidated. This manuscript describes the study of voltage dependent conformational changes of P2X2 using voltage clamp fluorometry of the fluorescent unnatural amino acid Anap that substituted P2X2 amino acid residues. 96 positions in different structural domains were scanned by substituting with Anap, and voltage dependent fluorescence signals were detected only at two positions, A337 and I341 in the TM2 domain. A fast and linear voltage dependence of fluorescence suggested that the membrane voltage converged at and around these two positions. With a mutation K308R that was supposed to enhance voltage dependent conformational changes, Anap at the A337 position showed a time and voltage dependent fluorescence. The authors concluded that this result indicated a voltage dependent conformational change. Structure guided mutations suggested that F44 in TM1 might move to interact with A337 in response to voltage. In this study the fluorescence signals were small, but the authors made a great effort and managed to obtain the data that are convincing. The experiments were well designed and the manuscript is clearly reasoned. Considering that among all the positions that were tested only at the two positions in the TM2 segment Anap showed voltage dependent fluorescence, and that the F44 mutations abolished voltage dependence of the P2X2 currents, the conclusion that voltage converges at the A337/I341/F44 and induces a conformational change seems to be well supported.

Reviewer #2 (Public Review):

The goal of this work is to advance knowledge of the neural bases of color perception. Color vision has been a model system for understanding how what we see arises from the coordinated action of neurons; detailed behavioral measurements revealed color vision's dependence upon three types of photoreceptors (trichromacy) and three second stage retinal circuits that compute sums and differences of the cone signals (color opponency). The processing of color at later, cortical stages has remained poorly understood however, and studies of human cortex have been hampered by methodologies that abandoned the detailed approach. Typical past work simply compared neural responses in two conditions, the presentation of colorful (formally, chromatic) vs grayscale (luminance) images. The present work returns to the older tradition that proved so successful.

The project's specific goals were to measure functional MRI responses in human cortex to a large range of colors, and equally importantly, capture the pattern responses with a quantitative model that can be used to predict response to many additional colors with just a few parameters. The reported work achieved these goals, establishing both a comprehensive data set and a modeling framework that together will provide a strong basis for future investigations. I would not hesitate to query the data further or to use the QCM model the paper provides to characterize other data sets.

The strengths of the work include its methodological rigor, which gives high confidence that the goals were achieved. Specifically:

1) The visual presentation equipment was uniquely sophisticated, allowing it to correct for possible confounds due to differences in photoreceptor responses across the retina.

2) The testing of the model was quite rigorous, aided by distinct replications of the experiment planned prior to data collection.

3) The fMRI methods were also state of the art.

The work was well-situated within the literature, comparing its findings to past results. The limitations and assumptions of the present work were also clearly stated, and conclusions were not overstated.

Weaknesses of the current draft are relatively minor, however, I believe:

1) The data could be presented in a way to make them more comparable to prior fMRI work, e.g. by using percent change units in more places, comparing the R^2 of model fits reported here to those reported in other papers, and explaining and exploring how the spatially uniform stimuli, used here but not in other fMRI studies, limited responses in visual areas beyond V1.

2) Comparison between the two models, the GLM and QCM is not quite complete.

3) The present results are not discussed in context with past results using EEG, and Brouwer and Heeger's model of fMRI responses to color.

4) Implications of the basic pattern of response for the cortical neurons producing the data are discussed less than they could be.

Reviewer #2 (Public Review):

The manuscript by Myers et al provides new insight into the mechanism of transient muscle in myotonia congenita, a question that has escaped understanding since its first description over >40 years ago. The authors use a complementary set of approaches (including measurements of in situ muscle force production, membrane voltage and ion currents) to determine the membrane conductances that underlie transient weakness in muscle from both genetic (Clc1-/- adr mice) and pharmacologic (9-AC-treated WT mice) models of myotonia congenita. The authors utilize a combination of a non-conducting Cav1.1 mouse and treatment with ranolazine to dissect the relative contribution of Cav1.1 and persistent Nav1.4 conductances, respectively, to sustained plateau membrane depolarizations observed following myotonic runs, which are proposed to underlie the transient weakness observed following myotonic runs.

Reviewer #2 (Public Review):

Levi-Ferber and colleagues showed in their previous paper that ER stress regulates germline transdifferentiation in a way that is IRE-1 dependent, but XBP-1 independent. An open question at that time was how IRE-1 activation could mediate this signaling. The authors present several experiments in this manuscript that support the idea that neuronal Ire-1 can cell non-autonomously control germline differentiation through regulation of the neuropeptide FLP-6. Mechanistically, the authors characterize that FLP-6 is a target of IRE-1 RIDD activity. This is the first demonstration of RIDD in C. elegans, an important finding given that no RIDD targets have yet been identified in this organism. Using a wide range of mutants, the authors were also able to identify a neuronal circuit that can control the germline ectopic differentiation (GED) phenotype, involving the sensory neuron ASE, the interneuron AIY, and the motor neuron HSN. The data presented in the manuscript are sound, the mapping of a pivotal three-neuron circuit is impressive, and the findings are likely to be of high interest to a broad readership. However, some more evidence is required to support some of the conclusions made, in particular the characterization of flp-6 as a substrate for RIDD.

Reviewer #2 (Public Review):

This is an interesting paper showing that prolonging the integrated stress response provides protection to oligodendrocytes in the presence of an inflammatory cytokine. For their experiments, the authors use the cuprizone model in transgenic mice overexpressing IFNg in an inducible manner in combination with a genetic and pharmacological approach to enhance the integrated stress response. The experiments are well conducted and the results clearly presented in the text. The Popko lab has previously demonstrated in a series of papers the importance of the integrated stress response for oligodendrocyte function. The novel aspect of this work is that targeting the integrated stress response requires a neuroinflammtory environment for the protective effects to occur.

It is important to improve the introduction. As written it is not clear what was known before and how this paper goes beyond the existing literature.

The rational for combining for combining BZA and Seph needs to be explained.

The figures and legends could be improved according to the following suggestions:

The evidence that Sephin1 promotes remyelination in the EAE model shown in Figure 1 is only based on differences in g-ratio with the overall number of myelinated axons being unchanged. It is difficult to make conclusion based on these results. It is difficult to obtain accurate g-ratios in lesions. Maybe the authors could extend the analysis by performing histology and counting the number of oligodendrocytes.

Figure 2 contains only a scheme. Figure 2 should be combined with Figure 3. In addition, a scheme showing the time line of the cuprizone treatment and recovery from the treatment would be helpful. I assume W0 is at the time of treatment, W5 after 5 weeks of cuprizone and W8 represents 5 weeks of cuprizone and 3 weeks of recovery. If yes, it is not clear why the ASPA cell count shown it not reduced between W0 and W5. The numbers seem to be similar for W0, W5 and W8 in the absence of IFNg. In addition, the comparison shown in Figure 3 are incomplete. W0 is only shown without IFNg but not with. Does IFNg affect ASPA number in the absence of cuprizone?

Panel B and C in Figure 5 could be combined to be able to compare the analyses and to evaluate the recovery of cell number by Seph at W8. The number of mice per group is borderline (only 3 mice).

Same issue as above: Panel B and C in Figure 6 should be combined and a multiple comparison should be performed between W0, W5 and W8.

The rational for combining BZA and Seph as shown in Figure 8 should be explained in the text. The figure and legends should be improved to clarify at which time point the analyses were performed. The panel number stated in the legends do not match with what is shown in the figure. I assume the analyses were done at W8. Only g-ratios change, whereas the number of ASPA cells and amount of myelinated axons are not affected by the combined treatment. The interpretation of this result is not easy, and the emphasis of this result should be removed from the abstract.

Reviewer #2:

Ziółkowska et al. investigate synaptic processes in the dorsal hippocampal CA1(dCA1) region with the goal of testing the role of postsynaptic density protein 95 (PSD-95) dynamics in contextual fear extinction. They conclude that 1) extinction increases synaptic dCA1 PSD-95 levels and induces remodeling of dendritic spines, 2) extinction-related PSD-95 changes are mediated by phosphorylation of PSD-95 at serine 73, and 3) phosphorylation of PSD-95 at serine 73 as well as dCA1 activity are required to "update a partially extinguished fear memory". The experiments provide new insight and address a timely and important issue. The major strengths of the paper lie in the use of a wide range of complementary technical approaches, and the significance of addressing specific molecular mediators of fear attenuation. However, some of the analysis is based on inadequately justified or inappropriate measures (e.g. that do not directly assay the phenomenon under investigation), and there are concerns about independent effects of viral overexpression in this system as well as the relevance of the behavioral analysis. The conclusions from the paper, if true, would appear to support a very intricate model involving PSD95 phosphorylation and synaptic accumulation after extinction, but because of weaknesses in the underlying evidence, these mechanisms and their relationship to extinction memory were not persuasively demonstrated. Following are some specific concerns:

1) The mean intensity of PSD95 labeling per spine appears to be affected in some hippocampal layers (Fig. 1), but this might be attributable in some cases to elimination of spines that have relatively lower PSD-95, rather than a change in PSD-95 levels, per se.

2) The quantification of overexpressed PSD-95 in Fig. 2 makes unclear what specifically has been measured. The methods suggest that % area is defined as the total area of mCherry labeling divided by the total image area. This is not a direct measure of PSD-95 levels, rather than morphological or protein localization changes. Furthermore, the localization of overexpressed PSD-95 (Fig. 2) is clearly very different from that of endogenous PSD-95 (Fig. 1) in that it accumulates throughout the dendrites. This makes it unclear what a "puncta" represents, or whether the analysis implies anything about synaptic function.

3) The authors argue that S73 phosphorylation is required for synapse elimination during extinction, but Fig. S2 (which is not referenced or discussed in the manuscript) and Fig. 3 indicate that the effect of S73A overexpression is to dramatically reduce spine density in both behavioral groups. It is therefore not clear whether the manipulation interacted with extinction to prevent spine removal, or simply occluded such an effect because spine density was already at an artificial floor prior to any behavioral training. Overexpression of the wildtype construct also reduced spine density to a similar degree. Furthermore, the S73A mutant protein dramatically increased PSD area (Fig. 3d), which apparently contradicts the notion that phosphorylation of this site is required for synaptic accumulation, when applying the same logic used elsewhere in the paper. These are serious confounding issues because the central claim of the paper is that S73 phosphorylation mediates PSD95 synaptic accumulation and synaptic strengthening.

4) The authors suggest that successive days of extinction represent a distinct process called updating of a partly extinguished memory, which they seem to imply has different molecular requirements. There appears to be no basis in the literature for this idea.

5) The analysis of extinction relies on measurement of within-session decreases in freezing. However, within-session extinction has been shown to be neither sufficient nor essential for between-session extinction. It is not even clear that within-session extinction is really even extinction at all, rather than, for example, habituation. It is essential to examine the retention of decreased freezing across days in order to establish that the formation of long-term memory is involved.

6) Finally, numerous comparisons are made between animals that received FC, with no further manipulation, and extinguished animals. This design leaves open the possibility that any differences are attributable not to an extinction process but instead to context exposure independent of fear regulation. A behavioral control in which animals receive context exposures, but no shocks, would be very useful.

Reviewer #2 (Public Review):

Parker et al attempted to show that the FPA protein functions to regulate the widespread premature transcription termination of the Arabidopsis NLR genes. Using in vivo interaction proteomic-mass spectrometry, FPA was shown to co-purified with the mRNA 3' end processing machinery. Metagene analysis was used to show that FPA co-localized with Pol II phosphorylated at Ser2 of the CTD heptad repeat at the 3' end of Arabidopsis genes. Using a combination of Illumina RNA-Seq, Helicos, and nanopore DRS technologies, FPA was found to affect RNA processing by promoting poly(A) site choice, and hence controls the processing of NLR transcripts whereas such process is independent of IBM1.

Overall, it is a potentially important research. The data is rich and could be useful. However, the biological stories described are not thoroughly supported by the data presented, especially when the authors tried to touch on several aspects without some important validations and strong connections among different parts. Some special comments are provided below:

1) The title of this manuscript is "The expression of Arabidopsis NLR immune response genes is modulated by premature transcription termination and this has implications for understanding NLR evolutionary dynamics". Therefore, the readers will expect some functional connections between the FPA and the novel NLR isoforms due to premature transcription termination. However, the transcript levels of plant NLR genes are under strict regulation (e.g. Mol. Plant Pathol. 19:1267). Since the functions of NLR genes are related to effector-triggered immunity, it is more important to study the function of FPA on premature transcription termination when the plants are challenged with pathogens. In this manuscript, most transcript analyses are based on samples under normal growth conditions. It is therefore a weak link between the genomic studies and the functional aspects. For instance, it is more important to identify unique NLR isoforms produced upon pathogen challenges that are regulated by FPA. The authors will need to provide some of these data to fill this gap.

2) Since the function of FPA is to regulate NLR immune response genes, we should expect a change in plant defense phenotype in FPA loss-of-function mutants. Could the authors provide more information on this? On the contrary, in line 728 of this manuscript, the authors found that at least for some pathogens, "loss of FPA function does not reduce plant resistance". It is not consistent with the hypothesis that FPA is important to regulate NLR immune response genes.

3) Furthermore, the authors mentioned in lines 729-731 "Greater variability in pathogen susceptibility was observed in the fpa-8 mutant and was not restored by complementation with pFPA::FPA, possibly indicating background EMS mutations affecting susceptibility." Does it mean that fpa-8 contains other mutations? Will these additional mutations complicate the results of the RNA processing? Could the authors outcross the fpa-8 mutation to a clean background?

4) In line 318, the authors found 285 and 293 APA events in the fpa-8 mutant and the 35S::FPA:YFP construct respectively, but only 59 loci (line 347) exhibited opposite APA events (about one fifth). The low overlapping frequency suggests that some results could be false positive.

5) In line 732-736: "In contrast, 35S::FPA:YFP plants exhibited a similar level of sporulation to the pathogen-sensitive Ksk-1 accession (median 3 sporangiophores per plant). This suggests that the premature exonic termination of RPP7 caused by FPA has a functional consequence for Arabidopsis immunity against Hpa-Hiks1." It is contradictory to the statement in line 728 that "loss of FPA function does not reduce plant resistance". Is it possible that overexpression of FPA:YFP had generated an artificial condition that is not related to the natural function of FPA?

6) The fpa-8 mutant has a delayed flower phenotype (Plant Cell 13:1427). Could the 35S::FPA:YFP fusion protein construct reverse this phenotype and the plant defense response phenotype? It is important to interpret the data when the 35S::FPA:YFP construct was used to represent the overexpression of FPA.

7) Under the subheading "FPA co-purifies with the mRNA 3' end processing machinery". The results were based on in vivo interaction proteomics-mass spectrometry. MS prompts to false positives and will need proper controls and validations. Have the authors added the control of 35S:YFP instead of just the untransformed Col-0? At least for the putative interacting partners in Figure 1A, could the authors perform validations of some important targets, using techniques such as reverse co-IP, or to show direct protein-protein interaction between FPA to a few of the important targets by in vitro pull-down, BiFC, or FRET, etc.

8) In Fig. 3, the data show that the last exon of the FPA gene is missing in the FPA transcripts generated from the 35S::FPA:YFP construct. Will the missing of this exon affect the function of the transcript and the encoded protein?

9) The function of FPA is still ambiguous. There was a quantitative shift toward the selection of distal poly(A) sites in the loss-of-function fpa-8 mutant and a strong shift to proximal poly(A) site selection when FPA is overexpressed (35S::FPA:YFP) in some cases (Fig. 3, Fig. 5, Fig. 8). But the situation could be kind of reversed in other cases (Fig. 6). What is the mechanism behind it?

10) Under the subheading: "The impact of FPA on NLR gene regulation is independent of its role in controlling IBM1 expression". IBM1 is a common target of FPA and IBM2. Indeed, FPA and IBM2 share several common targets (Plant Physiol. 180:392). It may be more meaningful to compare the impact of FPA and IBM2 on NLR gene instead.

11) In lines 423-425, the authors described "Consistent with previous reports, the level of mRNA m6A in the hypomorphic vir-1 allele was reduced to approximately 10% of wild-type levels (Parker et al., 2020b; Ruzicka et al., 2017) (Figure 4 - supplement 3)." This data could not be found.

12) In line 426: "However, we did not detect any differences in the m6A level between genotypes with altered FPA activity." Which data is this statement referring to?

Reviewer #2 (Public Review):

In this manuscript, Anchimiuk et al reported that B. subtillis SMC can collide with each other, and that the collision is modulated by several factors including the number, strength, distribution of parS sites, the residence time of SMC on DNA, the translocation rate, and the cellular abundance of SMC. The authors suggested that these parameters are fine-tuned in the wild-type B. subtillis to minimize SMC collision. In my opinion, the finding is interesting, the experimental setup is creative, and the experiments were beautifully executed. Arguably, these experiments can only be performed in B. subtilis since parAB- and the insertion of another parS site at the mid-arm are not detrimental to cell viability (in Caulobacter crescentus, insertion of another parS mid-arm affects chromosome segregation, hence cell viability severely). Furthermore, the rare set of arm-modified SMCs from the Gruber lab also gives this manuscript a unique mechanistic angle. Given the available data, the conclusion of the manuscript is safe. I especially appreciate that the authors did not bias towards the model of SMC traversing each other by Z-loop formation.

Reviewer #2 (Public Review):

The authors present a compelling study that aims to resolve the extent to which synaptic responses mediated by metabotropic GABA receptors (i.e. GABA-B receptors) summate. The authors address this question by evaluating the synaptic responses evoked by GABA released from cortical (L1) neurogliaform cells (NGFCs), an inhibitory neuron subtype associated with volume neurotransmission, onto Layer 2/3 pyramidal neurons. While response summation mediated by ionotropic receptors is well-described, metabotropic receptor response summation is not, thereby making the authors' exploration of the phenomenon novel and impactful. By carrying out a series of elegant and challenging experiments that are coupled with computational analyses, the authors conclude that summation of synaptic GABA-B responses is linear, unlike the sublinear summation observed with ionotropic, GABA-A receptor-mediated responses.

The study is generally straightforward, even if the presentation is often dense. Three primary issues worth considering include:

1) The rather strong conclusion that GABA-B responses linearly summate, despite evidence to the contrary presented in Figure 5C.

2) Additional analyses of data presented in Figure 3 to support the contention that NGFCs co-activate.

3) How the MCell model informs the mechanisms contributing to linear response summation.

These and other issues are described further below. Despite these comments, this reviewer is generally enthusiastic about the study. Through a set of very challenging experiments and sophisticated modeling approaches, the authors provide important observations on both (1) NGFC-PC interactions, and (2) GABA-B receptor mediated synaptic response dynamics.

The differences between the sublinear, ionotropic responses and the linear, metabotropic responses are small. Understandably, these experiments are difficult – indeed, a real tour de force – from which the authors are attempting to derive meaningful observations. Therefore, asking for more triple recordings seems unreasonable. That said, the authors may want to consider showing all control and gabazine recordings corresponding to these experiments in a supplemental figure. Also, why are sublinear GABA-B responses observed when driven by three or more action potentials (Figure 5C)? It is not clear why the authors do not address this observation considering that it seems inconsistent with the study's overall message. Finally, the final readout – GIRK channel activation – in the MCell model appears to summate (mostly) linearly across the first four action potentials. Is this true and, if so, is the result inconsistent with Figure 5C?

Presumably, the motivation for Figure 3 is that it provides physiological context for when NGFCs might be coactive, thereby providing the context for when downstream, PC responses might summate. This is a nice, technically impressive addition to the study. However, it seems that a relevant quantification/evaluation is missing from the figure. That is, the authors nicely show that hind limb stimulation evokes responses in the majority of NGFCs. But how many of these neurons are co-active, and what are their spatial relationships? Figure 3D appears to begin to address this point, but it is not clear if this plot comes from a single animal, or multiple? Also, it seems that such a plot would be most relevant for the study if it only showed alpha-actin 2-positive cells. In short, can one conclude that nearby, presumptive NGFCs co-activate, and is this conclusion derived from multiple animals?

The inclusion of the diffusion-based model (MCell) is commendable and enhances the study. Also, the description of GABA-B receptor/GIRK channel activation is highly quantitative, a strength of the study. However, a general summary/synthesis of the observations would be helpful. Moreover, relating the simulation results back to the original motivation for generating the MCell model would be very helpful (i.e. the authors asked whether "linear summation was potentially a result of the locally constrained GABAB receptor - GIRK channel interaction when several presynaptic inputs converge"). Do the model results answer this question? It seems as if performing "experiments" on the model wherein local constraints are manipulated would begin to address this question. Why not use the model to provide some data – albeit theoretical – that begins to address their question?

In sum, the authors present an important study that synthesizes many experimental (in vitro and in vivo) and computational approaches. Moreover, the authors address the important question of how synaptic responses mediated by metabotropic receptors summate. Additional insights are gleaned from the function of neurogliaform cells. Altogether, the authors should be congratulated for a sophisticated and important study.

Reviewer #2 (Public Review):

In "Evolution of cytokine production capacity in ancient and modern European populations", Dominguez-Andrés et al. collect a large amount of trait association data from various studies on immune-mediated disorders and cytokine production, and use this data to create polygenic scores in ancient genomes. They then use the scores to attempt to test whether the Neolithic transition was characterized by strong changes in the adaptive response to pathogens. The impact of pathogens in human prehistory and the evolutionary response to them is an intriguing line of inquiry that is now beginning to be approachable with the rapidly increasing availability of ancient genomes.

While the study shows a commendable collection of association data, great expertise in immune biology and an interesting study question, the manuscript suffers from severe statistical issues, which makes me doubt the validity and robustness of their conclusions. I list my concerns below, in rough order of how important I believe they are to the claims of the paper:

— In addition to the magnitude of an effect away from the null, P-values are a function of the amount of data one has to fit a model or test a hypothesis. In this case, the authors have vastly more data after the Neolithic Revolution than before, and so have much higher power to reject the null hypothesis of "no relationship to time" after the revolution than before. One can see this in the plots the authors provided, which show vastly more data after the Neolithic, and consequently a greater ability to fit a significant linear model (in any direction) afterwards as well.

— The authors argue that Figure S2 makes their results robust to sample size differences, but showing a consistency in direction before and after downsampling in the post-neolithic samples is not enough, because:

1) you still lack power to detect changes in direction before the Neolithic.

2) even for the post-Neolithic, the relationship may be in the same direction but no longer significant after downsampling. How much the significance of the linear model fit is affected by the downsampling is not shown.

— The authors chose to test "relationship between PRS with time" before and after the Neolithic as a way to demonstrate that "the advent of the Neolithic was a turning point for immune-mediated traits in Europeans". A more appropriate way to test this would be creating a model that incorporates both sets of scores together, accounts for both sample size and genetic drift in the change of polygenic scores, and shows a significant shift occurs particularly in the Neolithic, rather in any other time period, instead of choosing the Neolithic as an "a priori" partition of the data. My guess is that one could have partitioned the data into pre- and post-Mesolithic and gotten similar results, largely due to imbalances in data availability.

— The authors only talk about partitions before and after the Neolithic, but plots are colored by multiple other periods. Why is the pre- and post-Neolithic the only transition that is mentioned?

