Reviewer #2 (Public Review):

Cuevas et al. investigate the stimulus selectivity of surround-induced responses in the mouse primary visual cortex (V1). While classical experiments in non-human primates and cats have generally demonstrated that stimuli in the surround receptive field (RF) of V1 neurons only modulate activity to stimuli presented in the center RF, without eliciting responses when presented in isolation, recent studies in mouse V1 have indicated the presence of purely surround-induced responses. These have been linked to prediction error signals. In this study, the authors build on these previous findings by systematically examining the stimulus selectivity of surround-induced responses.

Using neuropixels recordings in V1 and the dorsal lateral geniculate nucleus (dLGN) of head-fixed, awake mice, the authors presented various stimulus types (gratings, noise, surfaces) to the center and surround, as well as to the surround only, while also varying the size of the stimuli. Their results confirm the existence of surround-induced responses in mouse V1 neurons, demonstrating that these responses do not require spatial or temporal coherence across the surround, as would be expected if they were linked to prediction error signals. Instead, they suggest that surround-induced responses primarily reflect the representation of the achromatic surface itself.

The literature on center-surround effects in V1 is extensive and sometimes confusing, likely due to the use of different species, stimulus configurations, contrast levels, and stimulus sizes across different studies. It is plausible that surround modulation serves multiple functions depending on these parameters. Within this context, the study by Cuevas et al. makes a significant contribution by exploring the relationship between surround-induced responses in mouse V1 and stimulus statistics. The research is meticulously conducted and incorporates a wide range of experimental stimulus conditions, providing valuable new insights regarding center-surround interactions.

However, the current manuscript presents challenges in readability for both non-experts and experts. Some conclusions are difficult to follow or not clearly justified.

I recommend the following improvements to enhance clarity and comprehension:

(1) Clearly state the hypotheses being tested at the beginning of the manuscript.

(2) Always specify the species used in referenced studies to avoid confusion (esp. Introduction and Discussion).

(3) Briefly summarize the main findings at the beginning of each section to provide context.

(4) Clearly define important terms such as "surface stimulus" and "early vs. late stimulus period" to ensure understanding.

(5) Provide a rationale for each result section, explaining the significance of the findings.

(6) Offer a detailed explanation of why the results do not support the prediction error signal hypothesis but instead suggest an encoding of the achromatic surface.

These adjustments will help make the manuscript more accessible and its conclusions more compelling.

Reviewer #2 (Public Review):

Summary:

The manuscript presenting the discovery of a heparan-sulfate (HS) binding domain in monkeypox virus (MPXV) H3 protein as a new anti-poxviral drug target, presented by Bin Zhen and co-workers, is of interest, given that it offers a potentially broad antiviral substance to be used against poxviruses. Using new computational biology techniques, the authors identified a new alpha-helical domain in the H3 protein, which interacts with cell surface HS, and this domain seems to be crucial for H3-HS interaction. Given that this domain is conserved across orthopoxviruses, authors designed protein inhibitors. One of these inhibitors, AI-PoxBlock723, effectively disrupted the H3-HS interaction and inhibited infection with Monkeypox virus and Vaccinia virus. The presented data should be of interest to a diverse audience, given the possibility of an effective anti-poxviral drug. 

Strengths:

In my opinion, the experiments done in this work were well-planned and executed. The authors put together several computational methods, to design poxvirus inhibitor molecules, and then they test these molecules for infection inhibition.

Weaknesses:

One thing that could be improved, is the presentation of results, to make them more easily understandable to readers, who may not be experts in protein modeling programs. For example, figures should be self-explanatory and understood on their own, without the need to revise text. Therefore, the figure legend should be more informative as to how the experiments were done.

Reviewer #3 (Public Review):

Summary: Through a rigorous methodology, the authors demonstrated that within 11 different primates, the shape of the brain followed a universal scaling law with fractal properties. They enhanced the universality of this result by showing the concordance of their results with a previous study investigating 70 mammalian brains, and the discordance of their results with other folded objects that are not brains. They incidentally illustrated potential applications of this fractal property of the brain by observing a scale-dependant effect of aging on the human brain.

Strengths:<br /> - New hierarchical way of expressing cortical shapes at different scales derived from previous report through implementation of a coarse-graining procedure<br /> - Investigation of 11 primate brains and contextualisation with other mammals based on prior literature<br /> - Proposition of tool to analyse cortical morphology requiring no fine tuning and computationally achievable<br /> - Positioning of results in comparison to previous works reinforcing the validity of the observation.<br /> - Illustration of scale-dependance of effects of brain aging in the human.

Weaknesses:<br /> - The notion of cortical shape, while being central to the article, is not really defined, leaving some interpretation to the reader<br /> - The organization of the manuscript is unconventional, leading to mixed contents in different sections (sections mixing introduction and method, methods and results, results and discussion...). As a result, the reader discovers the content of the article along the way, it is not obvious at what stages the methods are introduced, and the results are sometimes presented and argued in the same section, hindering objectivity.<br /> To improve the document, I would suggest a modification and restructuring of the article such that: 1) by the end of the introduction the reader understands clearly what question is addressed and the value it holds for the community, 2) by the end of the methods the reader understands clearly all the tools that will be used to answer that question (not just the new method), 3) by the end of the results the reader holds the objective results obtained by applying these tools on the available data (without subjective interpretations and justifications), and 4) by the end of the discussion the reader understands the interpretation and contextualisation of the study, and clearly grasps the potential of the method depicted for the better understanding of brain folding mechanisms and properties.

Reviewer #3 (Public Review):

In the manuscript titled "Structure and Evolution of Alanine/Serine Decarboxylases and the Engineering of Theanine Production," Wang et al. solved and compared the crystal structures of Alanine Decarboxylase (AlaDC) from Camellia sinensis and Serine Decarboxylase (SerDC) from Arabidopsis thaliana. Based on this structural information, the authors conducted both in vitro and in vivo functional studies to compare enzyme activities using site-directed mutagenesis and subsequent evolutionary analyses. This research has the potential to enhance our understanding of amino acid decarboxylase evolution and the biosynthetic pathway of the plant specialized metabolite theanine, as well as to further its potential applications in the tea industry.

Reviewer #3 (Public Review):

This is an interesting manuscript that builds off of this group's previous work focused on the interface between Hsf1, heat shock protein (HSP) mRNA production, and 3D genome topology. Here the group subjects the yeast Saccharomyces cerevisiae to either heat stress (HS) or ethanol stress (ES) and examines Hsf1 and Pol II chromatin binding, Histone occupancy, Hsf1 condensates, HSP gene coalescence (by 3C and live cell imaging), and HSP mRNA expression (by RT-qPCR and live cell imaging). The manuscript is well written, and the experiments seem well done, and generally rigorous, with orthogonal approaches performed to support conclusions. The main findings are that both HS and ES result in Hsf1/Pol II-dependent intergenic interactions, along with formation of Hsf1 condensates. Yet, while HS results in rapid and strong induction of HSP gene expression and Hsf1 condensate resolution, ES result in slow and weak induction of HSP gene expression without Hsf1 condensate resolution. Thus, the conclusion is somewhat phenomenological - that the same transcription factor can drive distinct transcription, topologic, and phase-separation behavior in response to different types of stress. While identifying a mechanistic basis for these results would be a tough task perhaps beyond the scope of this study, it would nevertheless be helpful to place these results in context with a series of other studies demonstrating across various organisms showing Hsf1 driving distinct activities dependent on the context of activation. Perhaps even more importantly, this work left out PMID: 32015439 which is particularly relevant considering that it shows that it is human HSF1 condensate resolution rather than simple condensate formation that is associated with HSF1 transcriptional activity - which are similar to the findings here with this particular dose of HS resulting in resolution and high transcriptional activity versus ES resulting in resolution failure and lower activity. It is also worth noting that the stresses themselves are quite different - ethanol can be used as a carbon source and so beyond inducing proteotoxic stress, the yeast are presumably adapting to this distinct metabolic state. Basically, it is not clear whether these differences are due to the dose of stress, versus we are looking at an early timepoint as ES initiates a genome-wide chromatin restructuring and gene expression reprogramming that goes beyond a response to proteotoxic stress. This reviewer is not suggesting a barrage of new experiments, but perhaps discussion points to contextualize results.

Comments on latest version:

The authors have addressed my concerns.

Reviewer #2 (Public Review):

Summary:

This manuscript titled "Identification of pharmacological inducers of a reversible hypometabolic state for whole organ preservation" reports the effects of delta opioid receptor activator SNC80 and its modified analog WB3 with ~1,000 times less delta opioid receptor binding activity on metabolic state.

Strengths:

This is an interesting study with potentially broad implications for organ preservation.

Weaknesses:

However, there are several limitations which raise concerns.

(1) The authors developed an analog of a known delta opioid receptor activator SNC80 with three orders of magnitude lesser binding with the delta opioid receptor WB3. This will likely reduce the undesirable effects of SNC80 while preserving metabolic slowing needed for organ preservation. Yet, most experiments were done with SNC80, not the superior modification, WB3, shown in only a limited set of experiments, Figure 3.

(2) The heart is one of the most challenging organs to preserve, and some experiments are done to establish the metabolic effects of SNC80. However, the biodistribution study, shown in Figure 2, conspicuously omitted the heart.

(3) I do not understand the design of the electrophysiology and contractility experiments with the porcine hearts. How did you defibrillate the hearts after removal and establishing perfusion? Lines 173-175 on Page 7 state: "After defibrillation with epinephrine, the P and QRS waveforms were visible in ECGs from 3 of 4 SNC80-treated hearts (Table S1), suggesting that those hearts regain atrial and ventricular polarization." Please clarify. Defibrillation is done with an electric shock. Also, please show the ECG recordings to support your conclusions about "polarization." What did you mean by "polarization"? Depolarization? Repolarization? Or resting potential. To establish a normal physiological state, please show ECG waveforms and present data on basic ECG characteristics: heart rate, PQ and QT intervals, and P and QRS durations. I recommend perfusion of the porcine heart with WB3, not only SNC80.

(4) Pathology data also raises concerns. The histology images shown in Figure 4f are not quantified, and they show apparently higher levels of tissue disruption in SNC80-treated tissue vs vehicle-treated. The test (lines 169-171) confirms this concern: "In some hearts treated with SNC80, greater waviness of muscle fibers was observed, possibly indicating a state of muscle contraction." It will be helpful to measure markers of apoptosis and necrosis and to apply TTC viability staining.

(5) The apparent state of contracture suggests a higher degree of myocardial damage and a high intracellular calcium level in SNC80-treated hearts. The authors suggested that the sodium-calcium exchanger NCX is a possible target of SNC80 and could be responsible for the "hypometabolic state." However, NCX1 is critically important in the extrusion of cytosolic Ca2+ during the diastolic phase. Failure to remove excessive calcium and restore ionic homeostasis would lead to calcium overload and heart failure.

(6) I am surprised the authors did not consider using the gold standard assay for measuring mitochondrial function in cells by the Seahorse Cell Mito Stress Test.

Comments on revised version:

I am satisfied with the revisions. The authors addressed major concerns with new data and/or provided satisfactory rebuttal.

Reviewer #2 (Public Review):

The authors use ThT dye as a Nernstian potential dye in E. coli. Quantitative measurements of membrane potential using any cationic indicator dye are based on the equilibration of the dye across the membrane according to Boltzmann's law.

Ideally, the dye should have high membrane permeability to ensure rapid equilibration. Others have demonstrated that E.coli cells in the presence of ThT do not load unless there is blue light present, that the loading profile does not look like it is expected for a cationic Nernstian dye. They also show that the loading profile of the dye is different for E.coli cells deleted for the TolC pump. I, therefore, objected to interpreting the signal from the ThT as a Vm signal when used in E.coli. Nothing the authors have said has suggested that I should be changing this assessment.

Specifically, the authors responded to my concerns as follows:

(1) 'We are aware of this study, but believe it to be scientifically flawed. We do not cite the article because we do not think it is a particularly useful contribution to the literature.' This seems to go against ethical practices when it comes to scientific literature citations. If the authors identified work that handles the same topic they do, which they believe is scientifically flawed, the discussion to reflect that should be included.

(2)'The Pilizota group invokes some elaborate artefacts to explain the lack of agreement with a simple Nernstian battery model. The model is incorrect not the fluorophore.'<br /> It seems the authors object to the basic principle behind the usage of Nernstian dyes. If the authors wish to use ThT according to some other model, and not as a Nernstian indicator, they need to explain and develop that model. Instead, they state 'ThT is a Nernstian voltage indicator' in their manuscript and expect the dye to behave like a passive voltage indicator throughout it.

(3)'We think the proton effect is a million times weaker than that due to potassium i.e. 0.2 M K+<br /> versus 10-7 M H+. We can comfortably neglect the influx of H+ in our experiments.'<br /> I agree with this statement by the authors. At near-neutral extracellular pH, E.coli keeps near-neutral intracellular pH, and the contribution from the chemical concentration gradient to the electrochemical potential of protons is negligible. The main contribution is from the membrane potential. However, this has nothing to do with the criticism to which this is the response of the authors. The criticism is that ThT has been observed not to permeate the cell without blue light. The blue light has been observed to influence the electrochemical potential of protons (and given that at near-neutral intracellular and extracellular pH this is mostly the membrane potential, as authors note themselves, we are talking about Vm effectively). Thus, two things are happening when one is loading the ThT, not just expected equilibration but also lowering of membrane potential. The electrochemical potential of protons is coupled via the membrane potential to all the other electrochemical potentials of ions, including the mentioned K+.

(4) 'The vast majority of cells continue to be viable. We do not think membrane damage is dominating.' In response to the question on how the authors demonstrated TMRM loading and in which conditions (and while reminding them that TMRM loading profile in E.coli has been demonstrated in Potassium Phosphate buffer). The request was to demonstrate TMRM loading profile in their condition as well as to show that it does not depend on light. Cells could still be viable, as membrane permeabilisation with light is gradual, but the loading of ThT dye is no longer based on simple electrochemical potential (of the dye) equilibration.

(5) On the comment on the action of CCCP with references included, authors include a comment that consists of phrases like 'our understanding of the literature' with no citations of such literature. Difficult to comment further without references.

(6) 'Shielding would provide the reverse effect, since hyperpolarization begins in the dense centres of the biofilms. For the initial 2 hours the cells receive negligible blue light. Neither of the referee's comments thus seem tenable.'<br /> The authors have misunderstood my comment. I am not advocating shielding (I agree that this is not it) but stating that this is not the only other explanation for what they see (apart from electrical signaling). The other I proposed is that the membrane has changed in composition and/or the effective light power the cells can tolerate. The authors comment only on the light power (not convincingly though, giving the number for that power would be more appropriate), not on the possible changes in the membrane permeability.

(7) 'The work that TolC provides a possible passive pathway for ThT to leave cells seems slightly niche. It just demonstrates another mechanism for the cells to equilibrate the concentrations of ThT in a Nernstian manner i.e. driven by the membrane voltage.' I am not sure what the authors mean by another mechanism. The mechanism of action of a Nernstian dye is passive equilibration according to the electrochemical potential (i.e. until the electrochemical potential of the dye is 0).

(8) 'In the 70 years since Hodgkin and Huxley first presented their model, a huge number of similar models have been proposed to describe cellular electrophysiology. We are not being hyperbolic when we state that the HH models for excitable cells are like the Schrödinger<br /> equation for molecules. We carefully adapted our HH model to reflect the currently understood electrophysiology of E. coli.'

I gave a very concrete comment on the fact that in the HH model conductivity and leakage are as they are because this was explicitly measured. The authors state that they have carefully adopted their model based on what is currently understood for E.coli electrophysiology. It is not clear how. HH uses gKn^4 based on Figure2 here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1392413/pdf/jphysiol01442-0106.pdf, i.e. measured rise and fall of potassium conductance on msec time scales. I looked at the citation the authors have given and found a resistance of an entire biofilm of a given strain at 3 applied voltages. So why n^4 based on that? Why does unknown current have gqz^4 form? Sodium conductance in HH is described by m^3hgNa (again based on detailed conductance measurements), so why unknown current in E.coli by gQz^4? Why leakage is in the form that it is, based on what measurement?

Throughout their responses, the authors seem to think that collapsing the electrochemical gradient of protons is all about protons, and this is not the case. At near neutral inside and outside pH, the electrochemical potential of protons is simply membrane voltage. And membrane voltage acts on all ions in the cell.

Authors have started their response to concrete comments on the usage of ThT dye with comments on papers from my group that are not all directly relevant to this publication. I understand that their intention is to discredit a reviewer but given that my role here is to review this manuscript, I will only address their comments to the publications/part of publications that are relevant to this manuscript and mention what is not relevant.

Publications in the order these were commented on.

(1) In a comment on the paper that describes the usage of ThT dye as a Nernstian dye authors seem to talk about a model of an entire active cell.<br /> 'Huge oscillations occur in the membrane potentials of E. coli that cannot be described by the SNB model.' The two have nothing to do with each other. Nernstian dye equilibrates according to its electrochemical potential. Once that happens it can measure the potential (under the assumption that not too much dye has entered and thus lowered too much the membrane potential under measurement). The time scale of that is important, and the dye can only measure processes that are slower than that equilibration. If one wants to use a dye that acts under a different model, first that needs to be developed, and then coupled to any other active cell model.

(2) The part of this paper that is relevant is simply the usage of TMRM dye. It is used as Nernstian dye, so all the above said applies. The rest is a study of flagellar motor.

(3) The authors seem to not understand that the electrochemical potential of protons is coupled to the electrochemical potentials of all other ions, via the membrane potential. In the manuscript authors talk about, PMF~Vm, as DeltapH~0. Other than that this publication is not relevant to their current manuscript.

(4) The manuscript in fact states precisely that PMF cannot be generated by protons only and some other ions need to be moved out for the purpose. In near neutral environment it stated that these need to be cations (K+ e.g.). The model used in this manuscript is a pump-leak model. Neither is relevant for the usage of ThT dye.

Further comments include, along the lines of:

'The editors stress the main issue raised was a single referee questioning the use of ThT as an indicator of membrane potential. We are well aware of the articles by the Pilizota group and we believe them to be scientifically flawed. The authors assume there are no voltage-gated ion channels in E. coli and then attempt to explain motility data based on a simple Nernstian battery model (they assume E. coli are unexcitable<br /> matter). This in turn leads them to conclude the membrane dye ThT is faulty, when in fact it is a problem with their simple battery model.'

The only assumption made when using a cationic Nernstian dye is that it equilibrates passively across the membrane according to its electrochemical potential. As it does that, it does lower the membrane potential, which is why as little as possible is added so that this is negligible. The equilibration should be as fast as possible, but at the very least it should be known, as no change in membrane potential can be measured that is faster than that.

This behaviour should be orthogonal to what the cell is doing, it is a probe after all. If the cell is excitable, a Nernstian dye can be used, as long as it's still passively equilibrating and doing so faster than any changes in membrane potential due to excitations of the cells. There are absolutely no assumptions made on the active system that is about to be measured by this expected behaviour of a Nernstian dye. And there shouldn't be, it is a probe. If one wants to use a dye that is not purely Nernstian that behaviour needs to be described and a model proposed. As far as I can find, authors do no such thing.

There is a comment on the use of a flagellar motor as a readout of PMF, stating that the motor can be stopped by YcgR citing the work from 2023. Indeed, there is a range of references such as https://doi.org/10.1016/j.molcel.2010.03.001 that demonstrate this (from around 2000-2010 as far as I am aware). The timescale of such slowdown is hours (see here Figure 5 https://www.cell.com/cell/pdf/S0092-8674(10)00019-X.pdf). Needless to say, the flagellar motor when used as a probe, needs to stay that in the conditions used. Thus one should always be on the lookout at any other such proteins that could slow it down and we are not aware of yet or make the speed no longer proportional to the PMF. In the papers my group uses the motor the changes are fast, often reversible, and in the observation window of 30min. They are also the same with DeltaYcgR strain, which we have not included as it seemed given the time scales it's obvious, but certainly can in the future (as well as stay vigilant on any conditions that would render the motor a no longer suitable probe for PMF).

Reviewer #2 (Public Review):

Summary:<br /> Mistri et al explore the role of SLAM-SAP signaling in the developmental programming of innate-like gd T cell subsets. Using proteo-genomics, they determined that abrogation of SLAM-SAP signaling altered that programming, reducing some IL-17 producing subsets, including a novel Vγ4 γδT1 subset, and diverting gdTCR-expressing precursors to the ab fate. Altogether, this is a very thorough, thoughtfully interpreted study that adds significantly to our understanding of the contribution of the SLAM-SAP pathway to lineage specification. A particularly interesting element is the role of SLAM-SAP in preventing gd17 progenitors from switching fates and adopting the ab fate.

Comments on revised version:

The authors have addressed the minor issues raised in the original submission.

Reviewer #2 (Public Review):

Summary:

This work demonstrates that when E. coli cells divide, and division is not quite symmetric, the smaller cell has a higher growth rate than the larger cell at the beginning, but not the end, of the cell cycle. The authors then demonstrate that smaller cells have a higher ribosome concentration than larger cells, which is consistent with the idea that the two cells receive roughly equal numbers of ribosomes at division because, as they also observe, ribosomes are excluded by the nucleoid from the middle of the mother cell. The experimental observations are reproduced by a mathematical model that assumes growth is driven by ribosome concentration, with contributions from metabolism and active feedback.

Strengths:

The work provides strong evidence in support of the growing consensus that cells correct size fluctuations by modulating growth rate, within a cell cycle and on a single-cell basis. It also offers a plausible explanation for the correction mechanism by showing that ribosomes are excluded from the middle of a mother cell and have a higher concentration in the smaller daughter cell. The work is clearly written and benefits from a strong coupling between the experimental and modeling results. It provides a solid contribution to the field of single-cell bacterial growth control.

Weaknesses:

Although the results strongly suggest it, the work does not explicitly demonstrate (e.g. by direct perturbation) that higher ribosome concentration is the cause of the higher growth rate. Also, it is unclear why an active compensation mechanism is needed in the model, i.e., why size-dependent growth (via ribosome concentration) does not correct growth rate perturbations within a cell cycle automatically.

https://www.wikidata.org/wiki/Q82069695

https://en.m.wikipedia.org/wiki/SARS-CoV-2

Reviewer #2 (Public Review):

Summary:

This work describes the structure of Heparan-alpha-glucosaminide N-acetyltransferase (HGSNAT), a lysosomal membrane protein that catalyzes the acetylation reaction of the terminal alpha-D-glucosamine group required for degradation of heparan sulfate (HS). HS degradation takes place during the degradation of the extracellular matrix, a process required for restructuring tissue architecture, regulation of cellular function and differentiation. During this process, HS is degraded into monosaccharides and free sulfate in lysosomes.

HGSNAT catalyzes the transfer of the acetyl group from acetyl-CoA to the terminal non-reducing amino group of alpha-D-glucosamine. The molecular mechanism by which this process occur has not been described so far. One of the main reasons to study the mechanism of HGSNAT is that multiple mutations spanning the entire sequence of the protein, such as, nonsense mutations, splice-site variants, and missense mutations lead to dysfunction that causes abnormal accumulation of HS within the lysosomes. This accumulation is a cause of mucopolysaccharidosis IIIC (MPS IIIC), an autosomal recessive neurodegenerative lysosomal storage disorder, for which there are no approved drugs or treatment strategies.<br /> This paper provides a 3.26A structure of HGSNAT, determined by single-particle cryo-EM. The structure reveals that HGSNAT is a dimer in detergent micelles, and a density assigned to acetyl-CoA. The authors speculate about the molecular mechanism of the acetylation reaction, map the mutations known to cause MPS IIIC on the structure and speculate about the nature of the HGSNAT disfunction caused by such mutations.

Strengths:

The paper describes a structure of HGSNAT a member of the transmembrane acyl transferase (TmAT) superfamily. The high-resolution of a HGSNAT bound to acetyl-CoA is important for our understanding of HGSNAT mechanism. The density map is of high-quality, except for the luminal domain. The location of the acetyl-CoA allows speculation about the mechanistic role of multiple residues surrounding this molecule. The authors thoroughly describe the architecture of HGSNAT and map the mutations leading to MPS IIIC.

Reviewer #2 (Public Review):

Summary:

This paper utilizes a neural network model to investigate how the brain employs an adaptive chunking strategy to effectively enhance working memory capacity, which is a classical and significant question in cognitive neuroscience. By integrating perspectives from both the 'slot model' and 'limited resource models,' the authors adopted a neural network model encompassing the prefrontal cortex and basal ganglia, introduced an adaptive chunking strategy, and proposed a novel hybrid model. The study demonstrates that the brain can adaptively bind various visual stimuli into a single chunk based on the similarity of color features (a continuous variable) among items in visual working memory, thereby improving working memory efficiency. Additionally, it suggests that the limited capacity of working memory arises from the computational characteristics of the neural system, rather than anatomical constraints.

Strengths:

The neural network model utilized in this paper effectively integrates perspectives from both slot models and resource models (i.e., resource-like constraints within a slot-like system). This methodological innovation provides a better explanation for the limited capacity of working memory. By simulating the neural networks of the prefrontal cortex and basal ganglia, the model demonstrates how to optimize working memory storage and retrieval strategies through reinforcement learning (i.e., the efficient management of access to and from working memory). This biologically plausible simulation offers a novel perspective on human working memory and potentially provides a novel explanation for the working memory difficulties observed in patients with Parkinson's disease and other disorders. Furthermore, the effectiveness of the model is validated through computational simulation experiments, yielding reliable and robust predictions.

Weaknesses:

The model employs a spiking neural network, which is relatively complex. Additionally, while this paper validates the effectiveness of chunking strategies used by the brain to enhance working memory efficiency through computational simulations, further comparison with related phenomena observed in cognitive neuroscience experiments on limited working memory capacity, such as the recency effect, is necessary to verify its generalizability.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Shore et al. investigate the consequent changes in excitability and synaptic efficacy of diverse neuronal populations in an animal model of juvenile epilepsy. Using electrophysiological patch-clamp recordings from dissociated neuronal cultures, the authors find diverging changes in two major populations of inhibitory cell types, namely somatostatin (SST)- and parvalbumin (PV)-positive interneurons, in mice expressing a variant of the KCNT1 potassium channel. They further suggest that the differential effects are due to a compensatory increase in the persistent sodium current in PV interneurons in pharmacological and in silico experiments. It remains unclear why this current is selectively enhanced in PV-interneurons.

Strengths:

(1) Heterozygous KCNT1 gain of function variant was used which more accurately models the human disorder.

(2) The manuscript is clearly written, and the flow is easy to follow. The authors explicitly state the similarities and differences between the current findings and the previously published results in the homozygous KCNT1 gain of function variant.

(3) This study uses a variety of approaches including patch clamp recording, in silico modeling and pharmacology that together make the claims stronger.

(4) Pharmacological experiments are fraught with off-target effects and thus it bolsters the authors' claims when multiple channel blockers (TTX and VU170) are used to reconstruct the sodium-activated potassium current.

Weaknesses:

(1) This study mostly relies on recordings in dissociated cortical neurons. Although specific WT interneurons showed intrinsic membrane properties like those reported for acute brain slices, it is unclear whether the same will be true for those cells expressing KCNT1 variants, especially when the excitability changes are thought to arise from homeostatic compensatory mechanisms. The authors do confirm that mutant SST-interneurons are hypoexcitable using an ex vivo slice preparation which is consistent with work for other KCTN1 gain of function variants (e.g. Gertler et al., 2022). However, the key missing evidence is the excitability state of mutant PV-interneurons, given the discrepant result of reduced excitability of PV cells reported by Gertler et al in acute hippocampal slices.

Reviewer #2 (Public Review):

Summary:

Complexin (Cplx) is expressed at nearly all chemical synapses. Mammalian Cplx comes in four different paralogs which are differentially expressed in different neurons or secretory cell types, either selectively or in combination with one or two other Cplx isoforms. Cplx binds with high affinity to assembled SNARE complexes and promotes evoked synchronous release. Cplx is assumed to preclude premature SV fusion by preventing full SNARE assembly, thereby arresting subsequent SNARE-driven fusion ("fusion-clamp" theory). The protein has multiple domains, the functions of which are controversially discussed. Cplx's function has been studied in a variety of model organisms including mouse, fly, worm, and fish with seemingly conflicting results which led to partly contradicting conclusions.<br /> Makee et al. study the function of mammalian Cplx2 in chromaffin cells by making use of Cplx2 ko mice to overexpress and functionally characterize mutant Cplx2 forms in cultured chromaffin cells. The main conclusion of the present study are:

The hydrophobic character of the amphipathic helix in Cplx's C-terminal domain is essential for inhibiting premature vesicle fusion at a [Ca2+]i of several hundreds of nM (pre-flash [Ca2+]i). The Cplx-mediated inhibition of fusion under these conditions does not rely on expression of either Syt1 or Syt7.

Slow-down of exocytosis by N-terminally truncated Cplx mutants in response to a [Ca2+]i of several µM (peak flash [Ca2+]i) occurs regardless of the presence or absence of Syt7 demonstrating that Cplx2 does not act as a switch favoring preferential assembly of the release machinery with Syt1,2 rather than the "slow" sensor Syt7.

Cplx's N-terminal domain is required for the Cplx2-mediated increase in the speed of exocytosis and faster onset of exocytosis which likely reflect an increased apparent Ca2+ sensitivity and faster Ca2+ binding of the release machinery.

Strengths:

The authors perform systematic truncation/mutational analyses of Cplx2. They analyze the impact of single and combined deficiencies for Cplx2 and Syt1 to establish interactions of both proteins.<br /> State-of-the-art methods are employed: Vesicle exocytosis is assayed directly and with high resolution using capacitance measurements. Intracellular [Ca2+] is controlled by loading via the patch-pipette and by UV-light induced flash-photolysis of caged [Ca2+]. The achieved [Ca2+ ] is measured with Ca2+ -sensitive dyes.<br /> The data is of high quality and the results are compelling.

Weaknesses:

With the exception of mammalian retinal ribbon synapses (and some earlier RNAi knock down studies which had off-target effects), there is little experimental evidence for a "fusion-clamp"-like function of Cplxs at mammalian synapses. At conventional mammalian synapses, genetic loss of Cplx (i.e. KO) consistently decreases AP-evoked release, and generally either also decreases spontaneous release rates or does not affect spontaneous release, which is inconsistent with a "fusion-clamp" theory. This is in stark contrast to invertebrate (D. m. and C. e.) synapses where genetic Cplx loss is generally associated with a strong upregulation of spontaneous release.

There are alternative scenarios explaining how Cplx may phenomenological "clamp" vesicle fusion rates without mechanistically assigning a "clamping" function to Cplx (Neher 2010, Neuron). In fact, changes in asynchronous release kinetics following conditioning AP trains observed at Cplx1 ko calyx of Held synapses do not favor a "fusion clamp" model (Chang et al., 2015, J.Neurosci.), while an alternative model, assigning Cplx the role of a "checkpoint" protein in SNARE assembly, quantitatively reproduces all experimental observations (Lopez et al., 2024, PNAS). It might be helpful for a reader to mention such alternative scenarios.

Reviewer #2 (Public Review):

In this manuscript, Rachubinski and colleagues provide a comprehensive clinical, immunological, and autoantibody assessment of autoimmune/inflammatory manifestations of patients with Down syndrome (DS) in a large number of patients with this disorder. These analyses confirm prior results of excess interferon and cytokine signals in DS patients and extend these observations to highlight early-onset immunological aberrancies, far before symptoms occur, as well as characterizing novel autoantibody reactivities in this patient population. Then, the authors report the interim analysis of an open-label, Phase II, clinical trial of the JAK1/3 inhibitor, tofacitinib, that aims to define the safety, clinical efficacy, and immunological outcomes of DS patients who suffer from inflammatory conditions of the skin. The clinical trial analysis indicates that the treatment is tolerated without serious adverse effects and that the majority of patients have experienced clinical improvement or remission in their corresponding clinical cutaneous manifestations as well as improvement or normalization of aberrant immunological signals such as cytokines.

The major strength of the study is the recruitment and uniform, systematic evaluation of an impressive number of DS patients. Moreover, the promising early results from the tofacitinib clinical trial pave the way for analysis of a larger number of patients within the Phase II trial and otherwise, which may lead to improved clinical outcomes for affected patients. An inherent weakness of such studies is the descriptive nature of several parameters and the relatively small size of tofacitinib-treated DS patients. However, the descriptive nature of some of the correlative research analyses is of scientific interest and is useful to generate hypotheses for future additional (including mechanistic) work, and treatment of 10 DS patients in a formal clinical trial at interim analysis is not a trivial task for a disease like this. The manuscript achieves the aims of the authors and the results support their conclusions. The authors appropriately acknowledge areas that require more research and areas that are not well understood. The results are represented in a useful manner and statistical methods and analyses appear sound.

Reviewer #2 (Public Review):

Summary:<br /> In this manuscript, the authors use the Drosophila model system to study the impact of mild head trauma on sex-dependent brain deficits. They identify Sex Peptide as a modulator of greater negative outcomes in female flies. Additionally, they observe that increased age at the time of injury results in worse outcomes, especially in females, and that this is due to chronic suppression of innate immune defense networks in mated females. The results demonstrate a novel signaling pathway that promotes age- and sex-dependent outcomes after head injury.

Strengths:<br /> The authors have modified their previously reported TBI model in flies to mimic mild TBI, which is novel. Methods are explained in detail, allowing for reproducibility. Experiments are rigorous with appropriate statistics. A number if important controls are included. The work tells a complete mechanistic story and adds important data to increase our understanding of sex-dependent differences in recovery after TBI. The Discussion is comprehensive and puts the work in context of the field.

Weaknesses: None<br /> The authors answered the following concerns, and I have no other concerns:<br /> A very minor weakness is that exact n values should be included in the figure legends. There should also be confirmation of knockdown by RNAi in female flies either by immunohistochemistry or qRT-PCR if possible.

Reviewer #2 (Public Review):

Wnt signaling is the name given to a cell-communication mechanism that cells employ to inform on each other's position and identity during development. In cells that receive the Wnt signal from the extracellular environment, intracellular changes are triggered that cause the stabilization and nuclear translocation of β-catenin, a protein that can turn on groups of genes referred to as Wnt targets. Typically these are genes involved in cell proliferation. Genetic mutations that affect Wnt signaling components can therefore affect tissue expansion. Loss of function of APC is a drastic example: APC is part of the β-catenin destruction complex, and in its absence, β-catenin protein is not degraded and constitutively turns on proliferation genes, causing cancers in the colon and rectum. And here lies the importance of the finding: β-catenin has for long been considered to be regulated almost exclusively by tuning its protein turnover. In this article, a new aspect is revealed: Ctnnb1, the gene encoding for β-catenin, possesses tissue-specific regulation with transcriptional enhancers in its vicinity that drive its upregulation in intestinal stem cells. The observation that there is more active β-catenin in colorectal tumors not only because the broken APC cannot degrade it, but also because transcription of the Ctnnb1 gene occurs at higher rates, is novel and potentially game-changing. As genomic regulatory regions can be targeted, one could now envision that mutational approaches aimed at dampening Ctnnb1 transcription could be a viable additional strategy to treat Wnt-driven tumors.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Zhang et al. examine neural activity in the motor cortex as monkeys make reaches in a novel target interception task. Zhang et al. begin by examining the single neuron tuning properties across different moving target conditions, finding several classes of neurons: those that shift their preferred direction, those that change their modulation gain, and those that shift their baseline firing rates. The authors go on to find an interesting, tilted ring structure of the neural population activity, depending on the target speed, and find that (1) the reach direction has consistent positioning around the ring, and (2) the tilt of the ring is highly predictive of the target movement speed. The authors then model the neural activity with a single neuron representational model and a recurrent neural network model, concluding that this population structure requires a mixture of the three types of single neurons described at the beginning of the manuscript.

Strengths:

I find the task the authors present here to be novel and exciting. It slots nicely into an overall trend to break away from a simple reach-to-static-target task to better characterize the breadth of how the motor cortex generates movements. I also appreciate the movement from single neuron characterization to population activity exploration, which generally serves to anchor the results and make them concrete. Further, the orbital ring structure of population activity is fascinating, and the modeling work at the end serves as a useful baseline control to see how it might arise.

Weaknesses:

While I find the behavioral task presented here to be excitingly novel, I find the presented analyses and results to be far less interesting than they could be. Key to this, I think, is that the authors are examining this task and related neural activity primarily with a single-neuron representational lens. This would be fine as an initial analysis since the population activity is of course composed of individual neurons, but the field seems to have largely moved towards a more abstract "computation through dynamics" framework that has, in the last several years, provided much more understanding of motor control than the representational framework has. As the manuscript stands now, I'm not entirely sure what interpretation to take away from the representational conclusions the authors made (i.e. the fact that the orbital population geometry arises from a mixture of different tuning types). As such, by the end of the manuscript, I'm not sure I understand any better how the motor cortex or its neural geometry might be contributing to the execution of this novel task.

Main Comments:

My main suggestions to the authors revolve around bringing in the computation through a dynamics framework to strengthen their population results. The authors cite the Vyas et al. review paper on the subject, so I believe they are aware of this framework. I have three suggestions for improving or adding to the population results:

(1) Examination of delay period activity: one of the most interesting aspects of the task was the fact that the monkey had a random-length delay period before he could move to intercept the target. Presumably, the monkey had to prepare to intercept at any time between 400 and 800 ms, which means that there may be some interesting preparatory activity dynamics during this period. For example, after 400ms, does the preparatory activity rotate with the target such that once the go cue happens, the correct interception can be executed? There is some analysis of the delay period population activity in the supplement, but it doesn't quite get at the question of how the interception movement is prepared. This is perhaps the most interesting question that can be asked with this experiment, and it's one that I think may be quite novel for the field--it is a shame that it isn't discussed.

(2) Supervised examination of population structure via potent and null spaces: simply examining the first three principal components revealed an orbital structure, with a seemingly conserved motor output space and a dimension orthogonal to it that relates to the visual input. However, the authors don't push this insight any further. One way to do that would be to find the "potent space" of motor cortical activity by regression to the arm movement and examine how the tilted rings look in that space (this is actually fairly easy to see in the reach direction components of the dPCA plot in the supplement--the rings will be highly aligned in this space). Presumably, then, the null space should contain information about the target movement. dPCA shows that there's not a single dimension that clearly delineates target speed, but the ring tilt is likely evident if the authors look at the highest variance neural dimension orthogonal to the potent space (the "null space")--this is akin to PC3 in the current figures, but it would be nice to see what comes out when you look in the data for it.

(3) RNN perturbations: as it's currently written, the RNN modeling has promise, but the perturbations performed don't provide me with much insight. I think this is because the authors are trying to use the RNN to interpret the single neuron tuning, but it's unclear to me what was learned from perturbing the connectivity between what seems to me almost arbitrary groups of neurons (especially considering that 43% of nodes were unclassifiable). It seems to me that a better perturbation might be to move the neural state before the movement onset to see how it changes the output. For example, the authors could move the neural state from one tilted ring to another to see if the virtual hand then reaches a completely different (yet predictable) target. Moreover, if the authors can more clearly characterize the preparatory movement, perhaps perturbations in the delay period would provide even more insight into how the interception might be prepared.

Reviewer #2 (Public Review):

Summary:<br /> After manually labelling 144 human adult hemispheres in the lateral parieto-occipital junction (LPOJ), the authors 1) propose a nomenclature for 4 previously unnamed highly variable sulci located between the temporal and parietal or occipital lobes, 2) focus on one of these newly named sulci, namely the ventral supralateral occipital sulcus (slocs-v) and compare it to neighbouring sulci to demonstrate its specificity (in terms of depth, surface area, gray matter thickness, myelination, and connectivity), 3) relate the morphology of a subgroup of sulci from the region including the slocs-v to the performance in a spatial orientation task, demonstrating behavioural and morphological specificity. In addition to these results, the authors propose an extended reflection on the relationship between these newly named landmarks and previous anatomical studies, a reflection about the slocs-v related to functional and cytoarchitectonic parcellations as well as anatomic connectivity and an insight about potential anatomical mechanisms relating sulcation and behaviour.

Strengths:<br /> - To my knowledge, this is the first study addressing the variable tertiary sulci located between the superior temporal sulcus (STS) and intra-parietal sulcus (IPS).<br /> - This is a very comprehensive study addressing altogether anatomical, architectural, functional and cognitive aspects.<br /> - The definition of highly variable yet highly reproductible sulci such as the slocs-v feeds the community with new anatomo-functional landmarks (which is emphasized by the provision of a probability map in supp. mat., which in my opinion should be proposed in the main body).<br /> - The comparison of different features between the slocs-v and similar sulci is useful to demonstrate their difference.<br /> - The detailed comparison of the present study with state of the art contextualises and strengthens the novel findings.<br /> - The functional study complements the anatomical description and points towards cognitive specificity related to a subset of sulci from the LPOJ<br /> - The discussion offers a proposition of theoretical interpretation of the findings<br /> - The data and code are mostly available online (raw data made available upon request).

Weaknesses:<br /> - While the identification of the sulci has been done thoroughly with expert validation, the sulci have not been labelled in a way that enables the demonstration of the reproducibility of the labelling.

The proposed methodology is convincing in identifying and studying the relationship between highly variable sulci and cognition. This improves our refined understanding of the general anatomical variability in the LPOJ and its potential functional/cognitive correlates. This work is important to the understanding of sulcal variability and its implications on functional and cognitive aspects.

Comments on revised version:

Thank you for the elegant and informative work.

Reviewer #2 (Public Review):

Summary:

This study shows that when excitatory DREADD receptors are expressed in the ventral area of the cervical spinal cord containing phrenic motoneurons, the systemic administration of the DREADD ligand J60 increases diaphragm EMG activity without altering respiratory rate. The authors took a non-selective expression approach in wild-type mice, as well as a more selective Cre-dependent approach in Chat-Cre mice and Chat-Cre rats to stimulate cervical motoneurons in the spinal cord. This is a proof of principle study that supports the use of DREADD technology to stimulate the motor output to the diaphragm.

Strengths:

The strengths of the study lie in the use of both mice and rats and testing activation of diaphragmatic activity with multiple experimental approaches to show that diaphragm EMG and tidal volume are increased.

Weaknesses:

Weaknesses of the study consist in the lack of some important control experiments to consolidate the findings: a test of DREADD ligand effects in the absence of viral construct; repeated respiratory challenges within the same recording session in whole body plethysmographs that could compromise the behaving experiments; and lastly, a limited qualitative analysis of the histological data that does not allow for confirmation of expression in phrenic motoneurons.

Reviewer #2 (Public Review):

Summary:

The authors set out to determine the role of Rtf1 in Cryptococcal biology, and demonstrate that Rtf1 acts independently of the Paf1 complex to exert regulation of Histone H2B monoubiquitylation (H2Bub1). The biological impact of the loss of H2Bub1 was observed in defects in morphogenesis, reduced production of virulence factors, and reduced pathogenic potential in animal models of cryptococcal infection.

Strengths:

The molecular data is quite compelling, demonstrating that the Rtf1-depednent functions require only this histone modifying domain of Rtf1, and are dependent on nuclear localization. A specific point mutation in a residue conserved with the Rtf1 protein in the model yeast demonstrates the conservation of that residue in H2Bub1 modification. Interestingly, whereas expression of the HMD alone suppressed the virulence defect of the rtf1 deletion mutant, it did not suppress defects in virulence factor production.

Weaknesses:

The authors use two different species of Cryptococcus to investigate the biological effect of Rtf1 deletion. The work on morphogenesis utilized C. deneoformans, which is well-known to be a robust mating strain. The virulence work was performed in the C. neoformans H99 background, which is a highly pathogenic isolate. The study would be more complete if each of these processes were assessed in the other strain to understand if these biological effects are conserved across the two species of Cryptococcus. H99 is not as robust in morphogenesis, but reproducible results assessing mating and filamentation in this strain have been performed. Similarly, C. deneoformans does produce capsule and melanin.

There are some concerns with the conclusions related to capsule induction. The images reported in Figure B are purported to be grown under capsule-inducing conditions, yet the H99 panel is not representative of the induced capsule for this strain. Given the lack of a baseline of induction, it is difficult to determine if any of the strains may be defective in capsule induction. Quantification of a population of cells with replicates will also help to visualize the capsular diversity in each strain population.

The authors demonstrate that for specific mating-related genes, the expression of the HMD recapitulated the wild-type expression pattern. The RNA-seq experiments were performed under mating conditions, suggesting specificity under this condition. The authors raise the point in the discussion that there may be differences in Rtf1 deposition on chromatin in H99, and under conditions of pathogenesis. The data that overexpression of HMD restores H2Bub1 by western is quite compelling, but does not address at which promoters H2Bub1 is modulating expression under pathogenesis conditions, and when full-length Rtf1 is present vs. only the HMD.

Reviewer #2 (Public Review):

Summary:

The manuscript expands the current bulk sequencing data deconvolution toolkit to include ATAC-seq. The EPIC-ATAC tool successfully predicts accurate proportions of immune cells in bulk tumour samples and EPIC-ATAC seems to perform well in benchmarking analyses. The authors achieve their aim of developing a new bulk ATAC-seq deconvolution tool.

Strengths:

The manuscript describes simple and understandable experiments to demonstrate the accuracy of EPIC-ATAC. They have also been incredibly thorough with their reference dataset collections and have been robust in their benchmarking endeavours and measured EPIC-ATAC against multiple datasets and tools. This tool will be valuable to the community it serves.

Reviewer #2 (Public Review):

Summary:

In this study, the authors identified a previously unrecognized organ interaction where limb immobilization induces thermogenesis in BAT. They showed that limb immobilization by cast fixation enhances the expression of UCP1 as well as amino acid transporters in BAT, and amino acids are supplied from skeletal muscle to BAT during this process, likely contributing to increased thermogenesis in BAT. Furthermore, the experiments with IL-6 knockout mice and IL-6 administration to these mice suggest that this cytokine is likely involved in the supply of amino acids from skeletal muscle to BAT during limb immobilization.

Strengths:

The function of BAT plays a crucial role in the regulation of an individual's energy and body weight. Therefore, identifying new interventions that can control BAT function is not only scientifically significant but also holds substantial promise for medical applications. The authors have thoroughly and comprehensively examined the changes in skeletal muscle and BAT under these conditions, convincingly demonstrating the significance of this organ interaction.

Weaknesses:

Through considerable effort, the authors have demonstrated that limb-immobilized mice exhibit changes in thermogenesis and energy metabolism dynamics at their steady state. However, The impact of immobilization on the function of skeletal muscle and BAT during cold exposure has not been thoroughly analyzed.

Reviewer #2 (Public Review):

Intrinsic properties of a neuron refer to the ion channels that a neuron expresses. These ion channels determine how a neuron responds to its inputs. How intrinsic properties link to behavior remains poorly understood. Medina and Margoliash address this question using the zebra finch, a well-studied songbird. Previous studies from their lab and other labs have shown that the intrinsic properties of adult songbird basal-ganglia projecting premotor neurons, are more similar within a bird than across birds. Across birds, this similarity is related to the extent of similarity in the songs; the more similar the song between two birds, the more similar the intrinsic properties between the neurons of these two birds. Finally, the intrinsic properties of these neurons change over the course of development and are sensitive to intact auditory feedback. However, the song features that relate to these intrinsic properties and the function of the within-bird homogeneity of intrinsic properties are unclear.

In this manuscript, the authors address these two questions by examining the intrinsic properties of basal-ganglia projecting premotor neurons in zebra finch brain slices. Specifically, they focus on the Ih current (as this is related to rhythmic activity in many pattern-generating circuits) and correlate the properties of the Ih current with song features. They find that the sag ratio (a measure of the driving force of the Ih current) and the rebound area (a measure of the post-inhibitory depolarisation) are both correlated with the temporal features of the song. First, they show the presence of correlations between the length of the song motif and the length of the longest syllable (most often a harmonic stack syllable). Based on this, they conclude that longer song motifs are composed of longer syllables. Second, they show that HVCX neurons within a bird have more similar sag ratios and rebound areas than across birds. Third, the mean sag ratio and mean rebound areas across birds were correlated with the duration of the longest harmonic stack within the song. These two results suggest that IPs are correlated with the temporal structure of the song. To further test this, the authors used natural and experimental tutoring procedures to have birds that learned two different types of songs that only differed in length; the longer song had an extra harmonic stack at the end. Using these two sets of birds, the authors find larger sag ratios and higher firing frequencies in birds with longer songs. Fifth, they show that the post-inhibitory rebound area allows neurons to respond to excitatory inputs and produce spikes. Neurons with a larger rebound area have a larger time window for responding to excitatory inputs. Based on this, they speculate that HVCX neurons with larger rebound areas integrate over larger time windows. Finally, they make a network model of HVC and show that one specific model could explain sequence-specific bursting of HVCX neurons.

Strengths

The question being addressed is an interesting question and the authors use appropriate techniques. The authors find a new temporal structure within the song, specifically, they find that longer songs typically have more syllables and longer syllables. As far as I know, this has not been shown earlier. The authors build on existing literature to suggest that IPs of HVCX neurons are correlated with the temporal structure of songs.

Weaknesses

I have a number of concerns with the statistics and interpretation of the results, insufficient controls for one experiment, and the specifics of the model that affect the implications of these results. These concerns are listed in the recommendations for the authors.

Reviewer #2 (Public Review):

Summary:

Hebin et al reported a fascinating story about antibiotic persistence in the biofilms. First, they set up a model to identify the increased persisters in the biofilm status. They found that the adhesion of bacteria to the surface leads to increased c-di-GMP levels, which might lead to the formation of persisters. To figure out the molecular mechanism, they screened the E.coli Keio Knockout Collection and identified the HipH. Finally, the authors used a lot of data to prove that c-di-GMP not only controls HipH over-expression but also inhibits HipH activity, though the inhibition might be weak.

Strengths:

They used a lot of state-of-the-art technologies, such as single-cell technologies as well as classical genetic and biochemistry approaches to prove the concept, which makes the conclusions very solid. Overall, it is a very interesting and solid story that might attract diverse readers working with c-di-GMP, persisters, and biofilm.

Weaknesses:

(1) Is HipH the only target identified by screening the E.coli Keio Knockout Collection?

(2) Since the story is complicated, a diagrammatic picture might be needed to illustrate the whole story. And the title does not accurately summarize the novelty of this study.

(3) The ratio of mVenus NB to mScarlet-I (R) negatively correlates with the concentration of c-di-GMP. Therefore, R -1 demonstrates a positive correlation with the concentration of c-di-GMP. Is this method validated with other methods to quantify c-di-GMP， or used in other studies？

(4) References are missing throughout the manuscript. Please add enough references for every conclusion.

(5) The novelty of this study should be clearly written and compared with previous references. For example, is it the first study to report the mechanism that the adhesion of bacteria to the surface leads to increased persister formation?

(6) in vitro DNA cleavage assay. Why not use bacterial genomic DNA to test the cleaving of HipH on the bacterial genome?

(7) C-di-gmp -HipH is not a TA, it does not fit in the definition of the TA systems. You can say C-di-gmp is an antitoxin based on your study, but C-di-gmp -HipH is not a TA pair.

Reviewer #2 (Public Review):

Summary:

The manuscript by Munday et al. presents real-time predictions of geographic spread during an Ebola epidemic in north-eastern DRC. Predictions were elicited from individual experts engaged in outbreak response and from two mathematical models. The authors found comparable performance between experts and models overall, although the models outperformed experts in a few dimensions.

Strengths:

Both individual experts and mathematical models are commonly used to support outbreak response but rarely used together. The manuscript presents an in-depth analysis of the accuracy and decision-relevance of the information provided by each source individually and in combination.

Weaknesses:

A few minor methodological details are currently missing.

Reviewer #2 (Public Review):

Summary:<br /> The authors begin with the stated goal of gaining insight into the known repression of autophagy by Ezrin, a major membrane-actin linker that assembles signaling complexes on membranes. RNA and protein expression analysis is consistent with upregulation of lysosomal proteins in Ezrin-deficient MEFs, which the authors confirm by immunostaining and western blotting for lysosomal markers. Expression analysis also implicates EGF signaling as being altered downstream of Ezrin loss, and the authors demonstrate that Ezrin promotes relocalization of EGFR from the plasma membrane to endosomes. Ezrin loss impacts downstream MAPK/Akt/mTORC1 signaling, although the mechanistic links remain unclear. An Ezrin mutant Medaka fish line wa then generated to test Ezrin's role in retinal cells, which are known to be sensitive to changes in autophagy regulation. Phenotypes in this model appear generally consistent with observations made in cultured cells, though mild overall.

Strengths:<br /> Data on the impact of Ezrin-loss on relocalization of EGFR from the plasma membrane are extensive, and thoroughly demonstrate that Ezrin is required for EGFR internalization in response to EGF.

A new Ezrin-deficient in vivo model (Medaka fish) is generated.

Strong data demonstrates that Ezrin loss suppresses Akt signaling. Ezrin loss also clearly suppresses mTORC1 signaling in cell culture, although examination of mTORC1 activity is notably missing in Ezrin-deficient fish.

Weaknesses:<br /> LC3 is used as a readout of autophagy, however the lipidated/unlipidated LC3 ratio generally does not appear to change, thus there does not appear to be evidence that Ezrin loss is affecting autophagy in this study.

The conclusion is drawn that Ezrin loss suppresses EGF signaling, however this is complicated by a strong increase in phosphorylation of the p38 MAPK substrate MK2. Without additional characterization of MAPK and Erk signaling, the effect of Ezrin loss remains unclear.

Causative conclusions between effects on MAPK, Akt, and mTORC1 signaling are frequently drawn, but the data only demonstrate correlations. For example, many signaling pathways can activate mTORC1 including MAPK/Erk, thus reduced mTORC1 activity upon Ezrin-loss cannot currently be attributed to reduced Akt signaling. Similarly, other kinases can phosphorylate TSC2 at the sites examined here, so the conclusion cannot be drawn that Ezrin-loss causes a reduction in Akt-mediated TSC2 phosphorylation. In Figure 7, the conclusion cannot be drawn that retinal degeneration results from aberrant EGFR signaling.

It is unclear why TSC1 is highlighted in the title, as there does not appear to be any specific regulation of TSC1 here.

In Figure 1 the conclusion is drawn that there is an increase in lysosome number with Ezrin KO, however it does not appear that the current analysis can distinguish an increased number from increased lysosome size or activity. Similarly, conclusions about increased lysosome "biogenesis" could instead reflect decreased turnover.