— Extrapolating polygenic scores to the distant past is especially problematic given recent findings about the poor portability of scores across populations (Martin et al. 2017, 2019) and the sensitivity of tests of polygenic adaptation to the choice of GWAS reference used to derive effect size estimates (Berg et al. 2019, Sohail et al. 2019). In addition to being more heavily under-represented, paleolithic hunter-gatherers are the most differentiated populations in the time series relative to the GWAS reference data, and so presumably they are also the genomes for which PGS estimates built using such a reference would have higher error (see, e.g. Rosenberg et al. 2019). Some analyses showing how believable these scores are is warranted (perhaps by comparing to phenotypes in distant present-day populations with equivalent amounts of differentiation to the GWAS panel).

— In multiple parts of the paper, the authors mention "adaptation" as equivalent to the patterns they claim to have found, but alternative hypotheses like genetic drift are not tested (see e.g. Guo et al. 2018 for a review of methods that could be used for this).

— 250 kb window is too short a physical distance for ensuring associated loci that are included in the score are not in LD, and much shorter than standard approaches for building polygenic scores in a population genomic context (e.g. see Berg et al. 2019, Berisa et al. 2016). Is this a robust correction for LD?

— If one substitutes dosage with the average genotyped dosage for a variant from the entire dataset, then one is biasing towards the partitions of the dataset that are over-represented, in this case, post-Neolithic samples.

— It seems from Figure 2, that some scores are indeed very sensitive to the choice of P-value cutoff (e.g., Malaria, Tuberculosis) and to the amount of missing data (e.g. HIV). This should be highlighted in the main text.

— Some of the score distributions look a bit strange, like the Tuberculosis ones in Figure 2, which appear concentrated into particular values. Could this be because some of the scores are made with very few component SNPs?

Reviewer #2 (Public Review):

The authors examined the role of Rab25 during cell division within a developing epithelia. Strikingly, they found that the RabGTPase, Rab25, localized to mitotic structures such as centrosomes and cytokinetic midbodies in dividing cells of the developing zebrafish embryo. They went on to create maternal-zygotic Rab25a and Rab25b mutant embryos where they clearly demonstrate that apical cytokinetic bridges fail to undergo abscission leading to anisotropic cell morphologies that likely contribute to a delayed epiboly.

The major strengths of this study is the clear cell biology defects found in a developing embryo that lead to downstream developmental defects (delayed epiboly). The rab25 localization is beautiful. The examination of the viscoelastic properties is also compelling. The main improvements would be to expand upon the spatio-temporal localization of Rab25a and Rab25b during cell division at different stages of epiboly, present Rab11 localization patterns in the Rab25 mutant embryos, and clearly demonstrate that changes in viscoelasticity are also in their multinucleated cells that occur in Rab25 mutant conditions. These additions will help the authors support their conclusions that Rab25 localization/regulation of endomembranes (potentially recycling endosomes) regulates abscission and subsequently the viscoelastic properties of the developing tissue.

This study has identified novel roles for Rab25 in cytokinesis/abscission and opens the doors for examining it in regulating mitotic centrosome function. It is paradigm shifting in that it creates a new way to think about Rab25 and potentially its relationship with Rab11 and recycling endosomes during division in the early embryo.

Reviewer #2 (Public Review):

This manuscript set out to address several outstanding questions concerning the impact of 'eusocial' behaviour in mammals, here represented by the experimental model of the Damaraland mole-rat, on skeletal remodelling. Specifically, the transition to breeding status (queen) for some individuals in the colony is accompanied by changes that support high fecundity. The authors investigate the extent to which changes are localised in the skeleton and the underlying regulatory changes that are associated with these morphological features. The paper is well-written, the experiments have been planned thoughtfully and described carefully, and the panel figures convey information without over-crowding. Overall, I thoroughly enjoyed reading this manuscript, which represents as a multi-pronged approach to advancing understanding of the unusual biology and phenotype of queen mole rats.

Reviewer #2 (Public Review):

The authors investigated how alternative polyadenylation (APA) is modulated in yeast using appropriate transcriptomic methodologies.

The authors found that mutants for mRNA 3' end formation factors and cordycepin treatment alter alternative polyadenylation in the same manner, generating transcripts with longer 3'UTRs, due to a switch to distal polyadenylation sites (PAS). Most mutants analyzed cause a PAS switch, in particular mutants for RNA14, PCF11, YSH1, FIP1, NAB4 and PAP1. They also found that MPA and a rpb1 mutant, with a slower transcription elongation rate, reverts the cordycepin effect of distal PAS selection. This implies that in yeast, as in higher organisms, APA is modulated by RNAPII elongation. There is nucleosome depletion in the 3' end of convergent genes that undergo cordycepin-driven APA alterations, which is a new finding.

On the basis of their data, the authors propose a kinetic model for APA in yeast that is regulated by the concentration of core mRNA 3' end factors and nucleotide levels, which in turn modulates RNAPII elongation. This integrative model has been already described in higher organisms, but not in yeast, and overall this study covers an impressive body of work that makes an important contribution to the field.

1) The authors show that cordycepin have the same effect in APA as most of the 3' end factors mutants used, but there is a lack of integration between the two sets of PAS-seq data. The cordycepin APA effect may be due to decreased expression of mRNA 3' end factors but this hypothesis was not fully explored. Treating those mRNA 3' end mutants with cordycepin could shed some light on this.

2) A new role for SEN1 in APA for a subset of protein coding was observed. The SEN1 mechanism could be clarified if the authors show that SEN1 is within the subset of convergent genes analyzed, and also if SEN1 expression changes upon cordycepin treatment.

Reviewer #2 (Public Review):

This study induced tactile percepts through microstimulation via two multi-electrode arrays implanted over a quadriplegic's primary somatosensory hand region. The report focuses on manipulation of the stimulation frequency of microstimulation, though further manipulations were tested and are briefly reported.

For different stimulation sites, the perceived intensity was highest at different stimulation frequencies. This result contradicted the expectation that higher stimulation frequency would be related to higher perceived intensity. This expectation derived from previous work in non-human primates that showed lower detection thresholds for higher-frequency stimulation. The authors show that the same result is obtained in their human patient, suggesting that differences exist between near- and supra-threshold perceived stimuli and that, accordingly, generalizing from non-human primate work has its traps.

The authors grouped stimulation sites according to optimal stimulation frequency into low, intermediate, and high frequency preferring sites. These three classes were spatially clustered, and related to different patterns of reported perceptual qualities (such as vibration, pressure etc).

The paper's results are important for practical developments of sensory feedback in brain-machine interfaces. Understanding the perceptual result of brain stimulation requires reports by human participants, as underlined by the differences uncovered here between near- and supra-threshold stimulation. They furthermore reveal new aspects of the cortical organisation of primary somatosensory cortex.

The conclusion of clustered patches sensitive to specific frequencies is tentative. As an inherent limitation of intracranial recordings, the total number of stimulation sites is small, and some electrodes did not produce significant results, further reducing the number of analysable sites. Therefore, it is possible that stimulation doesn't truly fall into three distinct clusters (even if such clustering is statistically supported with the current data set), but are actually continuous or divide into a larger number of classes. Notably, this critique does not invalidate the main finding that different patches of cortex show specific frequency preferences.

Reviewer #2 (Public Review):

Hallast et al. have performed an extensive genetic analysis of a cohort of men with idiopathic infertility, for whom many have accompanying phenotypic data in the form of andrological parameters. The complex genetic architecture of repeating sequences on the Y chromosome gives rise to recurrent AZFc deletions that affect male infertility. However, while partial deletions of AZFc are reasonably frequent, they have less clear phenotypic effects. gr/gr and b2/b3 deletions seem to be a risk factor for spermatogenic impairment in some populations but are fixed in others. Hallast et al. focus on these partial AZFc deletions in a reference cohort and a cohort with idiopathic infertility from the same geographic population, characterising further structural and sequence variation, Y-chromosomal haplogroups, and gene dosage.

While the gr/gr deletion is present in the reference group of individuals with normal andrological parameters, Hallast et al. show that this deletion is enriched among patients, with 2.2-fold increased susceptibility to infertility. As observed in other European populations, the prevalence of b2/b3 deletion was similar in the reference group and the patient group, suggesting that it is not a spermatogenic impairment risk factor for this Estonian population either.

A quarter of Estonian gr/gr deletion carriers belonged to the Y chromosomal haplogroup R1a1-M458. Within this Y haplogroup, an inversion has occurred that promotes subsequent deletion, likely causing severe spermatogenic failure in the majority of carriers as this complex rearrangement is enriched 8.6-fold in individuals with severe spermatogenic impairment.

Some major strengths of this paper are the size of the groups recruited (1,190 patients and 1,134 reference individuals) from a single national population, the extensive accompanying andrological data, and the genomic characterisation of many individuals to elucidate the relationship between specific structural variants and effects on fertility.

The discovery of the fixed inversion infertility risk factor on a specific Y haplogroup is a useful contribution that could aid genetic counselling efforts through carrier identification and risk mitigation.

However, I am seeking clarity on multiple testing correction for microdeletion association with specific andrological parameters. Besides this, the main conclusions of this paper are supported by other data presented.

Reviewer #2 (Public Review):

Aly et al. investigated anticipatory signals in the cortex by analysing data in which participants repeatedly watched the same movie clip. The authors identified events using an HMM-based data-driven event segmentation method and examined how the timing of events shifted between the initial and repeated presentation of the same video clip. A number of brain regions were identified in which event timings were shifter earlier in time due to repeated viewing. The main findings is that more anterior brain regions showed more anticipation than posterior brain regions. The reported findings are very interesting, the approach the authors used is innovative and the main conclusions are supported by the results and analyses. However, many cortical regions did not show any anticipatory effects and it is not clear why that is. In part, this may be due to a number of suboptimal aspects in the analysis approach. In addition, the analyses of behavioural annotations are open to multiple interpretations.

Methods and Results:

1) The paper shows that across multiple regions in the cortex, there is significant evidence for anticipation of events with repeated viewing. However, there are also many areas that do not show evidence for anticipation. It is not clear whether this is due to a lack of anticipation in those areas, or due to noise in the data or low power in the analyses. There are two factors that may be causing this issue. First, the data that were used are not optimal, given the short movie clip and relatively low number of participants. Second, there are a number of important issues with the analyses that may have introduced noise in the observed neural event boundaries (see points 2-4 below).

2) Across all searchlights, the number of estimated events was fixed to be the same as the number of annotated events. However, in previous work, Baldassano and colleagues (2017) showed that there are marked differences between regions in the timescales of event segmentation across the cortex. Therefore, it may be that in regions such as visual cortex, that tends to have very short events, the current approach identifies a mixture of neural activity patterns as one 'event'. This will add a lot of noise to the analysis and decrease the ability of the method to identify anticipatory event timings, particularly for regions lower in the cortical hierarchy that show many more events than tend to be observed in behavioural annotations.

3) If I understand correctly, the HMM event segmentation model was applied to data from voxels within a searchlight that were averaged across participants. Regular normalization methods typically do not lead to good alignment at the level of single-voxels (Feilong et al., 2018, Neuroimage). Therefore, averaging the data without first hyperaligning them may lead to noise due to functional alignment issues within searchlights.

4) In the analyses the five repeated viewings of the clips were averaged into a single dataset. However, it is likely that participants' ability to predict the upcoming information still increased after the first viewing. That is especially true for perceptual details that may not have been memorised after watching the clip once, but will be memorised after watching it five times. It is not clear why the authors choose to average viewings 2-6 rather than analyse only viewing 6, or perhaps even more interesting, look at how predictive signals varied with the number of viewings. I would expect that especially for early sensory regions, predictive signals increase with repeated viewing.

5) In the analyses of the alignment between the behavioural and neural event boundaries, the authors show the difference in correlation between the initial and repeated viewing without taking the estimated amount of anticipation into account. I wonder why the authors decided on this approach, rather than estimating the delay between the neural and behavioural event boundaries. The finding that is currently reported, i.e. a lower correlation between neural and annotated events in the repeated viewing condition, does not necessarily indicate anticipation. It could also suggest that with repeated viewing, participants' neural events are less reflective of the annotated events. Indeed the results in figure 5 suggest that the correlations are earlier but also lower for the repeated viewing condition.

6) To do the comparison between neural and annotated event boundaries, the authors refit the HMM model to clusters of significant voxels in the main analysis. I wonder why this was done rather than using the original searchlights. By grouping larger clusters of voxels, which cover many searchlights with potentially distinct boundary locations, the authors may be introducing noise into the analyses.

Discussion:

7) To motivate their use of the HMM model, the authors state that: "This model assumes that the neural response to a structured narrative stimulus consists of a sequence of distinct, stable activity patterns that correspond to event structure in the narrative." If neural events are indeed reflective of the narrative event structure, what does it mean if these neural events shift in time? How does this affect the interpretation the association between neural events and narrative events?

Reviewer #2 (Public Review):

This manuscript provides convincing evidence that the ICEBs1 conjugative element confers a fitness advantage on the model bacterium B. subtilis during biofilm formation and sporulation. This effect is frequency dependent and is effected in large measure via an element gene, named devI, by an unknown mechanism that probably decreases the concentration of Spo0A-P. The data are well presented and successfully make the case for a fitness advantage conferred by the mobile element during biofilm formation and sporulation. It is likely that a mechanistic exploration of DevI will follow and will provide another facet to the regulation of Spo0A, a gift that keeps on giving.

Delaying sporulation in a mixed culture confers an advantage for the delayers. This has been convincingly shown. But I wonder about the effects in a clonal population of cells carrying ICEBs1 in competition with a null population. I appreciate that the delay in sporulation is transient, as pointed out in lines 404-407. But a delay of a few hours may be critical in this type of competition between populations as resources become limiting. This is presumably why sporulation is so exquisitely regulated on so many levels and in response to many external an internal signals. If so, ICEBs1 would have a deleterious effect and the element might be in danger of extinction. I suppose that an analogous discussion could be considered for biofilm formation.

Reviewer #2 (Public Review):

This study builds on a previously published paper from this group showing that KLF10 is under circadian control, and it in turn affects the oscillation of a set of metabolic genes in the liver. While the previous study utilized a systemic Klf10 KO mouse model, here, Ruberto et al. generated a conditional hepatocyte-specific Klf10 KO mouse model (Klf10Δhep).

The authors find that the absence of hepatocyte KLF10 alters the circadian oscillation of a number of metabolic genes. In response to sugar consumption, Klf10Dhep mice demonstrate exacerbated adverse effects as well as significantly increased hepatic expression of many glycolysis, gluconeogenesis, and lipogenesis related genes. They conclude that Klf10 normally acts as a "transcriptional brake" to protect animals against the effects of high sugar consumption and show via ChIP-seq that KLF10 is present at a wide range of metabolic genes, particularly at those involved in acetyl-CoA metabolism. The findings are interesting, particularly in the context of the burgeoning burden of metabolic disease and its relation to high sugar consumption, and are supported by the experimental findings.

Reviewer #2 (Public Review):

This manuscript by Nicholas Strash et al. compares the effects of several potential mitogens on cell cycle of the two most used in vitro models of cardiomyocytes (CMs): neonatal rat ventricular myocytes (NRVMs) and human induced pluripotent stem cell (hiPSC)-derived CMs. In addition, they use a 3D model of NRVMs as a model that represents more mature, non-proliferating CMs. The work is interesting for researchers working in the field of cardiac regeneration and provides the first direct comparison of several potential mitogens. The inclusion of several in vitro models to account for potential species differences strengthens the data. The results support previously published findings and the main conclusions are supported by the data presented.

The authors used a 3D model, cardiobundles made from NRVMs, as a more mature CM model. However, these cardiobundles still had a considerable number of CMs in active cell cycle in basal conditions. Whether this reflects true proliferation or the postnatal multinucleation process of rat cardiomyocytes, is unclear. Furthermore, post-mitotic human CMs were not studied. These can be obtained from hiPSC-CMs by prolonged culture or using metabolic stimuli as shown by Mills et al. 2017 (PNAS).

The authors demonstrate that the known mitogenic pathway for CMs, Erbb2-mediated signalling, promotes cell cycle activation in 2D cultures or NRVMS and hiPSC-CMs as well as in 3D cardiobundles. Although cell cycle activity was clearly induced, no actual proof of cytokinesis has been presented. For the cardiobundle work, it remains unclear if the increase in cross-sectional size of cardiobundles induced by Erbb2 signalling is due to increased number of CMs or increased size of CMs. Both the physiological ligand of Erbb3, Neuregulin-1, and the downstream ERK pathway are known to induce CM hypertrophy (see for example Zurek et al. 2020 Circulation; Bueno and Molkentin 2002 Circ Res).

The data analysis and statistics raise some concerns, which require clarification. First, the N numbers are really big and according to the Table 1 it is unclear if they all indeed represent independent samples. For example, one field in a monolayer (Table 1, definition of n in Figures 1J, 1P, 4C, 4E, 4G) should not be considered to represent n=1, if several images were analysed from the same sample and/or if several technical replicates (samples prepared from the same cell isolation or differentiation and treated similarly) were analysed. Only samples from separate differentiations or cell isolations should be considered as representatives of n and the results from technical replicates should be averaged to form the n=1 data. Second, the selection of statistical tests is a concern. It is unclear if the data were analysed for equal variances before selecting the test (parametric vs. non-parametric). It is also unclear why the authors carried out multiple t tests instead of using ANOVA or its variations, which are generally considered more suitable for multiple comparisons.

Reviewer #2 (Public Review):

Rosello et al. present very compelling evidence that Cytosine base editors can be used to introduce G:C to A:T base conversions with high efficiency in zebrafish. Furthermore, they describe engineering and validation of a base editor targeting the NAA PAM sequence. Finally, they have developed a potential novel model of the Noonan syndrome. The manuscript represents an important and much needed advance in precision genome editing in the zebrafish model system.

Reviewer #2 (Public Review):

The manuscript "Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways" by Bowerman and colleagues describes a study of archaeasome dynamics combining molecular simulations, cryo-EM, and sedimentation velocity analytical ultracentrifugation. How chromatin evolved is a fundamental question in biology, marking a striking departure from the bacterial nucleoid. Indeed, ever since the first description of archaeal nucleosomes and histones HmfA/B (Sandman and Reeves mid-80s) from thermophilic archaea, this question has fascinated and puzzled the field.

Recent work from the Luger lab figured out the organization of these archaeal chromatin fibers as a continuous loop structure. Here, the authors extend this question further. MD analyses show that Arc90 has two preferred states (closed and flexible ends), but the same 5T5K structure on 120 or 180 bp of DNA prefer a single state (closed). Sedimentation velocity analytical ultracentrifugation showed that Arc207 sediments slower than the H3 mononucleosome, implying that that Arc207 has a shape with higher anisotropy, resulting in excessive drag compared to a mononucleosome. Subsequently, high-resolution cryoEM showed that at least two distinct classes for Arc207 exist, where one class represents a 5-mer and another class represent a 7-mer. The latter has a unique shape in that the 7-mer forms an L-shape (or open clam) with a 3-mer hinging on a 4-mer.

Overall, these data provide exciting structural insights into how archaeal chromatin is folded up at its basic unit level, which the authors describe as most fittingly as a "slinkie". Because so little is known about how nucleosomes evolved during the transition from archaea to eukaryotes, we found this interdisciplinary report well written and with compelling data, that will be of interest to the chromosome biology field at large. We suggest a minor revision in which a few technical points are addressed.

Considerations:

1) The cryoEM data showed two main groups of particles: 5-mer protecting 150 bp and a 7-mer protecting either 90bp or 120bp. A few times in the manuscript (both in the results and discussion section) the authors mention a 30-bp MNase digestion ladder is observed. The Mnase data should be included, as this provides evidence that the structures observed by cryoEM indeed represent physiological structures, especially if strong discrete bands are observed at 90, 120, and 150 bp.

2) The two main classes found by cryoEM give the impression that adding dimers results in altered structures. The 7-mer shows an angled structure, which is interpreted as an open structure. The 5-mer shows a more uniform structure, which is interpreted as a closed structure. The former structure protects the full length of DNA on which HTkA histones were reconstituted, whereas the latter might be an incomplete reconstitution or a partially disassembled structure. It also raises the question if the length of the DNA is a limiting factor. What if HTkA was reconstituted on 170 bp or 307 bp instead? Would this in turn only permit the formation of the 5-mer on the 170 bp construct and two 5-mers on the 307 bp construct? The authors should consider addressing this point because the reconstitution might be constrained by the length of the DNA construct used. Indeed, a related topic might be AT content- what does archaeal DNA look like from the perspective of DNA sequence for chromatin (Jon Widom's group had a ChIPSeq paper on this a few years ago, just after his untimely passing).

3) In the discussion the authors cite that in one archaeal species the Mg2+ concentration is ~120 mM, more than a magnitude greater than that tested in Figure 5. What happens to reconstituted archaeasomes at higher Mg+? This is relevant because in vivo, archaea are thought to have 10x the concentration of Mg+ (amongst other ions) relative to us humble eukaryotes who would probably die of kidney failure at those ionic concentrations. Indeed at high ionic conditions, eukaryotic chromatin can be made to precipitate out of solution (for e.g. 10mM Mg+, 3M NaCl). An AUC assay with higher Mg2+ concentrations seems a doable and physiologically relevant addition to the ms that would strengthen it. It is relevant to consider that in vivo structure in these halophilic and thermophilic organisms might be dependent on the concentration of various salts and temperature, it would be nice to read the authors' thoughts on this issue.

Reviewer #2 (Public Review):

Bifulco et al. performed a large-scale in silico study to test whether the spatial fibrosis distribution measured via LGE-MRI in 45 patient with embolic stroke of undetermined source (ESUS) as compared to the distribution in 45 atrial fibrillation (AFib) patients without stroke leads to differences in reentrant arrhythmia inducibility of dynamics.

1) This study comprises a high number of simulations and is one of the computational electrophysiology studies that covers the most anatomical and structural variability on the atrial level. In their comprehensive analysis, Bifulco et al. answered their question and found no pronounced differences in arrhythmia inducibility and dynamics between ESUS and AFib models. It would be interesting to learn how the spatial fibrosis distributions compare in terms of the previously suggested features density and entropy (Zahid et al.). This might also influence the statements in L170/L207.

2) The authors chose to exclude patients with stroke from the AFib group, the reasons for this choice are not entirely clear. The same holds for the fact that the ESUS models included AFib-induced electrophysiological remodeling even though these patients have not been diagnosed with AFib (by definition).

3) An acknowledged limitation of the study is the assumption of fixed conduction velocity and action potential duration/effective refractory period. Bifulco et al. base this assumption on previous studies by the group (e.g. L312), which, however, concluded that reentrant driver locations and inducibility are sensitive to changes of action potential and conduction velocity (Deng et al.). For conduction velocity, wider ranges have been reported since the publication of the supporting reference (35) in 1994, e.g. Verma et al.; Roney et al.

4) The number of pacing sites is rather low for a comprehensive in silico arrhythmia inducibility test but likely a good balance of coverage and computational feasibility considering that the primary goal of this research was to check whether the two groups of models show differences when undergoing the same (but not necessarily exhaustive) protocol.