Immunoprecipitation data for a role for Ezrin as a signaling scaffold appear minimal and seem to lack important controls.

In Figure 3A it seems difficult to conclude that EGFR dimerization is reduced since the whole blot, including the background between lanes, is lighter on that side.

In Figure 6C specificity controls for the TSC1 and TSC2 antibodies are not included, but seem necessary since their localization patterns appear very different from each other in WT cells.

In Figure 7 the signaling effects in Ezrin-deficient fish are mild compared to cultured cells, and effects on mTORC1 are not examined. Further data on the retinal cell phenotypes would strengthen the conclusions.

In Figure 7F there appears to be more EGFR throughout the cell, so it is difficult to conclude that more EGFR at the PM in Ezrin-/- fish means reduced internalization.

Reviewer #2 (Public Review):

Summary:

This study investigates in mice neural mechanisms generating sighs, which are periodic large-amplitude breaths occurring during normal breathing that subserve physiological pulmonary functions and are associated with emotional states such as relief, stress, and anxiety. Sighs are generated by a structure called the preBötzinger complex (preBötC) in the medulla oblongata that generates various forms of inspiratory activity including sighs. The authors have previously described a circuit involving neurons producing bombesin-related peptides Neuromedin B (NMB) and gastrin-releasing peptide (GRP) that project to preBötC neurons expressing receptors for NMB (NMBRs) and GRP (GRPRs) and that activation of these preBötC neurons via these peptide receptors generates sighs. In this study, the authors further investigated mechanisms of sigh generation by applying optogenetic and chemogenetic strategies to selectively activate the subpopulations of preBötC neurons expressing NMBRs and/or GRPRs, and a separate subpopulation of neurons expressing somatostatin (SST) but not NMBRs and GRPRs. The authors present convincing evidence that sigh-like inspirations can be evoked by photostimulation of the preBötC neurons expressing NMBRs or GRPRs. Photostimulation of SST neurons can independently evoke sighs, and chemogenetic inhibition of these neurons can abolish sighs. The results presented support the authors' conclusion that the preBötC neurons expressing NMBRs or GRPRs produce sighs via pathways to downstream SST neurons. Thus, these studies have identified some of the preBötC cellular elements likely involved in generating sighs.

Strengths:

(1) This study employs an effective combination of electrophysiological, transgenic, optogenetic, chemogenetic, pharmacological, and neuron activity imaging techniques to investigate sigh generation by distinct subpopulations of preBötC neurons in mice.

(2) The authors extend previous studies indicating that there is a peptidergic circuit consisting of NMB and GRP expressing neurons that project from the parafacial (pF) nucleus region to the preBötC and provides sufficient input to generate sighs, since photoactivation of either pF NMB or GRP neurons evoke ectopic sighs in this study.

(3) Convincing evidence is presented that sighs can be evoked by direct photostimulation of preBötC neurons expressing NMBRs and/or GRPRs, and also a separate subpopulation of neurons expressing somatostatin (SST) but not NMBRs and GRPRs.

(4) The mRNA-expression data presented from in situ hybridization indicates that most preBötC neurons expressing NMBR, GRPR (or both) are glutamatergic and excitatory.

(5) Measurements in slices in vitro indicate that only the NMBR-expressing neurons are normally rhythmically active during normal inspiratory activity and endogenous sigh activity.

(6) Evidence is presented that activation of preBötC NMBRs and/or GRPRs is not necessary for sigh production, suggesting that sighs are not the unique product of the preBötC bombesin-peptide signaling pathway.

(7) The novel conclusion is presented that the preBötC neurons expressing NMBRs and/or GRPRs produce sighs via the separate downstream population of preBötC SST neurons, which the authors demonstrate can independently generate sighs, whereas chemogenetic inhibition of preBötC SST neurons selectively abolishes sighs generated by activating NMBRs and GRPRs.

Weaknesses:

(1) While these studies have identified subpopulations of preBötC neurons capable of episodically evoking sigh-like inspiratory activity, mechanisms producing the normal slow sigh rhythm were not investigated and remain unknown.

(2) Several key technical aspects of the study require further clarification to aid in interpreting the experimental results, including issues relating to the validation of the transgenic mouse lines and virally transduced expressions of proteins utilized for optogenetic and chemogenetic experiments, as well as justifying the optogenetic photostimulation paradigms used to evoke sighs.

Reviewer #2 (Public Review):

Summary:

Exploring the DEP-MAP database and two drug-screen databases, the authors identify WSB2 as an interactor of several BCL2 proteins. In follow-up experiments, they show that CRL5/WSB2 controls NOXA protein levels via K48 ubiquitination following direct protein-protein interaction, and cell death sensitivity in the context of BH3 mimetic treatment, where WSB2 depletion synergizes with drug treatment.

Strengths:

The authors use a set of orthogonal methods across different model cell lines and a new WSB2 KO mouse model to confirm their findings. They also manage to correlate WSB2 expression with poor prognosis in prostate and liver cancer, supporting the idea that targeting WSB2 may sensitize cancers for treatment with BH3 mimetics.

Weaknesses:

The conclusions drawn based on the findings in cancer patients are very speculative, as regulation of NOXA cannot be the sole function of CRL5/WSB2 and it is hence unclear what causes correlation with patient survival. Moreover, the authors do not provide a clear mechanistic explanation of how exactly higher levels of NOXA promote apoptosis in the absence of WSB2. This would be important knowledge, as usually high NOXA levels correlate with high MCL1, as they are turned over together, but in situations like this, or loss of other E3 ligases, such as MARCH, the buffering capacity of MCL1 is outrun, allowing excess NOXA to kill (likely by neutralizing other BCL2 proteins it usually does not bind to, such as BCLX). Moreover, a necroptosis-inducing role of NOXA has been postulated. Neither of these options is interrogated here.

Reviewer #2 (Public Review):

The manuscript by Chen et al. describes how low levels of CPT1A in colorectal cancer (CRC) confer radioresistance by expediting radiation-induced ROS clearance. The authors propose that this mechanism of ROS homeostasis is regulated through FOXM1. CPT1A is known for its role in fatty acid metabolism via beta-oxidation of long-chain fatty acids, making it important in many metabolic disorders and cancers.

Previous studies have suggested that the upregulation of CPT1A is essential for the tumor-promoting effect in colorectal cancers (CRC) (PMID: 32913185). For example, CPT1A-mediated fatty acid oxidation promotes colorectal cancer cell metastasis (PMID: 2999587), and repression of CPT1A activity renders cancer cells more susceptible to killing by cytotoxic T lymphocytes (PMID: 37722058). Additionally, inhibition of CPT1A-mediated fatty-acid oxidation (FAO) sensitizes nasopharyngeal carcinomas to radiation therapy (PMID: 29721083). While this suggests a tumor-promoting effect for CPT1A, the work by Chen et al. suggests instead a tumor-suppressive function for CPT1A in CRC, specifically that loss or low expression of CPT1A confers radioresistance in CRC. This makes the findings important given that they oppose the previously proposed tumorigenic function of CPT1A. However, the data presented in the manuscript is limited in scope and analysis.

Major Limitations:

(1) Analysis of Patient Samples

- Figure 1D shows that CPT1A levels are significantly lower in COAD and READ compared to normal tissues. It would be beneficial to show whether CPT1A levels are also significantly lower in CRC compared to other tumor types using TCGA data.<br /> - The analysis should include a comparison of closely related CPT1 isoforms (CPT1B and CPT1C) to emphasize the specific importance of CPT1A silencing in CRC.<br /> - Figure 2 lacks a clear description of how IHC scores were determined and the criteria used to categorize patients into CPT1A-high and CPT1A-low groups. This should be detailed in the text and figure legend.<br /> - None of Figure 2B or 2C show how many patients were assigned to the CPT1A-low and CPT1A-high groups.

(2) Model Selection and Experimental Approaches

- The authors primarily use CPT1A knockout (KO) HCT116 cells and CPT1A overexpression (OE) SW480 cells for their experiments, which poses major limitations.<br /> - The genetic backgrounds of the cell lines (e.g., HCT116 being microsatellite instable (MSI) and SW480 not) should be considered as they might influence treatment outcomes. This should be acknowledged as a major limitation.<br /> - Regardless of their CPT1A expression levels, for the experiments with HCT116 and SW480 cells in Figure 3C-F, it would be useful to see whether HCT116 cells can be further sensitized to radiotherapy in overexpression and whether SW480 cells can be desensitized through CPT1A KO.<br /> - The use of only two CRC cell lines is insufficient to draw broad conclusions. Additional CRC cell lines should be used to validate the findings and account for genetic heterogeneity. The authors should repeat key experiments with additional CRC cell lines to strengthen their conclusions.

(3) Pharmacological Inhibition

Several studies have reported beneficial outcomes of using CPT1 pharmacological inhibition to limit cancer progression (e.g., PMID: 33528867, PMID: 32198139), including its application in sensitization to radiation therapy (PMID: 30175155). Since the authors argue for the opposite case in CRC, they should show this through pharmacological means such as etomoxir and whether CPT1A inhibition phenocopies their observed genetic KO effect, which would have important implications for using this inhibitor in CRC patients.

(4) Data Representation and Statistical Analysis

- The relative mRNA expression levels across the seven cell lines (Supplementary Figure 1C) differ greatly from those reported in the DepMap (https://depmap.org/portal/). This discrepancy should be addressed.<br /> - The statistical significance of differences in mRNA and protein levels between RT-sensitive and RT-resistant cells should be shown (Supplementary Figure 1C, D).

Conclusion

The study offers significant insights into the role of CPT1A in CRC radioresistance, proposing a tumor-suppressive function. However, the scope and depth of the analysis need to be expanded to fully validate these claims. Additional CRC cell lines, pharmacological inhibition studies, and a more detailed analysis of patient samples are essential to strengthen the conclusions.

Reviewer #2 (Public Review):

Summary:

This manuscript by Wei et al studies the role of ZFP36L1, an RNA-binding protein, in promoting PD-L1 expression in gastric cancer (GC). They used human gastric cancer tissues from six patients and performed H3K27ac CUT&Tag to unbiasedly identify SE specific for the infiltrative type. They identified an SE driving the expression of ZFP36L1 and immune evasion through upregulation of PD-L1. Mechanistically, they show that SPI1 binds to ZFP36L1-SE and ZFP36L1 in turn regulates PD-L1 expression through modulation of the 3'UTR of HDAC3. This mechanism of PD-L1 regulation in gastric cancer is novel, and ZFP36L1 has not been previously implicated in GC progression. However, the data presented are largely correlations and no direct proof is presented that the identified SE regulates ZFP36L1 expression. Furthermore, the effect of ZFP36L1 manipulation elicited a modest effect on PDL1 expression. In fact, several cell lines (XGC1, MNK45) express abundant ZFP36L1 but no PD-L1, suggesting the ZFP36L1 per se is not a key stimulant of PD-L1 expression as IFNg is. Thus, the central conclusions are not supported by the data.

Strengths:

Use of human GC specimens to identify SE regulating PD-L1 expression and immune evasion.

Weaknesses:

Major comments:

(1) The difference in H3K27ac over the ZFP36L1 locus and SE between the expanding and infiltrative GC is marginal (Figure 2G). Although the authors establish that ZFP36L1 is upregulated in GC, particularly in the infiltrative subtype, no direct proof is provided that the identified SE is the source of this observation. CRISPR-Cas9 should be employed to delete the identified SE to prove that it is causatively linked to the expression of ZFP36L1.

(2) In Figure 3C the impact of shZFP36L1 on PD-L1 expression is marginal and it is observed in the context of IFNg stimulation. Moreover, in XGC-1 cell line the shZFP36L1 failed to knock down protein expression thus the small decrease in PD-L1 level is likely independent of ZFP36L1. The same is the case in Figure 3D where forced expression of ZFP36L1 does not upregulate the expression of PDL1 and even in the context of IFNg stimulation the effect is marginal.

(3) In Figure 4, it is unclear why ELF1 and E2F1 that bind ZFP36L1-SE do not upregulate its expression and only SPI1 does. In Figure 4D the impact of SPI overexpression on ZFP36L1 in MKN45 cells is marginal. Likewise, the forced expression of SPI did not upregulate PD-L1 which contradicts the model. Only in the context of IFNg PD-L1 is expressed suggesting that whatever role, if any, ZFP36L1-SPI1 axis plays is secondary.

(4) The data presented in Figure 6 are not convincing. First, there is no difference in the tumor growth (Figure 6E). IHC in Figure 6I for CD8a is misleading. Can the authors provide insets to point CD8a cells? This figure also needs quantification and review from a pathologist.

Reviewer #2 (Public Review):

Trac, Huang, et al used the AZ Drug Combination Prediction DREAM challenge data to make a new random forest-based model for drug synergy. They make comparisons to the winning method and also show that their model has some predictive capacity for a completely different dataset. They highlight the ability of the model to be interpretable in terms of pathway and target interactions for synergistic effects. While the authors address an important question, more rigor is required to understand the full behavior of the model.

Major Points

(1) The authors compare DIPx to the winning method of the DREAm challenge, TAJI to show that from molecular features alone they retrain TAJI to create TAJI-M without the monotherapy data inputs. They mention that "of course, we could also use such data in DIPx...", but they never show the behaviour of DIPx with these data. The authors need to demonstrate that this statement holds true or else compare it to the full TAJI.

(2) It would be neat to see how the DIPx feature importance changes with monotherapy input. For most realistic scenarios in which these models are used robust monotherapy data do exist.

(3) In Figure 2, the authors compare DIPx and TAJI-M on various test sets. If I understood correctly, they also bootstrapped the training set with n=100 and reported all the model variants in many of the comparisons. While this is a nice way of showing model robustness, calculating p-values with bootstrapped data does not make sense in my opinion as by increasing the value of n, one can make the p-value arbitrarily small. The p-value should only be reported for the original models.

(4) From Figures 2 and 3, it appears DIPx is overfit on the training set with large gaps in Spearman correlations between Test Set 2/ONeil set and Test Set 1. It also features much better in cases where it has seen both compounds. Could the authors also compare TAJI on the ONeil dataset to show if it is as much overfit?

Reviewer #2 (Public Review):

Summary:

In this manuscript, Guayasamin et al. show that early-life stress (ELS) can induce a shift in fear generalisation in mice. They took advantage of a fear conditioning paradigm followed by a discrimination test and complemented learning and memory findings with measurements for anxiety-like behaviors. Next, astrocytic dysfunction in the lateral amygdala was investigated at the cellular level by combining staining for c-Fos with astrocyte-related proteins. Changes in excitatory neurotransmission were observed in acute brains slices after ELS suggesting impaired communication between neurons and astrocytes. To confirm the causality of astrocytic-neuronal dysfunction in behavioral changes, viral manipulations were performed in unstressed mice. Occlusion of functional coupling with a dominant negative construct for gap junction connexin 43 or reduction in astrocytic calcium with CalEx mimicked the behavioral changes observed after ELS suggesting that dysfunction of the astrocytic network underlies ELS-induced memory impairments.

Strengths:

Overall, this well-written manuscript highlights a key role for astrocytes in regulating stress-induced behavioral and synaptic deficits in the lateral amygdala in the context of ELS. Results are innovative, and methodological approaches relevant to decipher the role of astrocytes in behaviors. As mentioned by the authors, non-neuronal cells are receiving increasing attention in the neuroscience, stress, and psychiatry fields.

Weaknesses:

I do have several suggestions and comments to address that I believe will improve the clarity and impact of the work. For example, there is currently a lack of information on the timeline for behavioral experiments, tissue collection, etc.

Notice that many fake news stories begin from a place of fear. This fear hijacks our brains and triggers fight or flight options in our system I circuitry and actively prevent the use of the rational parts of system II which would quickly reveal problems in the information.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors use a combination of transgenic animals, intersectional viruses, retrograde tracing, and ex-vivo slice electrophysiology to show that VTA projection neurons synapse locally. First, the authors injected a cre-dependent channelrhodopsin into the VTA of PV, SST, MOR, and NTS-Cre mice. Importantly, PV, SST, MOR, and NTS are molecular markers previously used to describe VTA interneurons. Imaging of known VTA target regions identified that these neurons are not localized to the VTA and instead project to the PFC, NAc, VP, and LHb. Next, the authors used an intersectional viral strategy to label projection neurons with both GFP (membrane localized) and Syn:Ruby (release sites). These experiments identified that VTA projection neurons also make intra-VTA synapses. Finally, the authors use a combination of optogenetics and ex-vivo slice electrophysiology to show that neurons projecting from the VTA to the NAc/VP/PFC also synapse locally. Overall, most of the conclusions seem to be well supported by the data.

Strengths:

Previous literature has described Pvalb, Sst, Oprm1, and Nts as selective markers of VTA interneurons. Here, the authors make use of cre driver lines to show that neurons defined by these genes are not interneurons and project to known VTA target regions. Additionally, the authors convincingly use intersectional viral approaches and slice electrophysiology to show that projection neurons synapse onto neighboring cells within the VTA

Weaknesses:

While the authors use several cre driver lines to identify GABAergic projection neurons, they then use wild-type mice to show that projection neurons synapse onto neighboring cells within the VTA. This does not seem to lend evidence to the idea that previously described "interneurons" are projection neurons that collateralize within the VTA.

Reviewer #2 (Public Review):

Summary:

Franke et al. characterize the representation of color in the primary visual cortex of mice, highlighting how this changes across the visual field. Using calcium imaging in awake, head-fixed mice, they characterize the properties of V1 neurons (layer 2/3) using a large center-surround stimulation where green and ultra-violet colors were presented in random combinations. Clustering of responses revealed a set of functional cell-types based on their preference to different combinations of green and UV in their center and surround. These functional types were demonstrated to have different spatial distributions across V1, including one neuronal type (Green-ON/UV-OFF) that was much more prominent in the posterior V1 (i.e. upper visual field). Modelling work suggests that these neurons likely support the detection of predator-like objects in the sky.

Strengths:

The large-scale single-cell resolution imaging used in this work allows the authors to map the responses of individual neurons across large regions of the visual cortex. Combining this large dataset with clustering analysis enabled the authors to group V1 neurons into distinct functional cell types and demonstrate their relative distribution in the upper and lower visual fields. Modelling work demonstrated the different capacity of each functional type to detect objects in the sky, providing insight into the ethological relevance of color opponent neurons in V1.

Weaknesses:

It is unfortunate the authors were unable to provide stronger mechanistic insights into how color opponent neurons in V1 are formed.

Overall, this study will be a valuable resource for researchers studying color vision, cortical processing, and the processing of ethologically relevant information. It provides a useful basis for future work on the origin of color opponency in V1 and its ethological relevance.

Reviewer #3 (Public Review):

Summary:<br /> Animals can evaluate food quality in many ways. In contrast to the rapid sensory evaluation with smell and taste, the mechanism of slow nutrient sensation and its impact on food choice is unexplored. The authors utilize C. elegans larvae and their bacterial food as an elegant model to tackle this question and reveal the detailed molecular mechanism to avoid nutrient-poor foods.

Strength:<br /> The strength of this study is that they identified the molecular identities of the critical players in bacterial food and C. elegans using unbiased approaches, namely metabolome analysis, E. coli mutant screening, and RNA sequencing. Furthermore, they strengthened their findings by thorough experiments combining multiple methods such as genetics, fluorescent reporter analysis, and Western blot.

Weakness:<br /> The major caveat of this study is the reporter genes; specifically, transcriptional reporters used to monitor the UPRER and immune responses in the intestine of C. elegans. However, their tissue-specific rescue experiments suggest that the genes in the UPRER and immune response function in the neurons. Thus, we should carefully interpret the results of the reporter genes. Another point to be aware of is that although they show that lack of carbohydrates elicits the response to "low-quality" food, carbohydrate supplementation with heat-killed E. coli was insufficient to support animal growth.

Overall, this work provides convincing data to support their model. In the C. elegans field, the behaviors of larvae are not well studied compared to adults. This work will pose an interesting question about the difference between larvae and adults in nutrition sensing in C. elegans and provide a framework and candidate molecules to be studied in other organisms.

Reviewer #2 (Public Review):

Summary:

This manuscript by Peters, Rakateli, et al. aims to characterize the contribution of miR-26b in a mouse model of metabolic dysfunction-associated steatohepatitis (MASH) generated by a Western-type diet on the background of Apoe knock-out. In addition, the authors provide a rescue of the miR-26b using lipid nanoparticles (LNPs), with potential therapeutic implications. In addition, the authors provide useful insights into the role of macrophages and some validation of the effect of miR-26b LNPs on human liver samples.

Strengths:

The authors provide a well-designed mouse model, that aims to characterize the role of miR-26b in a mouse model of metabolic dysfunction-associated steatohepatitis (MASH) generated by a Western-type diet on the background of Apoe knock-out. The rescue of the phenotypes associated with the model used using miR-26b using lipid nanoparticles (LNPs) provides an interesting avenue to novel potential therapeutic avenues.

Weaknesses:

Although the authors provide a new and interesting avenue to understand the role of miR-26b in MASH, the study needs some additional validations and mechanistic insights in order to strengthen the author's conclusions.

(1) Analysis of the expression of miRNAs based on miRNA-seq of human samples (see https://ccb-compute.cs.uni-saarland.de/isomirdb/mirnas) suggests that miR-26b-5p is highly abundant both on liver and blood. It seems hard to reconcile that despite miRNA abundance being similar in both tissues, the physiological effects claimed by the authors in Figure 2 come exclusively from the myeloid (macrophages).

(2) Similarly, the miRNA-seq expression from isomirdb suggests also that expression of miR-26a-5p is indeed 4-fold higher than miR-26b-5p both in the liver and blood. Since both miRNAs share the same seed sequence, and most of the supplemental regions (only 2 nt difference), their endogenous targets must be highly overlapped. It would be interesting to know whether deletion of miR-26b is somehow compensated by increased expression of miR-26a-5p loci. That would suggest that the model is rather a depletion of miR-26.

UUCAAGUAAUUCAGGAUAGGU mmu-miR-26b-5p mature miRNA<br /> UUCAAGUAAUCCAGGAUAGGCU mmu-miR-26a-5p mature miRNA

(3) Similarly, the miRNA-seq expression from isomirdb suggests also that expression of miR-26b-5p is indeed 50-fold higher than miR-26b-3p in the liver and blood. This difference in abundance of the two strands is usually regarded as one of them being the guide strand (in this case the 5p) and the other being the passenger (in this case the 3p). In some cases, passenger strands can be a byproduct of miRNA biogenesis, thus the rescue experiments using LNPs with both strands in equimolar amounts would not reflect the physiological abundance miR-26b-3p. The non-physiological overabundance of miR-26b-3p would constitute a source of undesired off-targets.

(4) It would also be valuable to check the miRNA levels on the liver upon LNP treatment, or at least the signatures of miR-26b-3p and miR-26b-5p activity using RNA-seq on the RNA samples already collected.

(5) Some of the phenotypes described, such as the increase in cholesterol, overlap with the previous publication by van der Vorst et al. BMC Genom Data (2021), despite in this case the authors are doing their model in Apoe knock-out and Western-type diet. I would encourage the authors to investigate more or discuss why the initial phenotypes don't become more obvious despite the stressors added in the current manuscript.

(6) The authors have focused part of their analysis on a few gene makers that show relatively modest changes. Deeper characterization using RNA-seq might reveal other genes that are more profoundly impacted by miR-26 depletion. It would strengthen the conclusions proposed if the authors validated that changes in mRNA abundance (Sra, Cd36) do impact the protein abundance. These relatively small changes or trends in mRNA expression, might not translate into changes in protein abundance.

(7) In Figures 5 and 7, the authors run a phosphorylation array (STK) to analyze the changes in the activity of the kinome. It seems that a relatively large number of signaling pathways are being altered, I think that should be strengthened by further validations by Western blot on the collected tissue samples. For quite a few of the kinases, there might be antibodies that recognise phosphorylation. The two figures lack a mechanistic connection to the rest of the manuscript.

Reviewer #2 (Public Review):

Li and colleagues investigate the enzymatic activity-independent function of IDH1 in regulating erythropoiesis. This manuscript reveals that IDH1 deficiency in the nucleus leads to the redistribution of histone marks (especially H3K79me3) and chromatin state reprogramming. Their findings suggest a non-typical localization and function of the metabolic enzyme, providing new insights for further studies into the non-metabolic roles of metabolic enzymes. However, there are still some issues that need addressing:

(1) Could the authors show the RNA and protein expression levels (without fractionation) of IDH1 on different days throughout the human CD34+ erythroid differentiation?

(2) Even though the human CD34+ erythroid differentiation protocol was published and cited in the manuscript, it would be helpful to specify which erythroid stages correspond to cells on days 7, 9, 11, 13, and 15.

(3) It is important to mention on which day the lentiviral knockdown of IDH1 was performed. Will the phenotype differ if the knockdown is performed in early vs. late erythropoiesis? In Figures 1C and 1D, on which day do the authors begin the knockdown of IDH1 and administer NAC and GSH treatments?

(4) The authors validate that IDH1 regulates erythropoiesis in an enzymatic activity-independent manner by adding ROS scavengers or α-KG. Given the complexity of metabolic pathways, these two strategies may not suffice. Mutating the enzymatic active site could provide a clearer explanation for this point.

(5) While the cell phenotype of IDH1 deficiency is quite dramatic, yielding cells with larger nuclei and multi-nuclei, the authors only attribute this phenotype to defects in chromatin condensation. Is it possible that IDH1-knockdown cells also exhibit primary defects in mitosis/cytokinesis (not just secondary to the nuclear condensation defect)?), given the function of H3K79Me in cell cycle regulation?

(6) Why are there two bands of Histone H3 in Figure 4A?

(7) Are the density and localization of histone modifications (not just H3K79me3) in Sg-NEG-IDH1 HuDEP2 cells similar to those in IDH1-shRNA erythroid cells compared to control cells?

(8) Displaying a heatmap and profile plots in Figure 5A between control and IDH1-deficient cells will help illustrate changes in H3K79me3 density in the nucleus after IDH1 knockdown.

(9) Are the distribution and intensity of H3K79me3 in primary healthy erythroid cells in the bone marrow similar to or distinct from those in AML and MDS cells? The authors could present at least one sample of healthy donor cells for comparison.

(10) In Figure 7E, why are the bands of Luciferase-shRNA in the input and probe both light, while the bands of IDH1-shRNA are both dark? This suggests that the expression of KLF1 is much higher in IDH1-shRNA cells than in control cells. Therefore, this result may not strongly support the increased binding of KLF1 at the SIRT1 promoter after IDH1 knockdown.

Reviewer #2 (Public Review):

The authors present a computational methodology for de-biasing/denoising high-throughput genomic signals using optimal transport techniques, thus allowing disparate datasets to be merged and jointly analysed. They apply this methodology on liquid biopsy data and they demonstrate improved performance (compared to simpler bias-correcting approaches) for cancer detection using common machine learning algorithms. This is a theoretically interesting and potentially useful approach for addressing a very common practical problem in computational genomics.

I have the following recommendations:

(1) When comparing performance metrics between different approaches (e.g., tables 3 and 4), 95% confidence intervals should also be provided and a pairwise statistical test should be applied to establish whether the observed difference in each performance metric between the proposed method and the alternatives is statistically significant, thus justifying the claim that the proposed method offers an improvement over existing methodologies.