5) The discussion does a good job in putting the results into context. Two interesting observations that deserve more attention are that i) the Inducibility Score was always higher for AFib vs. ESUS (Figure 6A, no statistical test performed). However, this did not translate to a difference in silico arrhythmia burden (inducibility). ii) Reentrant drivers were about twice as likely to localize to the left pulmonary veins than the right pulmonary veins in the AFib models (Figure 6D).

6) The study succeeded in answering the question it posed in the sense that no marked difference was found between the ESUS and AFib models. This leads to the question what the stroke-inducing mechanism is in the ESUS patients. A hypothesis for future work could be that the fibrotic infiltrations in the ESUS patients reduce the hemodynamic efficacy of the left atrium and render clot formation (e.g. in the atrial appendage) more likely in this way.

7) The negative finding in this study (no difference between groups) does not naturally allow us to draw clinical implications for diagnosis or stratification. Additional ways to put the hypothesis proposed by the authors (fewer arrhythmogenic triggers in the ESUS patients) to test could be to consider readouts/surrogate measures of the autonomic nervous system.

Reviewer #2 (Public Review):

The authors used several approaches to define a discrete population of Langerhans cell-like (LC-like) dendritic cells (DC) in the dermis of mice. By flow cytometry, these cells expressed langerin/CD207 and EpCAM/CD236 and were found in the CD103-CD11b- fraction of dermal cells. It was also shown that LC-like cells, rather than LC, are the main contributors to CD103- langerin+ cells in the lymph node. By single cell RNAseq of dermal cells they clustered with Langerhans cells but lacked expression of DC-SIGN/CD209. Fate-mapping with Kitmercremer/Rosa26loxPSTOPloxPeYFP showed a similar origin to other dermal DC, with no yolk sac signal as observed in LC. Bone marrow chimeras, however, indicated a much slower turnover compared with other dermal DC. Independence from LC and other DCSIGN+ DC was also demonstrated by unchanged kinetics during continuous ablation of DCSIGN+ fractions in a DTR model.

The results explain the expression of langerin on two fractions of dermal DC observed several years ago (CD103+ and CD103-). The demonstration that epidermal LC do not contribute to LN populations in the steady state is completely unexpected and raises an important question of the in vivo function of the LC-like subset. LC-like cells appear to be related to LC but a more in-depth analysis of their gene expression differences compared with LC would be interesting. Also, their potential relationships with other DC (cDC1 or cDC2), was not defined. Langerin expression by human cDC2 is well described and possibly correlated with these observations in mice. Finally, the turnover of LC-like cells was slow, yet they contributed as many langerin+ cells to the resting lymph node as cDC1, which turnover quickly. Proliferation in situ might explain this observation but there were no data on this.

Reviewer #2:

In this study, entitled “APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy” Rae et al. describe a method to improve the visualization of the staining for genetically encoded probes that they described in previous studies (namely APEX2 constructs).

These techniques are very powerful as they increase the sensitivity for detecting low level of expression of the tagged proteins (e.g. compared to GFP tagged proteins). The novelty in this study is that the reaction product (DAB precipitates) is revealed by the nucleation of silver/gold precipitates. Such enhancement has been used extensively in the past for pre-embedding immuno-peroxidase techniques, but has never been combined with the use of APEX2. This has one major advantage: that the contrast of the positive staining can stand out from the contrast of the surrounding ultrastructure, making the sample preparation more adapted to 3D EM techniques, especially volume SEM where contrast is a bottleneck. Moreover, the sensitivity of the technique is shown to be compatible with the detection of endogenous levels of expression.

The technique is very well detailed and elegantly illustrated by convincing applications on cultured cell systems. The apparent simplicity of use, together with a growing interest in the community for the APEX2 based techniques (also in correlative imaging), significantly raises the potential for it to become a standard in the field, and should thus be shared with the community.

Reviewer #2:

Miningou and Blackwell in their manuscript titled "Temporal pattern and synergy influence activity of ERK signaling pathways during L-LTP induction" explored the contributions of upstream pathways to ERK activation during LTP. The authors expanded on their previously published LTP model to assess the influence on ERK activation of each of the upstream pathways originating from cAMP or Ca+2 activated with differing temporal patterns. This manuscript's aim is quite germane, since 1) ERK plays such a central role in learning and memory and its cellular proxy LTP; 2) the Ca+2/cAMP/PKA system is highly complex and nonlinear, with multiple feedback loops. The resulting manuscript has the potential to be impactful. The approach of using a stochastic reaction-diffusion model is state of the art and appropriate for the modeling of these subcellular events in spines. And the modeling insights are very intriguing as the authors predict that ERK activation by cAMP/PKA or Ca+2 pathways differ in their linearity, these pathways can synergize during LTP and this may involve a novel feedforward loop containing synGAP. The authors do a marvelous job placing their findings within the huge body of LTP literature.

There are, however, a couple of points that I feel should be addressed:

1) There needs to be additional technical detail on how the original models were expanded. The model presented here was developed by merging Jȩdrzejewska-Szmek et al., 2017 and Jain and Bhalla, 2014 models. These models were developed based on experimental data and validated with independent experimental datasets in a rigorous manner. It is not clear how the combining these two models, and the additional molecules and reactions added have affected the dynamics of ERK activation, and how comparable they are to the original experimental data used for model development in the previous modeling efforts. It is not clear if the model was reparameterized.

2) Beyond the ERK activation traces, it would be useful for clarity sake to also include the simulated traces for the activation of the upstream molecules (PKA, RAS, RAP, etc). Given how additional changes have been made additional information should be provided to ensure that the contribution of each pathway is accurately represented.

Reviewer #2:

In this work, Hofmann and colleagues conduct a study investigating the relationship between EEG alpha and subjective arousal in naturalistic (as opposed to controlled experimental) settings. Participants completed an immersive virtual reality experience while EEG was recorded, and continuously rated their subjective arousal while a video of the experience was replayed. Three different decoding methods were evaluated (Source Power Comodulation, Common Spatial Patterns, and Long Short-Term Memory Recurrent Neural Networks), each of which demonstrated above chance levels of performance, substantiating a link between lower levels of parietal/occipital alpha and subjective arousal. This work is notable because the roller-coaster simulation is a well-controlled, yet dynamic manipulation of arousal, and in its comparison of multiple decoding approaches (that can model the dynamics of affective responses). Indeed, this is an interesting proof of concept that shows it is possible to decode affective experience from brain activity measured during immersive virtual reality.

Major concerns:

The authors advocate that naturalistic experiments are needed to study emotional arousal, because "static" manipulations are not well-suited to capture the continuity and dynamics of arousal. This point is well-taken, but no comparisons were made between static and dynamic methods. Thus, although the work succeeds in showing it is possible to use machine learning to decode the subjective experience of arousal during virtual reality, it is not clear what new insights naturalistic manipulations and the machine learning approaches employed have to offer.

The methods used to assess model performance are also a concern. Decoding models were evaluated separately for each subject using 10-fold cross-validation, and inference on performance was made using group-level statistics. Because time-series data are being decoded, if standard cross-validation was performed the results could be overly optimistic. Additionally, hyperparameters were selected to maximize model performance which can also lead to biased estimates. This is particularly problematic because overall decoding performance is not very high.

Reviewer #2:

This paper proposes a novel and relevant evolutionary model that explains many aspects of replication origin statistics in a family of yeast species. It is a step forward in our understanding of the evolutionary pressures that affect the distribution of replication origins in Eukaryotes. I recommend the authors address the following issue:

1) Many of the conclusions of the paper are based on the claim that the extending the model by adding an efficiency bias to the origin death rate makes the model fit the data better; in particular, they say in line 213 that "the observed huge divergence in efficiency between lost origins and their neighbors is absent in the model simulations." This is reinforced in line 243, and in other parts of the text. But inspecting Fig 3, the two models (with and without a death rate bias) yield almost identical box-plots; if anything, the box-plots for the lost/nearest fractions of the pure double-stall aversion model seem visually to match the data marginally better. So why do the authors claim that the model with death rate bias is a much better fit? This is far from clear by just inspecting the data. I see no "huge difference" in the plots. There is a difference, but it is far from huge - the differences in the mean are much smaller than the size of the boxes. It seems to me unjustified to use this to choose one model over another. One way to ascertain this is to do rigorous statistical tests to determine if the differences in the means of the simulated and observed data are statistically significant; for example, a t-test.

Reviewer #2:

The conclusion was quite surprising from their anatomical differences and connectivity to the cortex, however, implies different mechanisms underlie for species specific circuit organization.

The manuscript is well-organized and well-written with strong figures. I have only a few comments/suggestions to further improve the overall quality of this manuscript.

I understand obtaining human and NHP tissue is difficult and hard to perform numbers of ISH. Therefore, there is a database that provides additional information on gene expression in NHP LGN (https://gene-atlas.brainminds.riken.jp/). From this database, it is possible to obtain parvocellular specific and magnocellular specific gene expression by fine structure search, which may be worth comparing with the results in the current paper. Many researchers have realized that marmoset is one of the good animal models to understand human brain function and dysfunction, therefore, it is worth including marmoset for comparative analysis for community interest.

Reviewer #2:

The paper investigates the temporal signatures of single-neuron activity (the autocorrelation timescale and latency) in two frontal areas, MCC and LPFC. These signatures differ between the two areas and cell classes, and form an anatomical gradient in MCC. Moreover, the intrinsic timescales of single neurons correspond with their coding of behaviorally relevant information on different timescales. The authors develop a detailed biophysical network model which suggests that after-hyperpolarization potassium and inhibitory GABA-B conductances may underpin the potential biophysical mechanism that explains diverse temporal signatures observed in the data. The results appear exciting, as the proposed relationship between the intrinsic timescales, coding of behavioral timescales, and anatomical properties (e.g., the amount of local inhibition) in the two frontal areas is novel. The use of the biophysically detailed model is creative and interesting. However, there are serious methodological concerns undermining the key conclusions of this study, which need to be addressed before the results can be credited.

Major Concerns:

1) One of the key findings is the correspondence between the intrinsic timescales of single neurons and their coding of information on different behavioral timescales (Fig. 4). However, the method for estimating the intrinsic timescales has serious problems which can undermine the finding.

1.1 The authors developed a new method for estimating autocorrelograms from spike data but the details of this method are not specified. It is stated that the method computes the distribution of inter-spike-intervals (ISIs) up to order 100, which was "normalized", but how it was normalized is not described. The correct normalization is crucial, as it converts the counts of spike coincidences (ISI distribution) into autocorrelogram (where the coincidence counts expected by chance are subtracted) and can produce artifacts if not performed correctly.

1.2 The new method, described as superior to the previous method by Murray et al, 2014, appears to have access to more spikes than the Murray's method (Fig. 2). Where is this additional data coming from? While Murray's method was applied to the pre-cue period, the time epoch used for the analysis with the new method is not stated clearly. It seems that the new method was applied to the data through the entire trial duration and across all trials, hence more spikes were available. If so, then changes in firing rates related to behavioral events contribute to the autocorrelation, if not appropriately removed. For example, the Murray's method subtracts trail-averaged activity (PSTH) from spike-counts, similar to shuffle-correction methods. If a similar correction was not part of the new method, then changes in firing rates due to coding of task variables will appear in the autocorrelogram and estimated timescales. This is a serious confound for interpretation of the results in Fig. 4. For example, if the firing rate of a neuron varies slowly coding for the gauge size across trials, this will appear as a slow timescale if the autocorrelogram was not corrected to remove these rate changes. In this case, the timescale and GLM are just different metrics for the same rate changes, and the correspondence between them is expected. Before results in Fig. 4 can be interpreted, details of the method need to be provided to make sure that the method measures intrinsic timescales, and not timescales of rate changes triggered by the task events. This is an important concern also because recent work showed that there is no correlation between task dependent and intrinsic timescales of single neurons, including in cingulate cortex and PFC (Spitmaan et al., PNAS, 2020).

2) The balanced network model with a variety of biophysical currents is interesting and it is impressive that the model reproduces the autocorrelation signatures in the data. However, we need to better understand the network mechanism by which the model operates.

2.1 The classical balanced network (without biophysical currents such as after-hyperpolarization potassium) generates asynchronous activity without temporal correlations (Renart et al., Science, 2010). The balanced networks with slow adaptation currents can generate persistent Up and Down states that produce correlations on slow timescales (Jercog et al., eLife, 2017). Since slow after-polarization potassium current was identified as a key ingredient, is the mechanism in the model similar to the one generating Up and Down states, or is it different? Although the biophysical ingredients necessary to match the data were identified, the network mechanism has not been studied. Describing this network mechanism and presenting the model in the context of existing literature is necessary, otherwise the results are difficult to interpret for the reader.

2.2 Does the model operate in a physiologically relevant regime where the firing rates, Fano factor etc. are similar to the data? It is hard to judge from Fig. 5b and needs to be quantified.

2.3 The latency of autocorrelation is an interesting feature in the data. Since the model replicates this feature (which is not intuitive), it is important to know what mechanism in the model generates autocorrelation latency.

3) HMM analysis is used to demonstrate metastability in the model and data, but there are some technical concerns that can undermine these conclusions.

3.1 HMM with 4 states was fitted to the data and model. The ability to fit a four-state HMM to the data does not prove the existence of metastable states. HMM assumes a constant firing rate in each "state", and any deviation from this assumption is modeled as state transitions. For example, if some neurons gradually increase/decrease their firing rates over time, then HMM would generate a sequence of states with progressively higher/lower firing rates to capture this ramping activity. In addition, metastability implies exponential distributions of state durations, which was not verified. No model selection was performed to determine the necessary number of states. Therefore, the claims of metastable dynamics are not supported by the presented analysis.

3.2 HMM was fit to a continuous segment of data lasting 600s, and the data was pooled across different recording sessions. However, different sessions have potentially different trial sequences due to the flexibility of the task. How were different trial types matched across the sessions? If trial-types were not matched/aligned in time, then the states inferred by the HMM may trivially reflect a concatenation of different trial types in different sessions. For example, the same time point can correspond to the gauge onset in one session and to the work trial in another session, and vice versa at a different time. If some neurons respond to the gauge and others to the work, then the HMM would need different states to capture firing patterns arising solely from concatenating the neural responses in this way. This confound needs to be addressed before the results can be interpreted.

Reviewer #2:

A state of the art imaging of the dynamics of astroglial glutamate transporters that certainly add novel perspective into this, quite important and hot field. Experiments and clean and convincing, the data obtained fully support conclusions.

Comments:

1) The authors mention the importance of efficient glutamate uptake in the development of neuropathological conditions, but do not discuss this in regards to their results. Such a discussion would seem relevant.

2) Authors conclude that the membrane turnover pathway should be a particularly important GLT-1 resupply mechanism near excitatory synapses as some earlier studies have found the lowest lateral membrane mobility of GLT-1 there. In this context, it would be of interest to have some quantitative tips as to the relationship between the level of excitatory activity and the occupancy of local GLT-1.

3) There is a recent work implicating the C-terminus in the surface assembly of GLT-1 (Peacy et al Mol Pharm 2020), which seems relevant to the present findings. Please discuss further.

4) Functional activity of glutamate transporters is linked to (and is being regulated by) astroglial Na signalling; any suggestions how proposed turnover cycle may affect cytosolic Na+ dynamics

5) The Fig. 5A imaging data seem to nicely provide both surface and cytosol labelling of the same cell. Perhaps the authors could thus assess the distribution of surface-to-volume ratios across live astroglia: to my knowledge, such data has not yet been available.

6) Figure 1B: Please provide further detail regarding fast-exchange solution application, its physical arrangement, etc.

7) Figure 2, whole-cell photobleaching: Please expand on what is 'tornado' mode scanning and how it has been applied.

8) Figure 3, dSTORM data: Please provide further details regarding the numbers of sampled ROIs and/or individual molecules / distances analysed.

Reviewer #2:

This manuscript addresses the question of whether duplication of tumor suppressors occurred coincidently with the enlarged body size and reduced cancer risk evolved independently in Afrotherians. Using the human genome as reference, the authors systematically searched for gene duplications in 13 publicly available Afrotherian genomes, including 9 extant and 4 extinct species. The authors also reconstructed the ancestral body sizes, cancer risks and gene duplication events across the Afrotherian phylogeny. These data showed that both increased body sizes and reduced cancer risks are gradually evolved. Reactome pathway enrichment analysis for gene duplicates showed unexpectedly that gene duplicates in both lineages with or without major increases in body size/lifespan/decreases in cancer risk are enriched in many cancer related pathways. However, the authors found that 157 genes duplicated in Proboscidean stem-lineage, in which extremely large species evolved, were uniquely enriched in 12 cancer pathways. These genes might facilitate further body enlargement and cancer resistance evolution in Proboscidean. Most interestingly, the authors found that several genes both upstream and downstream of a famous tumor suppressor TP53 have also been duplicated, either before or after initial TP53 duplication. These genes are involved in transcriptional regulation of TP53 and may have facilitated re-functionalization of TP53 retroduplicates. Overall, this is an important and interesting study that can help us understand the evolution of body size, lifespan and cancer risk in mammals more deeply.

Major comments:

1) In general, the evolutionary fate of gene duplication includes: 1) Conservation of gene function; 2) Neofunctionalization; 3) Pseudogenization; 4) Subfunctionalization (doi:10.1016/S01695347(03)00033-8). To execute the function of tumor suppression, as this study focused on, gene duplicates were supposed to be functionally conserved or subfunctionalized. Gene duplicates that have been neofunctionalized or pseudogenized will not be helpful (also mentioned by authors in the Caveats section). Therefore, it might be more convincing to investigate the functional status of each gene duplicate, especially those in Fig 4C/D. In many cases, however, a related function, rather than an entirely new function, evolves by neofunctionalization after gene duplication, and also that to check new functions for a batch of genes is not realistic, the authors could simply check the coding sequences to ensure these genes duplicates are not pseudogenes and are functional. This is necessary because in Fig 4D, many genes have only 2 copies expressed. If one of them is a young pseudogene, it could be stochastically expressed and will encode a dysfunctional protein.

2) In Results section 3, the cancer pathway frequency data of many nodes seems not consistent with data shown in Table 2. For example, Line 293-296: "55.8% (29/52) of the pathways that were enriched in the Tethytherian stem-lineage..., 27.8% (20/72) of the pathways that were enriched in the Proboscidean stem-lineage...were related to tumor suppression", the cancer pathway percentages shown in Table 2 for these 2 nodes are 63.4% and 38.81%, respectively. While the frequency data in Table 2 are consistent with Supplementary Data File S3: "Atlantogenata_Reactome_ORA.xlsx". It is possible that the frequency data shown in the main text are specific to pathways of tumor suppression, rather than cancer related pathways. If this is the case, more detailed data should be shown somewhere else.

3) The titles of Results section 3 and section 4 are highly similar and actually the data in section 4 seems to be used to further solidify the conclusion of section 3. Therefore, is it possible to merge them into one single section?

Reviewer #2:

When animals are given a choice between drug and nondrug reinforcers, they will most often choose the nondrug alternative even when presented with highly reinforcing drugs of abuse. This is difficult to reconcile with known behavior in humans and for modeling aspects of addiction that are critical to the disorder, such as choosing to use drugs above all other reinforcers. Recent work by this same group has reported that responding for nondrug reinforcer is, surprisingly, insensitive to devaluation. This suggests that the choice for the nondrug reinforcer is under habitual, rather than the presumed goal-directed, control and may explain why animals most often choose the nondrug reinforcer over drug reinforcers. Moreover, because there is no devaluation procedure for determining whether drug choice is habitual or goal directed, it's not known if choice for drug is also habitual or remains goal-directed.

The manuscript by Vandaele et al., therefore, sought to develop a procedure for determining whether behavior of rats making choices between saccharin and cocaine reinforcers was habitual or goal-directed based on reaction times (RT). Based on previous theories, the authors argue that goal-directed behavior should have slower RTs on choice trials versus sampling trials (e.g., because animals are deliberating between the alternatives) whereas habitual behavior should have similar RTs across both sampling and choice trials. The authors also present a third possibility in which options are evaluated sequentially, rather than simultaneously, resulting in RTs being longer in the sampling versus choice trials. The authors report that rats with minimal training and who are presumed to be goal-directed have slower RTs in choice trials compared to sample trials whereas rats that have had extensive training have similar RTs in the choice and sampling phases. These findings are consistent with their hypotheses. Moreover, they demonstrate that in the small subset of rats that prefer cocaine over saccharin, RTs in the sampling trials are longer than that in the choice trial suggesting that cocaine preferring rats are not evaluating each of the options. These data are the first to evaluate habitual responding for a drug reinforcer and suggest that comparing latencies across different task phases could be used to measure habitual and goal-directed behaviors.

Reviewer #2:

This manuscript by Mathsyaraja et al. studies the oncogenic loss of the Max-gene-associated (MGA) protein due to deletion or mutation in cell-lines, in mice and in human cancers (cell-lines and tumors). The authors knocked out MGA by aerosol-delivered, CRISPR-CAS expressing lentiviruses that simultaneously Cre-activated a Lox-stop Kras oncogene. The loss of MGA accelerated proliferation and oncogenesis, and shortened survival. Oncogenesis was further enhanced by enforced TP53 deletion in these lung tumors. RNA-seq and ChIP-seq of MGA+ or - cell-lines demonstrated the up and downregulation of various gene classes (thousands of genes) according to function and regulation including of PRC1.6 targets, meiosis regulators, TGF-beta signaling pathway components, EMT regulators, anti-tumor immunity, as well as of MYC, E2F, etc. Different cell lines exhibited both overlapping and distinct target sets. MGA knockout cells were more migratory and invasive and displayed actin-protrusions in accord with this behavior. They show that a Domain of Unknown Function in the mid-region of MGA engages PRC1.6 and is required to depress proliferation. The DUF is also required to limit actin-protrusions. Human colon organoids were studied since MGA mutations and deletions are also apparent in colon cancer. Again, shared and distinct targets of MGA action were inferred.

The authors make a strong case that MGA is an important tumor suppressor that operates through PRC1.6 for some of its actions.

Reviewer #2:

1) The authors hint towards the involvement of c-di-GMP signaling via the YcgR protein. This hypothesis can be tested by knocking down the ycgr gene and repeating the assay, but this has not been done or reported. Addition of these data to the manuscript would make the paper significantly stronger.

2) Do other chemoreceptors (Tar, Tsr, Tap) also act in the same way with their respective ligands? It would be useful to know if this effect is specific to Trg or if it is also found in the other chemoreceptors.

3) In figure 3C, what is the reason that the GFP intensity and the speed do not have the same range? In other words, why is the slope not equal to 1? Since there is 1:1 correspondence between the number of MotB and the number of GFP, shouldn't the slope be 1?

4) The authors do not cite or discuss the recent literature on load-dependent stator remodeling (e.g. PMIDs: 29183968, 31142644). It would be helpful to have a more in-depth discussion on how the observed stator unit recruitment relates to stator remodeling in response to load.