(2) The commonly used center-and-scale and GC debias approaches presented by the authors are fairly simple. How does their methodology compare to more elaborate approaches, such as tangent normalisation (https://academic.oup.com/bioinformatics/article/38/20/4677/6678978) and robust PCA (https://github.com/mskilab-org/dryclean)?

(3) What is the computational cost of the proposed methodology and how does it compare to the alternatives?

(4) The proposed approach relies on a reference dataset, against which a given dataset is adapted. What are the implications for cross-validation experiments (which are essential for assessing the out-of-sample error of every methodology), particularly with regards to the requirement to avoid information leakage between training and validation/test data sets?

In conclusion, this is an interesting and potentially useful paper and I would like to encourage the authors to address the above points, which hopefully will strengthen their case.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors investigated whether a salticid spider, Phidippus regius, recognizes other individuals of the same species. The authors placed each spider inside a container from which it could see another spider for 7 minutes, before having its view of the other spider occluded by an opaque barrier for 3 minutes. The spider was then either presented with the same individual again (habituation trial) or a different individual (dishabituation trial). The authors recorded the distance between the two spiders during each trial. In habituation trials, the spiders were predicted to spend more time further away from each other and, in dishabituation trials, the spiders were predicted to spend more time closer to each other. The results followed these predictions, and the authors then considered whether the spiders in habituation trials were generally fatigued instead of being habituated to the appearance of the other spider, which may have explained why they spent less time near the other individual. The authors presented the spiders with a different (novel) individual after a longer period of time (which they considered to be a long-term dishabituation trial), and found that the spiders switched to spending more time closer to the other individual again during this trial. This suggested that the spiders had recognized and had habituated to the individual that they had seen before and that they became dishabituated when they encountered a different individual.

Strengths:

It is interesting to consider individual recognition by Phidippus regius. Other work on individual recognition by an invertebrate has been, for instance, known for a species of social wasp, but Phidippus regius is a different animal. Importantly and more specifically, P. regius is a salticid spider, and these spiders are known to have exceptional eyesight for animals of their size, potentially making them especially suitable for studies on individual recognition. In the current study, the results from experiments were consistent with the authors' predictions, suggesting that the spiders were recognizing each other by being habituated to individuals they had encountered before and by being dishabituated to individuals they had not encountered before. This is a good start in considering individual recognition by this species.

Weaknesses:

The experiments in this manuscript (habituation/dishabituation trials) are a good start for considering whether individuals of a salticid species recognize each other. I am left wondering, however, what features the spiders were specifically paying attention to when recognizing each other. The authors cited Sheehan and Tibbetts (2010) who stated that "Individual recognition requires individuals to uniquely identify their social partners based on phenotypic variation." Also, recognition was considered in a paper on another salticid by Tedore and Johnsen (2013).

Tedore, C., & Johnsen, S. (2013). Pheromones exert top-down effects on visual recognition in the jumping spider Lyssomanes viridis. The Journal of Experimental Biology, 216, 1744-1756. doi: 10.1242/jeb.071118

In this elegant study, the authors presented spiders with manipulated images to find out what features matter to these spiders when recognizing individuals.

Part of the problem with using two living individuals in experiments is that the behavior of one individual can influence the behavior of the other, and this can bias the results. However, this issue can be readily avoided because salticids are well known, for example, to be highly responsive to lures (e.g. dead prey glued in lifelike posture onto cork disks) and to computer animation. These methods have already been successful and helpful for standardizing the different stimuli presented during many different experiments for many different salticid spiders, and they would be helpful for better understanding how Phidippus regius might recognize another individual on the basis of phenotypic variation. There are all sorts of ways in which a salticid might recognize another individual. Differences in face or body structure, or body size, or all of these, might have an important role in recognition, but we won't know what these are using the current methods alone. Also, I didn't see any details about whether body size was standardized in the current manuscript.

For another perspective, my thoughts turn to a paper by Cross et al.

Cross, F. R., Jackson, R. R., & Taylor, L. A. (2020). Influence of seeing a red face during the male-male encounters of mosquito-specialist spiders. Learning & Behavior, 48, 104-112. doi: 10.3758/s13420-020-00411-y

These authors found that males of Evarcha culicivora, another salticid species that is known to have a red face, become less responsive to their own mirror images after having their faces painted with black eyeliner than if their faces remained red. In all instances, the spiders only saw their own mirror images and never another spider, and these results cannot be interpreted on the basis of habituation/dishabituation because the spiders were not responding differently when they simply saw their mirror image again. Instead, it was specifically the change to the spider's face which resulted in a change of behavior. The findings from this paper and from Tedore and Johnsen can help give us additional perspectives that the authors might like to consider. On the whole, I would like the authors to further consider the features that P. regius might use to discern and recognize another individual.

Reviewer #2 (Public Review):

Summary:

The present article by Tesler et al proposes a 3-population model of the striatum input-output function including the direct pathway (D1) striatal projection neurons (dSPNs), the indirect pathway (D2) striatal projection neurons (iSPNs), and the fast-spiking striatal interneurons. The authors derive a mean-field version of the model where the firing rate of each population follows the transfer function obtained from a spiking (AdEx) neuron model for each cell population. They report the response of the mean-field circuit to oscillatory inputs from the cortex, the effect of dopamine on dSPNs and iSPNs, and how a simple reinforcement learning rule at cortico-striatal synapses would adapt the model's output in the face of 2 distinct inputs.

Strengths:

The model is simple and easy to understand.

Weaknesses:

Feedforward inhibition from FSI and interconnections between dSPNs and iSPNs does not seem to have any significant impact on the input-output response of dSPNs and iSPNs to cortical inputs. Therefore, all of the results shown can be derived relatively easily from the basic knowledge we have about mean-field neuronal models and their responses to external inputs: all populations have an output that linearly follows the input. Concerning the reinforcement learning paradigm, showing that 2 distinct inputs can be associated with opposite outputs based on a tri-partite synaptic learning rule does not appear new either. As it is, it's unclear to me how this model contributes to new knowledge concerning striatal neuronal activity. Moreover, the assumptions made concerning the effect of dopamine and the synaptic plasticity rules appear rather simplistic and relatively outdated.

Many of the goals set in the introduction do not appear met:

"understanding and modelling the complex dynamics and functions of the striatum constitutes a very relevant and challenging task".<br /> I'm not sure if the authors aim to understand and model the complex dynamics of the striatum here: there are no complex dynamics that are revealed or explained in the model, as the dSPNs and iSPNs mainly appear to have a linear relationship to their inputs (with added noise) in 3 for example. I did not find any non-trivial dynamics highlighted in the presentation of the results either.

"modelling and studying the functions of the striatum and its associated neuronal dynamics requires to investigate these cellular/microcircuits mechanisms, and how the small-scale mechanisms affect large-scale behavior"<br /> I also did not find a statement about the effect of cellular/microcircuit mechanisms on behavior or large-scale activity in the results or discussion. The effects of micro-circuits are rather transparent as dSPNs and iSPNs do not seem to differ from feedforward responses to cortical inputs.

"existing mean-fields are based on generic models (sometimes inspired by cortical circuits) [7, 8], which do not consider the rich and specific cellular and synaptic variability observed along brain regions."<br /> The authors argue here that specific input-output relationships of striatal neurons may contribute to the circuit dynamics. However, the input-output they derive from a spiking neuron model (AdEx) in Figure 2, are very typical IF curves used in most mean-field models. Apart from a slight saturation effect at large rates (which is incorporated in many mean-field models and may not even be relevant here given the max firing of these cells), the I-F curve looks exactly like what is expected from the most basic rate model neuron with a rectifying transfer function in the presence of synaptic noise. What cellular or synaptic properties would the authors like to highlight here? Linking to molecular and cellular parameters, as advertised in the intro, seems much beyond the current achievements of the present model.

"This approach permits an efficient transition between scales and, furthermore, it allows to explore the effects of cellular parameters at the network level, as we will show for the case of dopaminergic effects in the striatum."<br /> If the authors mean the excitation of D1 SPNS and the inhibition of D2 SPNs by dopamine, this statement seems slightly oversold. It's very well known that dopaminergic effects cannot simply be resumed by a change in excitability as it acts on non-linear currents and complex synaptic parameters. They model it as follows: "To model these effects of dopamine in dSPN cells we will assume the increase of excitability due to D1 activation in dPSNs can be described as an increase in the glutamatergic conductance (Qe in our model) together with the action of a depolarizing current" Which basically means an additional excitatory input and a depolarizing current. The expected effect on the firing rate of these 2 effects is rather simple and does not require circuit modelling I believe.

This effect of dopamine is referred to in the discussion as: "This analysis allowed us to show how modifications at the cellular level can be incorporated within the mean-field model which can in turn predict and capture the emergent changes at the network level generated by them, and in addition has provided further validation to our model."<br /> Again, I don't see any emergent property or model validation here. Maybe the authors can be a bit more precise about what emergent property they refer to.

"In addition it illustrates how changes at the cellular level can lead to emerging effects at the network level, which can be captured by the mean-field model"<br /> I did not find any description of 'emerging effects at the network level" in the results or discussion. Maybe the authors could elaborate on what they mean here.

"shows the capabilities of the model to reproduce specific brain functions"<br /> The capacity of a network to associate stim A to a positive output and stim B to a negative one through reward-driven synaptic plasticity is rather well described and is a bit far from 'specific brain functions'. Concerning the discussion, it highlights how the model 'could be useful' rather than highlighting any strength of the model or relation to existing work. In particular, the (large) literature on circuit modelling in the striatum and BG circuits is not cited at all beyond self-citations, except in one book chapter (Houk et al, 1995) and one paper (Bogacz, 2020).

"The RL model proposed can very easily be improved to capture more biologically complex scenarios"<br /> Why did the authors not implement such an 'easy' improvement?

DOI: 10.1002/cne.24001

Resource: (ZFIN Cat# ZDB-GENO-060623-2,RRID:ZFIN_ZDB-GENO-060623-2)

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-GENO-060623-2

What is this?

DOI: 10.1002/cne.24001

Resource: (ZFIN Cat# ZDB-GENO-060623-2,RRID:ZFIN_ZDB-GENO-060623-2)

Curator: @gabimpine

SciCrunch record: RRID:ZFIN_ZDB-GENO-060623-2

What is this?

DOI: 10.1002/cne.24042

Resource: (ZFIN Cat# ZDB-GENO-060619-2,RRID:ZFIN_ZDB-GENO-060619-2)

Curator: @gabimpine

SciCrunch record: RRID:ZFIN_ZDB-GENO-060619-2

What is this?

Reviewer #2 (Public Review):

Summary:

In the manuscript "Metabolic heterogeneity of colorectal cancer as a prognostic factor: insights gained from fluorescence lifetime imaging" by Komarova et al., the authors used fluorescence lifetime imaging and quantitative analysis to assess the metabolic heterogeneity of colorectal cancer. Generally, this work is logically well-designed, including in vitro and in vivo animal models and ex vivo patient samples. Although the key parameter (BI index) used in this study was already published by this group, it was shown that heterogeneity of patients' samples had associations with clinical characteristics of tumors. Additional samples from 8 patients were added to the data pool during the revision process, which is helpful and important for the conclusions that the authors are trying to draw. Overall, the revisions that the authors have made greatly strengthen this study.

Strengths:

(1) Solid experiments are performed and well-organized, including in vitro and in vivo animal models and ex vivo patient samples;

(2) Attempt and efforts to build the association between the metabolic heterogeneity and prognosis for colorectal cancer.

Weaknesses:

(1) Although additional data acquired from 8 patients were collected, maybe more patients should be involved in the future for reliable diagnosis and prognosis.

Reviewer #2 (Public Review):

This work makes substantial progress towards understanding physical aspects of formation locomotion, notably the hydrodynamic stability of groups of flappers and the modifications to energy costs associated with flow interactions.

Major strengths pertain to the fact that this topic is timely, interesting and complex, and the authors have advanced the understanding through their characterizations.

The weaknesses may relate to the many idealizations employed in the simulations and models, which may raise questions about how to interpret their results and whether the outcomes hold generally. But given the complexity of the problem, simplifications are necessary. The authors have certainly provided a clear presentation with appropriate details and caveats that will help the reader extract the main messages and form their own conclusions.

Overall, the work is a positive addition to the growing set of studies into schooling, flocking and related problems where unsteady flow interactions lead to interesting collective effects.

Reviewer #2 (Public Review):

A limitation in using SNPs to understand recent histories of genomes is their low mutation frequency. Tellier et al. explore the possibility of adding hypermutable markers to SNP based methods for better resolution over short time frames. In particular, they hypothesize that epimutations (CG methylation and demethylation) could provide a useful marker for this purpose. Individual CGs in Arabidopsis tends to be either close to 100% methylated or close to 0%, and are inherited stably enough across generations that they can be treated as genetic markers. Small regions containing multiple CGs can also be treated as genetic markers based on their cumulative methylation level. In this manuscript, Tellier et al develop computational methods to use CG methylation as a hypermutable genetic marker and test them on theoretical and real data sets. They do this both for individual CGs and small regions. My review is limited to the simple question of whether using CG methylation for this purpose makes sense at a conceptual level, not at the level of evaluating specific details of the methods. I have a small concern in that it is not clear that CG methylation measurements are nearly as binary in other plants and other eukaryotes as they are in Arabidopsis. However, I see no reason why the concept of this work is not conceptually sound. Especially in the future as new sequencing technologies provide both base calling and methylating calling capabilities, using CG methylation in addition to SNPs could become a useful and feasible tool for population genetics in situations where SNPs are insufficient.

Reviewer #2 (Public Review):

Summary:

The manuscript by Ziegler et al, entitled 'Structural characterization and dynamics of AdhE ultrastructure from Clostridium thermocellum: A containment strategy for toxic intermediates?" presents the atomic resolution cryo-EM structure of C. thermocellum AdhE showing that it show dominantly an extended form while E.coli AdhE shows dominantly a compact form. With comparative analysis of their C. thermocellum structure and the previous E.coli AdhE structure, they tried to reveal the mechanism by which C.thermocellum and E.coli show different dominant conformations. In addition, they also analyzed the substrate channel by comparative and computational approaches. Lastly, their computational analysis using CryoDRGN reveals conformational heterogeneity in the sample. Despite this the manuscript is very descriptive and does not provide a mechanistic understanding by which AdhE works, this work will provide structural frame works to further investigate the function and mechanism of AdhE dynamics.

Strengths:

This manuscript provides the first C. thermocellum (Ct) AdhE structure and comparatively analyzed this structure with E.coli AdhE.

Weaknesses:

This work is very descriptive and does not provide mechanistic understanding of the function and dynamics of AdhE.

Reviewer #2 (Public Review):

Summary:

Peled et al identified HER2 mutations in connection with resistance to the anti-HER2 antibody Pertuzumab-mediated therapy. After constructing a yeast display library of Pertuzumab variants with 3.86×10^11 sequences for targeted screening of variant combinations in chosen 6 out of 14 residues, the authors performed experimental screening to obtain the clones that bind to HER2 WT and/or mutants (S310Y and S310F), and then combined new variations to obtain antibodies with a broad spectrum binding to both WT and two HER2 mutants. These are interesting studies of clinical impact and translational potential.

Strengths:

(1) Deep computational analyses of large datasets of clinical data provide useful information about HER2 mutations and their potential relevance to antibody therapy resistance.

(2) There is valuable information analyzing the residues within or near the interface between the antigen HER2 and the Pertuzumab antibody (heavy chain).<br /> The experimental antibody library screening obtained 90+ clones from 3.86×10^11 sequences for further functional validation.

Weaknesses:

(1) There is lack of assessment for antibody variant functions in cancer cell phenotypes in vitro (proliferation, cell death, motility) or in vivo (tumor growth and animal survival). The only assay was the western blotting of phosphopho-HER3 in Figure 4. However, HER2 levels and phosphor-HER2 were not analyzed.

(2) There is misleading impression from the title of computational engineering of a therapeutic antibody and the statement in the abstract "we designed a multi-specific version of Pertuzumab that retains original function while also bindings these HER2 variants" for a few reasons:

a. The primary method used for variant antibody identification for HER2 mutant binding is rather traditional experimental screening based on yeast display instead of computational design of a multi-specific version of Pertuzumab.

b. There is insufficient or lack of computational power in the antibody design or prioritization in choosing variant residues for the library construction of 3.86×1011 sequences. It seems random combinations from 6 residues out of 4 groups with 20 amino acid options.<br /> c. The final version of tri-binding variant is a combination of screened antibody clones instead of computation design from scratch.<br /> d. There is incomplete experimental evidence about the therapeutic values of newly obtained antibody clones.

Comments on revised version:

Two major comments remain and have not been well addressed. Comment 1 is expecting any cellular phenotypic analysis if not in vivo. Comment 2 requires some modifications to avoid overstating.

Reviewer #2 (Public Review):

This manuscript explores the utility of AlphaFold2 (AF2) and the author's own AF2-RAVE method for drug discovery. As has been observed elsewhere, the predictive power of docking against AF2 structures is quite limited, particularly for proteins like kinases that have non-trivial conformational dynamics. However, using enhanced sampling methods like RAVE to explore beyond AF2 starting structures leads to a significant improvement.

Comments on revised version:

I'm happy with the changes made.

Reviewer #2 (Public Review):

Vangl2, a core planar cell polarity protein involved in Wnt/PCP signaling, cell proliferation, differentiation, homeostasis, and cell migration. Vangl2 malfunctioning has been linked to various human ailments, including autoimmune and neoplastic disorders. Interestingly, it was shown that Vangl2 interacts with the autophagy regulator p62, and autophagic degradation limits the activity of inflammatory mediators, such as p65/NF-κB. However, the possible role of Vangl2 in inflammation has not been investigated. In this manuscript, Lu et al. describe that Vangl2 expression is upregulated in human sepsis-associated PBMCs and that Vangl2 mitigates experimental sepsis in mice by negatively regulating p65/NF-κB signaling in myeloid cells. Their mechanistic studies further revealed that Vangl2 recruits the E3 ubiquitin ligase PDLIM2 to promote K63-linked poly-ubiquitination of p65. Vangl2 also facilitated the recognition of ubiquitinated p65 by the cargo receptor NDP52. These molecular processes caused selective autophagic degradation of p65. Indeed, abrogation of PDLIM2 or NDP52 functions rescued p65 from autophagic degradation, leading to extended p65/NF-κB activity in myeloid cells. Overall, the manuscript presents convincing evidence for novel Vangl2-mediated control of inflammatory p65/NF-kB activity. The proposed pathway may expand interventional opportunities restraining aberrant p65/NF-kB activity in human ailments.

IKK is known to mediate p65 phosphorylation, which instructs NF-kB transcriptional activity. In this manuscript, Vangl2 deficiency led to an increased accumulation of phosphorylated p65 and IKK also at 30 minutes post-LPS stimulation; however, autophagic degradation of p-p65 may not have been initiated at this early time point. Therefore, this set of data put forward the exciting possibility that Vangl2 could also be regulating the immediate early phase of inflammatory response involving the IKK-p65 axis - a proposition that may be tested in future studies.

Reviewer #2 (Public Review):

Summary:<br /> I believe the authors have done a wonderful job at dissecting a very complex topic, starting with basic building blocks of locomotion and introducing a powerful simulation approach to the exploring the landscape of growth and form in intelligent behavior.

Strengths:<br /> This is a very original, timely, and robust piece of work that I believe can inspire further computational studies in evo-devo-etho.

Weaknesses:<br /> More detail on the simulations and also greater clarity regarding the generalizability of their claims would improve the message and further studies.

Reviewer #2 (Public Review):

Panel 2N and 2O should have been done with and without SCRV treatment, so that the reader can assess whether SCRV induces additional IFN activation (on top of MDA5 and STING autoactivation). I would recommend the authors include a sentence in the text to explain that ectopic expression of MDA5 or STING (i.e. overexpression from a plasmid) induces autoactivation of these proteins. Therefore, the IFN induction that is seen in panel 2N is likely due to MDA5/STING overexpression. SCRV treatment may further boost IFN induction, but this cannot be assessed without the 'mock' conditions. This information will help the readers to interpret Fig. 2N and 2O correctly.

Reviewer #2 (Public Review):

The authors characterized the activity of the dorsal periaqueductal gray (dPAG) - basolateral amygdala (BLA) circuit. They show that BLA cells that are activated by dPAG stimulation are also more likely to be activated by a robot predator. These same cells are also more likely to display synchronous firing.

The authors also replicate prior results showing that dPAG stimulation evokes fear and the dPAG is activated by a predator.

Lastly, the report performs anatomical tracing to show that the dPAG may act on the BLA via the paraventricular thalamus (PVT). Indeed, the PVT receives dPAG projections and also projects to the BLA. However, the authors do not show if the PVT mediates dPAG to BLA communication with any functional behavioral assay.

The major impact in the field would be to add evidence to their prior work, strengthening the view that the BLA can be downstream of the dPAG.

Reviewer #2 (Public Review):

Summary:<br /> This work identifies two variants in CAPSL in two generation familial exudative vitreoretinopathy (FEVR) pedigrees, and using a knockout mouse model, they link CAPSL to retinal vascular development and endothelial proliferation through the MYC pathway. Together, these findings suggest that the identified variants may be causative and that CAPSL is a new FEVR-associated gene.

Strengths:<br /> The authors data provides compelling evidence that loss of the poorly understood protein CAPSL can lead to reduced endothelial proliferation in mouse retina and suppression of MYC signaling, consistent with the disease seen in FEVR patients. The paper is clearly written, and the data generally support the author's hypotheses.

Weaknesses:<br /> (1) Both pedigrees described suggest autosomal dominant inheritance in humans, but no phenotype was observed in Capsl heterozygous mice. Additional studies would be needed to determine the cause of this disparity.

(2) Additional discussion of the hypothesized functional mechanism of the p.L83F variant would have improved the manuscript. While the human genetic data is compelling, it remains unclear how this variant may effect CAPSL function. In vitro, p.L83F protein appears to be normally localized within the cell and it is unclear why less mutant protein was detected in transfected cells. Was the modified protein targeted for degradation?

(3) Authors did not describe how the new crispr-generated Capsl-loxp mouse model was screened for potential off-target gene editing, raising the possibility that unrelated confounding mutations may have been introduced.

Reviewer #2 (Public Review):

Summary:<br /> In their manuscript, Multi-dimensionality of tree communities structure host-parasitoid networks and their phylogenetic composition, Wang et al. examine the effects of tree diversity and environmental variables on communities of reed-nesting insects and their parasitoids. Additionally, they look for the correlations in community composition and network properties of the two interacting insect guilds. They use a data set collected in a subtropical tree biodiversity experiment over five years of sampling. The authors find that the tree species, functional, and phylogenetic diversity as well as some of the environmental factors have varying impacts on both host and parasitoid communities. Additionally, the communities of the host and parasitoid showed correlations in their structures. Also, the network metrices of the host-parasitoid network showed patterns against environmental variables.

Strengths:<br /> The main strength of the manuscript lies in the massive long-term data set collected on host-parasitoid interactions. The data provides interesting opportunities to advance our knowledge on the effects of environmental diversity (tree diversity) on the network and community structure of insect hosts and their parasitoids in a relatively poorly known system.

Weaknesses:<br /> To me, there are no major issues regarding the manuscript, though sometimes I disagree with the interpretation of the results and some of the conclusions might be too far-fetched given the analyses and the results (namely the top-down control in the system). Additionally, the methods section (especially statistics) was lacking some details, but I would not consider it too concerning. Sometimes, the logic of the text could be improved to better support the studied hypotheses throughout the text. Also, the results section cannot be understood as a stand-alone without reading the methods first. The study design and the rationale of the analyses should be described somewhere in the intro or presented with the results.

Reviewer #2 (Public Review):

Summary:

This study examines how local DNA features around the amino acid permease gene GAP1 influence adaptation to glutamine-limited conditions through changes in GAP1 Copy Number Variation (CNV). The study is well motivated by the observation of numerous CNVs documented in many organisms, but difficulty in distinguishing the mechanisms by which they are formed, and whether or how local genomic elements influence their formation. The main finding is convincing and is that a nearby Autonomous Replicating Sequence (ARS) influences the formation of GAP1 CNVs and this is consistent with a predominate mechanism of Origin Dependent Inverted Repeat Amplification (ODIRA). These results along with finding and characterizing other mechanisms of GAP1 CNV formation will be of general interest to those studying CNVs in natural systems, experimental evolution, and in tumor evolution. While the results are limited to a single CNV of interest (GAP1), the carefully controlled experimental design and quantification of CNV formation will provide a useful guide to studying other CNVs and CNVs in other organisms.

Strengths:

The study was designed to examine the effects of two flanking genomic features next to GAP1 on CNV formation and adaptation during experimental evolution. This was accomplished by removing two Long Terminal Repeats (LTRs), removing a downstream ARS, and removing both LTRs and the ARS. Although there was some heterogeneity among replicates, later shown to include the size and breakpoints of the CNV and the presence of an unmarked CNV, both marker-assisted tracking of CNV formation and modeling of CNV rate and fitness effects showed that deletion of the ARS caused a clear difference compared to the control and the LTR deletion.

The consequence of deletion of local features (LTR and ARS) was quantified by genome sequencing of adaptive clones to identify the CNV size, copy number and infer the mechanism of CNV formation. This greatly added value to the study as it showed that i) ODIRA was the most common mechanism but ODIRA is enhanced by a local ARS, ii) non-allelic homologous recombination (NAHR) is also used but depends on LTRs, and iii) de novo insertion of transposable elements mediate NAHR in strains with both ARS and LTR deletions. Together, these results show how local features influence the mechanism of CNV formation, but also how alternative mechanisms can substitute when primary ones are unavailable.

Weaknesses:

The CNV mutation rate and its effect on fitness are hard to disentangle. The frequency of the amplified GFP provides information about mutation rate differences as well as fitness differences. The data and analysis show that each evolved population has multiple GAP1 CNV lineages within it, with some being unmarked by GFP. Thus, estimates of CNV fitness are more of a composite view of all CNV amplifications increasing in frequency during adaptation. Another unknown but potential complication is whether the local (ARS, LTR) deletions influence GAP1 expression and thus the fitness gain of GAP1 CNVs. The neural network simulation-based inference does a good job at estimating both mutation rates and fitness effects, while also accounting for unmarked CNVs. However, the model does not account for the population heterogeneity of CNVs and their fitness effects. Despite these limitations of distinguishing mutation rate and fitness differences, the authors' conclusions are well supported in that the LTR and ARS deletions have a clear impact on the CNV-mediated evolutionary outcome and the mechanism of CNV formation.

Reviewer #2 (Public Review):

Summary:

The authors aim to address the clinical challenge of treating endometriosis, a debilitating condition with limited and often ineffective treatment options. They propose that inhibiting KMO could be a novel non-hormonal therapeutic approach. Their study focuses on:<br /> • Characterising KMO expression in human and mouse endometriosis tissues.<br /> • Investigating the effects of KMO inhibitor KNS898 on inflammation, lesion volume, and pain in a mouse model of endometriosis.<br /> • Demonstrating the efficacy of KMO blockade in improving histological and symptomatic features of endometriosis.

Strengths:

• Novelty and Relevance: The study addresses a significant clinical need for better endometriosis treatments and explores a novel therapeutic target.<br /> • Comprehensive Approach: The authors use both human biobanked tissues and a mouse model to study KMO expression and the effects of its inhibition.<br /> • Clear Biochemical Outcomes: The administration of KNS898 reliably induced KMO blockade, leading to measurable biochemical changes (increased kynurenine, increased kynurenic acid, reduced 3-hydroxykynurenine).

Weaknesses:

• Limited Mechanistic Insight: The study does not thoroughly investigate the mechanistic pathways through which KNS898 affects endometriosis. Specifically, the local vs. systemic effects of KMO inhibition are not well differentiated.<br /> • Statistical Analysis Issues: The choice of statistical tests (e.g., two-way ANOVA instead of repeated measures ANOVA for behavioral data) may not be the most appropriate, potentially impacting the validity of the results.<br /> • Quantification and Comparisons: There is insufficient quantitative comparison of KMO expression levels between normal endometrium and endometriosis lesions, and the systemic effects of KNS898 are not fully explored or quantified in various tissues.<br /> • Potential Side Effects: The systemic accumulation of kynurenine pathway metabolites raises concerns about potential side effects, which are not addressed in the study.

Achievement of Aims:

• The authors successfully demonstrated that KMO is expressed in endometriosis lesions and that KNS898 can induce KMO blockade, leading to biochemical changes and improvements in endometriosis symptoms in a mouse model.

Support of Conclusions:

• While the data supports the potential of KMO inhibition as a therapeutic strategy, the conclusions are somewhat overextended given the limitations in mechanistic insights and statistical analysis. The study provides promising initial evidence but requires further exploration to firmly establish the efficacy and safety of KNS898 for endometriosis treatment.

Impact on the Field:

• The study introduces a novel therapeutic target for endometriosis, potentially leading to non-hormonal treatment options. If validated, KMO inhibition could significantly impact the management of endometriosis.

Utility of Methods and Data:

• The methods used provide a foundation for further research, although they require refinement. The data, while promising, need more rigorous statistical analysis and deeper mechanistic exploration to be fully convincing and useful to the community.

Reviewer #2 (Public Review):

Summary:<br /> In agriculture, nitrogen fertilizers are used to allow for optimum growth and yield of crops. The use of these fertilizers has a large negative impact on the environment and climate. In this report McMahon et al. have inoculated maize seeds with a nitrogen fixing bacterium: Gluconacetobacter diazotrophicus. It has been demonstrated before that nitrogen fixed by this bacterium can be incorporated in a plant. In this study the spatial distribution of the incorporated nitrogen was revealed using NanoSIMS. The nitrogen was strongly enriched in the chloroplasts and especially the stromal region where the Calvin-Benson cycle enzymes are located.

Strengths:<br /> The topic is very interesting as nitrogen supply is of great importance for agriculture. The study is well designed, and the data convincingly show enrichment of 15N (fixed by the bacterium) in the chloroplasts.

Weaknesses:<br /> Some of the data that is discussed is not presented in the (supplement) of the paper. First, in the abstract it is mentioned "help explain the observation of enhanced growth rates in plants containing this nitrogen fixing bacterium". It is unclear if this refers to literature or to this study. Either, it should be mentioned in the introduction, or the data should be shown in the paper. Second, it is mentioned that the chloroplast had a significantly higher nitrogen isotope ratio value compared to the nuclei and the xylem cell walls. Please provide the numbers of the ratios (preferably also an image of the xylem cell wall) and the type of statistical analysis that has been performed.

The paper could benefit from a more in-depth analysis of why the nitrogen isotope ratio is higher in the chloroplast. It seems to be correlated with the local nitrogen abundance, did the authors plot the two against each other? What would it mean if it is correlated? What minimal nitrogen concentration/signal should there be to make a reliable estimate of the ratio? Does the higher ratio mean that the turnover rate of the Calvin-Benson cycle enzymes is higher than for other proteins?

For the small structures that could be the nitrogen fixing bacteria the 15N enrichment is up to 270x the natural ratio. Does this mean that 100% (270*0.0036=1) of their nitrogen is fixed from the provided atmosphere?

Could one also provide the absolute ratio in the chloroplasts? It would be nice if the authors discuss, based on their data, the potential of using nitrogen fixing bacteria to provide nitrogen to crops.

Reviewer #2 (Public Review):

Fuchs et al. propose a framework for action recognition based on pose estimation. They integrate functions from DeepLabCut and MMAction2, two popular machine-learning frameworks for behavioral analysis, in a new package called ASBAR.

They test their framework by

- Running pose estimation experiments on the OpenMonkeyChallenge (OMC) dataset (the public train + val parts) with DeepLabCut.

- Annotating around 320 image pose data in the PanAf dataset (which contains behavioral annotations). They show that the ResNet-152 model generalizes best from the OMC data to this out-of-domain dataset.

- They then train a skeleton-based action recognition model on PanAf and show that the top-1/3 accuracy is slightly higher than video-based methods (and strong), but that the mean class accuracy is lower - 33% vs 42%. Likely due to the imbalanced class frequencies. This should be clarified. For Table 1, confidence intervals would also be good (just like for the pose estimation results, where this is done very well).

Reviewer #1 (Public Review):

This is a very relevant study, clearly with the potential of having a high impact on future research on the evolution of chemical defense mechanisms in animals. The authors present a substantial number of new and surprising experimental results, i.e., the presence in low quantities of alkaloids in amphibians previously deemed to lack these toxins. These data are then combined with literature data to weave the importance of passive accumulation mechanisms into a 4-phases scenario of the evolution of chemical defense in alkaloid-containing poison frogs.

In general, the new data presented in the manuscript are of high quality and high scientific interest, the suggested scenario compelling, and the discussion thorough. Also, the manuscript has been carefully prepared with a high quality of illustrations and very few typos in the text. Understanding that the majority of dendrobatid frogs, including species considered undefended, can contain low quantities of alkaloids in their skin provides an entirely new perspective to our understanding of how the amazing specializations of poison frogs evolved. Although only a few non-dendrobatids were included in the GCMS alkaloid screening, some of these also included minor quantities of alkaloids, and the capacity of passive alkaloid accumulation may therefore characterize numerous other frog clades, or even amphibians in general.

While the overall quality of the work is exceptional, major changes in the structure of the submitted manuscript are necessary to make it easier for readers to disentangle scope, hypotheses, evidence and newly developed theories.

Reviewer #2 (Public Review):

Summary:

Yamawaki et al., conducted a series of neuroanatomical tracing and whole-cell recording experiments to elucidate and characterise a relatively unknown pathway between the endopiriform (EN) and CA1 of the ventral hippocampus (vCA1) and to assess its functional role in social and object recognition using fibre photometry and dual vector chemogenetics. The main findings were that the EN sends robust projections to the vCA1 that colateralise to the prefrontal cortex, lateral entorhinal cortex, and piriform cortex, and these EN projection neurons terminate in the stratum lacunosum-moleculare (SLM) layer of distal vCA1, synapsing onto GABAergic neurons that span across the Pyramidal-Stratum Radiatum (SR) and SR-SML borders. It was also demonstrated that EN input disynaptically inhibits vCA1 pyramidal neurons. vCA1 projecting EN neurons receive afferent input from the piriform cortex, and from within EN. Finally, fibre photometry experiments revealed that vCA1 projecting EN neurons are most active when mice explore novel objects or conspecifics, and pathway-specific chemogenetic inhibition led to an impairment in the ability to discriminate between novel vs. familiar objects and conspecifics.

This is an interesting mechanistic study that provides valuable insights into the function and connectivity patterns of afferent input from the endopiriform to the CA1 subfield of the ventral hippocampus. The authors propose that the EN input to the vCA1 interneurons provides a feedforward inhibition mechanism by which novelty detection could be promoted. The experiments appear to be carefully conducted, and the methodological approaches used are sound. The conclusions of the paper are supported by the data presented on the whole.

However, some aspects of methodology and data interpretation will need to be clarified and further evidence provided to enhance the utility of the data to the rest of the field.

The authors used dual retrograde tracing and observed that the highest percentage (~30%) of vCA1 projecting EN cells also projected to the PFC. They then employed an intersectional approach to show the presence of collaterals in other cortical areas such as the entorhinal cortex and piriform cortex in addition to the PFC. However, they state that 'Projection to prefrontal cortex was sparse relative to other areas, as expected based on the retrograde labeling data' (referring to Figure 2K) and subsequently appear to dismiss the initial data set indicating strong axonal projections to the PFC.

Since this is a relatively unknown connection, it would be helpful if some evidence/discussion is provided for whether the EN projects to other subfields (CA3, DG) of the ventral hippocampus. This is important, as the retrograde tracer injections depicted in Figure 1B clearly show a spread of the tracer to vCA3 and potentially vDG and it is not possible to ascertain the regional specificity of the pathway.

The vCA1 projecting EN cells appear to originate from an extensive range along the AP axis. Is there a topographical organization of these neurons within the vCA1? A detailed mapping of this kind would be valuable.

Given this extensive range in the location of vCA1 EN originating cells, how were the targets (along the AP axis) in EP selected for the calcium imaging?

The vCA1 has extensive reciprocal connections with the piriform cortex as well, which is in close proximity to the EN. How certain are the authors that the chemogenetic targeting was specific to the EN-vCA1 connection?

Raw data for the sociability and discrimination indices should be provided so that the readers can gain further insight into the nature of the impairment.

Line 222: It is unclear how locomotor activity informs anxiety in the behavioral tests.

Figure 7 title; It is stated that activity of EN neurons 'predict' social/object discrimination performance. However, caution must be exercised with this interpretation as the correlational data are underpowered (n=5-8). Furthermore, the results show a significant correlation between calcium event ratios and the discrimination index in the social discrimination test but not the object discrimination test.

While both male and female mice were included in the anatomical tracing and recording experiments, only male mice were used for behavioral tests.

Reviewer #2 (Public Review):

Summary:

The paper considers a recurrent network with neurons driven by external input. During the external stimulation predictive synaptic plasticity adapts the forward and recurrent weights. It is shown that after the presentation of constant stimuli, the network spontaneously samples the states imposed by these stimuli. The probability of sampling stimulus x^(i) is proportional to the relative frequency of presenting stimulus x^(i) among all stimuli i=1,..., 5.

Methods:

Neuronal dynamics:

For the main simulation (Figure 3), the network had 500 neurons, and 5 non-overlapping stimuli with each activating 100 different neurons where presented. The voltage u of the neurons is driven by the forward weights W via input rates x, the inhibitory recurrent weights G, are restricted to have non-negative weights (Dale's law), and the other recurrent weights M had no sign-restrictions. Neurons were spiking with an instantaneous Poisson firing rate, and each spike-triggered an exponentially decaying postsynaptic voltage deflection. Neglecting time constants of the postsynaptic responses, the expected postsynaptic voltage reads (in vectorial form) as

u = W x + (M - G) f (Eq. 5)

where f =; phi(u) represents the instantaneous Poisson rate, and phi a sigmoidal nonlinearity. The rate f is only an approximation (symbolized by =;) of phi(u) since an additional regularization variable h enters (taken up in Point 4 below). The initialisation of W and M is Gaussian with mean 0 and variance 1/sqrt(N), N the number of neurons in the network. The initial entries of G are all set to 1/sqrt(N).

Predictive synaptic plasticity:

The 3 types of synapses were each adapted so that they individually predict the postsynaptic firing rate f, in matrix form

ΔW ≈ (f - phi( W x ) ) x^T<br /> ΔM ≈ (f - phi( M f ) ) f^T<br /> ΔG ≈ (f - phi( M f ) ) f^T but confined to non-negative values of G (Dale's law).

The ^T tells us to take the transpose, and the ≈ again refers to the fact that the ϕ entering in the learning rule is not exactly the ϕ determining the rate, only up to the regularization (see Point 4).

Main formal result:

As the authors explain, the forward weight W and the unconstrained weight M develop such that, in expectations,

f =; phi( W x ) =; phi( M f ) =; phi( G f ) ,

consistent with the above plasticity rules. Some elements of M remain negative. In this final state, the network displays the behaviour as explained in the summary.

Major issues:

Point 1: Conceptual inconsistency

The main results seem to arise from unilaterally applying Dale's law only to the inhibitory recurrent synapses G, but not to the excitatory recurrent synapses M.

In fact, if the same non-negativity restriction were also imposed on M (as it is on G), then their learning rules would become identical, likely leading to M=G. But in this case, the network becomes purely forward, u = W x, and no spontaneous recall would arise. Of course, this should be checked in simulations.

Because Dale's law was only applied to G, however, M and G cannot become equal, and the remaining differences seem to cause the effect.

Predictive learning rules are certainly powerful, and it is reasonable to consider the same type of error-correcting predictive learning rule, for instance for different dendritic branches that both should predict the somatic activity. Or one may postulate the same type of error-correcting predictive plasticity for inhibitory and excitatory synapses, but then the presynaptic neurons should not be identical, as it is assumed here. Both these types of error-correcting and error-forming learning rules for same-branches and inhibitory/excitatory inputs have been considered already (but with inhibitory input being itself restricted to local input, for instance).

Point 2: Main result as an artefact of an inconsistently applied Dale's law?

The main result shows that the probability of a spontaneous recall for the 5 non-overlapping stimuli is proportional to the relative time the stimulus was presented. This is roughly explained as follows: each stimulus pushes the activity from 0 up towards f =; phi( W x ) by the learning rule (roughly). Because the mean weights W are initialized to 0, a stimulus that is presented longer will have more time to push W up so that positive firing rates are reached (assuming x is non-negative). The recurrent weights M learn to reproduce these firing rates too, while the plasticity in G tries to prevent that (by its negative sign, but with the restriction to non-negative values). Stimuli that are presented more often, on average, will have more time to reach the positive target and hence will form a stronger and wider attractor. In spontaneous recall, the size of the attractor reflects the time of the stimulus presentation. This mechanism so far is fine, but the only problem is that it is based on restricting G, but not M, to non-negative values.

Point 3: Comparison of rates between stimulation and recall.

The firing rates with external stimulations will be considerably larger than during replay (unless the rates are saturated).

This is a prediction that should be tested in simulations. In fact, since the voltage roughly reads as<br /> u = W x + (M - G) f,<br /> and the learning rules are such that eventually M =; G, the recurrences roughly cancel and the voltage is mainly driven by the external input x. In the state of spontaneous activity without external drive, one has<br /> u = (M - G) f ,<br /> and this should generate considerably smaller instantaneous rates f =; phi(u) than in the case of the feedforward drive (unless f is in both cases at the upper or lower ceiling of phi). This is a prediction that can also be tested.

Because the figures mostly show activity ratios or normalized activities, it was not possible for me to check this hypothesis with the current figures. So please show non-normalized activities for comparing stimulation and recall for the same patterns.

Point 4: Unclear definition of the variable h.<br /> The formal definition of h = hi is given by (suppressing here the neuron index i and the h-index of tau)

tau dh/dt = -h if h>u, (Eq. 10)<br /> h = u otherwise.

But if it is only Equation 10 (nothing else is said), h will always become equal to u, or will vanish, i.e. either h=u or h=0 after some initial transient. In fact, as soon as h>u, h is decaying to 0 according to the first line. If u is >0, then it stops at u=h according to the second line. No reason to change h=u further. If u<=0 while h>u, then h is converging to 0 according to the first line and will stay there. I guess the authors had issues with the recurrent spiking simulations and tried to fix this with some regularization. However as presented, it does not become clear how their regulation works.

BTW: In Eq. 11 the authors set the gain beta to beta = beta0/h which could become infinite and, putatively more problematic, negative, depending on the value of h. Maybe some remark would convince a reader that no issues emerge from this.

Added from discussions with the editor and the other reviewers:

Thanks for alerting me to this Supplementary Figure 8. Yes, it looks like the authors did apply there Dale's law for both the excitatory and inhibitory synapses. Yet, they also introduced two types of inhibitory pathways converging both to the excitatory and inhibitory neurons. For me, this is a confirmation that applying Dale's law to both excitatory and inhibitory synapses, with identical learning rules as explained in the main part of the paper, does not work.

Adding such two pathways is a strong change from the original model as introduced before, and based on which all the Figures in the main text are based. Supplementary Figure 8 should come with an analysis of why a single inhibitory pathway does not work. I guess I gave the reason in my Points 1-3. Some form of symmetry breaking between the recurrent excitation and recurrent inhibition is required so that, eventually, the recurrent excitatory connection will dominate.

Making the inhibitory plasticity less expressive by applying Dale's law to only those inhibitory synapses seems to be the answer chosen in the Figures of the main text (but then the criticism of unilaterally applying Dale's law).

Applying Dale's law to both types of synapses, but dividing the labor of inhibition into two strictly separate and asymmetric pathways, and hence asymmetric development of excitatory and inhibitory weights, seems to be another option. However, introducing such two separate inhibitory pathways, just to rescue the fact that Dale's law is applied to both types of synapses, is a bold assumption. Is there some biological evidence of such two pathways in the inhibitory, but not the excitatory connections? And what is the computational reasoning to have such a separation, apart from some form of symmetry breaking between excitation and inhibition? I guess, simpler solutions could be found, for instance by breaking the symmetry between the plasticity rules for the excitatory and inhibitory neurons. All these questions, in my view, need to be addressed to give some insights into why the simulations do work.

Overall, Supplementary Figure 8 seems to me too important to be deferred to the Supplement. The reasoning behind the two inhibitory pathways should appear more prominently in the main text. Without this, important questions remain. For instance, when thinking in a rate-based framework, the two inhibitory pathways twice try to explain the somatic firing rate away. Doesn't this lead to a too strong inhibition? Can some steady state with a positive firing rate caused by the recurrence, in the absence of an external drive, be proven? The argument must include the separation into Path 1 and Path 2. So far, this reasoning has not been entered.

In fact, it might be that, in a spiking implementation, some sparse spikes will survive. I wonder whether at least some of these spikes survive because of the other rescuing construction with the dynamic variable h (Equation 10, which is not transparent, and that is not taken up in the reasoning either, see my Point 4).

Perhaps it is helpful for the authors to add this text in the reply to them.

Reviewer #3 (Public Review):

Summary: The authors investigate the effect of high concentrations of the lipid aldehyde trans-2-hexadecenal (t-2-hex) in a yeast deletion strain lacking the detoxification enzyme. Transcriptomic analyses as global read out reveal that a large range of cellular functions across all compartments are affected (transcriptomic changes affect 1/3 of all genes). The authors provide additional analyses, from which they built a model that mitochondrial protein import caused by modification of Tom40 is blocked.

Strengths:<br /> Global analyses (transcriptomic and functional genomics approach) to obtain an overview of changes upon yeast treatment with high doses of t-2-hex.

Weaknesses:<br /> The use of high concentrations of t-2-hex in combination with a deletion of the detoxifying enzyme Hfd1 limits the possibility to identify physiological relevant changes. From the hundreds of identified targets the authors focus on mitochondrial proteins, which are not clearly comprehensible from the data. The main claim of the manuscript that t-2-hex targets the TOM complex and inhibits mitochondrial protein import is not supported by experimental data as import was not experimentally investigated. The observed accumulation of precursor proteins could have many other reasons (e.g. dissipation of membrane potential, defects in mitochondrial presequence proteases, defects in cytosolic chaperones, modification of mitochondrial precursors by t-2-hex rendering them aggregation prone and thus non-import competent). However, none of these alternative explanations have been experimentally addressed or discussed in the manuscript.<br /> Furthermore, many of the results have been reported before (interaction of Tom22 and Tom70 with Hfd1) or observed before (TOM40 as target of t-2-hex in human cells).

Reviewer #3 (Public Review):

Summary:

In this manuscript, the authors extend previous work on the role of predator interference in species coexistence. Previous theoretical work (for example, using the Beddington-DeAngelis model) has shown that predator interference allows for multiple predators to coexist on the same prey. While the Beddington-DeAngelis has been influential in theoretical ecology, it has also been criticized at times for several unusual assumptions, most critically, that predators interfere with each other regardless of whether they are already engaged in another interaction. There has been considerable work since then which has sought either to find sets of assumptions that lead to the B-D equation or to derive alternative equations from a more realistic set of assumptions (Ruxton et al. 1992; Cosner et al. 1999; Broom et al. 2010; Geritz and Gyllenberg 2012). This paper represents another effort to more rigorously derive a model of predator interference by borrowing concepts from chemical reaction kinetics (the approach is similar to previous work: Ruxton et al. 1992). The main point of difference is that the model in the current manuscript allows for 'chasing pairs', where a predator and prey engage with one another to the exclusion of other interactions, a situation Ruxton et al. (1992) do not consider. While the resulting functional response is quite complex, the authors show that under certain conditions, one can get an analytical expression for the functional response of a predator as a function of predator and resource densities. They then go on to show that including intraspecific interference allows for the coexistence of multiple species on one or a few resources, and demonstrate that this result is robust to demographic stochasticity. This work provides additional support for the idea that predator interference allows multiple predators to persist with a shared resource.

Strengths:

I appreciate the effort to rigorously derive interaction rates from models of individual behaviors. As currently applied, functional responses (FRs) are estimated by fitting equations to feeding rate data across a range of prey or predator densities. In practice, such experiments are only possible for a limited set of species. This is problematic because whether a particular FR allows stability or coexistence depends on not just its functional form, but also its parameter values. The promise of the approach taken here is that one might be able to derive the functional response parameters of a particular predator species from species traits or more readily measurable behavioural data.

Weaknesses:

The main weakness of this paper is that while it is technically sound, it doesn't change the fundamental intuition gained from more phenomenological models of predator interference: as one species becomes more common, it limits its own growth (manifested by less time spent searching for/handing resources due to interference), such that it does not exclude the existence of a competitor species. However, given the authors use a different model formulation that has been used in past studies, it suggests that predator interference will likely tend to promote coexistence regardless of some of the technical details in how it is formulated in a model.

The formulation of chasing-pair engagements assumes that prey being chased by a predator are unavailable to other predators. While this may hold in some predator-prey, it does not hold for many others, perhaps limiting some results' generality.

Summary:

The manuscript by Kang et al investigates how the consideration of pairwise encounters (consumer-resource chasing, intraspecific consumer pair, and interspecific consumer pair) influences the community assembly results. To explore this, they presented a new model that considers pairwise encounters and intraspecific interference among consumer individuals, which is an extension of the classical Beddington-DeAngelis (B-D) phenomenological model, incorporating detailed considerations of pairwise encounters and intraspecific interference among consumer individuals. Later, they connected with several experimental datasets.

Strengths:

They found that the negative feedback loop created by the intraspecific interference allows a diverse range of consumer species to coexist with only one or a few types of resources. Additionally, they showed that some patterns of their model agree with experimental data, including time-series trajectories of two small in-lab community experiments and the rank-abundance curves from several natural communities. The presented results here are interesting and present another way to explain how the community overcomes the competitive exclusion principle.

Weaknesses:

The authors did a great job of satisfactorily addressing each of my concerns raised in the previous round. I did not detect additional weaknesses.

Reviewer #2 (Public Review):

The neural dynamics underlying decision-making have long been studied across different species (e.g., primates and rodents) and brain areas (e.g., parietal cortex, frontal eye fields, striatum). The key question is to what extent neural firing rates covary with evidence accumulation processes as proposed by evidence accumulation models. It is often assumed that the evidence-accumulation process at the neural level should mirror the evidence-accumulation process at the behavioral level. The current paper shows that the neural dynamics of three rat brain regions (the FOF, ADS, and PCC) all show signatures of evidence accumulation, but in distinct ways. Especially the role of the FOF appears to be distinct, due to its dependence on early evidence compared to the other regions. This sheds new light and a new interpretation of the role of the FOF in decision-making - previously, it has been described as a region encoding the choice that is currently being committed to; this new analysis suggests it is instead strongly influenced by early evidence.

A major strength of the paper is that the results are achieved through joint modelling of the behavioral and neural data, combined with information on the physical stimulus at hand. Joint models were shown to provide more information on the underlying processes compared to behavioral or neural models alone. Especially the inclusion of the neural data seemed to have greatly improved the quality of inferences. This is a key contribution that illustrates that the sophisticated modelling of multiple sources of data at the same time, pays off in terms of the quality of inferences. Yet, it should be added here, that due to the nature of the task, the behavioral data contained only choices, and not response times, which tend to contain more information regarding the evidence accumulation process than choice alone. It would be interesting to additionally discuss how choice decision times can be modeled with the proposed modelling framework.

A main limitation of the paper is that it does not appear to address a seemingly logical follow-up question: If these three brain regions individually accumulate evidence in distinct manners, how do these multiple brain regions then each contribute to a final choice? The joint models fit each region's data separately, so how well does each region individually 'explain' or 'predict' behavior, and how does the combined neural activity of the regions lead to manifest behavior? I would be very interested in the authors' perspectives on these questions.

There are some remaining questions regarding the specific models used, that I was hoping the authors could clarify. Specifically, in equations 10-11, I was wondering to what extent there might be a collinearity issue. Equation 10 proposes that the firing rates of neurons can vary across time due to two mechanisms: (1) The dependence of the firing rate on the accumulated evidence, and (2) a time-varying trial average (as detailed in Equation 11). If firing rates of the neuron indeed covary with the accumulated evidence and therefore increase across time, how can the effects of mechanisms 1 and 2 be disentangled? Relatedly, the independent noise models model each neuron separately and thereby include many more parameters, each informed by less data. Is it possible that the relatively poor cross-validation of the independent noise model may be a consequence of the overfitting of the independent noise model?<br /> Another related question is how robust the parameter recovery properties of these models are under a wider range of data-generating parameter settings. I greatly appreciate the inclusion of a parameter recovery study (Figure S1C) using a single synthetic dataset, but it could be made even stronger by simulating multiple datasets with a wider range of parameter settings. Such a simulation study would help understand how robust and reliable the estimated parameters of all models are. Similarly, it would be helpful if also the \theta_{y} parameters are shown, which aren't shown in Figure S1C.

An aspect of the paper that initially raised confusion with me is that the models fit on the choice data and stimulus information alone, make different predictions for the evidence accumulation dynamics in different regions (e.g., Figure 5A, 6A) and also led to different best-fitting parameters in different regions (Figure S9A). It took me a while to realize that this is due to the data being pooled across different rats and sessions - as such, the behavioral choice data are not the same across regions, and neither is the resulting fit models. This could easily be clarified by adding a few notes in the captions of the relevant figures.

Combined, this manuscript represents an interesting and welcome contribution to an ongoing debate on the neural dynamics of decision-making across different brain regions. It also introduced new joint modelling techniques that can be used in the field and raised new questions on how the concurrent activity of neurons across different brain regions combined leads to behavior.

Reviewer #2 (Public Review):

Summary:

Schmidlin & Apodaca et al. aim to distinguish mutants that resist drugs via different mechanisms by examining fitness tradeoffs across hundreds of fluconazole-resistant yeast strains. They barcoded a collection of fluconazole-resistant isolates and evolved them in different environments with a view to having relevance for evolutionary theory, medicine, and genotype-phenotype mapping.

Strengths:

There are multiple strengths to this paper, the first of which is pointing out how much work has gone into it; the quality of the experiments (the thought process, the data, the figures) is excellent. Here, the authors seek to induce mutations in multiple environments, which is a really large-scale task. I particularly like the attention paid to isolates with are resistant to low concentrations of FLU. So often these are overlooked in favour of those conferring MIC values >64/128 etc. What was seen is different genotype and fitness profiles. I think there's a wealth of information here that will actually be of interest to more than just the fields mentioned (evolutionary medicine/theory).