Reviewer #2:

Overall, this is a very well written paper that presents software that fills an interesting niche: interactive, real-time simulations of complex multicellular systems that can run in a web browser, without any need for users to install or configure software. As the authors describe, this enables new modes of education, science communication, and multidisciplinary collaboration. The software itself is impressive, and the supplied examples are clean and beautifully fluid. It is eye-opening that Javascript can run these models so well. The authors also did a fantastic and complete job in sharing their full source code, from the overall software down to individual scripts used to generate figures.

Some points that the authors should address in a revision:

1) Suitability of the software for researchers:

a. Artistoo simulations do not appear to have any method to save data for external manipulation and archival. This makes their use somewhat less applicable to robust simulation-driven investigations, particularly where postprocessing and further analyses are required.

b. It is unclear if Artistoo-based models can be exported into other cellular Potts (CP) frameworks such as CC3D or Morpheus. This may leave researcher end users without a clear "upgrade path" after exploring model ideas in Artistoo and moving to larger simulations (e.g., larger or more complex domains), running simulations in high throughput on HPC resources, or adapting approximate Bayeseian techniques for parameter estimation that require automating many simulation runs. Without an upgrade path, such users may wish to immediately begin in research-focused platforms rather than start with Artistoo and re-implement in another framework later.

c. Similarly, it is unclear if a model developed in Morpheus or CC3D can be directly imported into Artistoo. If such an import were possible rather than re-implementing models in Aristoo, research-focused users would be more likely to use Artistoo for scientific communication and outreach.

2) Need for improved educational scaffolding: The examples provided in the paper are excellent. However, they lack context on what the parameters mean or do. (For example, what are max_act and lambda_act in the cell migration model?) This may limit the educational impact because users will be unclear on what to change, and how the parameters relate to cell biophysical processes.

The authors should include more background information with each model, define parameters, and give end users some idea of what to expect when parameters are changed. We have also found it useful to help guide a new user's exploration of a model by suggesting parameter sets and describing what they should see. This can serve as an educational scaffolding to help learners build and grow.

The authors' sample models should serve as a template to Artistoo users on best practices for communicating models to diverse audiences.

3) New developments in online cellular Potts simulators: The authors should note that CompuCell3D has recently been ported to run interactively online in a web browser. See https://nanohub.org/resources/compucell3d. This recent development should be addressed in the paper.

4) Narrow review of interactive, "zero install" simulation frameworks: The authors focus too narrowly by only comparing Artistoo with other cellular Potts frameworks, while the main use case for Artistoo is for interactively sharing and communicating complex simulation models online.

The authors should discuss non-CP frameworks that worked towards this, such as CC3D on nanoHUB (see above), online Tellurium (https://nanohub.org/resources/tellurium), current practice to share R models online as Shiny apps, and recent work to use xml2jupyter to automatically convert research-focused (command line) PhysiCell models to interactive Jupyter notebooks that can be shared as interactive webapps on nanoHUB (e.g., https://nanohub.org/tools/pc4cancerimmune). All of these serve similar purposes of creating zero-install, interactive versions of models for science education and communication. The authors should briefly discuss these to further contextualize their work.

5) While this is a more minor point, I would feel more comfortable if the supplementary information had convergence and accuracy testing. Are there limits on computational step sizes for numerically accurate simulations, particularly for large energies or when including diffusion processes?

Overall, this is some fantastic work.

Reviewer #2:

This manuscript interrogates function of Ihog and Boi adhesion molecules in cytoneme-based transport of the Hedgehog morphogen in Drosophila. The cell biology of how cytonemes are regulated to deliver morphogen signals is not yet well understood, so the work addresses an important topic that will be of interest to a broad audience. However, much of the study refines previous work from the same group to provide only a modest advance in understanding of how Ihog impacts cytoneme behavior.

The authors use genetic strategies in Drosophila to investigate how Ihog and Boi influence cytoneme dynamics. They find that the two proteins act differently with regard to cytoneme function. Boi effects are not exhaustively analyzed, but a number of genetic experiments are performed to interrogate Ihog. The authors reveal that the extracellular domains of Ihog interact with the glypicans Dally and Dlp to stabilize cytonemes that originate from Ihog over-expressing cells. Knockdown of Ihog does not alter cytoneme dynamics.

The most novel aspect of the study - that Boi functions differently than Ihog in cytonemes - is, unfortunately, not expanded upon. Some experiments lack controls or are presented in a manner that prevents clear interpretation of results.

Key points to be addressed:

Figure 1: Null alleles and RNAi silencing are used interchangeably to reduce Ihog, Boi, Dally and Dlp function in vivo. Results between methods are directly compared. Oftentimes, controls are not included to confirm the level of knockdown following RNAi. If possible use null alleles due to consistency. However, if this is not possible due to experimental reasons, give an explanation and state impact in the discussion.

Ihog levels decrease following loss of Dally or Dlp and Boi levels appear to increase following knockdown of Ihog, Dally, or Dlp. These stability changes have previously been reported. The mechanism is not clear, so should have been investigated here - especially the increased Boi protein level. How does this occur? Is stabilization occurring at the protein level or is gene expression changing? Is this a compensatory upregulation?

Based upon the supplement for Figure 2, it looks like the Ihog truncation mutants show variable stability. Might this be affecting the extent to which they alter Dally or Dlp stability? The western blot data are presented as crops of single bands adjacent to crops of a molecular weight ladder. Blots should be shown as intact images, preferable with all variants compared across a single gel with a loading control. As presented, relative stability/expression levels are impossible to assess.

Figures 3-4: Ihog mutant transgenes are tagged with either HA or RFP. Best to be consistent with tags when mutant function is being directly compared. Given that the HA tag is a small epitope and the RFP is a protein tag, they may differentially alter protein functionality. To be consistent it would be preferable to use the same tags. However, if this is not possible due to experimental reasons, the technical implication can also be mentioned in the discussion.

Figure 5: Investigation of histoblast cytonemes reaching into ttv, botv mutant clones: The ability of cytonemes to invade double mutant clones is altered only under the engineered situation of glypican dysfunction combined with Ihog over-expression. From this, it is concluded that Ihog is acting with glypicans to stabilize cytonemes. This may be the case, but they ability to see it only under an engineered situation of compound mutation plus Ihog over-expression leads this review to question the physiological relevance of the observation. Of similar concern is that the authors state the ability of Ihog over-expressing cell cytonemes to cross small vs. large ttv, botv clones differs. The difference is very difficult to appreciate from the results presented.

Figure 6: The apparent functional difference between Ihog and Boi in the ability to stabilize cytonemes is potentially very interesting, but is not investigated, which limits the advance of the current study.

Reviewer #2:

Using this new Trypanosoma carassii infectious model in larval zebrafish, Jacobs et al. have developed a new clinical scoring system to reliably separate high-and low-infected larvae in order to investigate their individual innate immune responses, with a special emphasis on macrophages and neutrophils.

In summary the separation system used in this allows us i) to identify a strong macrophage and neutrophil proliferation response by high-and low-infected larvae, although happening a bit earlier, 5 dpi, for macrophages in low-infected larvae, and ii) to observe a differential distribution and morphology of macrophages, associated to the unique presence of more rounded foamy macrophages with a high pro-inflammatory profile into the vessels of high-infected zebrafish larvae. Together, this study constitutes the first report of the occurrence of foamy macrophages during an extracellular trypanosome infection.

Although the paper is well-written and the findings are interesting as they bring new insights into the development of foamy macrophages in response to an extracellular pathogen, i.e. Trypanosoma carassii, using a zebrafish larvae model, I have a few concerns regarding the following:

• The experimental infectious model in zebrafish: figure 2 summarizes that only 15% of the infected larvae, named low-infected larvae, are able to survive the infection. As an explanation the authors refer to the trypanosuceptible vs. trypanotolerant background of the host observed in non-zebrafish models. However, in this particular setting, all the larvae possess an identical genetic background. Therefore, why would the larvae behave differently in response to a similar pathogen? In addition, there is no clear differences in neither parasitic load at 2 dpi (figure 3F) nor myeloid cells accumulation at 3 dpi (figure 4AB), which could lead to a drastic difference in parasitic load based on mRNA expression at 4 dpi (figure 3F). The authors should discuss this shortly.

• Figure 4: the representative pictures from Fig4B do not seem to clearly match the histograms depicted in Fig4C. For example, from the pictures in Fig4B, it seems that there is a decrease in red fluorescence in the representative pictures from 7 dpi to 9 dpi low-infected larvae, which is not reflected in the histogram. Also, a representative picture of 7 hi-infected larvae seems to show at least equal or even more red fluorescence compared to 9 dpi low-infected larvae.

• Lines 494-496 states "No significant difference was observed between high-and low-infected fish, confirming that macrophages react to the presence and not to the number of trypanosomes.", reflecting that there is no differences in total macrophages nor in their proliferation between low- and high-infected zebrafish larvae (Figure 5B&C). Therefore it is not sufficiently clear on which basis the authors states a few lines later as a conclusion that "Altogether, these data confirm that T. carassii infection triggers macrophage proliferation and that proliferation is higher in low-infected compared to high-infected individuals, possibly due to a higher haematopoietic activity." Therefore the authors should revise this conclusion or bring stronger data to reinforce their results. Also, similar conclusions need to be adjusted in the discussion section and bring new elements to explain the higher number of macrophages observed in figure 4.

Reviewer #2:

This manuscript, "Lactobacilli in a clade ameliorate age-dependent decline of thermotaxis behavior in Caenorhabditis elegans," is focused on the impact of diet on age-dependent behavioral decline. The authors utilize a thermotaxis screen using different lactic acid bacteria (LAB) and identify strains of LAB with the ability to ameliorate age dependent decline in thermotaxis behavior. The study introduces some interesting results, including the finding that many LAB strains of the same clade can improve thermotaxis in older nematodes, despite disparate results on longevity. However, there were some questions remaining about methodology, and more importantly, there is very little evidence provided on what the molecular mechanism might be behind this phenomenon. Overall, this study contains interesting findings that are not developed thoroughly enough.

Major Comments/Questions:

1) How is LAB different from Ecoli? Does metabolic composition of LAB dictate its impact on thermotaxis behavior of worms? In the manuscript the authors argue that LAB are a "better" food source than E. coli. How does one define better for something as broad as a food source? There is a difference here but it is very unclear what aspects of LAB physiology may play a role.

2) Does this phenomenon require eating LAB, or just perceiving it? The assays did not test whether perception of LAB diet is sufficient for its effect on thermotaxis, rather whether more time on LAB leads to better thermotaxis.

3) Showing a potential daf-16 interaction is plausible, given that daf-16 interacts with many key pathways in the worm, but it is unclear whether this interaction is direct or indirect, or whether daf-16 is a major player in this pathway or just necessary for maintenance of health. What sensory pathways are activated when worms are fed on LAB diet, and how it finally interacts with daf-16?

4) Similarly, the pha-4 and eat-2 data are interesting, but are not developed in any way. This is another avenue that could in principle lead toward a better mechanistic understanding.

Reviewer #2:

Park et al. report on an analysis of existing semi-longitudinal NSPN 2400 data to learn how the projections of high-dimensional structural connectivity patterns onto a three dimensional subspace change with age during adolescence. They employ a non-linear manifold learning algorithm (diffusion embedding), thereby linking the maturation of global structural connectivity patterns to an emerging approach in understanding brain organization through spatial gradient representations. As might be expected based on the large body of literature indicating changes in structural connectivity in specific brain regions during adolescence, the authors find corresponding changes in the embedding of the structural connectivity patterns.

While this work touches on an important topic, ties nicely with the increasing body of papers on global brain gradients, and its overall conclusions are warranted, I am not (yet) convinced that it offers fundamentally new insights that could not have been gleaned from previous work (after all, manifold learning simply displays a shadow of the underlying patterns; if the patterns change, so does their shadow). I am also not convinced by the rationale for employing diffusion embedding: the authors state that the ensuing gradients are heritable, conserved across species, capture functional activation patterns during task states, and provide a coordinate system to interrogate brain structure and function, but that would be true for any method that adequately captures biologically meaningful variance in the structural connectivity patterns.

Other comments:

The authors show that the maturational change of the manifold features predict intelligence at follow-up, but did not show that intelligence itself exhibited changes that exceeded the error bounds of the regression line. Why not predict IQ change?

The slight improvements in prediction accuracy observed after adding maturational change and subcortical features to the features at baseline will necessarily happen by adding more regression parameters and may not be meaningful.

Reviewer #2:

The present study investigates how CSF-contacting neurons (CSFcNs) of the mouse spinal cord integrate and translate different synaptic inputs using distinct calcium-dependent spike mechanisms. Indeed two different types of voltage-gated calcium channels can be activated, resulting in the generation of spikes with different amplitudes. T-type Ca2+ channels would be involved in the generation of low amplitude spikes while HVA-Ca2+ channels participate in the generation of large amplitude spikes. Then these distinct spikes allow signaling different neurotransmitter systems. Consequently, the data provided here argue in favor of CSF-contacting neurons acting as a sensory system that uses Ca2+ channels-dependent spike activity with graded amplitude corresponding to the activation of different neurotransmitter receptors. This study is based on two-photon calcium imaging performed on spinal cord slices preparations obtained from young and adult mice. My comments are as follows:

1) All data are based on calcium imaging. Therefore, traces correspond to calcium-dependent fluorescent changes in the cells of interest. Can the author provide at least one sample showing that these calcium events are indeed linked to the generation of spikes; i.e., electrophysiological recordings? In addition, is there any electrophysiological evidence for the existence of calcium-dependent conductances in the CSFcNs? In the same vein, the authors conclude that spontaneous activity of CSFcNs depends upon calcium- but not sodium-spikes as TTX has apparently no effect. But, are the authors sure that in their experimental conditions individual sodium spikes could be detected given the genetic encoded probe used, the kinetic of such spikes and the frequency of the sampling during image acquisition? Note that this does not preclude the conclusion that CSFcNs express calcium-dependent spikes. See also comment 4 below.

2) Using the activation of different calcium channels to trigger spikes of different amplitude to code distinct signaling pathways associated with distinct neurotransmitter systems is a very attractive mechanism. I was wondering whether the authors ever observed the two processes in one single cell, meaning: did they ever try to apply Ach and ATP on the same cell? To my point of view, this would be an extremely elegant way to show that spikes of variable amplitudes imply the activation of distinct calcium-dependent conductances and are linked to different neurotransmitter signaling in one neuron. This should be possible as they said that 100% of the examined cells responded to Ach, suggesting that the only limitation would be to find a cell that also expresses purinergic receptors (should be highly feasible). In addition, this would strongly demonstrate how much this coding mechanism is valuable if this is present in a single cell, otherwise one could consider that the coding system just depends upon each cell, the neurotransmitter and its associated receptor signaling that by definition can involve distinct calcium-dependent channels. Then it would rather be a mechanism specific to each receptor than a sophisticated coding system.

3) As a general comment on figures, I would suggest to the authors to provide samples that are more illustrative of the results they claim on. For example on Figure 3 they state that TTX has no effect on spike amplitude and frequency, but the two traces shown (in blue and green) rather indicate a decrease in spike frequency and even an increase in spike amplitude after a few minutes of recording (green trace). [See also comment 4 below]. Another example is in Figure 6 in which one important data is the distinct amplitude of spikes triggered by either Ach or ATP. While this is properly illustrated in panels C, D and E, in contrast the samples chosen for panels A and B show events with the exact same amplitude. Please choose other traces. By the way, panel C is not necessary because the same info are included in panels D and E. I would suggest removing panel C. Finally, in Figure 7 it is stated in the text that in some cells ATP induced first a decrease in fluorescence followed by a large Ca2+ spike, while this specific spike looks much smaller than all the other ones illustrated in the study (Fig 7G). Also, the spike triggered by UTP looks different than the one triggered by ATP. Is it a typical response?

4) Several experimental details must be provided. First, the justification for the choice of VGAT promoter to drive the GCaMP6f indicator into PKD2L1 neurons is missing. Second, drug concentrations are not justified. This is important as the authors argue that Ach and ATP trigger Ca2+ spikes with different amplitudes, but isn't there the possibility that this is dose-dependent? Did the authors try different concentrations? Third, on TTX experiments (Fig 3), after how long under TTX exposure were measurements performed? While this is a crucial parameter, this is not indicated in the paper. Given the traces provided different conclusions could be reached depending on this timing.

5) It remains unclear to me why only some of the data (for example Fig 7) make a distinction between dorsal and ventral CSF-contacting neurons. In the zebrafish it is established that ventral and dorsal CSFC neurons have different developmental origins and distinct types of projections related to different functions. Then, if these neurons are suspected to play different roles depending on their ventro-dorsal position also in mice, the entire study should take this into account.

Reviewer #2:

The manuscript "A naturalistic environment to study natural social behaviors and cognitive tasks in freely moving monkeys" describes a large-scale system of rooms allowing for non-human primates to, potentially, freely engage in several different behaviors and neuroscientific experiments to be performed. The study is well intended, but in its current form with many claims, but few if any results does not, in my view, meet scientific standards.

The paper presents the testing environment consisting of different rooms. Compared to earlier work (e.g. Berger et al., 2018), the main innovation is the inclusion of an eye tracking system. Data supports the notion that this works in principle. But there is no analysis of data quality and accuracy. We also do not know whether the system works on every trial, or how often the eye is not detected or the tracker loses the signal.

The authors claim novelty of this testing environment, but similar ones have been used in behavioral research for decades and in recent years in neuroscience.

The authors claim that it is easier to place a testing system into a separate cage then in the home cage. It remains unclear what this claim is based on. Motivation of animals in these social settings should be more difficult than in the home cage environment. So, this is a potentially interesting result. It is also a conceptually important claim for the paper's logic, if the social setting should really be beneficial for training. But the claim needs to be substantiated.

The authors claim that natural behavior can be analyzed because a CCTV camera is mounted in the cage. There are no results or analyses to demonstrate that.

The authors mention neural recordings on multiple occasions, but do not show any. EM shielding is neither necessary nor new.

Automatic training appears to be a one-to-one copy of that in Berger et al. 2018, but citation is missing, except for Supplemental Information.

The authors report an anecdote of one animal (n=1) learning socially from others. There is no indication that this subject might have performed differently without social learning. The interpretation is a just-so story and appears rather anthropomorphic.

There are no results in the manuscript.

The manuscript is not organized well. The Methods section reads like a Discussion, important information on methods is distributed across Supplemental Information and Results. Results, as mentioned, does not contain any results or data.

Reviewer #2:

In this manuscript, Knight et al examine the genetic diversity in >12,000 publicly available C. difficile genomes in order to characterize genomic evidence of taxonomic incoherence among this genomically diverse pathogen. Their primary analysis employs average nucleotide identity thresholds to identify species boundaries, with secondary analyses examining core genome size changes, gene content, and estimated emergence dates. The authors' main conclusion is that the previously identified C. difficile cryptic clades CI-III are genomically divergent enough from the main clades C1-5 to warrant classification as different genomospecies. This paper is a useful contribution in benchmarking our understanding of the genetic diversity of C. difficile using all currently publicly available genomes, but the results are largely unsurprising given previous phylogenetic analyses involving clades 1-5 and CI-III, and is therefore probably best suited for a specialty journal. Additionally, in some instances, the methods lack details, reducing their interpretability and reproducibility.

Major Comments:

1) There are some claims that are too strong and not supported by the data or literature, including the claim that the rise of community-associated CDI is likely due to presence of C. difficile in livestock (Lines 53-54 - far too little evidence to make such a sweeping claim), the statement of apparent rapid population expansion into clades C1-4 (Lines 278-279 - only shown for certain sequence types and greatly impacted by observation bias), the statement that these findings "impacts the diagnosis of CDI worldwide" (Lines 37-38 -too grandiose given limited evidence of the clinical importance of the cryptic clades).

2) Generally, it is hard to discern which sets of genomes and variants were used for each of the bioinformatic analyses that are described. If there are a limited number of genome sets it might be useful to define them in the results to allow the reader to more easily follow along and understand the scope of different analyses.

3) The dated phylogenomic analyses methods would benefit from a more thorough assessment of model assumptions along with more description of the sources of bias and uncertainty at play. Specific questions are:

• Was the temporal signal in the data evaluated?

• What are the potential impacts of using a single clock model and demographic prior for such a diverse set of taxa?

• Was the clock rate restricted to the cited 2.5x10-9 - 1.5 x 10-8 range? What clock prior distribution was applied?

• Were relaxed clock priors explored?

• What went into the selection of the demographic model prior in BEAST? Were alternative models evaluated?

• The significant uncertainty in the divergence estimates should be emphasized/listed as a limitation.

4) Similarly, the pangenome analyses could be more thoroughly described, and the relevance of the core-genome size changes more robustly explored. Specifically:

• How did the core genome change when excluding any of C1-5? Were these changes much different than when excluding CI-III?

• The differences between Roary and Panaroo are notable, and potentially important for the microbial genomics community. More details should be provided on these results and how sensitive they are to the input parameters of the respective programs (e.g. collapsing paralogs in Roary and percent identity for orthologs). In addition, it is important to know if any filtering was done with respect to the quality of assemblies, which could have a significant impact on Roary's behavior.

Reviewer #2:

Recombinant antibodies are the most common and powerful reagents in life science research to identify and study proteins. Yet, every single antibody should always be validated and carefully tested for its relevant application, to ensure constructive and reproductive scientific endeavor. I was thus extremely pleased to review the manuscript of Terkild Buus et al, as it provides a careful assessment of oligo-conjugated antibody signal in CITE-seq. The authors tested four variables (antibody concentration, staining volume, cell numbers and tissue origin) and clearly showed that antibody titration is a crucial step to optimize CITE-seq panel. The authors found that, as a general rule, concentration in the 0.625 and 2.5 µg/mL range provides the best results while recommended concentrations by vendors, 5 to 10 µg/mL range, increase background signal.

In my opinion, the study is well-performed and may serve as a guideline to accurately validate antibodies for CITE-seq, as a consequence I have only minor comments.

• As stated by the authors, the starting concentration used for each antibody was based on historical experience and assumptions about the abundance of the epitopes. This approach may not be ideal, and the optimal concentration may have been missed. Do the authors think that a proper titration would be an advantage? Maybe this could be discussed in the text.

• The authors showed by testing four variables (see above) that they could define the optimal conditions to reduce background signal and increase sensitivity of antibodies and thus this way improves CITE-seq outcome. Nevertheless, the authors rely on the fact that all antibodies used in their panel are specific for their targeted antigens. I am not asking here to test the specificity of every single antibody used in the study as this would be a colossal amount of work. But I feel that this aspect should be discussed in the manuscript, especially when an "uncommon" antibody is intended to be used in the CITE-seq panel; the specificity of this antibody should be indeed tested prior to its use.

Reviewer #2:

In this paper, Numssen and co-workers focus on the functional differences between hemispheres to investigate the "domain-role" of IPL in different types of mental processes. They employ multivariate pattern-learning algorithms to assess the specific involvement of two IPL subregions in three tasks: an attentional task (Attention), a semantic task (Semantics) and a social task (Social cognition). The authors describe how, when involved in different tasks, each right and left IPL subregion recruits a different pattern of connected areas.

The employed tasks are "well established", and the results confirm previous findings. However, the novelty of the paper lies in the fact that the authors use these results as a tool to observe IPL activity when involved in different domains of cognition.

The methodology is sound, well explained in the method section, the analyses are appropriate, and the results clear and well explained in the text and in graphic format.

However, a solid experimental design is required to provide strong results. To the reviewer's view, the employed design can provide interesting results about functional connectivity, but not about the functional role of IPL in the investigated functions.

I think the study would be correct and much more interesting if only based on functional connectivity data. Note that rewriting the paper accordingly would lead to a thorough discussion about how anatomical circuits are differently recruited based on different cognitive demands and about the variable role of cortical regions in functional tasks. This issue is neglected in the present discussion, and this concept is in disagreement with the main results, suggesting (probably beyond the intention of the authors) that different parts of the right and left IPL are the areas responsible for the studied functions.

Major points:

1) The 3 chosen tasks explore functions that are widespread in the brain, and are not specifically aimed at investigating IPL. The results (see. e.g. fig 1) confirm this idea, but the authors specifically focus on IPL. This seems a rather arbitrary and not justified choice. If they want to explore the lateralization issue, they should consider the whole set of involved areas or use tasks showing all their maximal activation in IPL.

2) The authors aims to study lateralization using an attentional task, considering the violation of a prevision (invalid>valid), a linguistic task, looking for an activation related to word identification (word>pseudoword) and a social task, considering correct perspective taking (false belief>true belief), but they do not consider that in all cases a movement (key press) is required. It is well known that IPL is a key area also for creating motor commands and guiding movements. Accordingly, the lateralization bias observed could be due more to the unbalance between effectors while issuing the motor command, than to a different involvement of IPL regions in the specific tasks functions.

3) Like point 2, the position of keys is also crucial if the authors want to explore lateralization. This is especially important if one considers that IPL plays a major role in spatial attention (e.g. Neglect syndrome). In the Methods, the authors simply say "Button assignments were randomized across subjects and kept identical across sessions", this should be explained in more detail.

4) The authors show to know well the anatomical complexity of IPL, however their results are referred to two large-multiareal-regions. This seems to the reader at odds with all the descriptions related to fig.2. If they don't find any more subtle distinction within these 2 macro-regions, they should at least discuss this discrepancy.

5) The part about Task-specific network connectivity is indeed very interesting, I would suggest to the authors to focus exclusively on this part. (Note that the results of this part seems to confirm that only the linguistic task is able to show a clear lateralization).

Reviewer #2:

The main analyses of the study compare previously published experimental observations from Hi-C and ORCA to predictions of the author's "futile cycle" model. The predictions are derived from simulations and differential equations analysis of the model as a dynamical system. Given its centrality to the manuscript, we recommend describing this overall strategy in more detail in Results. For example, at line 124 (Pg. 4) the authors could talk about how the simulations are done, including where the variability comes from (e.g., random starting conditions vs. probabilistic events vs. different parameters).

Xiao et al. make several key assumptions to dramatically simplify their model. Namely, it is assumed that promoter modification and transcription are equivalent and that enhancer-promoter contact influences transcription instead of transcription influencing structure. Steady-state equilibrium must also be assumed. It would be helpful if the authors explicitly stated these assumptions and provided references to support their being reasonable.

It is not totally clear why the authors decide to call their proposed approach the futile cycle model. There are similarities to other well-known models in biochemistry and biophysics that should be noted. It might make sense to simply call this a mechanistic model of cooperative promoter activation. If the authors stick with "futile cycle", the relationship between promoter activation through tags and metabolic signaling should be described in more detail.

There is also an opportunity to emphasize that the proposed model is not necessarily absolutely correct, but one of many plausible models that can produce a non-linear relationship between genome structure (enhancer-promoter contact) and transcription. Any thoughts on other models that could generate similar dynamics would be a useful discussion point. There are parallels to both sigmoidal dose-response curves, where drug concentration is plotted against response, and transcription factor binding curves, where free ligand concentration is plotted against the fraction bound. We recommend providing background context on these types of models or the Hill equation to illustrate why non-linear behavior is or is not surprising given the proposed model.

For clarity, it would be helpful to discuss model parameters in greater detail. First, we suggest noting which parameters shift the location of the curve and which increase the steepness of the curve. Second, we recommend including a phase diagram exploring when sigmoidal behavior and any other key model predictions arise across parameter space. In what circumstances does hypersensitivity or time lag emerge? The authors demonstrate that a narrow set of parameters is sufficient to produce a super-linear relationship between enhancer-promoter contact and transcription in Figure 6. One potential dilemma is this model's ability to explain many experimental observations by indicating that minimal changes all occur in the sub-linear regime while observable changes occur in the super-linear regime. Given that one needs specific parameters to replicate an example of the hyper-linear regime (including at least three degrees of stimulation and increasing stimulation of the successive states), it could be valuable to demonstrate how large the plausible parameter space is. Without an exhaustive search across the space of minimal parameters, it is not clear when this property emerges or how common it is within the full parameter space. The authors could vary model parameters and plot a grid visualizing behavior (e.g., steepness of the curve or Hill coefficient).

Images throughout the manuscript are low resolution, making the figures difficult to read. Increase the resolution of figures throughout, especially those containing text (Fig 6A).

Reviewer #2:

This manuscript by Diamanti et al. describes their study on how visual neurons responded to identical visual stimuli at two different locations along a virtual linear track. Extending their previous result that spatial location modulates the neuronal activities in the primary visual cortex (V1), they now demonstrate that similar spatial modulation also occurred in the higher visual areas (HVAs), but not so much in a lower visual area, the lateral geniculate nucleus (LGN). In addition, they show that the modulation, measured by a spatial modulation index (SMI), was stronger when animals had more experience in the track and when the animals were actively performing a task rather than passively viewing the same virtual track. The authors have been responsive to comments by previous reviewers at a different journal. Data are appropriately analyzed and clearly presented.

Since the finding that visual neurons are spatially modulated similarly as hippocampal place cells in spatial navigation tasks (Ji and Wilson, 2007; Haggerty and Ji, 2015; Fiser at al, 2016; Saleem at al, 2018), there has been increasing interest in identifying the source(s) of this modulation. This study adds new evidence to this puzzle, suggesting that it is more likely either generated within the visual cortex or top-down propagated from higher brain areas, rather than bottom-up propagated from the thalamus. This is an important contribution. However, there are concerns, mainly on the data interpretation and the clarification of the main conclusion, as elaborated below.

1) Because experience and task engagement enhanced spatial modulation, the authors concluded in the abstract that "Active navigation in a familiar environment, therefore, determines spatial modulation...". This conclusion is too strong and not well-supported by the data. First, spatial modulation on Day 1, when the task was novel, was lower than on later days, but it was already much higher than 0 (Fig. 1h). Also the individual neuron data (Fig. 1e) display clear spatial modulation on Day 1. Therefore, "familiar environment" is not a requirement. Second, spatial modulation during passive viewing was much higher than 0 and was correlated with that during active navigation, as shown in Fig. 4e - Fig. 4l. Therefore, "active navigation" is not a requirement either. It is true that both active navigation and familiar environment enhanced spatial modulation. They did not "determine" spatial modulation.

2) Related to the point above, the presence of spatial modulation in passive viewing reminds us that these cells in the visual system were still mainly driven by visual stimuli. The data in Fig. 4e,f are especially telling: the modulation in V1 was similar and highly correlated between active navigation and running replay. In addition, it is clear from all the raw traces in Fig. 1 and Fig. 2 that these cells did respond to the two segments with identical stimuli reliably with two peaks. The spatial modulation was just a change in one of the peaks. So the nature of the modulation is a "rate remapping" of the expected, classical visual responses. I believe, in order to maintain the big picture of what drives the activities of these neurons, it is beneficial to clarify that the "spatial modulation" is a modulation on top of the expected visual responses. This message is not explicitly conveyed in the current manuscript.

3) The authors stated that spatial modulation is "largely absent in the main thalamic pathway into V1". This was based on the significantly weaker SMIs in LGN than those in V1 and HVAs. However, it is unclear whether the SMIs in LGN were still significant. The SMI values for both LGN buttons (Line #100) and LGN units (Line# 130) might be statistically significant from zero. The statistical comparison p-values should be given in both cases. Second, Figure 3 - figure supplement 1 b,f show that the SMI values in LGN could be predicted by spatial modulation, but not by visual stimuli alone or behavioral variations, just like those in V1 and HVAs. This seems to me good evidence for the presence of spatial modulation in LGN. Therefore, it is my opinion that the data do not support the complete lack of spatial modulation in LGN, but do clearly demonstrate weaker spatial modulation in LGN than in V1 and HVAs.

Reviewer #2:

In this manuscript, the authors set out to measure participant's decisions about when an item occurred in a short list of 3 or 4 items, where the first and last items were always at the beginning and end, respectively. They report two behavioral studies that examine time judgments to items in the intermediate positions. They show that time judgments (when did you see X item using a continuous line scale) are always a little off but, more importantly, they tend to be anchored to other items presented. The results are interesting and add to our knowledge of the representation of time in the brain mainly by introducing a new paradigm with which to study time. Within the broader context of research on timing capacities, it should not be surprising that participants do not have a continuous representation of time that lasts beyond traditional time interval training of a few hundred milliseconds to a few seconds. Furthermore, research has also shown that 'events' that require attentional resources do morph our perception and memory for time. So while the paradigm is worth expanding on, the behavioral results are not surprising given this past literature. I do feel however that this work is an important first step in developing a more firm model of memory for time.

Reviewer #2:

Borghesani and colleagues aimed to understand how dysfunction in the ATL alters the dynamic activity during semantic categorization. To achieve this, they contrast MEG responses between patients with svPPA and age-matched healthy controls. Both groups show similar profiles of behavioural performance on the task, and broad similarities in MEG responses. Critically, svPPA patients show enhanced gamma synchronization in the occipital lobe compared to controls, while gamma synchronization was correlated to task RTs.

In general, I found the manuscript interesting, and the major strength being the application of MEG analyses to a clinical population during a cognitive task. In terms of improvements, I think the results could be more fully characterized, which would allow for more expansive interpretations and inferences.

Major comments:

1) As the paper is about 'Neural dynamics', I felt this aspect could be developed, with the timing of the effects characterized further, and considered more in relation to the conclusions. For example, the main finding is the increased occipital gamma response in svPPA compared to controls. Looking at Figure 3, there is a peak in the svPPA group near 200 ms, and very little synchronized activity in the control group. This is interesting as there are many ways we could have seen svPPA > controls, but this suggests that the gamma synchronization response associated with compensation is specific to the svPPA group (and largely absent from controls - also from Supp fig 1), and is distinguished from an initial visual evoked response (peaking ~100 ms). I would recommend discussing and characterizing the dynamics of this effect more, such as what a later occipital effect could tell us about dynamics given ATL dysfunction? Is this increase a result of a lack of top-down effects from ATL? I think these kinds of issues could be explored and discussed more.

2) The occipital gamma effect looks like the primary visual cortex, which might suggest the effects are not related to higher-level perceptual features (such as has eyes, teeth) as the authors suggest, but rather low-level visual effects. Do the authors perhaps think the effects could relate to enhanced processing of visual details (as related to the ideas of Hochstein and Asher's reverse hierarchy), or whether the effects relate to additional visual input following a visual saccade?

3) The VBM results for the svPPA patients were surprising given that all the atrophy appeared in the left hemisphere. There can be hemispheric differences in svPPA, but is this a true lateral pattern (meaning the right ATL is intact) or a product of VBM being run so that the most atrophied hemisphere is shifted to the left side? If the VBM maps are correct, and the svPPA patients are only showing left hemisphere atrophy, then what does this suggest about the role of the right ATL, and the bilateral nature of occipital increased in svPPA?

4) Both svPPA patients and healthy controls achieved around 80% accuracy in the categorization task. This seems surprisingly low given, (1) the task (living vs. nonliving after seeing the image for 2 seconds), (2) that all the images were pretested and had high name agreement, and (3) that items were repeated on average 2.5 times. Is there something that explains this low performance for all individuals?

Reviewer #2:

Overall I think the authors collected an interesting dataset. Analyses should be adjusted to include all cells rather than sub-selecting for stability. Additionally, the language needs to be adjusted to better reflect the data. I wish there was any behavioral data included, but if the authors compare their data to publicly available data in V1 for a single recording session during a visually guided task, these concerns could be quelled a bit.

1) In general the language of this paper and title seem to mismatch the results. The fraction of cells that were 'stable' as the authors say on line 112 was very small, however the authors focus extensively on this small subset for the majority of analyses in the paper. Why ignore the bulk of data (line 119)? What happens if you repeat the same analysis and keep all cells in the dataset? The general language around stability of neural ensembles should be adjusted to better reflect the data (ex: lines 157, 225).

2) There are claims in this paper about how ensembles 'implement long-term memories' in the introduction and conclusion and yet the authors never link the activity of ensembles to any behavioral or stimulus dependent feature. This language reaches far beyond the evidence provided in this paper. The introduction could provide some better framing for expectations of stability vs. drift in neural activity rather than focus on the link between ensembles and memory given that there isn't much focus on the ensembles' contribution to memory throughout. For example, the last sentence of the paper is not supported by data in the paper. Where is the link between ensembles and memory in the data? What is the evidence that transient ensembles are related to new or degraded memories? This reads as though it was the authors' hypothesis before doing the experiments and was not adjusted in light of the results.

3) There is no discussion around the alternative to stability of neuronal ensembles. What are the current theories about representational drift? For example, in Line 34 the authors present an expectation for stability without any reasoning for why there need not be stability. This lack of framing makes their job of explaining results in line 217 more difficult. There is a possibility that the most stable cells aren't more important - what is the evidence that they are? Does an ensemble need a core? Would be interesting to include some discussion on the possibility of a drifting readout (Line 223). [https://doi.org/10.1016/j.conb.2019.08.005]

4) How do activations in V1 in this dataset compare to other data collected from V1 while the animal is performing a task (where for example the angle of the gradings is relevant to how the mouse should respond)? I would be interested to know if the authors compared statistics of their ensembles to publicly available data recorded in V1 during a visually guided behavior. Are the ensembles tuned to anything in particular? Could they be related to movement? [http://repository.cshl.edu/id/eprint/38599/]

5) The authors provide some hypotheses as to why fewer cells are active in the later imaging sessions (dead/dying cells?). This is worrisome in regards to how much it might have affected the imaged area's biology. One alternative hypothesis is that the animal is more familiar with the environment/ not running as much etc. Have the authors collected any behavioral data to compare over time?

6) How much do the results change when you vary the 50% threshold of preserved neurons within an ensemble (Line 146)? Does it make sense to call an ensemble stable when 50% of the cells change? Especially given that the cells analyzed as contributing to an ensemble are already sub-selected to be within the small population of stable cells (Line 119)?

7) Cells are referred to as 'stable' when they're active on 3 different sessions that are separated in time. However, the authors find a smaller number of cells are stable over extended time (43-46 days later). If we extrapolate this over more time, would we expect these cells to continue to be stable? Given these concerns, it might make more sense to qualify the language around stability by the timespan over which these cells were studied.

8) Filtering frames to only coactive neurons for ensemble identification seems strange to me. Authors may be overestimating the extent of coactivation. What happens when you don't do this? How much do the results change when you don't subselect for Jaccard similarity? I would be interested to see how the results vary as you vary this threshold (Line 136).

9) The term 'evoked activity' is misleading because the authors don't link these activations to the visual stimulus. There's no task, so the mice could be paying little attention to the stimulus. Should we really consider this activity to be visually driven? Could the authors provide any evidence of this?

10) A method like seqNMF could reveal ensembles that are offset in time. This looser temporal constraint could potentially reveal more structure. This should be run on the entire dataset (without stability sub-selection). I suggest this as a potential alternative or supplement to the method described by the authors. [https://elifesciences.org/articles/38471]

Reviewer #2:

In this manuscript, Barondeau and co-workers test a hypothesis for the role of the protein frataxin in iron-sulfur cluster assembly, seeking, inter alia, to explain the observation that mutations in the gene encoding this protein are associated with the incurable neurodegenerative disease, Friederich's ataxia. Their notion is that, whereas the bacterial versions of the sulfur-providing cysteine desulfurase are stable homodimers - in which the interactions between the monomers help to organize the mobile loop harboring the key cysteine residue that serves as general acid and nucleophile in the C-S-cleavage reaction that mobilizes the sulfur for incorporation into the cluster - the human enzyme (i) has a dimer interface that has been weakened through evolution, (ii) can be monomeric or form non-optimal dimeric forms, and (iii) can be driven to adopt the optimally active dimer form by intervention of accessory proteins (e.g., frataxin). Their approach was to perturb a bacterial (E. coli) cysteine desulfurase (IscS) by structure-guided mutagenesis in an attempt to introduce into it the behavior of the human enzyme, specifically its activation by accessory proteins (here CyaA and FXN). The experiments were successful in this goal. I like this paper and believe that it is interesting and important. I would point out two aspects that perhaps leave room for improvement.

1) In principle, it would have been a more powerful test of their hypothesis had they been able to perturb the human enzyme to get a constitutively active form, no longer dependent on the binding of the accessory proteins, either instead of, or in addition to, the converse perturbation of the bacterial system. Perhaps this approach was precluded by difficulties associated with the human enzyme?

2) The second criticism is that the effects on quinonoid form decay and activity are rather modest. However, I believe that important biological effects can arise from even such modest regulation of enzyme activity levels.

Reviewer #2:

This manuscript by Dingens et al. develops a novel application of mutational antigenic scanning to identify dominant neutralizing antibody epitopes in polyclonal sera from vaccinated animals, and compares the findings of such techniques with those from cryo-EM based unbiased mapping of binding antibodies and from conventional mutational mapping of neutralizing epitopes. Overall, I find the experiments and analyses to be of high quality, thorough and of sound reasoning, and the manuscript to be well written. I also commend the authors for the development of a facile and easy-to-use interactive viewer for exploring the mutational scanning data. I think the dual approach of mutational scanning and cryo-EM based mapping has the potential to be a powerful approach for dissecting antibody content of polyclonal sera post-vaccination or in infected hosts.

The only major concern I could identify is the following. One of the main advantages of the mutational scanning approach is that it can identify novel epitopes targeted by antibody responses in a high-throughput manner. It is a little disappointing that this advantage was not leveraged in the current manuscript, perhaps due to the choice of the vaccine (BG505 SOSIP trimers where the epitopes have been thoroughly mapped in the literature) and the selection of vaccinated animals. Looking at Fig. 2, animal 5727 was the only animal whose serum showed some selection signatures outside of the regions considered in depth (at sites 507 and 509) - have the authors analyzed these escape mutations? If not, and only if possible within reasonable workload, I urge the authors to pursue this example or any other example where a potential novel epitope discovery could be possible.

Reviewer #2:

The Hydra, in the phylum cnidaria, is a near microscopic freshwater animal that has recently resurfaced as an attractive model organism in neuroscience due to its optically accessible transparent body, sparsely distributed neural network, and simple behaviors. In this manuscript, Badhiwala and colleagues use calcium imaging of the Hydra neural network, combined with surgical resection and microfluidics pressure stimulation to identify body regions indispensable for mechanosensory activity. They report that while resection of the aboral region did not abolish the mechanical response, resection of the oral region attenuated this response, while combined resection of oral and aboral regions showed the greatest effect. They also find a correlation between reduced stimulated activity and spontaneous activity, suggesting a common mechanism that gives rise to both activities. While this study takes on an innovative approach by using a microfluidics device to mechanically stimulate the hydra under optical recording there are a number of conceptual and technical limitations. Perhaps my biggest reservation is that despite real potential, the data are rather low resolution (body transections and bulk calcium responses) and as such the conclusions that can be reasonably drawn do not extend what is known in a significant way.

Major comments:

1) The authors have designed a microfluidic device that allows them to simultaneously mechanically stimulate, monitor movement and functionally image a hydra. The highly quantifiable nature of the microfluidic device is a great asset, although this potential is not deeply explored. While I can see how the microfluidic stimulation could offer benefits over fluid jet or blunt probe, more in-depth characterization is needed.

2) What is the spatial distribution of the pressure pulse stimulus on the Hydra body? How far does the mechanical force spread from the region directly touching the pressure valve?

3) The use of the microfluidic device was limited. Have the authors attempted to map mechanical sensitivity across the Hydra body by stimulating different sites?

4) The authors have not attempted to record calcium responses from single neurons, but rather spatially average a population response from a large region of interest. This should be specifically stated in the results section. More importantly, to provide insight into network function much smaller ROIs over multiple sites are needed instead of the bulk activity of the entire peduncle. This seems like a real lost opportunity as the lure of the optically clear and small hyda is that neural representation and coding can be tracked over large portions of the network at cellular resolution.

5) It is unclear where the recorded signals are coming from and if movement is creating artifacts. Have authors made any attempts to correct for movement? The supplemental movies show a stationary region of interest and moving animal, in some cases parts of animal moving in and out. Furthermore, is background subtracted and how? There is a large fluorescent signal coming from the entire body/ middle columnar part of the body and spontaneous firing that makes interpretation of the data difficult.

6) Contraction is a behavioral response of the animal; however, the authors use 'contraction' do describe calcium imaging responses throughout the figures and text. This should be avoided.

7) I am unsure if the title of the paper is accurate. I do not think this work has demonstrated "multiple nerve rings" are important for coordinating mechanosensory behavior.

8) Furthermore, the claim that the observed "linear relationship" between the spontaneous contraction probability and resection type is evidence for shared neural pathways is a stretch. These data are fairly coarse resolution and include only 3 animals in each group with highly variable responses (Figure 4C). Additionally, they do not provide evidence to distinguish the motor circuits they hypothesized these neural nets converge upon.

Reviewer #2:

The authors asked how the brain uses different sensory signals to estimate self-motion for path integration in the presence of different movement dynamics. They used a new paradigm to show that path integration based on vision was mostly accurate, but vestibular signals alone led to systematic errors particularly for velocity-based control.

While I really like the general idea and approach, the conclusions of this study hinge on a number of assumptions for which it would be helpful if the authors could provide better justifications. I also have some clarification questions for certain parts of the manuscript.

1) Lines 26-7: "performance in all conditions was highly sensitive to the underlying control dynamics". This is hard to really appreciate from the residual error regressions in Fig 3 and seems to be contradicting Fig 5A (for vestibular condition). A more explicit demonstration of how tau affects performance would be helpful.

2) One of the main potential caveats I see in the study design is the fact that trial types (vest, visual, combined) were randomly interleaved. In the combined condition, this could potentially result in a form of calibration of the vestibular signal and/or a better estimate of tau that then is used for a subsequent vestibular-only trial. As such, you'd expect a history effect based on trial type more so (or in addition to) simple sequence effects. This is particularly true since you have a random walk design for across-trial changes of tau. In other words, my question is whether in the vestibular condition participants simply use their previous estimate of tau, since that would be on average close enough to the real tau?

3) I thought the experimental design was very clever, but I was missing some crucial information regarding the design choices and their consequences. First, has there been a psychophysical validation of GIA vs pure inertial acceleration? Second, were GIAs always well above the vestibular motion detection threshold? In other words could the worse performance in the vestibular condition be simply related to signal detection limitations? Third, how often did the motion platform enter the platform motion range limit regime (non-linear portion of sigmoid)?