Weaknesses:

Not picking up low fitness lineages - which the authors discuss and provide a rationale as to why. I can completely see how this has occurred during this research, and whilst it is a shame I do not think this takes away from the findings of this paper. Maybe in the next one!

In the abstract the authors focus on 'tradeoffs' yet in the discussion they say the purpose of the study is to see how many different mechanisms of FLU resistance may exist (lines 679-680), followed up by "We distinguish mutants that likely act via different mechanisms by identifying those with different fitness tradeoffs across 12 environments". Whilst I do see their point, and this is entirely feasible, I would like a bit more explanation around this (perhaps in the intro) to help lay-readers make this jump. The remainder of my comments on 'weaknesses' are relatively fixable, I think:

In the introduction I struggle to see how this body of research fits in with the current literature, as the literature cited is a hodge-podge of bacterial and fungal evolution studies, which are very different! So example, the authors state "previous work suggests that mutants with different fitness tradeoffs may affect fitness through different molecular mechanisms" (lines 129-131) and then cite three papers, only one of which is a fungal research output. However, the next sentence focuses solely on literature from fungal research. Citing bacterial work as a foundation is fine, but as you're using yeast for this I think tailoring the introduction more to what is and isn't known in fungi would be more appropriate. It would also be great to then circle back around and mention monotherapy vs combination drug therapy for fungal infections as a rationale for this study. The study seems to be focused on FLU-resistant mutants, which is the first-line drug of choice, but many (yeast) infections have acquired resistance to this and combination therapy is the norm.

Methods: Line 769 - which yeast? I haven't even seen mention of which species is being used in this study; different yeast employ different mechanisms of adaptation for resistance, so could greatly impact the results seen. This could help with some background context if the species is mentioned (although I assume S. cerevisiae). In which case, should aneuploidy be considered as a mechanism? This is mentioned briefly on line 556, but with all the sequencing data acquired this could be checked quickly?

I think the authors could be bolder and try and link this to other (pathogenic) yeasts. What are the implications of this work on say, Candida infections?

Reviewer #2 (Public Review):

In this work, Kashefi et al. investigate the planning of sequential reaching movements and how the additional information about future reaches affects planning and execution. This study, carried out with human subjects, extends a body of research in sequential movements to ask important questions: How many future reaches can you plan in advance? And how do those future plans interact with each other?

The authors designed several experiments to address these questions, finding that information about future targets makes reaches more efficient in both timing and path curvature. Further, with some clever target jump manipulations, the authors show that plans for a distant future reach can influence plans for a near future reach, suggesting that the planning for multiple future reaches is not independent. Lastly, the authors show that information about future targets is acquired parafoveally--that is, subjects tend to fixate mainly on the target they are about to reach to, acquiring future target information by paying attention to targets outside the fixation point.

The study opens up exciting questions about how this kind of multi-target planning is implemented in the brain. As the authors note in the manuscript, previous work in monkeys showed that preparatory neural activity for a future reaching movement can occur simultaneously with a current reaching movement, but that study was limited to the monkey only knowing about two future targets. It would be quite interesting to see how neural activity partitions preparatory activity for a third future target, given that this study shows that the third target's planning may interact with the second target's planning.

[Editors' note: The authors fully addressed the reviewers' comments on the original manuscript.]

Acord asociație pentru modficiări constructive

Reviewer #2 (Public Review):

Summary:

Numerous studies by the authors and other groups have demonstrated an important role for HIV gene expression kidney cells in promoting progressive chronic kidney disease, especially HIV associated nephropathy. The authors had previously demonstrated a role for protein kinase R (PKR) in a non-HIV transgenic model of kidney disease (Okamoto, Commun Bio, 2021). In this study, the authors used innovative techniques including bulk and single nuclear RNAseq to demonstrate that mice expressing a replication-incompetent HIV transgene have prominent dysregulation of mitochondrial gene expression and activation of PKR and that treatment of these mice with a small molecule PKR inhibitor ameliorated the kidney disease phenotype in HIV-transgenic mice. They also identified STAT3 as a key upstream regulator of kidney injury in this model, which is consistent with previously published studies. Other important advances include identifying the kidney cell types that express the HIV transgene and have dysregulation of cellular pathways.

Strengths:

Major strengths of the study include the use of a wide variety of state-of-the-art molecular techniques to generate important new data on the pathogenesis of kidney injury in this commonly used model of kidney disease and the identification of PKR as a potential druggable target for the treatment of HIV-induced kidney disease. The authors also identify a potential novel cell type within the kidney characterized by high expression of mitochondrial genes.

Weaknesses:

Though the HIV-transgenic model used in these studies results in a phenotype that is very similar to HIV-associated nephropathy in humans, the model has several limitations that may prevent direct translation to human disease, including the fact that mice lack several genetic factors that are important contributors to HIV and kidney pathogenesis in humans. Additional studies are therefore needed to confirm these findings in human kidney disease.

Reviewer #2 (Public Review):

Summary:

Most polymerases and nucleases use two or three divalent metal ions in their catalytic functions. The family of His-Me nucleases, however, use only one divalent metal ion, along with a conserved histidine, to catalyze DNA hydrolysis. The mechanism has been studied previously but, according to the authors, it remained unclear. By use of time resolved X-ray crystallography, this work convincingly demonstrated that only one M2+ ion is involved in the catalysis of the His-Me I-PpoI 19 nuclease, and proposed concerted functions of the metal and the histidine.

Strengths:

This work performs mechanistic studies, including the number and roles of metal ion, pH dependence, and activation mechanism, all by structural analyses, coupled with some kinetics and mutagenesis. Overall, it is a highly rigorous work. This approach was first developed in Science (2016) for a DNA polymerase, in which Yang Cao was the first author. It has subsequently been applied to just 5 to 10 enzymes by different labs, mainly to clarify two versus three metal ion mechanisms. The present study is the first one to demonstrate a single metal ion mechanism by this approach.<br /> Furthermore, on the basis of the quantitative correlation between the fraction of metal ion binding and the formation of product, as well as the pH dependence, and the data from site specific mutants, the authors concluded that the functions of Mg2+ and His are a concerted process. A detailed mechanism is proposed in Figure 6.<br /> Even though there are no major surprises in the results and conclusions, the time-resolved structural approach and the overall quality of the results represent a significant step forward for the Me-His family of nucleases. In addition, since the mechanism is unique among different classes of nucleases and polymerases, the work should be of interest to readers in DNA enzymology, or even mechanistic enzymology in general.

Weaknesses:

Two relatively minor issues are raised here for consideration by the authors:

p. 4, last para, lines 1-2: "we next visualized the entire reaction process by soaking I-PpoI crystals in buffer....". This is a little over-stated. The structures being observed are not reaction intermediates. They are mixtures of substrates and products in the enzyme-bound state. The progress of the reaction is limited by the progress of soaking of the metal ion. Crystallography is just been used as a tool to monitor the reaction (and provide structural information about the product). It would be more accurate to say that "we next monitored the reaction progress by soaking...."

p. 5, beginning of the section. The authors on one hand emphasized the quantitative correlation between Mg ion density and the product density. On the other hand, they raised the uncertainty in the quantitation of Mg2+ density versus Na+ density, thus they repeated the study with Mn2+ which has distinct anomalous signals. This is a very good approach. However, still no metal ion density is shown in the key figure 2A. It will be clearer to show the progress of metal ion density in a figure (in addition to just plots), whether it is Mg or Mn.

Revised version: The authors have properly revised the paper in response to both questions raised in the weakness section. The first issue is an important clarification for others working on similar approaches also. For the second issue, the metal ion density is nicely shown in Fig. S4 now.

Reviewer #2 (Public Review):

Summary:

The manuscript entitled "Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K" by Zheng et al. presents a neutron scattering study trying to elucidate if at the dynamical transition temperature water and protein motions are coupled. The origin of the dynamical transition temperature has been debated for decades, specifically its relation to hydration.

The study is rather well conducted, with a lot of effort to acquire the perdeuterated proteins, and some results are interesting.

Reviewer #2 (Public Review):

Summary:<br /> The manuscript by Zhu et al. describes phenotypes associated with the loss of the gene ifc using a Drosophila model. The authors suggest their findings are relevant to understanding the molecular underpinnings of a neurodegenerative disorder, HLD-18, which is caused by mutations in the human ortholog of ifc, DEGS1.<br /> The work begins with the authors describing the role for ifc during fly larval brain development, demonstrating its function in regulating developmental timing, brain size, and ventral nerve cord elongation. Further mechanistic examination revealed that loss of ifc leads to depleted cellular ceramide levels as well as dihydroceramide accumulation, eventually causing defects in ER morphology and function. Importantly, the authors showed that ifc is predominantly expressed in glia and is critical for maintaining appropriate glial cell numbers and morphology. Many of the key phenotypes caused by the loss of fly ifc can be rescued by overexpression of human DEGS1 in glia, demonstrating the conserved nature of these proteins as well as the pathways they regulate. Interestingly, the authors discovered that the loss of lipid droplet formation in ifc mutant larvae within the cortex glia, presumably driving the deficits in glial wrapping around axons and subsequent neurodegeneration, potentially shedding light on mechanisms of HLD-18 and related disorders.

Strengths:<br /> Overall, the manuscript is thorough in its analysis of ifc function and mechanism. The data images are high quality, the experiments are well controlled, and the writing is clear.

Weaknesses:<br /> (1) The authors clearly demonstrated a reduction in number of glia in the larval brains of ifc mutant flies. What remains unclear is whether ifc loss leads to glial apoptosis or a failure for glia to proliferate during development. The authors should distinguish between these two hypotheses using apoptotic markers and cell proliferation markers in glia.

(2) It is surprising that human DEGS1 expression in glia rescues the noted phenotypes despite the different preference for sphingoid backbone between flies and mammals. Though human DEGS1 rescued the glial phenotypes described, can animal lethality be rescued by glial expression of human DEGS1? Are there longer-term effects of loss of ifc that cannot be compensated by the overexpression of human DEGS1 in glia (age-dependent neurodegeneration, etc.)?

(3) The mechanistic link between the loss of ifc and lipid droplet defects is missing. How do defects in ceramide metabolism alter triglyceride utilization and storage? While the author's argument that the loss of lipid droplets in larval glia will lead to defects in neuronal ensheathment, a discussion of how this is linked to ceramides needs to be added.

(4) On page 10, the authors use the words "strong" and "weak" to describe where ifc is expressed. Since the use of T2A-GAL4 alleles in examining gene expression is unable to delineate the amount of gene expression from a locus, the terms "broad" and "sparse" labeling (or similar terms) should be used instead.

Reviewer #2 (Public Review):

Summary:

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

Strengths:

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

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

Weaknesses:

One way to define effective population size is by the inverse of the coalescent rate. This is where the geometric mean of Ne comes from. If Ne is defined this way, many of the paradoxes mentioned seem to resolve naturally. If we take this approach, one could easily show that a large N population can still have a low coalescent rate depending on the reproduction model. However, the authors did not discuss Ne in light of the coalescent theory. This is surprising given that Eldon and Wakeley's 2006 paper is cited in the introduction, and the multiple mergers coalescent was introduced to explain the discrepancy between census size and effective population size, superspreaders, and reproduction variance - that said, there is no explicit discussion or introduction of the multiple mergers coalescent.

The Wright-Fisher model is often treated as a special case of the Cannings 1974 model, which incorporates the variance in reproductive success. This model should be discussed. It is unclear to me whether the results here have to be explained by the newly introduced WFH model, or could have been explained by the existing Cannings model.

The abstract makes it difficult to discern the main focus of the paper. It spends most of the space introducing "paradoxes".

The standard Wright-Fisher model makes several assumptions, including hermaphroditism, non-overlapping generations, random mating, and no selection. It will be more helpful to clarify which assumptions are being violated in each tested scenario, as V(K) is often not the only assumption being violated. For example, the logistic growth model assumes no cell death at the exponential growth phase, so it also violates the assumption about non-overlapping generations.

The theory and data regarding sex chromosomes do not align. The fact that \hat{alpha'} can be negative does not make sense. The authors claim that a negative \hat{alpha'} is equivalent to infinity, but why is that? It is also unclear how theta is defined. It seems to me that one should take the first principle approach e.g., define theta as pairwise genetic diversity, and start with deriving the expected pair-wise coalescence time under the MMC model, rather than starting with assuming theta = 4Neu. Overall, the theory in this section is not well supported by the data, and the explanation is insufficient.

DOI: 10.1016/j.celrep.2024.114559

Resource: ZFIN_ZDB-GENO-141030-2

Curator: @vtello

SciCrunch record: RRID:ZFIN_ZDB-GENO-141030-2

What is this?

Reviewer #2 (Public Review):

The study presented by Paoli et al. explores temporal aspects of neuronal encoding of odors and their perception, using bees as a general model for insects. The neuronal encoding of the presence of an odor is not a static representation; rather, its neuronal representation is partly encoded by the temporal order in which parallel olfactory pathways participate and are combined. This aspect is not novel, and its relevance in odor encoding and recognition has been discussed for more than the past 20 years.

The temporal richness of the olfactory code and its significance have traditionally been driven by results obtained based on electrophysiological methods with temporal resolution, allowing the identification and timing of the action potentials in the different populations of neurons whose combination encodes the identity of an odor. On the other hand, optophysiological methods that enable spatial resolution and cell identification in odor coding lack the temporal resolution to appreciate the intricacies of olfactory code dynamics.

(1) In this context, the main merit of Paoli et al.'s work is achieving an optical recording that allows for spatial registration of olfactory codes with greater temporal detail than the classical method and, at the same time, with greater sensitivity to measure inhibitions as part of the olfactory code.

The work clearly demonstrates how the onset and offset of odor stimulation triggers a dynamic code at the level of the first interneurons of the olfactory system that changes at every moment as a natural consequence of the local inhibitory interactions within the first olfactory neuropil, the antennal lobe. This gives rise to the interesting theory that each combination of activated neurons along this temporal sequence corresponds to the perception of a different odor. The extent to which the corresponding postsynaptic layers integrate this temporal information to drive the perception of an odor, or whether this sequence is, in a sense, a journey through different perceptions, is challenging to address experimentally.

In their work, the authors propose a computational approach and olfactory learning experiments in bees to address these questions and evaluate whether the sequence of combinations drives a sequence of different perceptions. In my view, it is a highly inspiring piece of work that still leaves several questions unanswered.

(2) In my opinion, the detailed temporal profile of the response of projection neurons and their respective probabilities of occurrence provide valuable information for understanding odor coding at the level of neurons transferring information from the antennal lobes to the mushroom bodies. An analysis of these probabilities in each animal, rather than in the population of animals that were measured, would aid in better comprehending the encoding function of such temporal profiles. Being able to identify the involved glomeruli and understanding the extent to which the sequence of patterns and inhibitions is conserved for each odor across different animals, as it is well known for the initial excitatory burst of activity observed in previous studies without the fine temporal detail, would also be highly significant.

In my view, the computational approach serves as a useful tool to inspire future experiments; however, it appears somewhat simplistic in tackling the complexity of the subject. One question that I believe the researchers do not address is to what extent the inhibitions recorded in the projection neurons are integrated by the Kenyon cells and are functional for generating odor-specific patterns at that level.

Lastly, the behavioral result indicating a difference in conditioned response latency after early or delayed learning protocol is interesting. However, it does not align with the expected time for the neuronal representation that was theoretically rewarded in the delayed protocol. This final result does not support the authors' interpretation regarding the existence of a smell and an after-smell as separate percepts that can serve as conditioned stimuli.

Reviewer #2 (Public Review):

Summary:<br /> In "Speech-induced suppression and vocal feedback sensitivity in human cortex", Ozker and colleagues use intracranial EEG to understand audiomotor feedback during speech production using a speech production and delayed auditory feedback task. The purpose of the paper is to understand where and how speaker induced suppression occurs, and whether this suppression might be related to feedback monitoring. First, they identified sites that showed auditory suppression during speech production using a single word auditory repetition task and a visual reading task, then observed whether and how these electrodes show sensitivity to auditory feedback using a DAF paradigm. The stimuli were single words played auditorily or shown visually and repeated or read aloud by the participant. Neural data were recorded from regular- and high-density grids from the left and right hemisphere. The main findings were:<br /> • Speaker induced suppression is strongest in the STG and MTG, and enhancement is generally seen in frontal/motor areas except for small regions of interest in dorsal sensorimotor cortex and IFG, which can also show suppression.<br /> • Delayed auditory feedback, even when simultaneous, induces larger response amplitudes compared to the typical auditory word repetition and visual reading tasks. The authors presume this may be due to effort and attention required to perform the DAF task.<br /> • The degree of speaker induced suppression is correlated with sensitivity to delayed auditory feedback, and is strongest for ~200 ms of delayed auditory feedback.<br /> • pSTG (behind TTS) is more strongly modulated by DAF than mid-anterior STG

Strengths:<br /> Overall, I found the manuscript to be clear, the methodology and statistics to be solid, and the findings mostly quite robust. The large number of participants with high density coverage over both the left and right lateral hemispheres allows for a greater dissection of the topography of speaker induced suppression and changes due to audiomotor feedback. The tasks were well-designed and controlled for repetition suppression and other potential caveats.

Weaknesses:<br /> I am happy with the changes the authors made in response to my first round of comments.

The authors addressed my comments relating to plotting relative to the onset of articulation in Figure 1 and also addressed whether the amount of suppression varies according to more interfering delayed auditory feedback (though the correlations between sensitivity and suppression are a little noisy, they are positive). Finally, I am also satisfied with the inclusion of more group data in Figure 4.

Reviewer #2 (Public Review):

Summary:

The study tries to connect energy metabolism with immune tolerance during bacterial infection. The mechanism details the role of pyruvate transporter expression via ERRalpha-PGC1 axis, resulting in pro-inflammatory TNF alpha signalling responsible for acquired infection tolerance.

Strengths:

Overall, the study is an excellent addition to the role of energy metabolism during bacterial infection. The mechanism-based approach in dissecting the roles of metabolic coactivator, transcription factor, mitochondrial transporter and pro-inflammatory cytokine during acquired tolerance towards infections indicates a detailed and well-written study. The in vivo studies in mice nicely corroborate with the cell line-based data, indicating the requirement for further studies in human infections with another bacterial model system.

Weakness:

Revised version doesn't have much weakness as authors have performed some of the critical experiments to answer the concerns. Moreover, authors promted that a few concerns like public data sets, etc are out of scope of this work or they will perform such experiments in future.

Reviewer #2 (Public Review):

Summary:

The authors investigated how neuronal activity and metrics of plasticity using local electrical stimulation in the GPi were different between Parkinson's disease and dystonia patients.

Strengths:

The authors achieved their aims of comparing the dynamics related to stimulation induced metrics of plasticity in GPi between dystonia and PD, which has not been previously explored. These results could directly inform DBS protocols to improve treatment. The methods are clearly described and results are strong with measurements from a large population of patients for each disease group, and with distinct findings for each group. These results also may help provide insight as to the differences in terms of dynamics of therapeutic stimulation effects in the different disease groups.

Weaknesses:

After the revisions, the discussion contains many more details and comparisons to relevant literature, which will be helpful for readers to appreciate the importance of the results. The conclusion could have been strengthened as well, as it seems to be a very general summary of their findings without consideration of their clinical implications and importance. However, this may be a minor issue.

Reviewer #2 (Public Review):

Summary:<br /> The work by Klaassen & Rasch investigates the influence of word learning difficulty on sleep-associated consolidation and reactivation. They elicited reactivation during sleep by applying targeted memory reactivation (TMR) and manipulated word learning difficulty by creating words more similar (easy) or more dissimilar (difficult) to our language.<br /> In one group of participants, they applied TMR of easy words and in another group of participants, they applied TMR of difficult words (between-subjects design).<br /> They showed that TMR leads to higher memory benefits in the easy compared to the difficult word group. On a neural level, they showed an increase in spindle power (in the up-state of an evoked response) when easy words were presented during sleep.

Strengths:<br /> The authors investigate a research question relevant to the field, that is, which experiences are actually consolidated during sleep. To address this question, they developed an innovative task and manipulated difficulty in an elegant way.

Overall, the paper is clearly structured, results and methods are described in an understandable way. The analyses approach is solid.

Weaknesses:<br /> (1) Sample size<br /> For a between-subjects design, the sample size is too small (N = 22). The main finding (also found in the title "Difficulty in artificial word learning impacts targeted memory reactivation") is based on an independent samples t-test with 11 participants/group.<br /> The authors explicitly mention the small sample size and the between-subjects design as a limitation in their discussion. Nevertheless, making meaningful inferences based on studies with such a small sample size is difficult.

(2) Choice of task<br /> Even though the task itself is innovative, there would have been tasks better suited to address the research question. The main disadvantage the task and the operationalisation of memory performance (d') have is that single-trial performance cannot be calculated. Consequently, choosing individual items for TMR is not possible.<br /> Additionally, TMR of low vs. high difficulty is conducted between subjects (and independently of pre-sleep memory performance) which is a consequence of the task design.

Reviewer #2 (Public Review):

Summary:

This paper reports that mechanical stress from egg accumulation is a biological stimulus that drives the formation of extruded vesicles from the neurons of C. elegans ALMR touch neurons. Using powerful genetic experiments only readily available in the C. elegans system, the authors manipulate oocyte production, fertilization, embryo accumulation, and egg-laying behavior, providing convincing evidence that exopher production is driven by stretch-dependent feedback of fertilized, intact eggs in the adult uterus. Shifting the timing of egg production and egg laying alters the onset of observed exophers. Pharmacological manipulation of egg laying has the predicted effects, with animals retaining fewer eggs having fewer exophers and animals with increased egg accumulation having more. The authors show that egg production and accumulation have dramatic consequences to the viscera, and moving the ALMR process away from eggs prevents the formation of exophers. This effect is not unique to ALMR but is also observed in other touch neurons, with a clear bias toward neurons whose cell bodies are adjacent to the filled uterus. Embryos lacking an intact eggshell with reduced rigidity have impaired exopher production. Acute injection into the uterus to mimic the stretch that accompanies egg production causes a similar induction of exopher release. Together these results are consistent with a model where stretch caused by fertilized embryo accumulation, and not chemical signals from the eggs themselves or egg release, underlies ALMR exopher production seen in adult animals.

Strengths:

Overall, the experiments are very convincing, using a battery of RNAi and mutant approaches to distinguish direct from indirect effects. Indeed, these experiments provide a model generally for how one would methodically test different models for exopher production. The source and factors influencing exopher production had previously been unclear. This study addresses how and when they form in the animal using physiologically meaningful manipulations. The stage is now set to address at a cellular level how exophers like these are made and what their functions are.

Weaknesses:

Not many. The experiments are about as good as could be done. Some of the n's on the more difficult to work strains or experiments are comparatively low, but this is not a significant concern because the number of different, complementary approaches used. The microinjection experiment is very interesting, and the authors have added additional details on how these experiments were conducted in the revised manuscript. The authors have now included data from strains bearing a single-copy transgene that expresses mKate2 in the same neurons, showing that induced egg accumulation drives a similar degree of exopher production. This indicates that exposers seen are generated in response to specific biological conditions and not merely an artifact of mCherry protein over-expression.

Reviewer #2 (Public Review):

Kwon et al. used several conditional KO mice for the deletion of ric8a or app in different cell types. Some of them exhibited pial basement membrane breaches leading to neuronal ectopia in the neocortex.

They first investigated ric8a, a Guanine Nucleotide Exchange Factor for Heterotrimeric G Proteins. They observed the above-mentioned phenotype when ric8a is deleted from microglia and neural cells (ric8a-emx1-cre or dual deletion with cre combination cx3cr1 (in microglia) and nestin (in neural cells)) but not in microglia alone or neural cells alone (whether it is in CR cells (ric8a-Wnt3a-cre), post-mitotic neurons (nex-cre or dlx5/6-cre), or in progenitors and their progeny (nestin-cre or foxg1-cre). They also show that ric8a KO mutant microglia cells stimulated in vitro by LPS exhibit an increased TNFa, IL6 and IL1b secretion compared to controls (Fig 2). They therefore injected LPS in vivo and observed the neuronal ectopia phenotype in the ric8a-cx3cr1-cre (microglial deletion) cortices at P0 (Fig 2). They suggest that ric8a KO in neuronal cells mimics immune stimulation (but we have no clue how ric8a KO in neural cells would induce immune stimulation).

The authors then turned their attention on APP. They observed neuronal ectopia into the marginal zone when APP is deleted in microglia (app-cxcr3-cre) + intraperitoneal LPS injection (they did not show it, but we have to assume there would not be a phenotype without the injection of LPS) (Fig 3). (The phenotype is similar but not identical to ric8a-cx3cr1-cre + LPS. They suggest that the reason is because they had to inject 3 times less LPS due to enhanced immune sensitivity in this genetic background but it is only a hypothesis). After in vitro stimulation by LPS, app mutant microglia show a reduced secretion of TNFa and IL6 but not IL1b (this is the opposite to ric8a-cx3cr1-cre microglia cells) while peritoneal macrophages in culture show increased secretion of TNFa, IL1, IL6 and IL23 (fig 3 and Suppl. Fig 9).

Amyloid beta (Ab) being one of the molecules binding to APP, the authors showed that Ab40 monomers (they did not test Ab40 oligomers) partially inhibit cytokines (TNFa, IL6, IL1b, MCP-1, IL23a, IL10) secretion in vitro by microglia stimulated by LPS but does not affect secretion by microglia from app-cx3cr1-cre (tested for TNFa, IL6, IL1b, IL23a, IL10) (Fig 4, Suppl fig 10) (but still does it in aplp2-cx3cr1-cre) and does not affect secretion by ric8a-cx3cr1-cre microglia (tested for TNFa and IL6 but still suppress IL1b) (Therefore here is another difference between app and ric8a KO microglia).

The authors injected inhibitors of Akt or Stat3 in the ric8a-emx1-cre cortex and found it suppressed neuronal ectopia (Fig 5, Suppl fig 11). It is not clear whether it suppresses immune stimulation from neuronal cells or immune reaction from microglia cells.

Finally, the authors examined the activities of MMP2 and MMP9 in the developing cortex using gelatin gel zymography. The activity and protein levels of MMP9 but not MMP2 in the ric8a-emx1-cre cortex were claimed significantly increased (Fig 5, Suppl fig 12). Unfortunately, they did not show it in the app-cx3cr1-cre +LPS mouse. They make a connection between ric8a deletion and MMP9 but unfortunately do not make the connection between app deletion and MMP9, which is at the center of the pathway claimed to be important here). Then they injected BB94, a broad-spectrum inhibitor of MMPs or an inhibitor specific for MMP9 and 13. They both significantly suppress the number and the size of the ectopia in ric8a mutants (Fig5).

After reading the manuscript, I still do not know how ric8a in neural cells is involved in the immune inhibition. Is it through the control of Ab monomers? In addition, the authors did not show in vivo data supporting that Ab monomers are the key players here. As the authors said, this is not the only APP interactor. Finally, I still do not know how ric8a is linked to APP in microglia in the model.

While several of the findings presented in this manuscript are of potential interest, there are a number of shortcomings. Here are some suggestions that could improve the manuscript and help substantiate the conclusions:

(1) As the title suggests it, the focus is on Ab and APP functions in microglia. However, the analysis is more focused on ric8a. The connection between ric8a and APP in this study is not investigated, besides the fact that their deletion induces somewhat similar but not identical phenotypes. Showing a similar phenotype is not enough to conclude that they are working on the same pathway. The authors should find a way to make that connection between ric8a and app in the cells investigated here.