4) Lines 331-345: it's unclear to me why you did not propose a more normative framework as outlined here. Especially, a model that would "constrain the hypothesized brain computation and their neurophysiological correlates" would be highly desirable and really strengthen the future impact of this study.

5) I would highly recommend all data to be made available online in the same way as the analysis code has been made available.

Reviewer #2:

The article by Gould et al breaks new ground by demonstrating a role for lysosomal-mediated degradation in the mechanosensitive repression of Sclerostin levels in bone. Though the post-translational repression of Sclerostin has long been apparent, no one has yet unraveled the mechanisms. Therefore, this discovery is important to the skeletal biology community - both because of the findings themselves, and because the conditions/models used by this team to make these discoveries will be useful for other investigators, including their ability to manipulate and observe the rapid lysosome-dependent control of Sclerostin levels in vitro and in vivo in response to PTH or mechanical stimulation. In addition to the importance within this field, the work has broad impact on multiple levels including a) the clinical relevance for understanding and potentially treating osteoporosis and the skeletal phenotypes in individuals with lysosomal disease, and b) the mechanoregulation of lysosomal function and its relationships to crinophagy, which has implications not only for the regulation of Sclerostin, but also for other factors in and beyond the skeleton (RANKL, insulin).

The study is elegantly designed, clearly communicated, and rigorously conducted. The conclusions drawn in the manuscript are mostly supported by the data provided. In general, it is important to elaborate on what gives the authors confidence that the inhibitors were effective and act as expected throughout the study - but especially Bafilomycin A1 and Apocynin in vivo. If BafA1 and Apocynin treatment in vivo work as expected, they should prevent the rapid load-dependent repression of Sclerostin levels (shown in Figure 1D).

Other revisions or additions, described below, would improve the quality of the study:

1) Are Sclerostin levels insensitive to FSS or PTH in Gaucher cells (though it understandably may not be feasible to differentiate these cells in microfluidic devices)?

2) Since a sex-specific effect of exercise on bone anabolism has previously been described, and TRPV4 also has a sexually dimorphic effect on bone, were any differences observed between male and female animals here?

3) Can the authors discuss where the pathway used by PTH diverges from that activated by FSS/load?

4) Is it possible to detect load dependent changes in sclerostin localization in lysosomes in vivo?

5) Given the non-specific effects of hydrogen peroxide, Figure 6D may not add a great deal in light of the other data that was gathered with more rigorous approaches. Additional controls would give more confidence in the efficacy/specificity of this approach.

6) Please include how long the OCY454 cells were differentiated prior to the treatments applied.

7) Please identify the route by which inhibitory agents were administered to the mice (i.e. subcutaneous, intraperitoneal).

8) Please increase the N for experiments in Figure 4A and 5D, or remove these data and the corresponding conclusions.

Reviewer #2:

Summary:

This paper predicts intelligence using either coarse-grained functional connectivity (based on 360 ROIs) or fine-grained functional connectivity (vertex-wise) after hyperalignment. The results show a two-fold increase of variance explained in general intelligence between coarse-grained and fine-grained connectivity.

General:

This is a very clearly-written paper that presents an important result, which has the potential of great impact on the field of behavioral prediction. My comments below are relatively minor and primarily aimed at clarifying a few details in the article. Please find my detailed comments below, approximately in order of importance.

Major comments:

1) The fine-grained functional connectivity has richer features than coarse-grained, leading to higher dimensionality in the PCA step (supplementary figure S5). I wonder if this might contribute to improved prediction accuracy. Related to this, it appears that there may also be a relationship between PCA dimensionality and regularization parameter, such that more regularization may be needed when more PCs are used in the model. It would be interesting to test the effect of fixing the PCA dimensionality (and perhaps also the regularization) across all models to control model complexity.

2) The Glasser 360 parcellation was used throughout this work. There are subject-specific parcels and group-level parcels available for this parcellation. Please clarify which of these were used. If the group-level parcels were used, it might be interesting to see how the coarse-grained prediction accuracies might improve when using subject-specific parcels.

3) The residuals of fine-grained connectivity profiles were obtained after subtracting coarse-grain connectivity. Why was subtraction used here, rather than regressing out (i.e., orthogonalizing with respect to) the coarse-grained connectivity?

Reviewer #2:

This manuscript from Allio is an interesting mix of approach demonstration (population genomic sampling via roadkill) and application (demographic analyses, questions about taxonomic status, and phylogenomics). There are some valuable results from the application component of the paper. In particular, I appreciate the comparative approach for studying patterns of intra- vs. inter-species genetic diversity. However, there is some rework to fully normalize those comparisons, that I feel is required.

I would suggest the authors be more immediately forthcoming about the sizes of their samples, and perhaps consider changes to the introductory text to avoid giving any mis-impressions to readers about what data are ultimately presented in the manuscript. I had envisioned more of a landscape genetics-level sample and analyses, rather than n=3 individuals per each of the two species. Furthermore, while I think the reporting of the genome assembly qualities is important from confirmatory and quality control perspectives, and while presenting the new assemblies, in my view this shouldn't be set up to be a surprising result. These are very high-quality DNA samples, so we expect to be able to achieve DNA assembly qualities to whatever the invested level using current best-practices data generation and analytical methods.

On the general genetic diversity and taxonomic questions, from my own experience I know that genetic differentiation metrics are not necessarily precisely comparable between a new study based on genome sequence data and an existing published dataset. Sample size affects false positive and false negative SNP calling error rates and sequence coverage and the variation among samples can also make a difference. Thus, especially since this leads to a key result/conclusion (i.e. that the two subspecies of aardwolf may deserve species status), it isn't sufficient that "similar individual sampling was available" for the carnivoran comparative datasets. The datasets should be equalized with sample number and individual sequence coverage (using downsampling) and then SNPs re-called using the same approach, before making the comparison. From the methods it wasn't clear to me the extent to which this all was done. It does appear that the same number of samples were used, and that the SNP calling approach was likely re-done from the read data (although please be more explicit about this, in the description). However, it doesn't appear that the sequence read data were subsampled for equivalency across the samples, which should be incorporated. Hopefully the results are similar, but there can be big changes that affect interpretation, so a careful approach is required.

The study design and proposed expanded use of roadkill samples in population genomics led me to think of this study, one of my all-time favorites: Brown & Bomberger Brown (2013), Where has all the road kill gone?, Current Biology. For the present study, the question of potential biases in the sample for similar or related reasons is beyond the scope of investigation; this is not relevant for the sample sizes collected and analyses conducted. However, the importance of keeping this possibility in mind should at least be noted given the more expansive promotion of the wider inclusion of roadkill samples in population genomic studies. E.g. could the sample be biased towards individuals with genetically-mediated and/or culturally learned behavioral tolerance of human-disturbed habitats, etc., rather than a truly random sample representative of the overall landscape.

In the methods section, the collection process and permits for the four samples from South Africa are described in detail. (Could you preemptively explain that the IUCN status for these two species is Least Concern, and thus that CITES permits are not required for the international transport of the samples?). However, the same information is not provided for the two East African samples that were included in the study (also, I think that there should not be two separate sampling sections in the manuscript). Please provide these details or expanded explanations.

Reviewer #2:

In their manuscript, Kim et al address the role of PIE-1 sumoylation during C. elegans oogenesis. The authors favour a model in which sumoylated PIE-1 acts as a sort of E3-like factor 'enhancing' HDA-1 sumoylation. While the results are indeed very interesting, it is unclear to me whether there is enough data to support the author's model. I have list of comments, suggestions, questions, and concerns, which are listed below, which I hope will help the authors strengthen the manuscript:

Figure 1)

I) As with the accompanying manuscript, the extremely low level of SUMO modification should be factored in the model.

II) Is sumoylation also observed in untagged pie-1? As judged by figure 3A, the authors have a very good antibody to test this.

III) While the authors claim that PIE-1 sumoylation is not observed in embryos, that panel shows a lower exposure than the corresponding one in Adult (as judged by the co-purified unmodified PIE-1::FLAG). A longer exposure and/or more loading would be helpful.

IV) Their strategy and optimisation for purification of sumoylated proteins is excellent and will be useful for future research (along with other reagents the authors developed here). Is the 10xHis::smo-1 functional? Could this be tested in vitro and/or in vivo?

V) In vitro PIE-1 sumoylation would be a desirable addition to this figure.

VI) In addition to germline PIE-1 localisation, it would be interesting to see embryos and PIE-1(K68R).

VII) MW markers are missing in the blots.

Figure 2)

I) The generation of the ubc-9 ts allele is an exceptional tool. Could the authors show SUMO conjugation levels at permissive vs restrictive temperature? Just out of curiosity, is this a fast-acting allele?

II) The authors mention that gei-17 alleles are viable, could the authors mention any thoughts on why the tm2723 allele is lethal/sterile?

Figure 3)

I) Panel C is mentioned in the text in the wrong place. Also in C, what do the authors think about the big increase in MEP-1 sumoylation in the PIE-1(K68R) background?

II) I have the same comment for panel D as I had for figure 1 comment III: the exposure/loading for the embryo WB seems lower, as judged by the co-purifying, unmodified HDA-1. A positive control for sumoylated protein coming from embryos would be nice.

III) In general, the model of PIE-1 acting as a SUMO machinery recruiter should be tested with recombinant proteins. Even if compatible with some results in vivo, showing that this is a plausible mechanism in vitro would be extremely helpful and greatly support the authors' claim.

Figure 4)

I) The authors make a quantitative comparison of the HDA-1/MEP-1 interaction in the text. I think this is not correct. Even if these have been run in the same gel, this could just be a lower exposure. In this line, the HDA-1 blot in the 'Adult' IP would benefit from a longer exposure to better appreciate what seems a rather small difference between PIE-1 and PIE-1(K68R).

II) Since there still seems to be interaction between MEP-1 and HDA-1 in the PIE-1(K68R) background, does smo-1(RNAi) or ubc-9(G56R) reduce this further?

III) In panel B, the LET-418 blot on the right is massively overexposed.

IV) Once again, in vitro binding experiments to get some indication that the authors' model is plausible would be a great addition.

Figure 5)

I) Could the authors make some quantitation of the immunofluorescence data?

Overall, I think this manuscript proposes a very interesting model and the results support this model, although I am not convinced these are sufficient to strongly back the authors' claims. I would very much like to see a revised version with some in vitro data backing the authors' model.

Reviewer #2:

In their manuscript, Kim et al describe a role for HDAC1 (HDA-1) sumoylation in Argonaute-directed transcriptional silencing. The authors suggest that sumoylation of HDA-1 is important for proper assembly of the NuRD deacetylase complex. The role of SUMO modification in heterochromatin has been extensively documented and it is a very interesting topic. The current manuscript provides a very interesting set of results on this topic. I have list of comments, suggestions, questions, and concerns, which are listed below, especially related to the first half of the results:

1) A general question would be how can HDA-1 sumoylation, which is barely detectable, account for such a big 'positive' effect on complex assembly? HDA-1 SUMO modification seems around 10% after enriching for SUMO-modified proteins, which means that stoichiometry will be way lower than this. While this is common for SUMO-modified proteins, it does make it difficult to associate with a 'simple' model.

2) In Figure 1, a schematic of the sensor used throughout the study would benefit the reader.

3) In Figure 1, have the authors checked if the 10xHis::tagged smo-1 has the same effect as the 3xflag::smo-1 (i.e. is it also a partial loss of function allele)?

4) In Figure 1 it would be nice to see the global SUMO conjugation levels in the different conditions, particularly in the smo-1(RNAi), 3xflag::smo-1, and ubc-9(G56R).

5) Also Figure 1, was gei-17 depletion/deletion checked in any way (i.e. WB)? Did the authors consider other SUMO E3 ligase, such as the mms-21 orthologue?

6) While I am not a big fan of fusing SUMO to proteins, in this case it seems like a very reasonable thing to do, considering the modification sites are located very close to the C-terminal end of the protein. Did the authors check an N-terminal fusion?

7) In Figure 2B, it becomes very clear that the level of SUMO modification of HDA-1 is extremely small, barely detectable after an enrichment method. I also wonder why the gels were cropped so tightly, especially considering that in Figure 3 there is an additional band corresponding to ubiquitylated, sumoylated HDA-1. In vitro modification assays would be helpful. HDA-1 alongside a known and characterised SUMO substrate would indicate how good a substrate HDA-1 is.

8) In Figure 2D, is the difference between HDA-1(KKRR)::SUMO and HDA-1::SUMO significant?

9) In Figure 3A-C, it would be useful to control whether the GFP::HDA-1 fusion behaves as the untagged one in the sensor assay (wt vs. KKRR).

10) I have a few questions regarding Figure 3D:

I. Considering the extremely low level of HDA-1 sumoylation, did the authors detect SUMO and ub conjugated HDA-1 (not the SUMO usion)?

II. Is ub conjugated to SUMO or to HDA-1?

III. Does MEP-1 contain any obvious SIMs and or UIMs?

IV. To make a stronger case for the SUMO-dependent interaction model, in vitro interaction assays with recombinant proteins would be extremely useful.

11) In the discussion, the authors compare the lack of requirement for GEI-17 in their manuscript with the requirement for Su(var)2-10 in flies. It is very important to back this claim that the authors control GEI-17 depletion (as pointed out in 5).

Overall, I think this manuscript provides a very interesting set of results and I believe that, with the addition of some simple biochemical experiments, the quality and impact of the overall work would be much greater.

Reviewer #2:

Soucy and colleagues developed a thermoplastic microphysiological system (MPS) to investigate the mechanisms regulating adrenomedullary innervation. This system consists of 3D cultures of adrenal chromaffin cells and preganglionic sympathetic neurons within a contiguous bioengineered microtissue. Using this model, they report that adrenal chromaffin innervation is critical for hypoxia-induced catecholamine release. They also show that opioids and nicotine affect adrenal chromaffin cell response to hypoxia without impairing neurogenic control mechanisms. In addition to providing mechanistic insights on adrenomedullary catecholamine release, this study represents an elegant proof-of-concept that the MPS have the potential to become useful tools to study organ innervation.

Disclosure: I do not have the expertise to review the engineering aspects of this manuscript and will therefore share some concerns I have regarding the accuracy of this technology to mimic native tissues.

I understand that one advantage of the MPS over microfluidic devices using micro-posts or micro-tunnels is the presence of an unobstructed interface between the compartments that is similar to tissue interfaces. However, how better is it compared to other organs-on-chips constructs for reaching the biological complexity of an intact organ?

The system consists of adrenal chromaffin cells and preganglionic sympathetic neurons. I wonder if in this format it could lack the normal cellular heterogeneity of the adrenals. Can the absence of adrenal cortex cells producing aldosterone, androgens and glucocorticoids with important autocrine functions on chromaffin cells interfere with the ability of chromaffin cells to respond normally to a stimulus? Authors discuss that future efforts will incorporate additional adrenal cortical cell populations to better mimic the native physiology. Could they extend this discussion by highlighting the potential weaknesses of the model in its current format? Was any observations made that would suggest caveats?

In vivo, do all fibers innervating the medulla target the chromaffin cells or do some/most innervate the blood vessels or pericytes? If a majority of the innervation is to blood vessels, how does this system take into account potential changes in blood flow and perfusion of the adrenals that could occur and affect the oxygenation?

Early work suggests that adrenergic terminals innervate chromaffin cells and that the adrenal medulla receives a sympathetic and parasympathetic efferent and an afferent innervation (J Anat. 1993 Oct; 183: 265-276). How would this system allow to study such complex innervation? Is it possible to add additional neuronal types to this MPS?

In addition to the nicotinic cholinergic receptors, chromaffin cells express muscarinic receptors that may also be involved in catecholamine release. A quick profiling and comparison of the expression of the different receptors could reinforce the representative nature of the technology to model a biological system.

One important caveat of MPS is the challenge of delivering a drug in a physiologically realistic manner. Could the author comment on the doses of the different drugs used and how they are representative of what a chromaffin cell would normally "see" in vivo?

Could the authors comment on the culture media/conditions and how they are representative of a biological system? Would the use of blood or blood components be a better alternative to the system?

Reviewer #2:

The manuscript introduces a computational account of meta-control in value-based decision making. According to this account, meta-control can be described as a cost-benefit analysis that weighs the benefits of allocating mental effort against associated costs. The benefits of mental effort pertain to the integration of value-relevant information to form posterior beliefs about option values. Given a small set of parameters, as well as pre-choice value ratings and pre-choice uncertainty ratings as inputs to the model, it can predict relevant decision variables as outputs, such as choice accuracy, choice confidence, choice induced preference changes, response time and subjective effort ratings. The study fits the model to data from a behavioral experiment involving value-based decisions between food items. The resulting behavioral fits reproduce a number of predictions derived from the model. Finally, the article describes how the model relates to well-established accumulator models, such as the drift diffusion model or the race model.

Before I get into more detailed comments, I would like to highlight that this work addresses a timely and heavily debated subject, namely the role of cognitive control (or mental effort) in value-based decision making (see Shenhav et al., 2020). While there are plenty of models explaining value-based choice, and there is a growing number of computational accounts concerning effort-allocation, little theoretical work has been done to relate the two literatures (but see Major Comment 1). This work contributes a novel and interesting step in this direction. Moreover, I had the impression that the presented model can account for a broad range of behavioral phenomena and that the authors did a commendable amount of work to validate the model (but see Major Comments 2 and 3). The manuscript is also well written in that it seems accessible to a broad audience, including non-technical readers. However, while I remain curious about what the other reviewers have to say, the manuscript misses to address a few issues that I elaborate below.

Major Comments:

1) Model Comparison(s): While the manuscript compares the presented computational approach to existing accumulator models, it could situate itself better in the existing literature, ideally in the form of formal model comparisons. For instance, as someone less familiar with choice-induced preference changes in value-based decision making, I wonder how the model compares to existing computational work on this matter, e.g. the models described in Izuma & Murayama (2013) or the efficient coding account of Polanía, Woodford, & Ruff (2019). I do understand that the presented model can account for some phenomena that the other models cannot account for, at least without auxiliary assumptions (e.g. subjective effort ratings), but the interested reader might want to know how well the presented model can explain established decision-related variables, such as decision confidence, choice accuracy or choice-induced preference changes compared to existing models, by having them contrasted in a formal manner. Finally, it would seem fair to compare the presented account to emerging, more mechanistically explicit accounts of meta-control in value-based decision making (e.g. Callaway, Rangel & Griffiths, 2020; Jang, Sharma, & Drugowitsch, 2020). As these approaches are still in preprint, it may not be necessary to relate them in a formal model comparison. However, the manuscript might benefit from discussing how these approaches differ from the presented model in the text.

2) Fitting Procedure: This comment concerns the validation of the described model based on its fits to behavioral data. If I understand correctly, the authors first fit the model to each participant while "[a]ll five MCD dependent variables were [...] fitted concurrently with a single set of subject-specific parameters" and then evaluate whether model fits match the predicted qualitative relationship between experimental variables (e.g. pre-choice value ratings and pre-choice confidence ratings) and dependent variables (e.g. choice accuracy). I'm happy to be convinced otherwise, but it appears that the model's predictions could be tested in a more stringent manner. That is, it doesn't appear compelling to me that the model, once fitted, matches the behavior of participants -- please note that this is not to diminish the value of the results; I still think that these results are valuable to include in the manuscript. Instead, rather than fitting the model to all dependent variables at once, it would be more compelling to fit the model to a subset of established decision-related variables (e.g. accuracy, choice confidence, choice induced preference changes) and then evaluate how the fitted model can predict out-of-sample variables related to effort allocation (e.g. response time and subjective effort ratings). Again, I am happy to be convinced otherwise but the latter would seem like a much more stringent test of the model, and may serve to highlight its value for linking variables related to value-based decision making to variables related to meta-control.

3) Parameter Recoverability: Given that many of the results rely on model fits to human participants, it would seem appropriate to include an analysis of parameter recoverability. That is how well can the fitting procedure recover model parameters from data generated by the model? I apologize if I missed this, but the manuscript doesn't appear to report this kind of analysis.

References:

Callaway, F., Rangel, A., & Griffiths, T. L. (2020). Fixation patterns in simple choice are consistent with optimal use of cognitive resources. PsyArXiv: https://doi.org/10.31234/osf.io/57v6k

Izuma, K., & Murayama, K. (2013). Choice-induced preference change in the free-choice paradigm: a critical methodological review. Frontiers in psychology, 4, 41.

Jang, A. I., Sharma, R., & Drugowitsch, J. (2020). Optimal policy for attention-modulated decisions explains human fixation behavior. bioRxiv: 2020.2008.2004.237057.

Polania, R., Woodford, M., & Ruff, C. C. (2019). Efficient coding of subjective value. Nature neuroscience, 22(1), 134-142.

Shenhav, A., Musslick, S., Botvinick, M. M., & Cohen, J. D. (2020, June 16). Misdirected vigor: Differentiating the control of value from the value of control. PsyArXiv: https://doi.org/10.31234/osf.io/5bhwe

Reviewer #2:

This is a nice study that is clearly written and makes use of several datasets. The authors show that a gene signature associated with increased myelopoiesis in utero is associated with increased risk of pediatric asthma. Furthermore they show that cord blood serum PGLYRP -1 is associated with reduced risk of pediatric asthma and increased FEV1/FVC. Interestingly sIL6ra which is derived from neutrophils but not associated with neutrophil granules did not show any association with pulmonary outcomes. This suggests that it is the neutrophil granules rather than the neutrophils per se that are the problem association. The following should be addressed:

1) While the manuscript is clearly written, the message regarding PGLYRP-1 is at times confusing. The manuscript is clear that PGLYRP -1 is inversely associated with mid childhood asthma risk. The discussion however refers to animal models where PGLYRP -1 is proinflammatory and is associated with increased airway resistance and allergen sensitization. The apparent disparity should be clarified.

2) What is the proposed role of neutrophil degranulation in the pathogenesis or long term susceptibility to asthma?

3) While it was not the focus of the current study and maybe beyond the scope of the data it would be interesting to know if there is any association with the subsequent development of adult asthma.

Reviewer #2:

The paper submitted by Girard-Buttoz and colleagues asks whether and how early maternal loss affects cortisol levels and diurnal slopes among wild chimpanzees at Tai Forest, Côte d'Ivoire. The major claim of the paper is that, like humans, chimpanzees experience altered HPA functioning after maternal loss, including alterations to both diurnal slope and overall cortisol levels. However, their chimpanzee orphans exhibited patterns in diurnal slope that were opposite to their predictions (predicted blunted slopes, observed steeper slopes). The authors should be commended for their efforts in collecting a large number of samples for this analysis. However, I am not convinced that it is sufficient for investigating the hypotheses put forth here and, therefore I am also not convinced that their results are solid. I also have concerns about the theoretical grounding for the paper.

1) My principal concerns with this paper, as written, revolve around the methods/results. First and foremost, I am not convinced that the authors have the sufficient sample size to evaluate the predictions/hypotheses outlined in the introduction. While 849 urine samples is a large number, and again, their efforts here should be commended, the sample spread is actually quite thin once it is spliced up into appropriate categories, especially considering how many samples were collected per individual year, on average. As the authors indicate throughout and especially when describing their modeling approach, cortisol is inherently a very noisy hormone impacted by myriad factors- including age in at least one other densely-sampled chimpanzee community. I'm also surprised that time of day was modeled quadratically. It is my understanding that humans, other populations of chimpanzees, and other mammals follow a sigmoidal curve which should be modeled with a third-order term as well. For these reasons, it's difficult to tell whether model 1A is not significant because of insufficient sample or a true lack of predictive power. Additionally, I'm concerned that the paper seems to focus so much on the results from a single model term in a model that did not reach significance.

2) Despite acknowledging that the "significance of these predictors should be interpreted with caution" because model 1a did not reach significance, the authors make very strong claims about the results in the discussion- and also feature the finding of that model in the title of the paper. That seems problematic to me- especially because the insignificant model results (more intense diurnal slopes among immature orphans) diverge from the expectations set forth by other works in humans and non-humans. The finding that this is to do with higher-than-expected morning cortisol is puzzling given that evening levels are generally considered more responsive or plastic. However, this could also be an artefact of fitting the models without the third-order term for time.

3) The introduction needs refinement to help clarify and specify the authors' arguments.

(a) Does the biological embedding model always lead to negative fitness outcomes? Or is it possible that phenotypic adjustments might be adaptive, or even just making the best of a bad job (e.g. earlier death, but not death today)?

(b) Throughout the introduction it is unclear whether and where the authors refer to the human clinical literature as opposed to animal literature. It is also unclear how human patterns are similar versus different from those observed in animals. Further, I would recommend that the authors include a deeper review of the animal literature (e.g. early experimental work with macaques, cortisol at other chimpanzee field sites/captivity). It's also unclear whether and where the authors refer more broadly to early life adversity (and what this means for humans vs. animals) versus more specifically to maternal loss. Additionally, there should be further discussion specifically related early maternal loss (rather than "early life adversity" which can include a lot of different factors) focused on the nutritional and social obstacles associated with early maternal loss, how these related to HPA functioning, and how these effects are expected to change during development (Plasticity? Flexibility? The role of HPA in responding to changing environmental conditions?). What about the adaptive calibration model which posits that the HPA can readjust during particular periods of developmental reorganization?

4) It is difficult to assess the discussion without first dealing with the problems in the introduction/methods. However, despite their claims in the results section, it does not seem that the authors interpreted the results of model 1a with caution.

Reviewer #2:

The manuscript addresses an interesting question: whether genetic effects of common variants on educational attainment (EA) differ between individuals with and without psychiatric diagnoses. The dataset they use is ideally suited for such an analysis. The authors find evidence that the influence of common variants on EA is attenuated in individuals with a diagnosis of autism spectrum disorder (ASD) or ADHD.

My main concern with the paper is the statistical analyses used to support the authors' conclusions. The authors draw conclusions from dividing individuals into subgroups and comparing the R^2 of the EA PGS between those subgroups. This analysis is liable to bias due to range restriction: if the subgroups have been selected based on low/high education, then the R^2 of a predictor will tend to be lower in the subgroups than in the overall sample. Furthermore, here the selection into the subgroup (here diagnosis with ASD or ADHD) itself is related to both education and the EA PGS, which could be contributing to the differences in R^2 the authors observe between subgroups.

A more powerful and robust analysis would be to fit an interaction model in the full sample. The authors could regress individual's EA jointly onto their EA PGS, their diagnoses coded as binary variables, and the interactions between the EA PGS and the diagnoses codings. The authors could do this jointly for all diagnoses in the full sample, which would account for comorbidities between psychiatric disorders. If the influence of the EA PGS is truly weaker in ASD and ADHD cases, there should be a negative interaction effect between the EA PGS and ASD and ADHD diagnoses, which can be tested with a simple statistical test for a non-zero interaction effect.

It could also be worth first regressing the EA PGS onto the psychiatric diagnoses, and taking the residuals before assessing whether there are interactions between the EA PGS and ADHD/ASD diagnosis. It is possible that correlation between the EA PGS and ADHD/ASD diagnosis could generate a spurious interaction effect in the above analysis.

It is interesting that controlling for SES appears to mediate the (potential) interaction between EA PGS and ADHD diagnosis. However, I worry again that this could be a function of SES influencing ADHD diagnosis. SES and its interaction with both EA PGS and ADHD diagnosis could also be included in a full interaction model that could help interpret this finding.

The authors construct the PGS by using a pruning and thresholding approach. This is known to be suboptimal, which may explain why their R^2 is lower than in other studies. The authors could use LD-pred or other methods that account for linkage disequilibrium and non-infinitesimal genetic architectures. In the EA GWAS from which the score was constructed, the best R^2 was found by applying LD-pred to all variants without p-value thresholding.

The hypothesis that indirect genetic effects differ between psychiatric cases and controls is interesting. Do the authors have sufficient sibling data within their samples to test this?

Line 581: Closely related individuals were removed from the analysis. Why? How many were removed? Could inclusion of these help assess the hypothesis about indirect genetic effects and improve power? The authors could use a mixed model regression to control for relatedness without having to throw individuals out of their sample.

The grammar in the writing of the paper is a little odd at times. Often, definite or indefinite articles are omitted preceding nouns, such as in 'association of EA-PGS' in the abstract, which should be 'association of the EA-PGS'.

line 54: 'strongly influences', I think this is a little overconfident in its assignment of causality to highest level of education, perhaps 'strongly associated' would be better

Paragraph 3 of the introduction: the authors should mention population stratification and assortative mating as possible mediators of the association between EA PGS and EA, especially when referencing the drop in association strength in within-family designs

I found the decile based analyses a bit pointless. By arbitrarily dividing a continuous outcome into discrete subgroups, the authors are losing power and not gaining much compared to simply performing linear regression, which they already do. I would relegate these to supplementary figures.

Line 452: I think that the stated equivalence between low EA PGS and learning difficulties goes a bit too far here. I understand the point the authors are trying to make, but I think it should be phrased more carefully.

The authors used an MAF threshold of 5% for construction of the score. Typically, a threshold of 1% is used for construction of PGS from summary statistics by software such as LD-pred.

Line 580: the authors state that an EA PGS based on summary statistics from European samples cannot be used to predict EA in non-European samples. This is not true. It is true that the prediction accuracy is attenuated, but it is not zero.

Reviewer #2:

General assessment and major comments:

The study addresses a timely and important question of the role of potential modulations in perceptual decision-making in the atypicalities observed in perceptual processing of individuals diagnosed with autism. The manuscript is important, and the methods used are sound.

There are however some issues to consider:

Thresholds, or other indications of sensitivity and precision of performance in the task are not detailed (although judging by the individual psychometric functions presented in the figures, slopes seem less steep in ASD). Was sensitivity considered in any way in the analysis? wondering how the model fitting would look like and how it would interact with the biases. Bias magnitude could vary as a factor of noise or sensitivity.

Also, could larger consistency bias in the ASD group result from weaker performance, more lapses of attention etc.?

Age range is quite large. Did you check for age-related differences? I understand the sample size is not big enough to analyze data across different age groups but maybe as a covariate? (there is also the problematic issue of determining sample size of children based on the study in young adults).

Not sure why the effects of prior stimuli are considered adaptation effects, particularly in the first experiment where stimuli were briefly presented. Also, regarding the argument in the Introduction about Bayesian priors producing positive effects -- there are other prior effects that may cause 'negative effects' in relation to prior expectations (for example, in perceptual illusions such as the weight-brightness illusion).

Can you think of a reason why controls did not show significant consistency bias in their responses in the heading discrimination?

There is some wording in the reports of the statistics such as 'more significant' or 'more marginally' that needs to be rephrased.

Were the analyses corrected for multiple comparisons?

Usually RTs in this sort of perceptual task are longer in ASD. Wonder how this is not the case here, although instructions for the subjects emphasize speed and accuracy.

I agree with the authors. It is interesting to look at correlations between the effects of prior choices and clinical scores of repetitiveness and flexibility in ASD. Did you look at the correlation between the effects of prior choices and SCQ scores across the two groups? Previous work documenting correlation between autistic traits (AQ) and modulated perception provided important information about the generalization of the findings to the broader spectrum of autism in the wider, nonclinical population (see Lawson, Mathys, & Rees, 2017; Hadad, Scwartz, & Binur, 2019).

Reviewer #2:

Nonlinear microscopy is in the unique position that high-resolution images of cells and other tissue components can be obtained in live tissue. However, scattering and absorption limit the penetration depth. The impact of nonlinear microscopy in biomedicine and biology would be much improved if higher imaging depths can be achieved. Lately a few key studies have appeared achieving this. This manuscript contains a well-motivated extension of this research, in particular on the benefits of high-pulse-energy low-duty-cycle infrared excitation near 1300 and 1700 nm over 2-photon excitation, in heterogenous and dense tissue. The authors compare three types of excitation, at 1650 and 1300 nm at 1 MHz and at 1100 (or 1270) nm at 80MHz. They characterize photodamage in the tissue and determine the limits for power densities to stay below that. They study the achieved resolution at high depth for each of the processes and show a deeper imaging depth is resolved in bone and tumor core with 3P and 4P than with 2P. The article is a very solid and extensive study.

Though I have no major concerns with article, I do have some minor points:

l.57: Are the resolutions reported for 2-, 3-, or 4- photon processes. Do you not expect these to differ for the different processes? l.60 It is not explained that power is increased from X to Y, instead the peak power of 87 nJ in L 67 is not found back in fig. S2.

L. 103 Given is the power at the sample surface, after which the readout for cell stress via Ca imaging is done (very elegant). Is not the imaging depth of the readout relevant too, as it is probably the power density at the focus which matters. What imaging depths can be reached with this low power? This comes back later, but would be good to mention here.

L.110 The phrase 'Furthermore' confuses me. I guess the authors mean to say that with their 2.8-8.7 nJ of power they were well below the 100 mW level? Which is kind of obvious at 1 MHz?

L. 126 Some words are missing, 'but 1180'.

Why do some signals show a peak in intensity in fig. 3C and G rather than a slope?

Reviewer #2:

The authors quantify virulence factors in Cryptococcus neoformans and C. gattii in a large number of clinical isolates and correlate these virulence factors to survival in a g. mellonella infection model and to the clinical outcome. The authors found a correlation between secreted laccases and disease outcome in patients. In addition, the authors show that a faster melanization rate in C. neoformans correlated with phagocytosis evasion, virulence in the g. mellonella model and worse prognosis in humans.

The manuscript is well structured with an appropriate abstract summing the main findings, a clear introduction, well described methods section and appropriate number of figures and tables. The results are clearly described.

1) The authors identify and acknowledge the most important limitation of the study: line 365-366 the patients were treated with different regimens in distinct health services. This reviewers agrees this is a limitation. However, to get a feeling about the impact of these differences the authors should indicate how the patients were treated and whether there were differences in patients that died and survived. Without this information clearly presented, I cannot interpret the correlations between virulence factors and outcome found in this study. Perhaps the authors can show how many patients that were included in the phenotype-survival analysis, that died and survived were treated according to Brazilian guidelines.

2) The melanin production evaluation assay is an important tool that the authors use in this study and the measurements from these assays were correlated with G. mellonella and patients survival and thus are essential to the conclusions of the study. The method is well standardized, and the authors show elegantly that the outcomes are highly reproducible. Can the authors describe when melanization occurs: does it occur in mature colonies and may growth rate itself may influence the measurements? Do isolates with a high growth rate/colony maturation have a low T-HMM or high melanization Top. Have the final colonies of different species have a different final cell number after 7 days incubation and how does this correlate to melanization? And how does the growth rate/ budding rate/ colony maturation/ correlate to G. mellonella survival?

3) The figures 1-5 give a clear picture of the wide distribution and variation of virulence parameters e.g. the distribution of melanization kinetics parameters, the distribution of capsule sizes, GXM secretion and LC3 phagocytosis. But what does this distribution mean, it only shows that the isolates are not the same but does not contribute majorly to the final conclusion. Can the authors think of a way to give more meaning to these figures: e.g. indicate with colors which isolates were retrieved from patients that eventually died and which survived (although this may be inappropriate as not all clinical information is available. Figure 6 really gives meaning to the numbers displayed in figure 1-5. Perhaps move some figures to the supplementary file.

Reviewer #2:

The topic of this manuscript is the basis of continuous and episodic bursting electrical activity in developing spinal cords. The approach used is to employ a simple mathematical model as a representation of the central pattern generator underlying the bursting pattern, and examine how the properties of bursting change with variation in three key system parameters. Some of the model predictions are tested in an actual in vitro spinal cord preparation. Although I enjoyed reading the manuscript, I have some serious concerns about the model that is employed, which I discuss below.

Major concerns:

1) The model is a half-center oscillator (HCO) in which one cell inhibits the other, resulting in anti-phasic electrical activity of the two cells. (Each "cell" actually represents a cell population, so the model is a mean field model.) This is certainly one way to get electrical bursts. However, it is not at all clear that such a HCO structure exists in the developing spinal cord, or that there are neural populations with this anti-phasic activity. If such data exists, it is not mentioned in the paper or cited. Indeed, the recordings in Supp. Fig. 1 show extracellular neurogram recordings from ventral roots in different lumbar segments and in which the bursting appears to be synchronous. So I see no evidence that the HCO model reflects the actual neural circuit, other than the fact that it can produce bursting and episodic bursting. This does not mean that such a phenomenological model is without value, but it should be made clear to the reader that that is what the model is. Also, the next two points below do appear to cast doubt on the utility of this model.

2) In Fig. 3 it is shown that the inter-episode interval (IEI) is increased in the model when the conductance g_h is reduced. Because of this, the episode period (EP) also increases. The data, also in Fig. 3, show the opposite. They show that blocking the h-type current decreases the EP. This seems like a flaw in the model, since it is the h-type current that is responsible for episode production (at least I think it is, see point 4 below). The discrepancy is mentioned in the manuscript, but only briefly and it should be fully addressed.

3) In Fig. 5 it is shown that, in the model, there is a very small interval of g_NaP where episodic bursting is produced. Otherwise, the model produces continuous bursting (for larger g_NaP values) or silent cells (for smaller g_NaP values). However, the data that is also shown in the figure indicates that blocking the NaP channels has little effect on episodic bursting. This is another serious discrepancy between the model and the experimental data.

Points for clarification:

4) It appears from Fig. 1 that episodes stop when h-type current activation slowly moves to an insufficient level to kick off a new burst. Logically, a new episode would start once that activation grows back to a sufficiently large value. Is this right? The mechanism for episode production is never discussed, and it should be.

5) The model is deterministic, yet there is variation in burst duration and episode duration (see Fig. 3). What is the source of the variation? Does this mean that the episodes are not periodic?

6) The model has a multistable region in parameter space, and much is made of this in the Results and the Discussion. In Fig. 6, it was demonstrated that hyperpolarizing pulses could switch the system from one behavior to another. Can this be done experimentally in the in vitro prep? If so, was it tried?

Other:

7) Discussion is too long and touches on things that were far from the focus of the manuscript. For example, there is about a page and a half of text discussing short term motor memory (STMM) although the Results section did not focus at all on homeostatic functions of the circuit or STMM. Furthermore, some points were made several times during the Discussion, where one time would have been sufficient.

8) Almost two pages of the Discussion was dedicated to multistable zones, yet in the model the multistable zone was tiny, and there was no evidence that the experimental prep lies in or near that zone. The authors state that in actual neural circuitry there could be a much larger multistable zone, which is true, but there also may be none at all. This discussion appears irrelevant.

Reviewer #2:

Amyotrophic lateral sclerosis (ALS) used to be considered primarily a disease of motoneurons. Recent work using mouse models of ALS has revealed that pathological changes can also be detected in spinal interneurons, particularly inhibitory interneurons, and that some of these changes can be detected before birth. The present paper is the first to directly examine the electrical properties of spinal inhibitory interneurons in a mouse model of ALS and show that some of these are altered in the neonatal period well before the mice start to exhibit symptoms. The authors show that SOD1 Lamina IX neurons are smaller than the Lamina IX WT neurons whereas no differences were found between WT and SOD1 neurons outside Lamina IX. They also use whole cell recordings to reveal that putative 'Renshaw cells' are less excitable in SOD1 mice than wild type animals whereas non-Renshaw inhibitory SOD1 neurons are more excitable.

Major Comments

1) The authors claim that Renshaw cells are in lamina IX, when they have been shown to be located mostly in the ventral part of lamina VII, ventromedial to the motor nucleus (Alvarez and Fyffe, 2007). In addition, not all calbindin+ neurons in lamina VII are Renshaw cells. From the location of the whole cell recordings shown in fig.2, it seems likely that most of the recorded neurons are not Renshaw cells because they are outside the classical 'Renshaw' area. It is not clear why the authors are focusing on glycinergic neurons in lamina IX, as there is no evidence that they belong to a unique class or that they are presynaptic to motoneurons.

2) The concern about the identity of the Renshaw cells obviously undermines the statistical modeling to segregate Renshaw versus non-Renshaw cells. Furthermore, it was not clear from the text whether the model used both WT and SOD1 calbindin-positive neurons to define 'Renshaw cells'. Assuming it did, and given that there were changes in the electrical and morphological properties of the calbindin+ SOD1 neurons, is it not surprising that they could be grouped with the WT 'Renshaw cells'?

In addition, the characteristics the 'Renshaw cell' population used for the model are not clear. On line 186 that it states that 15/23 of the whole cell recorded interneurons were positive for calbindin. Does this refer to 15 WT and 23 SOD1 neurons? Thus 38 neurons were calbindin positive. Of the remaining 21 neurons how many were calbindin-negative and how many were not tested? How many of the 38 calbindin-positive neurons had their dendrites reconstructed sufficiently from the intracellular fill to be used in the model? The model predicted that 80% of the 59 patched interneurons were Renshaw cells. How many of these were in the calbindin-negative group and how many were in the not-tested group? The spatial distribution of these groups should also be plotted. However, it seems very unlikely that 80% of the recorded cells are Renshaw based on their location as shown in fig.2B.

Second it would have been useful apply the model to known non-Renshaw cells, to establish that it was not generating too many false positives. Another way the authors could test the model is to establish if it could distinguish WT and SOD1 neurons based on their morphology.

3) The authors suggest that the reduced excitability of 'Renshaw cells' might contribute to the excitability changes seen in motoneurons. However, based on their own data, this is not a straightforward conclusion. They find that 'non-Renshaw cells' are hyperexcitable and since this population would include 1a inhibitory interneurons and other premotor inhibitory interneurons, it is not clear what the overall effect on motoneuron excitability would be. Additionally, because the authors suggest that 'Renshaw cells' are less excitable this would presumably lead to reduced inhibition of 1a inhibitory interneurons counteracting a potential loss of inhibition onto motoneurons from Renshaw cells.

Reviewer #2:

Kandul et al. present an interesting study that could lead to important improvements on the use of homing-based gene drives. However, there are a number of things that should be addressed to improve the manuscript for better comprehension by readers.

Overall the manuscript presents a load of data. But the presentation of these data could be made in a better digestible way. The authors should go over their manuscript with a reader in mind, that is interested but not necessarily knows all the relevant literature in the very detail.

Abstract (line 18): Please remove "inherently confinable" from the abstract. The drive is indeed designed in a split drive design, however, all the experiments were done in a homozygous Cas9 background. Therefore, there are no experimental data for a split drive provided in this manuscript. The split situation seems to be here more for a practical reason to be allowed to do the experiments in a less stringent laboratory environment. Thus there are no experimental data that would support the confineable nature of this drive. Actually there are not even modelling data to this. Thus, such a statement should not be put in the abstract. This manuscript is not a demonstration of a confineable drive.

Results (line 124): How was Pol-gamma35 identified? It would be interesting to the reader to get to know about the exact reasoning, why this gene was chosen. Or were there several ones chosen before and this turned out to work the best or was the easiest to design. This could be very interesting considerations important to the field.

Results (lines 147-148 Fig. 1B; lines 155-156 Fig. 1C) and Methods (lines 698 and 706) and Figure 1 (both Figure and legend): The addressing of the Figure panels and the writing to it don't fit! Has there been a rearrangement of the Figure that was not worked through the text? When referring to "B" in the text, it is still about Act5C-Cas9 and the nos-Cas9 data are in the text referred to Fig1C! But Fig1C is BLM! In current panel Fig1B, what does "all" mean below the X-axis? This is not comprehensible. Panel C is not really described in the Figure legend!

Results (line 253), Discussion (lines 526-527), and supplementary Figure 1 (line 1101). "converting recessive non-functional resistant alleles into dominant deleterious /lethal mutations" is completely misleading! There is no "conversion" and how should that be done molecularly. There is a continuous removal of such alleles from the population because of lethal transheterozygous conditions caused in the drive. However, there is no active conversion of such alleles into dominant lethal ones. This needs to be clearly rewritten to avoid the misleading idea. Supplementary Figure 1 also seems to have a slight conceptual problem. What are "cells" (rectangles) with a red frame and a green core? Green means at least one wt allele (this must include the recoded rescue allele!). Red means biallelic knock-out: thus a red cell cannot have a wt allele. Thus what is a red-framed green core cell? To explain the removal of R2 alleles, a depiction of yellow framed red core cells in the germ line would be helpful, since this would explain how R2 alleles are selected against and might be continuously removed from the population!

Results (from line 424 to end of results): Before going into the modelling, the reader should be clearly informed about all the different approaches that are now to be compared. This is currently not done well, if at all! Thus moving current Fig 6 before current Fig. 5 might clearly help! Also a better explanation of the panels in Figure 6 is necessary as well as a correction of Fig6 Panel E! A comparison of a great number of the currently approached toxin-antidote (gene destruction - rescue, but not killer-rescue!) systems is greatly appreciated. However, the authors cannot expect the general reader to know about the small detailed differences between the systems that are compared here. Thus the authors need to provide some explanations and categorization of the different approaches here and also cite all the respective literature.

-First subdivision: Non-homing (interference-based drives) VERSUS Homing (thus overreplication-based drives). This will also help them to better understand why the interference-based drives (TARE and ClvR) are more sensitive to fitness parameters than overreplication drives.

-Second subdivision: same-site VERSUS distant site. This is important to understand the difference between the here modelled TARE and the CLvR. Actually ClvR is a TARE, but you use TARE here more specifically as the results in the respective paper are demonstrating only a same-site TARE! But this needs to be clearly stated here!

-Third subdivision: viable VERSUS haplosufficient VERSUS haploinsufficient. This also needs to be clearly depicted in labelling panels C to F of Figure 6, which are currently hard to grasp what the essential differences are, before looking at the panels in detail: C: HGD of viable gene (HGD) D: HGD of viable gene with rescue (HGD+R) E: HGD of haploinsufficient gene with rescue (HGD-hi+R). THIS PANEL NEEDS MAJOR CORRECTION!! F: HGD of haplosufficiant (essential) gene with rescue (HomeR)

-Forth subdivision: split VERSUS non-split. Here for the split HGD situation, the respective papers of which the current authors are co-authors should be cited: Kandul et al. 2020 (actually published end of 2019 and still cited as biorxiv Archives article 2019a!?) and Li et al. 2020, Elife). In addition, it is also important to state clearly that "split or two locus" is completely independent of the "distant site" concept! The reader needs to understand the differences of the systems that are compared here, without having the reader to go to the respective publications themselves and then try to find out what the differences really are. This is not so obvious and the current authors have a clear chance here to do that and help the reader in the mists of all this similar but still distinct approaches.