(2) This would help to show the appearance of breaches in the pial basement membrane leading to neuronal ectopia; to investigate laminin debris, cell identity, Wnt pathway for app-cxcr3-cre + LPS injection as you did for ric8a-emx1-cre.

(3) As a control, this would help to show that app-cxcr3-cre without the LPS injection does not display the phenotype.

(4) This would help to show the activity and protein levels of MMP9 and MMP2 and perform the rescue experiments with the inhibitors in the app-cx3cr1-cre cortex +LPS.

(5) Is MMP9 secreted by microglia cells or neural cells?

(6) The in vitro evidence indicates that one of the multiple APP interactors, ie Ab40 monomers, is less effective in suppressing the expression of some cytokines by microglia cells mutants for ric8a (TNFa and IL6 but still suppress IL1b) or APP (TNFa, IL6, IL1b, IL23a, IL10) when compared to WT. But there are other interactors for APP. In order to support the claim, it seems crucial to have in vivo data to show that Ab40 monomers are the molecules involved in preventing the breach in the pial basement membrane.

(7) In order to claim that this is specific to Ab40 monomers and not oligomers, it is necessary to show that the Ab40 oligomers do not have the same effect in vitro and in vivo. Also, an assay should be done to show that your Ab preparations are pure monomers or oligomers.

(8) Most of the cytokine secretion assays used microglia cells in culture. Two results draw my attention. Ric8a deletion increases TNFa and IL6 secretion after LPS stimulation in vitro on microglia cells while app deletion decreases their secretion. Then later, papers show that the decrease in IL1b induced by Ab on microglia cells is prevented by APP deletion but not ric8a deletion. Those two pieces of data suggest that ric8a and APP might not be in the same pathway. In addition, the phenotype from app-cxcr3-cre + LPS injection and ric8a-cxcr3-cre + LPS injection are not exactly the same. It could be due to the level of LPS as the author suggests or it might not be. More experiments are needed to prove they are in the same pathway.

(9) How do the authors reconcile the reduced TNFa and IL6 secretion upon stimulation of app mutant microglia with the model where app is attenuating immune response in vivo? Line 213 says that microglia exhibit attenuated immune response following chronic stimulation but I don't know if 3 hours of LPS in vitro is a chronic stimulation.

(10) Line 119: In their model, the authors suggest that there is a breach in pial basement membrane but that the phenotype is different from the retraction of the radial fibers due to reduced adhesion. So, could the author discuss to what substrate the radial fibers are attached to, in their model where the pial surface is destroyed?

(11) The authors should show that the increased cytokine secretion observed in vitro is also happening in vivo in ric8a-emx1-cre compared to WT mice and compared to ric8a-nestin-cre mice. Or when app is deleted in microglia (app-cxcr3-cre) + LPS injection compared to WT mice +LPS.

(12) The authors injected inhibitors of Akt or Stat3 in the ric8a-emx1-cre cortex and found that it suppressed neuronal ectopia (Fig 5, Suppl fig 11). Does it suppress immune stimulation from neuronal cells or immune reaction from microglia cells?

(13) Fig 5 and Supplementary fig 12: Please show a tubulin loading control in Fig 5i as you did in suppl fig 12 d (gel zymography). Please provide a gel zymography showing side by side Control, mutant and mutant +DM/S3I treatment. The same request for the MMP9 staining. Please provide statistics for control vs mutant for suppl fig 12c and d.

(14) Please provide the name and the source of the MMP9/13 inhibitor used in this study.

(15) The results show that deletion of ric8a in microglia and neural cells induced pia membrane breaches but no phenotype is apparent in ric8a deletion in microglia or neural cells alone. Then, the results showed that intraperitoneal injection of LPS induced the phenotype in ric8a-cxcr3-cre mutants. It would be beneficial as a control supporting the model to show that the insult induced by LPS injection does not induce the phenotype in the ric8a-foxg1-cre mice.

Reviewer #2 (Public Review):

Summary: This manuscript describes the creation and curation of a collection of genetic driver lines that specifically label small numbers of neurons, often just a single to handful of cell types, in the central nervous system of the fruit fly, Drosophila melanogaster. The authors screened over 77,000 split hemidriver combinations to yield a collection of 3060 lines targeting a range of cell types in the adult Drosophila central nervous system and 1373 lines characterized in third-instar larvae. These genetic driver lines have already contributed to several important publications and will no doubt continue to do so. It is a truly valuable resource that represents the cooperation of several labs throughout the Drosophila community.

Strengths:<br /> The authors have thoughtfully curated and documented the lines that they have created, so that they may be maximally useful to the greater community. This documentation includes confocal images of neurons labeled by each driver line and when possible, a list of cell types labeled by the genetic driver line and their identity in an EM connectome dataset. The authors have also made available some information from the other lines they created and tested but deemed not specific or strong enough to be included as part of the collection. This additional resource will be a valuable aid for those seeking to label cell types that may not be included in the main collection.

Weaknesses:<br /> None, this is a valuable set of tools that took many years of effort by several labs. This collection will continue to facilitate important science for years to come.

Reviewer #2 (Public Review):

Rodent studies of claustrum are complicated by the tube-like shape of this nucleus. As such, judicious viral strategies alone or in combination with existing Cre driver lines (Egr2, Gnb4, Slc17a6, and Tbx21) represent the current gold standard for claustrum structure and function investigation. Any improvement in tools that would allow better genetic access to the claustrum are always desired, as with any nucleus in brain. This paper describes the expression pattern of the gene Smim32 and characterization of new mouse transgenic lines expressing Cre/Flp recombinase driven by the Smim32 promoter. The authors should be applauded for the work to develop these new tools presented in the study. Overall, the strengths of the paper lie in the development of new mouse lines that are well-characterized in comparison to other molecular markers of the claustrum. Weaknesses lie in poor anatomical definitions of the claustrum (and endopiriform nucleus). Smim32 expression is used to define claustrum anatomical boundaries, rather than first using several structural, molecular, and connectivity lines of evidence to define the claustrum anatomically and then to assess whether Smim32 expression fits within this anatomical definition. Another major weakness is the fact that Cre/Flp expression driven by the Smim32 promoter is present in non-claustrum regions, including the neighboring cortex, striatum, and endopiriform nucleus as well as the more distant thalamic reticular nucleus. Despite this, the conclusion of the study, as communicated by the authors, is that selective interrogation of the claustrum is now possible with these Smim32-based tools. Therefore, the data do not support the claims and conclusions.

Very concerning is problematic language in the abstract and introduction sections that diminish the impact of several published studies (not cited) that have led to important findings regarding claustrum function. The authors Create an argument that all the research performed thus far on the claustrum is unreliable because targeting the structure has been sub-optimal. This is definitely not the case for several studies from multiple labs. If investigators new to the claustrum were to read this paper, they would conclude that all previous data hold little-to-no value and that using these tools set forth the possibility, at long last, to solve claustrum structural and functional queries. Here is an example from the abstract of the problematic language: "However, research on the CLA has been challenging due to difficulties in specifically and comprehensively targeting its neuronal populations. In various cases, this limitation has led to inconsistent findings and a lack of reliable data." (no references cited). Since Smim32 driven recombinase (in 61 or 62lrod) is not exclusively expressed in the claustrum, it is not clear how Smim32 is an advantage over possible Nr4a2 or, the more selective, GNB4 Cre driver lines. Taken together, the goal of the study as articulated in the Introduction: "Our goal was here to generate genetic tools capable of targeting the majority of mouse CLA projection neurons without affecting other brain cell populations, or tissues outside the brain" has not been met and, therefore, the conclusion of the study based on the data "With these genetic tools in hand, the comprehensive targeting and functional probing of the densely connected CLA is now possible" is unfortunately also unmet.

The manuscript does convincingly show that Smim32 targets excitatory neurons in the claustrum as evidenced by exclusive overlap of Smim32 expression with Vglut2 and not GAD (fig 1 and suppl fig 1). Additionally, the manuscript provides sufficient evidence that neurons in the claustrum area expressing Smim32 further co-express a number of other molecular markers of claustrum, including Nr4a2 (fig1), Lxn, Gnb4, and Oprk1 (fig 2), and Slc17a6 (suppl fig 1). The authors further show that Smim32 is not co-expressed with molecular markers of layer VI cortex like Ctgf and Rprm (fig 2). However, by limiting the line of evidence to molecular expression, the study fails to escape the limitations of molecular markers, which cannot by themselves be used to define the anatomical boundary of the claustrum. The expression of several of these markers in the neighboring endopiriform nucleus, including Smim32, is evidence that using molecular markers as a sole indicator of the anatomy of the claustrum is not warranted.

While the anatomical boundaries of the claustrum remain somewhat debated, several standards have emerged to delineate claustrum boundaries. These include immunoreactivity against Gng2 (or PV, especially in rat) to indicate claustrum or against Crym to counter-indicate claustrum. In addition, injection of retrograde tracers into the anterior cingulate cortex or retrosplenial cortex, for example, results in selective targeting of (large) subpopulations of claustrum neurons that help define claustrum location. Further targeting of neurons projecting to the anterior insula or thalamus has been used to delineate the boundaries of what some consider the claustrum shell and others consider the deep layers of the insula. The use of any of these approaches to delineate the claustrum anatomy should be used to describe the spatial distribution of Smim32 and Cre or FlpO in the transgenic lines.

The manuscript provides a description of Smim32 promoter-driven tdTomato in the three transgenic Cre lines during development. This shows strong expression in claustrum and not in surrounding regions. However, as the claustrum borders are not distinct without markers, the anatomical boundary of claustrum for this analysis is deemed arbitrary - an issue that is exacerbated when looking at the developing brain where atlases are less precise and boundaries of the claustrum are ill-defined.

Reviewer #2 (Public Review):

Summary:

The authors previously demonstrated that anterior-located a-Wave neurons (neuromeres A1-A3) extend axons anteriorly to connect to circuits inducing backward locomotion, while p-Wave axon (neuromeres A4-A7) project posteriorly to promote forward locomotion in Drosophila larvae. In the manuscript, the authors aim to determine the molecular mechanisms involved in wiring the segmentally homologous Wave neurons distinctively and thus are functionally different in modulating forward or backward locomotion. The genetic screen focused on Wnt/Fz-signaling due to its known anterior-to-posterior guidance roles in mammals and nematodes.

Strengths:

Knock-down (KD) DFz2 with two independent RNAi-lines caused ectopic posterior axon and dendrite extension for all a- and p-Wave neurons, with a-Wave axon extending into regions where p-Wave axons normally project. Both behavioral assays (optogenetic stimulation of all Wave neurons or tactile stimuli on heads using a von Frey filament) show that backward movement is reduced or absent and that the speed of evoked fast-forward locomotion is increased. This demonstrates that altered projections of Wave do alter behavior and the DFz2 KD phenotype is consistent with the potential aberrant wiring of a-Wave neurons to forward locomotion-promoting circuits instead of to backward locomotion-promoting circuits.

The main conclusion, that Wnt/Fz-signaling is essential for the guidance of Wave neurons and in diversifying their protection pattern in a segment-specific manner, is further supported by the results showing that DFz2 gain of function causes shortening of a-Wave but not p-Wave axon extensions towards the posterior end and that KD of DFz4 causes axonal shortening only in A6-p-Wave neurons but does not affect dendrites or processes of other Wave neurons. A role for ligand Wnt4 is demonstrated by results indicating that WNT4 mutants' posterior extension of a-Wave axons was elongated similar to DFz2 KD animals and p-Wave axon extension towards the posterior end was shortened similar to DFz2 KD animals. Finally, a DWnt4 gradient decreasing from the posterior (A8) to the anterior end (A2), similar to that described in other species, is supported by analyses of DWnt4 gene expression (using Wnt4 Trojan-Gal4) and protein expression (using antibodies). In contrast, DFz2 receptor levels seemed to decrease from the anterior (A2) to the posterior end (A5/6). Together the results support the conclusion that opposing Wnt/Fz ligand-receptor gradients contribute to the diversification of Wave neurons in a location-dependent manner and that DFz2 and DFz4 have opposing effects on axon extension.

Weaknesses:

Wave axon and dendrite projections are not exclusively determined by Wnt4, DFz2, and DFz4, and are likely to involve other Fz receptors, Wt ligands, and other types of receptor-ligand signaling pathways. This is in part supported by the fact that Wnt4 loss of function also resulted in phenotypes that do not mimic DFz2 KD or DFz4 KD (Figures 3D, E, and F) and that other Fz/Wnt mutants caused wave neuron phenotypes (Figure 1-supplement 2, D+E). This is not a weakness per se, since it doesn't affect the main conclusion of the manuscript. However, the description and analyses of the data in particular for Figure 1-supplement 2 D should be clarified in the legend. The number within the bars and the asterisks are not defined. It's presumed they refer to numbers of animals assessed and the asterisk next to DFz2 and DFz4 indicate statistically significant differences. However, only one p-value is provided in the legend. It is also unclear if p-values for the other mutants have not been determined or are non-significant. At least for mutants like Corin, which also exhibit altered axon projections, the p-values should be provided.

Figure 4 D, F. The gradient for Wnt4 was determined by comparison of expression levels of other segments to A8 but the gradient for DFz2 was by comparison to A2 and the data supports opposing gradients. However, for DFz2 (Figure 4, F) it seems that the gradient is bi-directional with the lowest being in A5 and increasing towards A2 as well as A8. Analysis should be performed in reference to A8 as well to determine if it is indeed bi-directional. While such a finding would not affect the interpretation of a-Wave neurons, it may impact conclusions about p-Wave neuron projections.

As discussed above, the DFz2 KD phenotypes are consistent with the potential aberrant wiring of a-Wave neurons to forward locomotion-promoting circuits instead of to backward locomotion-promoting circuits. However, since the axon and dendrites of a-Wave and p-Wave are affected the actual dendritic and axonal contributions for the altered behavior remain elusive. The authors certainly considered a potential contribution of altered dendrite projection of a-Wave neurons to the phenotype and their conclusion that altered axonal projections are involved is supported by the optogenetic experiment "bypassing" sensory input (albeit it seems unlikely that all Wave neurons are activated simultaneously when perceiving natural stimuli). However, the author should also consider that altered perception and projection of p-Wave neuron may directly (e.g. extended P-wave axon projections increase forward locomotion input thereby overriding backward locomotion) or indirectly (e.g. feedback loops between forward and backward circuits) contribute to the altered behavioral phenotypes in both assays. It is probably noteworthy that the more complex behavioral alterations observed with mechanical stimulation are likely to also be caused by altered dendritic projections.

Presynaptic varicosities of a-Wave neurons in DFz2 KD animals are indicated by orange arrows in Figure 1. However, no presynaptic markers have been used to confirm actual ectopic synaptic connections. At least the authors should more clearly define what parameters they used to "visually" define potential presynaptic varicosities. Some arrows seem to point to more "globular structures" but for several others, it's unclear what they are pointing at.

Reviewer #2 (Public Review):

Summary:

This manuscript examines the role of the dopamine receptor, Dop1R2, in memory formation. This receptor has complex roles in supporting different stages of memory, and the neural mechanisms for these functions are poorly understood. The authors are able to localize Dop1R2 function to the vertical lobes of the mushroom body, revealing a role in later (presumably middle-term) aversive and appetitive memory. In general, the experimental design is rigorous, and statistics are appropriately applied. While the manuscript provides a useful tool, it would be strengthened further by additional mechanistic studies that build on the rich literature examining the roles of dopamine signaling in memory formation. The claim that Dop1R2 is involved in memory formation is strongly supported by the data presented, and this manuscript adds to a growing literature revealing that dopamine is a critical regulator of olfactory memory. However, the manuscript does not necessarily extend much beyond our understanding of Dop1R2 in memory formation, and future work will be needed to fully characterize this reagent and define the role of Dop1R2 in memory.

Strengths:

(1) The FRT lines generated provide a novel tool for temporal and spatially precise manipulation of Dop1R2 function. This tool will be valuable to study the role of Dop1R2 in memory and other behaviors potentially regulated by this gene.

(2) Given the highly conserved role of Dop1R2 in memory and other processes, these findings have a high potential to translate to vertebrate species.

Weaknesses:

(1) The authors state Dop1R2 associates with two different G-proteins. It would be useful to know which one is mediating the loss of aversive and appetitive memory in Dop1R2 knockout flies.

(2) It would be interesting to examine 24hr aversive memory, in addition to 24hr appetitive memory.

(3) The manuscript would be strengthened by added functional analysis. What are the DANs that signal through Dop1R. How do these knockouts impact MBONs?

(4) Also in Figure 2, the lobe-specific knockouts might be moved to supplemental since there is no effect. Instead, consider moving the control sensory tests into the main figure.

(5) Can the single-cell atlas data be used to narrow down the cell types in the vertical lobes that express Dop1R2? Is it all or just a subset?

Reviewer #2 (Public Review):

Summary:

Bos and colleagues address the important question of how two major inhibitory interneuron classes in the neocortex differentially affect cortical dynamics. They address this question by studying Wilson-Cowan-type mathematical models. Using a linearized fixed point approach, they provide convincing evidence that the existence of multiple interneuron classes can explain the counterintuitive finding that inhibitory modulation can increase the gain of the excitatory cell population while also increasing the stability of the circuit's state to minor perturbations. This effect depends on the connection strengths within their circuit model, providing valuable guidance as to when and why it arises.

Overall, I find this study to have substantial merit. I have some suggestions on how to improve the clarity and completeness of the paper.

Strengths:

(1) The thorough investigation of how changes in the connectivity structure affect the gain-stability relationship is a major strength of this work. It provides an opportunity to understand when and why gain and stability will or will not both increase together. It also provides a nice bridge to the experimental literature, where different gain-stability relationships are reported from different studies.

(2) The simplified and abstracted mathematical model has the benefit of facilitating our understanding of this puzzling phenomenon. (I have some suggestions for how the authors could push this understanding further.) It is not easy to find the right balance between biologically detailed models vs simple but mathematically tractable ones, and I think the authors struck an excellent balance in this study.

Weaknesses:

(1) The fixed-point analysis has potentially substantial limitations for understanding cortical computations away from the steady-state. I think the authors should have emphasized this limitation more strongly and possibly included some additional analyses to show that their conclusions extend to the chaotic dynamical regimes in which cortical circuits often live.

(2) The authors could have discussed -- even somewhat speculatively -- how SST interneurons fit into this picture. Their absence from this modelling framework stands out as a missed opportunity.

(3) The analysis is limited to paths within this simple E,PV,SOM circuit. This misses more extended paths (like thalamocortical loops) that involve interactions between multiple brain areas. Including those paths in the expansion in Eqs. 11-14 (Fig. 1C) may be an important consideration.

DOI: 10.1038/s41467-021-22257-2

Resource: RRID:BDSC_31053

Curator: @olekpark

SciCrunch record: RRID:BDSC_31053

What is this?

DOI: 10.1038/s41467-021-26031-2

Resource: RRID:BDSC_66542

Curator: @olekpark

SciCrunch record: RRID:BDSC_66542

What is this?

DOI: 10.1038/s41598-021-99531-2

Resource: RRID:BDSC_24651

Curator: @olekpark

SciCrunch record: RRID:BDSC_24651

What is this?

Reviewer #2 (Public Review):

Summary:

This study, based on their previous findings that TFH cells can be converted into TR1 cells, conducted a highly detailed and comprehensive epigenetic investigation to answer whether TR1 differentiation from TFH is driven by epigenetic changes. Their evidence indicated that the downregulation of TFH-related genes during the TFH to TR1 transition depends on chromatin closure, while the upregulation of TR1-related genes does not depend on epigenetic changes.

Strengths:

A significant advantage of their approach lies in its detailed and comprehensive assessment of epigenetics. Their analysis of epigenetics covers chromatin open regions, histone modifications, DNA methylation, and using both single-cell and bulk techniques to validate their findings. As for their results, observations from different epigenetic perspectives mutually supported each other, lending greater credibility to their conclusions. This study effectively demonstrates that (1) the TFH-to-TR1 differentiation process is associated with massive closure of OCRs, and (2) the TR1-poised epigenome of TFH cells is a key enabler of this transdifferentiation process. Considering the extensive changes in epigenetic patterns involved in other CD4+ T lineage commitment processes, the similarity between TFH and TR1 in their epigenetics is intriguing.

They performed correlation analysis to answer the association between "pMHC-NP-induced epigenetic change" and "gene expression change in TR1". Also, they have made their raw data publicly available, providing a comprehensive epigenomic database of pMHC-NP-induced TR1 cells. This will serve as a valuable reference for future research.

Weaknesses:

A major limitation is that this study heavily relies on a premise from the previous studies performed by the same group on pMHC-NP-induced T-cell responses. This significantly limits the relevance of their conclusion to a broader perspective. Specifically, differential OCRs between Tet+ and naïve T cells were limited to only 821, as compared to 10,919 differential OCRs between KLH-TFH and naïve T cells (Figure 2A), indicating that the precursors and T cell clonotypes that responded to pMHC-NP were extremely limited. This limitation should be clearly discussed in the Discussion section.

This article uses peak calling to determine whether a region has histone modifications, claiming that the regions with histone modifications in TFH and TR1 are highly similar. However, they did not discuss the differences in histone modification intensities measured by ChIP-seq. For example, as shown in Figure 6C, IL10 H3K27ac modification in Tet+ cells showed significantly higher intensity than KLH-TFH, while in this article, it may be categorized as "possessing same histone modification region". This will strengthen their conclusions.

Last, the key findings of this study are clear and convincing, but some results and figures are unnecessary and redundant. Some results are largely a mere confirmation of the relationship between histone marks and chromatin status. I propose to reduce the number of figures and text that are largely confirmatory. Overall, I feel this paper is too long for its current contents.

Reviewer #3 (Public Review):

(1) Throughout the manuscript, hMT+ connectivity with the frontal cortex has been treated as an a priori hypothesis/space. However, there is no such motivation or background literature mentioned in the Introduction. Can the authors clarify the necessity of functional connectivity? In other words, can BOLD activity of hMT+ in the localizer task substitute for functional connectivity between hMT+ and the frontal cortex?

(2) There is an obvious mismatch between the in-text description and the content of the figure:

"In contrast, there was no correlation between BDT and GABA levels in V1 voxels (figure supplement 1a). Further, we show that SI significantly correlates with GABA levels in hMT+ voxels (r = 0.44, P = 0.01, n = 31, Figure 3d). In contrast, no significant correlation between SI and GABA concentrations in V1 voxels was observed (figure supplement 1b)."

(3) The authors' response to my previous round of review indicated that the "V1 ROIs" covered a substantial amount of V3 (32%). Therefore, it would no longer be appropriate to call these "V1 ROIs". I'd suggest renaming them as "Early Visual Cortex (EVC) ROIs" to be more accurate. Can the authors justify why choosing the left hemisphere for visual intelligence task, which is typically believed to be right lateralized?

(4) "Small threshold" and "large threshold" are neither standard descriptions, and it is unclear what "small threshold" refers to in the following figure caption. Additionally, the unit (ms) is confusing. Does it refer to timing?

"(f) Peason's correlation showing significant negative correlations between BDT and small threshold."

(5) In the response letter, the authors mentioned incorporating the neural efficiency hypothesis in the Introduction, but the revised Introduction does not contain such information.

Reviewer #2 (Public Review):

Summary:

This manuscript uses cell lines representative of germ line cells, somatic cells and pluripotent cells to address the question of how the endocrine disrupting compound BPS affects these various cells with respect to gene expression and DNA methylation. They find a relationship between the presence of estrogen receptor gene expression and the number of DNA methylation and gene expression changes. Notably, PGCLCs do not express estrogen receptors and although they do have fewer changes, changes are nevertheless detected, suggesting a nonconical pathway for BPS-induced perturbations. Additionally, there was a significant increase in the occurrence of BPS-induced epimutations near EREs in somatic and pluripotent cell types compared to germ cells. Epimutations in the somatic and pluripotent cell types were predominantly in enhancer regions whereas that in the germ cell type was predominantly in gene promoters.

Strengths:

The strengths of the paper include the use of various cell types to address sensitivity of the lineages to BPS as well as the observed relationship between the presence of estrogen receptors and changes in gene expression and DNA methylation.

Weaknesses:

The weakness, which has been addressed by the authors, includes the fact that exposures are more complicated in a whole organism than in an isolated cell line.

Reviewer #2 (Public Review):

In this study, the authors characterize the defensive responses of C. elegans to the predatory Pristionchus species. Drawing parallels to ecological models of predatory imminence and prey refuge theory, they outline various behaviors exhibited by C. elegans when faced with predator threats. They also find that these behaviors can be modulated by the peptide NLP-49 and its receptor SEB-3 in various degrees.

The conclusions of this paper are mostly well-supported, the writing and the figures are clear and easy to interpret. However, some of the claims need to be better supported and the unique findings of this work should be clarified better in text.

(1) Previous work by the group (Quach, 2022) showed that Pristionchus adopt a "patrolling strategy" on a lawn with adult C. elegans and this depends on bacterial lawn thickness. Consequently, it may be hypothesized that C. elegans themselves will adopt different predator avoidance strategies depending on predator tactics differing due to lawn variations. The authors have not shown why they selected a particular size and density of bacterial lawn for the experiments in this paper, and should run control experiments with thinner and denser lawns with differing edge densities to make broad arguments about predator avoidance strategies for C. elegans. In addition, C. elegans leaving behavior from bacterial lawns (without predators) are also heavily dependent on density of bacteria, especially at the edges where it affects oxygen gradients (Bendesky, 2011), and might alter the baseline leaving rates irrespective of predation threats. The authors also do not mention if all strains or conditions in each figure panel were run as day-matched controls. Given that bacterial densities and ambient conditions can affect C. elegans behavior, especially that of lawn-leaving, it is important to run day-matched controls.

(2) Both the patch-leaving and feeding in outstretched posture behaviors described here in this study were reported in an earlier paper by the same group (Quach, 2022) as mentioned by the authors in the first section of the results. While they do characterize these further in this study, these are not novel findings of this work.

(3) For Figures 1F-H, given that animals can reside on the lawn edges as well as the center, bins explored are not a definitive metric of exploration since the animals can decide to patrol the lawn boundary (especially since the lawns have thick edges). The authors should also quantify tracks along the edge from videographic evidence as they have done previously in Figure 5 of Quach, 2022 to get a total measure of distance explored.

(4) Where were the animals placed in the wide-arena predator-free patch post encounter? It is mentioned that the animal was placed at the center of the arena in lines 220-221. While this makes sense for the narrow-arena, it is unclear how far from the patch animals were positioned for the wide exit arena. Is it the same distance away as the distance of the patch from the center of the narrow exit arena? Please make this clear in the text or in the methods.

(5) Do exit decisions from the bacterial patch scale with number of bites or is one bite sufficient? Do all bites lead to bite-induced aversive response? This would be important to quantify especially if contextualizing to predatory imminence.

(6) Why are the threats posed by aversive but non-lethal JU1051 and lethal PS312 evaluated similarly? Did the authors characterize if the number of bites are different for these strains? Can the authors speculate on why this would happen in the discussion?

(7) The authors indicate that bites from the non-aversive TU445 led to a low number of exits and thus it was consequently excluded from further analysis. If anything, this strain would have provided a good negative control and baseline metrics for other circa-strike and post-encounter behaviors.