Figure 6 Panel E: This depiction is not consistent within itself, not consistent with the legend, and not consistent with the cited literature!

-Why should the rescuing drive construct over the wt allele be lethal as indicated in the right two boxes?

-The cited paper Champer et al. 2020b, which is by now also published in PNAS! clearly states that there is maternal carry over, which actually makes it so hard to use and is probably only working via male propagation. In the Figure legend, it is said that "maternal carryover and somatic expression ... are empirically unavoidable", which is in contrast with the depiction! The legend then also states that this is "unachievable". This should be better replaced by "hard to achieve", since the approach is published and seems to drive, even though probably just via the males! Thus the depiction of panel E needs to be thoroughly revised.

Discussion (lines 499-500): The haplolethal HGD works (admittingly poorly) despite the maternal carryover (Champer et al 2020b). Therefore, your statement needs to be refined or deleted: "requires germline-specific promoter that lacks maternal carryover" is not consistent with the published paper! The drive could go via the males because then you do not have maternal carry over! And homing based drives can go via males and do not necessarily have to be promoted through females, see also KaramiNejadRanjbar et al. 2018.

Discussion (lines 540 to 543). This sentence is based on an old but clearly overruled idea! NHEJ repair is not restricted to a time before the fusion of the paternal and maternal genetic material. It has been clearly demonstrated that R1 and R2 alleles are also generated in the early embryo after the zygote state (Champer et al 2017, KaramiNejadRanjbar et al. 2018). Actually, all of the authors' Figure 1C and Supplementary Figure 1 are about NHEJ mutation in the early embryo causing "BLM". Thus this sentence is inconsistent with current beliefs and also with the authors' own writing!

Figure 4: Panel C graph: Why is, in the controls, the transgene consistently and significantly higher inherited to the next generation (0). It is about 75% progeny sired by the transgenic fathers compared to the wild type fathers? Was there an age advantage of the transgenic ones or whatever other fitness factor? This is surprising and no explanation is given at all! In contrast, in the Cas9 background in generation 0, less than 50% carry the drive allele, which is probably due to induced lethality. But this should also be commented upon. In the legend it is stated that 7 of 9 flies carried an R1 allele heterozygous to an R2 allele. What about the other two?

Reviewer #2:

This work from Beier et al. elegantly dissects the rod circuits contributing to the mouse pupillary light reflex through ipRGCs. The authors combine multiple genetic mouse models with electrophysiology and behavior to demonstrate that the primary rod pathway is the primary driver of the dim light pupillary light reflex, and that the secondary pupillary light reflex cannot effectively compensate for this pathway if it is lost. My technical comments are minor. This will be a welcome addition to the field of ipRGC research. My main concern, which I will leave to the editors, is that the actual advance may not be substantial enough.

This is the first study to attribute the rod contribution to the PLR to the primary rod pathway. Though elegant, the fact that the primary rod pathway through ipRGCs is the major contributor in low light and that both primary and secondary pathways contribute to the photopic light PLR is not particularly surprising given the previous clear demonstration by the Hattar group that the rod pathway itself is required for the pupillary light reflex (Keenan et al., 2016).

The authors do convincingly show that the OFF pathway cannot drive the PLR, but again this is in agreement with data showing ipRGCs are the sole conduit for light to drive the PLR (Güler 2008; Chew 2015) and that all ipRGCs get info primarily or solely from the ON pathway (Dumitrescu et al. 2009 and Schmidt 2010, etc.).

Is 1 lux of mixed wavelength light truly in the scotopic regime? How was this calculation/determination made?

Was there any difference in the dark adapted pupil diameter between each of the mouse lines?

Reviewer #2:

In this study, Zhang et al. use a semi-novel method to track acyltransferase activity using fluorescently labeled palmitic acid (NBC-16:0) to track where specific lipids are incorporated with subcellular specificity. They show that NBD-16:0 can be incorporated into different lipid classes that segregate based previously known on subcellular specificity. While this is an interesting technique, it is difficult to determine how much fidelity this method has in recapitulating biological function without additional experimentation, orthogonal measurements, and a more descriptive methods section.

Comments:

1) The authors do not specify which lysophospholipids were used in their study. In the method section they specify that they came from Avanti, but there are >100 different lPLs in their catalog. Also, the authors give a range of lPL concentrations in the methods, but do not specify which concentration was used for which experiment. Without this information and other unspecified aspect of their studies, interpreting subsequent experiments is difficult.

2) One potential advantage of this method is that it is a method to track endogenous lipids in live cells, however the authors show the NBD-16:0 transporting to lipid species where palmitate is almost never measured. For example, the use of the transport of NBD-16:0 to CL as evidence this is working. However natural cardiolipins are almost completely devoid of 16:0. In mammalian cells >80% of the fatty acids in CL is 18:2 with most of the remaining being 18:1 and 18:3. Similarly (assuming you are using sn-1 lPL-16:0), phospholipids with two 16:0 are extremely rare in mammalian cells with the exception of lung surfactant. Further, 16:0 composes <5% of cholesteryl esters in typical cells. The authors should be clearer about how this discrepancy between natural sorting of palmitate and the sorting of NBD-16:0 supports this as an accurate model of acyltransferase activity and intracellular transport.

3) The authors state that PA is primarily remodeled in the ER and transported to the mitochondria as a precursor to CLs (lines 108-111). This statement needs a source. In most studies I am aware of, the vast majority of both PA and 16:0 are primarily converted to TGs or PC/PE with only a small fraction going towards the CDP-DAG pathway required for CL biosynthesis. Are C2C12 cells unique in this regard? Does lPA stimulation specificity induce CL production? Does any of the NBD get into the TG or phospholipid fractions?

4) This study would be much stronger if another fluorescently labeled fatty acid was added. A comparison of the sorting of 20:4 and 16:0 would be very informative. This is especially true if the studies were done in the context of a known acyltransferase, for example LPCAT3.

5) This study would also be strengthened by an orthogonal technique showing similar sorting. For example, separation of the organelles and measurement of labeled fatty acids by MS or nano-SIM analysis would greatly strengthen these studies.

6) In figure 1A, the authors draw a schematic with an sn-2 lyso-PL in the figure. Sn-2 lyso-PLs as labile and will acyl migrate to the sn-1 position without careful handling of the PL in a basic solution. The authors make no mention of this type of handling in the method section. This figure should either be corrected or more details of how they handled their lysophospholipids should be provided.

Reviewer #2:

I think this is a superb manuscript - it is written in a clear way, such that the story starts at the historical understanding of lipoprotein trafficking and builds up convincingly using various experimental methods to show that a new class of lipoproteins is trafficked via acylation of glycine, through the Aat secretion system.

It is highly exciting that a protein that does the acylation AND the secretion from the periplasm to the cell surface has been identified! Next step is to get a structure.

The data are convincing and the paper is extremely well-written. My comment is that I am not convinced by the argument that CexE would not be recognised by the lol system, when it is acylated it likely would be as the hydrophobic pocket of LolA and LolB are fairly indiscriminate - see e.g. the binding of small hydrophobic molecules to these proteins. The authors should comment on this aspect.

It is intriguing how glycine in particular is recognised for acylation.

Overall, a great paper - authors should be commended.

Reviewer #2:

The manuscript prepared by Kim and Colleagues provides a solid attempt at understanding the neural correlates associated with self-reassurance and self-criticism in relation to what they term neural pain. While it is well written and there is a clear story presented here, there appears to be insufficient details in the introduction and discussion. The methodology appears sound for the most part, but I have some concerns relating to stimuli and gender effects that I believe would make the findings more compelling if addressed.

Criticisms:

1) The example items of the neutral statements appear to involve an external agent (i.e., a reference to a friend), while the neural pain is purely about the self. Are there also references to other people in the neural pain condition? If not, how have the authors ensured that the neutral condition is actually neutral. It seems likely that the inclusion of an external agent for many of the neutral statements could pose problems with interpretation, especially when talking about self-criticism and self-reassurance. The presence of an external agent in the neutral statements changes the meaning from a purely self-oriented experience to a shared experience.

2) I am curious as to why the inverse contrasts (i.e., reassurance - criticism) were not run? Knowing whether there was a unique network associated with self-reassurance would provide a more comprehensive understanding of the authors' findings.

3) I am wondering why the authors did not accommodate for gender differences in their study? Given recent evidence (See citation) it seems likely that this may play a part in self-compassion. The authors report an almost equal distribution of males and females, so it should be possible. If the authors did explore this and found no difference with gender as a regressor then this should be noted in the manuscript. Mercadillo, R. E., Díaz, J. L., Pasaye, E. H., & Barrios, F. A. (2011). Perception of suffering and compassion experience: brain gender disparities. Brain and cognition, 76(1), 5-14.

4) It seems as though a whole body of literature is being very lightly touched on here but would benefit from inclusion. I think it would be useful to have some information in the introduction regarding moral emotions (i.e., compassion) and the link with empathy and emotion regulation (see work by Jean Decety). This would also be beneficial for the discussion as the authors are in essence describing empathy.

Reviewer #2:

The authors report on a model system to study the infiltration of growing thrombi by leukocytes using fluorescent microscopy. Such a system will facilitate studies on the role of leukocytes in the context of immuno-thrombosis and thrombus growth. I like the proposed model and I'm convinced about the utility of such a system. However, although the model is sound, I do have a couple of major concerns:

1) The authors describe crawling neutrophils; which methodology has been applied to guarantee that the crawling of the neutrophil is a general phenomenon in this system and not a feature of selected neutrophils? Has there been used a method of quantification (e.g. 86% of the neutrophils are crawling)?

2) The authors identify two types of granulocytes (uniform DiOC6-type A vs cluster-like DiOC6-type B granulocytes. Although the pictures provided (fig 2) do represent nice and clear examples of type A vs type B granulocytes, the experiment will reveal for sure staining patterns which have been less clear. What kind of systematic methodology has been applied to delineate type A from Type B neutrophils?

3) Figure 3 and 4 are nice figures showing differences in granulocytes/FOV and velocity- but it is not clear to the reader what percentage of the neutrophils visible in the FOV do move or not. Was there a minimal amount of neutrophils being in motion?

4) The authors want to point out the synergistic effects of neutrophils and platelets in the thrombus growth. To finally make the point they use whole blood of a WAS patient. However, since WAS affects neutrophil motility as well as platelet morphology/number the individual role of platelets and neutrophils in this process remains open. Therefore control experiments targeting either platelets (whole blood of a thrombocytopenic patient and/or platelet depletion) may contribute to identify the role of platelets in the model. On the other hand, inhibition of neutrophil activation/motility may illustrate the individual contribution of neutrophils in this setting.

Reviewer #2:

Summary and comments:

This study presents an analysis of five large datasets of cancer cell viability including both genetic and chemical perturbations and find that RNA-seq expression outperforms DNA-derived features in predicting cell viability response in nearly all cases, and the best results are typically driven by a small number of interpretable expression features. The authors suggest that both existing and new cancer targets are frequently better identified using RNA-seq gene expression than any combination of other cancer cell properties.

Overall, none of the main conclusions in the paper are surprising, and begs the question whether sequencing more cancer exomes is really meaningful? This is a question that deserves serious debate as major resources are being diverted to large-scale exome sequencing projects with low information content returns.

The paper is well written. And at first glance, the results seem to support the provocative title. Improved clarity around what the predictor and response variables are earlier in the paper would improve readability, particularly around what a "genomic" variable is. Most of the helpful details are buried in the methods.

The main benefits of the manuscript: (1) emphases on simplistic (i.e. few features) predictors that are themselves easily interpretable; and (2) the choice of random forest classifiers also makes interpretation of the predictions pretty straightforward. One concern is whether the breadth or depth (i.e. completeness) of the genomic predictor variables somehow unfairly bias the findings against the ability to predict with those variables compared to expression variables, which are quite easy to encode and interpret. This concern is alluded to in the discussion when reviewing the findings of previous, related publications, and could be further explored. For instance, while variations in mutant RAS (H, K or N) or B-RAF were the only dependencies noted to be predicted better by genomics (i.e. mutations), are all driver mutations known and represented in the data? One would expect that amplified EGFR or HER2 would be predicted well from genomics, but these are notably missing, presumably because they do not meet the filtering criteria.

A notable finding was that a single genes' expression data produced notably better results than gene set enrichment scores overall, despite having many more presumably irrelevant features. Predictive models for many vulnerabilities exhibit relationships expected to be specific to a single genes' expression (e.g. los of a paralog's expression predicts dependency on its partner). There is no biological validation for any of the predictions in the manuscript.

Specific comments:

What was the thought process for choosing 100 perturbations in each dataset to label as SSVs? Why not 82, or 105? Was there a systematic analysis done to pick this number (e.g. harmonic mean)?

Did the authors estimate the effect size they are measuring across the 100 selected SSVs? In other words, was there an estimation of fitness effect, single mutant fitness or degree of essentiality for the 100 SSVs and what range of effects are they exploring? One possible way to measure the fitness effect of each of the 100 vulnerabilities is to examine the dropout rate in pooled screens at the guide RNA level, looking for consistency in gRNA behaviour.

Did the authors include essential and non-essential genes as reference points in their analyses? This wasn't clear from the methods.

The authors describe a clear gradation of response to either TP53 or MDM2 knockout according to the magnitude of EDA2R expression observed in multiple datasets (i.e. Achilles, Project Score, RNAi, GDSC17, PRISM). Using EDA2R expression to infer TP53 activity could have clinical benefit and deserves more attention (i.e. validation).

Reviewer #2:

Asprosin, as identified by the authors' group, is reported to stimulate glucose release from the liver and also centrally act as an orexigenic hormone. The present study developed monoclonal antibodies for asprosin and demonstrated that antibody-based asprosin depletion lowered food intake, prevented diet-induced body weight gain, and lowered blood glucose levels in mice. Overall the data are supportive of the conclusion; however, several concerns were identified as follows:

1) One of the central issues is the specificity of the antibody action. The authors should demonstrate if the effect of the asprosin antibodies is blunted in mice that lack either asporosin or its receptor OR4M1.

2) Previous studies from the authors' group show that asprosin acts on hepatocytes and triggers cAMP signaling. The authors should examine if the neutral antibodies blunt the cAMP signaling in DIO mice.

3) Similarly, asprosin was shown to stimulate AgRP+ neurons. The authors need to demonstrate the effect of asprosin antibodies on AgRP+ neuronal activity.

4) A recent paper (von Herrath et al. Cell Metabolism 2019) challenged the author's observation of the metabolic action of asprosin. The authors claim that this is due to "due to use of poor quality recombinant asprosin". However, no scientific evidence was presented. This study needs a more rigorous assessment of data reproducibility.

5) Most of the bodyweight data are presented as "body-weight change". However, the authors should present them as whole-body weight.

6) Some of the data points and stat analyses require further clarification. e.g.) lack of SE in Fig.1c, statistical analysis of Fig.3, Sup Fig.1

Reviewer #2:

The authors investigate the neural correlates of second order conditioning in carefully designed behavioural experiments coupling multivariate fMRI and functional connectivity. They found that the lateral OFC in connection with the amygdala, plays an important role. I think the paper represents a valuable addition to the human cognitive literature, where second order conditioning is surprisingly under-investigated. I have only a few suggestions to make.

I encourage the authors to complement the multivariate analyses with a standard univariate analysis. To be clear, I am not without seeing the added value of the multivariate approach, however, given the extensive literature on the neural bases of conditioning using univariate analyses and the strong prediction about directionally of the effects in the OFC (which should positively encoded expected values and rewards), I think the paper would definitely benefit from including the univariate results for the main contrasts / variables.

I am also curious to see the reaction times in the attentional control task analyzed to check if they were affected by the underlying conditioning procedure. Following the Pavlovian-to-Instrumental transfer theory, we should observe that the reaction times are slower for negative (aversive) stimuli and faster for positive (appetitive) stimuli.

Reviewer #2:

In this work, Sims and colleagues use resting-state functional connectivity and diffusion tractography in human connectome project data to examine the connectivity of the central and peripheral aspects of the primary visual cortex. They find that central V1 connects more strongly to regions of the prefrontal cortex interpreted as the Fronto-parietal network than does peripheral V1.

The idea that central V1 may be directly connected to control-related networks is an interesting one, and has fascinating implications for the study of top-down modulation of visual cortex function. However, I must say I am somewhat skeptical of these findings, for several reasons.

First, I find the a priori anatomical basis for these proposed connections to be dubious. The authors themselves describe how Markov et al. explicitly conducted tract tracing with central V1 and found connections with posterior frontal and parietal cortex, but nothing with areas classically associated with the fronto-parietal cortex. The authors propose that the inferior fronto-occipital fasciculus may connect V1 with lateral prefrontal regions only in humans. However, they provide no evidence for this suggestion. Indeed, my understanding of the iFOF is that it connects to inferior and lateral occipital cortex (see e.g. figures from the Takemura study cited in this work). Can the authors better support the idea that the iFOF might be the route of connection between V1 and frontal cortex?

Second, I am concerned that both 1) the Central V1 ROI employed in this work and 2) the inferior frontal cortex region showing strong FC with that Central V1 ROI overlap very closely with regions where we have seen poor BOLD signal in our own fMRI data (I would like to attach a figure if possible).

We are not confident what the source of the poor signal might be in posterior occipital or inferior frontal cortex; we suspect the presence of large veins (possibly the transverse sinus in V1; see Winawer et al., 2010, Journal of Vision). In any case, the data quality is low enough that we believe our data should not be considered to represent actual neural function in those regions. Can the authors demonstrate convincingly that this is not the case in their HCP data?

Third, I have an issue with the localization of effects in this paper. The paper describes effects in the fronto-parietal network throughout the manuscript, including the title. How surprising, then, that the strongest effects are not in the FP network at all! Figure 4A makes it very clear that the largest effects are in the IFG, which is outside the green outlines describing the extent of the fronto-parietal network, but inside the Default network. Figure 3A also supports this Default-centric localization, with Central V1 effects in posterior lateral parietal, medial parietal, and superior frontal cortex, all outside FP but inside Default. Since the FC effects are not actually primarily in FP, I see no reason why FP should be used as a mask in Figure 5. Indeed, the authors should show the localization of SC effects throughout the cortex, not just in FP. I also see no reason why these V1-Default connections should be characterized in any way as "attention" or "control".

Fourth, I feel that these FC and SC differences are wildly over-interpreted. From the scale, the actual strength of FC and SC between central V1 and lateral parietal cortex is extremely weak (around Z(r) = .1 for FC and p-track = .1 for SC). Under no circumstances would I believe that either of those values represents any sort of real connection. Cortical regions with direct structural connections have much stronger FC values, as do regions that influence each other indirectly via multi-step connections. Further, very large portions of the brain probably have both stronger FC and SC to central V1 than these FP regions (the authors show this for FC but exclude this info for SC). Most glaringly, I certainly don't believe there is a "direct structural connection" as is claimed in the discussion--a claim based, strangely, on the spatial correspondence between the structural and functional maps, which really has nothing to do with any evidence for a direct connection.

Finally, the authors must note that p values may not be used for spatial correlations between brain maps. This is because these maps are always highly autocorrelated, which violates the independence assumption of the correlation procedure.

Reviewer #2:

In the manuscript, "Structural characterization of an RNA bound antiterminator protein reveals a successive binding mode," the authors present the solved crystal structure of Enterococcus faecalis EutV by itself as well as bound to its RNA substrate. In previous work, the RNA substrate was proposed to consist of a dual hairpin and the genetics strongly suggested that both hairpins of this feature were crucial to functional antitermination in vivo. The finding revealed by the crystal structure in this work is that the EutV dimer does not appear to bind both hairpins simultaneously. The structure shows one EutV chain binding a hairpin in one RNA molecule and the second binding a second hairpin in a separate RNA molecule. The orientation of the two ANTAR domains is such that it is not possible to bind one RNA molecule simultaneously. Based on their findings, the authors propose a model of successive antitermination in which EutV binds to the first hairpin as it is generated by RNA polymerase and then this somehow favors binding to the second hairpin overlapping the terminator sequence as soon as it is made to prevent terminator formation. My overall assessment is that this is potentially an important and interesting contribution to the fields of transcription termination/antitermination and RNA/protein structural biology. However, there are concerns with how conclusive the data is, how exactly the model can work, and a lack of experimental evidence for the model.

Major Comments:

1) One major concern about the structure is that it is of non-phosphorylated EutV bound to its RNA substrate. Two-component system regulators almost always undergo conformational changes upon phosphorylation and therefore I think it is still an open question whether the structure truly represents active EutV bound to RNA. Perhaps the ANTAR binding domains of the EutV dimer change orientation upon phosphorylation such that binding to both hairpins can occur.

2) If binding does only occur with one hairpin, then why are two necessary for activation? If it is impossible for one dimer to bind both hairpins simultaneously, how does binding to the first hairpin help binding to the second? This is not clearly explained. Also, no experimental evidence is presented to support the model.

3) Wording of the abstract does not well reflect the final model presented. The abstract makes it sound like the second hairpin is not important, which is not what is shown here or in the previous work. I think the authors should say a bit more about what the actual model is in the abstract to eliminate this misconception.

4) Ramesh et al. (2012) observed that EutV bound the eutP UTR with a higher KD (less efficiently) when just the P1 loop was used in an EMSA assay compared to P1/P2. This study found the same KD, whether P1, P2, or both are used in a SPR assay. Could the difference in these findings be related to the different techniques or the fact that slightly different versions of the EutV protein were used?

Reviewer #2:

The findings presented in this manuscript are really exciting. They show that selection is happening at multiple scales - among viruses within a cell - and between their host cells within a population. The conflict between these levels of selection results in evolved populations that are less fit than the ancestors. This result is exciting because it happens repeatedly in independently-evolving populations, showing that it can be a general result. It is also an example of how a non-transitive interaction can evolve de novo, as the authors claim in the manuscript. The experiments seem to rule out most alternative hypotheses. However, the authors could explain their reasoning more clearly in some cases.

1) In particular I found it difficult to understand some of their conclusions on page 9, in the first paragraph around lines 210 - 219, without rereading, rewriting results, and lots of thinking. On lines 211-213, they state that production of active toxin or maintenance of the virus has no detectable fitness cost to the host". There are a lot of comparisons to think through here to get to that conclusion, and I think the average reader needs to be taken through that. Even though I have some experience thinking about costs and how they can be estimated, I still spent quite a lot of time trying to follow the logic from figure A to that statement. In fact, I still do not understand how they are distinguishing between 'production of active toxin' and 'maintenance of the virus'. I also had to spend a lot of time thinking through the results in figure 3 and the conclusion stated on line 217.

2) I think it would be helpful to the reader, and interesting, if there were more of an explanation about WHY K+|+ cells have positive frequency-dependent fitness relative to K-|- cells. Why is the presence of an active virus and immunity more beneficial at higher frequencies?