8) For Figures 3 G and H, the reduction in bins explored (bins_none - bins_RS1594) due to the presence of predators should be compared between wildtype and mutants, instead of the difference between none and RS5194 for each strain.

(9) While the authors argue that baseline speeds of seb-3 are similar to wild type (Figure S3), previous work (Jee, 2012) has shown that seb-3 not only affects speed but also roaming/dwelling states which will significantly affect the exploration metric (bins explored) which the authors use in Figs 3G-H and 4E-F. Control experiments are necessary to avoid this conundrum. Authors should either visualize and quantify tracks (as suggested in 3) or quantify roaming-dwelling in the seb-3 animals in the absence of predator threat.

(10) While it might be beyond the scope of the study, it would be nice if the authors could speculate on potential sites of actions of NLP-49 in the discussion, especially since it is expressed in a distinct group of neurons.

Reviewer #2 (Public Review):

Summary:

Kan et al. present the discovery of oxydifficidin as a potential antimicrobial against N. gonorrhoeae, including multi-drug resistant strains. The authors show the role of DedA flippase-assisted uptake and the specificity of RplL in the mechanism of action for oxydifficidin. This novel mode of action could potentially offer a new therapeutic avenue, providing a critical addition to the limited arsenal of antibiotics effective against gonorrhea.

Strengths:

This study underscores the potential of revisiting natural products for antibiotic discovery of modern-day-concerning pathogens and highlights a new target mechanism that could inform future drug development. Indeed there is a recent growing body of research utilising AI and predictive computational informatics to revisit potential antimicrobial agents and metabolites from cultured bacterial species. The discovery of oxydifficidin interaction with RplL and its DedA-assisted uptake mechanism opens new research directions in understanding and combating antibiotic-resistant N. gonorrhoeae. Methodologically, the study is rigorous employing various experimental techniques such as genome sequencing, bioassay-guided fractionation, LCMS, NMR, and Tn-mutagenesis.

Weaknesses:

The scope is somewhat narrow, focusing primarily on N. gonorrhoeae. This limits the generalizability of the findings and leaves questions about its broader antibacterial spectrum. Moreover, while the study demonstrates the in vitro effectiveness of oxydifficidin, there is a lack of in vivo validation (i.e., animal models) for assessing pre-clinical potential of oxydifficidin. Potential SNPs within dedA or RplL raise concerns about how quickly resistance could emerge in clinical settings.

Reviewer #2 (Public Review):

Summary:

Directional migration is an integral aspect of sprouting angiogenesis and requires a cell to change its shape and sense a chemotactic or growth factor stimulus. Kondrychyn I. et al. provide data that indicate a requirement for zebrafish aquaporins 1 and 8, in cellular water inflow and sprouting angiogenesis. Zebrafish mutants lacking aqp1a.1 and aqp8a.1 have significantly lower tip cell volume and migration velocity, which delays vascular development. Inhibition of actin formation and filopodia dynamics further aggravates this phenotype. The link between water inflow, hydrostatic pressure, and actin dynamics driving endothelial cell sprouting and migration during angiogenesis is highly novel.

Strengths:

The zebrafish genetics, microscopy imaging, and measurements performed are of very high quality. The study data and interpretations are very well-presented in this manuscript.

Weaknesses:

Some of the findings and interpretations could be strengthened by additional measurements and further discussion. Also, a better comparison and integration of the authors' findings, with other previously published findings in mice and zebrafish would strengthen the paper.

Reviewer #2 (Public Review):

Summary:

The authors used 2-photon Ca2+-imaging to study the activity of ventral tegmental area (VTA) and locus coeruleus (LC) axons in the CA1 region of the dorsal hippocampus in head-fixed male mice moving on linear paths in virtual reality (VR) environments.

The main findings were as follows:<br /> - In a familiar environment, activity of both VTA axons and LC axons increased with the mice's running speed on the Styrofoam wheel, with which they could move along a linear track through a VR environment.<br /> - VTA, but not LC, axons showed marked reward position-related activity, showing a ramping-up of activity when mice approached a learned reward position.<br /> - In contrast, activity of LC axons ramped up before initiation of movement on the Styrofoam wheel.<br /> - In addition, exposure to a novel VR environment increased LC axon activity, but not VTA axon activity.

Overall, the study shows that the activity of catecholaminergic axons from VTA and LC to dorsal hippocampal CA1 can partly reflect distinct environmental, behavioral and cognitive factors. Whereas both VTA and LC activity reflected running speed, VTA, but not LC axon activity reflected the approach of a learned reward and LC, but not VTA, axon activity reflected initiation of running and novelty of the VR environment.

I have no specific expertise with respect to 2-photon imaging, so cannot evaluate the validity of the specific methods used to collect and analyse 2-photon calcium imaging data of axonal activity.

Strengths:

(1) Using a state-of-the-art approach to record separately the activity of VTA and LC axons with high temporal resolution in awake mice moving through virtual environments, the authors provide convincing evidence that activity of VTA and LC axons projecting to dorsal CA1 reflect partly distinct environmental, behavioral and cognitive factors.

(2) The study will help a) to interpret previous findings on how hippocampal dopamine and norepinephrine or selective manipulations of hippocampal LC or VTA inputs modulate behavior and b) to generate specific hypotheses on the impact of selective manipulations of hippocampal LC or VTA inputs on behavior.

Weaknesses:

(1) The findings are correlational and do not allow strong conclusions on how VTA or LC inputs to dorsal CA1 affect cognition and behavior. However, as indicated above under Strengths, the findings will aid the interpretation of previous findings and help to generate new hypotheses as to how VTA or LC inputs to dorsal CA1 affect distinct cognitive and behavioral functions.

(2) Some aspects of the methodology would benefit from clarification.<br /> First, to help others to better scrutinize, evaluate and potentially to reproduce the research, the authors may wish to check if their reporting follows the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines for the full and transparent reporting of research involving animals (https://arriveguidelines.org/). For example, I think it would be important to include a sample size justification (e.g., based on previous studies, considerations of statistical power, practical considerations or a combination of these factors). The authors should also include the provenance of the mice. Moreover, although I am not an expert in 2-photon imaging, I think it would be useful to provide a clearer description of exclusion criteria for imaging data (see below, Recommendations for the authors).<br /> Second, why were different linear tracks used for studies of VTA and LC axon activity (from line 362)? Could this potentially contribute to the partly distinct activity correlates that were found for VTA and LC axons?<br /> Third, the authors seem to have used two different criteria for defining immobility. Immobility was defined as moving at <5 cm/s for the behavioral analysis in Fig. 3a, but as <0.2 cm/s for the imaging data analysis in Fig. 4 (see legends to these figures and also see Methods, from line 447, line 469, line 498)? I do not understand why, and it would be good if the authors explained this.

(3) In the Results section (from line 182) the authors convincingly addressed the possibility that less time spent immobile in the novel environment may have contributed to the novelty-induced increase of LC axon activity in dorsal CA1 (Fig. 4). In addition, initially (for the first 2-4 laps), the mice also ran more slowly in the novel environment (Fig. 3aIII, top panel). Given that LC and VTA axon activity were both increasing with velocity (Fig. 1F), reduced velocity in the novel environment may have reduced LC and VTA axon activity, but this possibility was not addressed. Reduced LC axon activity in the novel environment could have blunted the novelty-induced increase. More importantly, any potential novelty-induced increase in VTA axon activity could have been masked by decreases in VTA axon activity due to reduced velocity. The latter may help to explain the discrepancy between the present study and previous findings that VTA neuron firing was increased by novelty (see Discussion, from line 243). It may be useful for the authors to address these possibilities based on their data in the Results section, or to consider them in their Discussion.

(4) Sensory properties of the water reward, which the mice may be able to detect, could account for reward-related activity of VTA axons (instead of an expectation of reward). Do the authors have evidence that this is not the case? Occasional probe trials, intermixed with rewarded trials, could be used to test for this possibility.

REVIEW OF THE REVISED MANUSCRIPT<br /> I thank the authors for their responses addressing some of the weaknesses I raised in my original comments.

Regarding their clarification of some methodological issues [Point 2) above], I have a few additional comments:<br /> - I appreciate that the authors clearly state the sample sizes contributing to the data. However, sample size justifications (e.g. based on previous studies, considerations of statistical power, practical considerations or a combination of these factors) are still lacking.<br /> - It is good that the authors have now clearly indicated how many mice they excluded due to lack of GCaMP expression or due to failure to reach the behavioral criteria. They also indicated that they discarded some of the collected datasets, based on the visual assessment of imaging sessions and the registration metrics output by suite2p. I appreciate that this may be common practice (although I am not using 2-photon imaging myself). However, I note that to minimize the risk of experimenter bias and improve reproducibility, it would be preferable to have more clearly defined quantitative criteria for such exclusions.<br /> - The authors clarified in their response why they used two different linear tracks for their studies of VTA and LC axon activity. I would encourage them to include this clarification in the manuscript. From the authors' response, I understand that they chose the different track lengths to facilitate comparison to previous studies involving LC and VTA axon recordings. However, given that the present paper aimed to compare LC and VTA axon recordings, the use of different track lengths for LC and VTA axon recordings remains a limitation of the present paper.

Reviewer #3 (Public Review):

Nitta et al. use a fly model of autosomal dominant optic atrophy to provide mechanistic insights into distinct disease-causing OPA1 variants. It has long been hypothesized that missense OPA1 mutations affecting the GTPase domain, which are associated with more severe optic atrophy and extra-ophthalmic neurologic conditions such as sensorineural hearing loss (DOA plus), impart their effects through a dominant negative mechanism, but no clear direct evidence for this exists particularly in an animal model. The authors execute a well-designed study to establish their model, demonstrating a mitochondrial phenotype and optic atrophy measured as axonal degeneration. They leverage this model to provide the first direct evidence for a dominant negative mechanism for 2 mutations causing DOA plus by expressing these variants in the background of a full hOPA1 complement.

Strengths of the paper include well-motivated objectives and hypotheses, and overall solid design and execution. There is a thorough discussion of the interpretation and context of the findings. The results technically support their primary conclusions with minor limitations. First, while only partial rescue of the most clinically relevant metric for optic atrophy in this model is now acknowledged, the result nevertheless hamstrings the mechanistic experiments that follow. Second, the results statistically support a dominant negative effect of DOA plus-associated variants, yet the data show a marginal impact on axonal degeneration for these variants. In added experiments, the ability of WT hOPA1 and I382M but not 2708del, D438V or R445H to rescue ROS levels or mitophagy in the context of dOPA1 knockdown serves to support axonal number as a valid measure of mitochondrial function in this context. However, the critical experiment demonstrating a dominant negative effect was performed in the context of expressing WT hOPA1 along with a pathogenic variant, in which no differences in ROS, COXII expression or mitophagy were seen. This makes it difficult to conclude that the dominant negative effect of D438V and R445H on axon number is related to mitochondrial function.

As an animal model of DOA that may serve for rapid assessment of suspected OPA1 variants, the results overall support utility of this model in identifying pathogenic variants but not in distinguishing haploinsufficiency from dominant negative mechanisms among those variants. The impact of this work in providing the first direct evidence of a dominant negative mechanism is under-stated considering how important this question is in development of genetic treatments for dominant optic atrophy.

Comments on revised version:

The authors have addressed the comments in my initial review. Through these modification and those related to the comments from the other reviewers, the manuscript is strengthened.

Comments on author responses to each of the reviews:

Reviewer 1:

Interpretation of data has been appropriately reorganized in the discussion.

Quantified mitochondria in the model show no difference in number. There is reduced size and structural abnormalities on electron microscopy.

Application of mito-QC revealed increased mitophagy.

Regarding partial rescue of axonal number in the mutant model, statistical significance between control and rescue is still not depicted in Figure 4D. Detailing possible explanations for this has been addressed in the discussion. However, only partial rescue of the most clinically relevant metric for optic atrophy in this model hamstrings subsequent mechanistic experiments that follow.

Discussion regarding variant I382M has been improved.

While reviewer 1's concerns about axonal number as a biomarker for OPA1 function are valid, it is worth noting that this is the most clinically relevant marker in the context of DOA. That said, I agree that the mechanistic DN/HI studies needed support using other measures of mitochondrial function, and the authors have done this. The ability of WT hOPA1 and I382M but not 2708del, D438V or R445H to rescue ROS levels or mitophagy in the context of dOPA1 knockdown serves to support axonal number as a valid measure of mitochondrial function in this context. However, the critical experiment demonstrating a dominant negative effect was performed in the context of expressing WT hOPA1 along with a pathogenic variant, in which no differences in ROS, COXII expression or mitophagy were seen. This makes it difficult to conclude that the (marginal) DN effect of D438V and R445H on axon number is related to mitochondrial function, and serves as a minor weakness of the paper.

Which exons are included in the transcript, and therefore, which isoforms are expressed in the model, has been addressed.

Reviewer 2:

The authors have addressed the need to include greater methodological details.

Language concerning the clinical utility of the model in informing treatment decisions has been appropriately modified. As pointed out by Reviewer 1, additional studies were needed to better establish the potential clinical utility of this model in screening DOA variants. The authors have completed those experiments, and the results overall support utility of this model in identifying pathogenic variants but not in distinguishing HI/DN mechanisms among those variants.

Reviewer 3:

The author has addressed the partial rescue effect as above.

The authors have not modified the text to acknowledge the marginal effect sizes in the critical experiment of the study that demonstrates a DN effect. Statistically, the results indeed support a dominant negative effect of DOA plus-associated variants, yet the data show a marginal impact on axonal degeneration for these variants. This remains a weakness of the study.

Reviewer #2 (Public Review):

In this manuscript, Cai et al use a combination of mouse transgenic lines to re-examine the question of the embryonic origin of telencephalic oligodendrocytes (OLs). Their tools include a novel Flp mouse for labelling mature oligodendrocytes and a number of pre-existing lines (some previously generated by the last author in Josh Huang's lab) that allowed combinatorial or subtractive labelling of oligodendrocytes with different origins. The conclusion is that cortically-derived OLs are the predominant OL population in the motor and somatosensory cortex and underlying corpus callosum, while the LGE/CGE generates OLs for the piriform cortex and anterior commissure rather than the cerebral cortex. Small numbers of MGE-derived OLs persist long-term in the motor, somatosensory and piriform cortex.

Strengths:

The strength and novelty of the manuscript lie in the elegant tools generated and used. These have enabled the resolution of the issue regarding the contribution of different telencephalic progenitor zones to the cortical oligodendrocyte population.

Comments on latest version:

The revised manuscript by Cai et al has addressed all the issues raised. I have some minor comments:

Figure 2: The y axis in figure 2L should be the same as the y axis in 2M to make the contribution to Mo and SS more clear.

Figure 3: Although this is clear in the figure, A an B should be labelled as classical model and new model to help the reader understand immediately what the two figures show.

Suppl Fig 2: It is not clear what 1-7 represent. It should be made clear in the legend which areas have been pooled into the different bins. The X axis should be labelled.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Otero-Coronel and colleagues use a combination of acoustic stimuli and electrical stimulation of the tectum to study MSI in the M-cells of adult goldfish. They first perform a necessary piece of groundwork in calibrating tectal stimulation for maximal M-cell MSI, and then characterize this MSI with slightly varying tectal and acoustic inputs. Next, they quantify the magnitude and timing of FFI that each type of input has on the M-cell, finding that both the tectum and the auditory system drive FFI, but that FFI decays more slowly for auditory signals. These are novel results that would be of interest to a broader sensory neuroscience community. By then providing pairs of stimuli separated by 50ms, they assess the ability of the first stimulus to suppress responses to the second, finding that acoustic stimuli strongly suppress subsequent acoustic responses in the M-cell, that they weakly suppress subsequent tectal stimulation, and that tectal stimulation does not appreciably inhibit subsequent stimuli of either type. Finally, they show that M-cell physiology mirrors previously reported behavioural data in which stronger stimuli underwent less integration.

The manuscript is generally well-written and clear. The discussion of results is appropriately broad and open-ended. It's a good document. Our major concerns regarding the study's validity are captured in the individual comments below. In terms of impact, the most compelling new observation is the quantification of the FFI from the two sources and the logical extension of these FFI dynamics to M-cell physiology during MSI. It is also nice, but unsurprising, to see that the relationship between stimulus strength and MSI is similar for M-cell physiology to what has previously been shown for behavior. While we find the results interesting, we think that they will be of greatest interest to those specifically interested in M-cell physiology and function.

Strengths:

The methods applied are challenging and appropriate and appear to be well executed. Open questions about the physiological underpinnings of M-cell function are addressed using sound experimental design and methodology, and convincing results are provided that advance our understanding of how two streams of sensory information can interact to control behavior.

Weaknesses:

Our concerns about the manuscript are captured in the following specific comments, which we hope will provide a useful perspective for readers and actionable suggestions for the authors.

Comment 1 (Minor):

Line 124. Direct stimulation of the tectum to drive M-cell-projecting tectal neurons not only bypasses the retina, it also bypasses intra-tectal processing and inputs to the tectum from other sources (notably the thalamus). This is not an issue with the interpretation of the results, but this description gives the (false) impression that bypassing the retina is sufficient to prevent adaptation. Adding a sentence or two to accurately reflect the complexity of the upstream circuitry (beyond the retina) would be welcome.

Comment 2 (Major):

The premise is that stimulation of the tectum is a proxy for a visual stimulus, but the tectum also carries the auditory, lateral line, and vestibular information. This seems like a confound in the interpretation of this preparation as a simple audio-visual paradigm. Minimally, this confound should be noted and addressed. The first heading of the Results should not refer to "visual tectal stimuli".

Comment 3 (Major):

Figure 1 and associated text.

It is unclear and not mentioned in the Methods section how phasic and tonic responses were calculated. It is clear from the example traces that there is a change in tonic responses and the accumulation of subthreshold responses. Depending on how tonic responses were calculated, perhaps the authors could overlay a low-passed filtered trace and/or show calculations based on the filtered trace at each tectal train duration.

Comment 4 (Minor):

Figure 3 and associated text.<br /> This is a lovely experiment. Although it is not written in text, it provides logic for the next experiment in choosing a 50ms time interval. It would be great if the authors calculated the first timepoint at which the percentage of shunting inhibition is not significantly different from zero. This would provide a convincing basis for picking 50ms for the next experiment. That said, I suspect that this time point would be earlier than 50m s. This may explain and add further complexity to why the authors found mostly linear or sublinear integration, and perhaps the basis for future experiments to test different stimulus time intervals. Please move calculations to Methods.

Comment 5 (Major):

Figure 4C and lines 398-410.<br /> These are beautiful examples of M-cell firing, but the text suggests that they occurred rarely and nowhere close to significantly above events observed from single modalities. We do not see this as a valid result to report because there is insufficient evidence that the phenomenon shown is consistent or representative of your data.

DOI: 10.1038/s41598-020-70236-2

Resource: SCR_00645

Curator: @anisehay

SciCrunch record: RRID:SCR_00645

What is this?

DOI: 10.1038/s42003-021-01685-2

Resource: SCR_00645

Curator: @anisehay

SciCrunch record: RRID:SCR_00645

What is this?

Reviewer #3 (Public Review):

In their article "The Geometric Basis of Epithelial Convergent<br /> Extension", Brauns and colleagues present a physical analysis of drosophila axis extension that couples in toto imaging of cell contours (previously published dataset), force inference, and theory. They seek to disentangle the respective contributions of active vs passive T1 transitions in the convergent extension of the lateral ectoderm (or germband) of the fly embryo.

The revision made by the authors has greatly improved their work, which was already very interesting, in particular the use of force inference throughout intercalation events to identify geometric signatures of active vs passive T1s, and the tension/isogonal decomposition. The new analysis of the Snail mutant adds a lot to the paper and makes their findings on the criteria for T1s very convincing.

About the tissue scale issues raised during the first round of review. Although I do not find the new arguments fully convincing (see below), the authors did put a lot of effort to discuss the role of the adjacent posterior midgut (PMG) on extension, which is already great. That will certainly provide the interested readers with enough material and references to dive into that question.

I still have some issues with the authors' interpretation on the role of the PMG, and on what actually drives the extension. Although it is clear that T1 events in the germ band are driven by active local tension anisotropy (which the authors show but was already well-established), it does not show that the tissue extension itself is powered by these active T1s. Their analysis of "fence" movies from Collinet et al 2015 (Tor mutants and Eve RNAi) is not fully convincing. Indeed, as the authors point out themselves, there is no flow in Tor mutant embryos, even though tension anisotropy is preserved. They argue that in Tor embryos the absence of PMG movement leaves no room for the germband to extend properly, thus impeding the flow. That suggests that the PMG acts as a barrier in Tor mutants - What is it attached to, then? The authors also argue that the posterior flow is reduced in "fenced" Eve RNAi embryos (which have less/no tension anisotropy), to justify their claim that it is the anisotropy that drives extension. However, previous data, including some of the authors' (Irvine and Wieschaus, 1994 - Fig 8), show that the first, rapid phase of germband extension is left completely unaffected in Eve mutants (that lack active tension anisotropy). Although intercalation in Eve mutants is not quantified in that reference, this was later done by others, showing that it is strongly reduced. Similarly, the Cyto-D phenotype from Clement et al 2017, in which intercalation is also strongly reduced, also displays normal extension.

Reviewer #2 (Public Review):

Summary:

Rademacher et al. present a paper showing that chronic chemogenetic excitation of dopaminergic neurons in the mouse midbrain results in differential degeneration of axons and somas across distinct regions (SNc vs VTA). These findings are important. This mouse model also has the advantage of showing a axon-first degeneration over an experimentally-useful time course (2-4 weeks). 2. The findings that direct excitation of dopaminergic neurons causes differential degeneration sheds light on the mechanisms of dopaminergic neuron selective vulnerability. The evidence that activation of dopaminergic neurons causes degeneration and alters mRNA expression is convincing, as the authors use both vehicle and CNO control groups, but the evidence that chronic dopaminergic activation alters circadian rhythm and motor behavior is incomplete as the authors did not run a CNO-control condition in these experiments.

Strengths:

This is an exciting and important paper.

The paper compares mouse transcriptomics with human patient data.

It shows that selective degeneration can occur across the midbrain dopaminergic neurons even in the absence of a genetic, prion, or toxin neurodegeneration mechanism.

Weaknesses:

Major concerns:

(1) The lack of a CNO-positive, DREADD-negative control group in the behavioral experiments is the main limitation in interpreting the behavioral data. Without knowing whether CNO on its own has an impact on circadian rhythm or motor activity, the certainty that dopaminergic hyperactivity is causing these effects is lacking.

(2) One of the most exciting things about this paper is that the SNc degenerates more strongly than the VTA when both regions are, in theory, excited to the same extent. However, it is not perfectly clear that both regions respond to CNO to the same extent. The electrophysiological data showing CNO responsiveness is only conducted in the SNc. If the VTA response is significantly reduced vs the SNc response, then the selectivity of the SNc degeneration could just be because the SNc was more hyperactive than the VTA. Electrophysiology experiments comparing the VTA and SNc response to CNO could support the idea that the SNc has substantial intrinsic vulnerability factors compared to the VTA.

(3) The mice have access to a running wheel for the circadian rhythm experiments. Running has been shown to alter the dopaminergic system (Bastioli et al., 2022) and so the authors should clarify whether the histology, electrophysiology, fiber photometry, and transcriptomics data are conducted on mice that have been running or sedentary.

Reviewer #2 (Public Review):

Summary:

The study reported by Trutti et al. uses high-field fMRI to test the hypothesized involvement of subcortical structure, particularly striatum, in WM updating. Specifically, participants were scanned while performing the Reference Back task (e.g., Rac-Lubashevsky and Kessler, 2016), which tests constructs like working memory gate opening and closing and substitution. While striatal activation was involved in substitution, it was not observed in gate opening. This observation is cited as a challenge to cortico-striatal models of WM gating, like PBWM (Frank and O'Reilly, 2005).

Strengths:

While there have been prior fMRI studies of the reference back task (Nir-Cohen et al., 2020), the present study overcomes limitations in prior work, particularly with regard to subcortical structures, by applying high-field imaging with a more precise definition of ROIs. And, the fMRI methods are careful and rigorous, overall. Thus, the empirical observations here are useful and will be of interest to specialists interested in working memory gating or the reference back task specifically.

Weaknesses:

I am less persuaded by the more provocative points regarding the challenge it presents to models like PBWM, made in several places by the paper. As detailed below, issues with conceptual clarity of the main constructs and their connection to models, like PBWM, along with some incomplete aspects of the results, make this stronger conclusion less compelling.

(1) The relationship of the Nir-Cohen et al. (2020) task analysis of the reference back task, with its contrasts like gate opening and closing, and the predictions of PBWM is far from clear to me for several reasons.

First, contrasts like gate opening and gate closing make strong finite state assumptions. As far as I know, this is not an assumption of PBWM, certainly not for gate opening. At a minimum, PBWM is default closed because of the tonic inhibition of cortico-thalamic dynamics by the globus pallidus. Indeed, this was even noted in the discussion of this paper, which seems to acknowledge this discrepancy, but then goes on to conclude that they have challenged the PBWM model anyway.

Second, as far as I know, PBWM emphasizes go/no-go processes around constructs of input- and output-gating, rather than state shifts between gate opening and closing. While this relationship is less clear in reference back, substituting task-relevant items into working memory does appear to be an example of input gating, as modeled by PBWM. Thus, it is not clear to me why the substitution contrast would not be more of a test of input gating than the gate opening contrast, which requires assumptions that are not clear are required by the model, as noted above.

Third, PBWM relies on striatal mechanisms to solve the problem of selective gating, inputting, or outputting items in memory while also holding on to others. Selective gating contrasts with global gating, in which everything in memory is gated or nothing. The reference back task is a test of global gating. It is an important distinction because non-striatal mechanisms that can solve global gating, cannot solve selective gating. Indeed, this limitation of non-striatal mechanisms was the rationale for PBWM adding striatum. The connectivity of the striatum with the cortex permits this selectivity. It is not clear that the reference back task tests these selective demands in the first place. That limitation in this task was the rationale behind the recent Rac-Lubashevsky and Frank (2022) paper using the reference back 2 procedure that modifies the original reference back for selective gating.

So, if the primary contribution of the paper is to test PBWM, as suggested by the first line of the abstract, then it is not clear that the reference back task in general, or the gate opening contrast in particular, is the best test of these predictions. Other contrasts (substitution), or indeed, tasks (reference back 2) would have been better suited.

(2) In general, observations of univariate activity in the striatum have been notoriously variable in the context of WM. Indeed, Chatham et al. (2014) who tested working memory output gating - notably in a direct test of the predictions of PBWM - noted this variability. They too did not observe univariate activation in the striatum associated with selective output gating. Rather they found evidence of increased connectivity between the striatum and cortex during selective output gating. They argued that one account of this difference is that striatal gating dynamics emerge from the balance between the firing of both Go and NoGo cell populations that decide whether to gate or not. It is not always clear how this balance should relate to univariate activation in the striatum. Thus, the present study might also test cortico-striatal connectivity, rather than relying exclusively on univariate activation, in their test of striatal involvement in these WM constructs.

(3) It is concerning that there was no behavioral cost for comparison switch vs. repeat trials. This differs from with prior observations from the reference back (e.g., Nir-Cohen et al., 2020), and in general, is odd given the task switch/cue interpretation component. This failure to observe a basic behavioral effect raises a concern about how participants approached this task and how that might differ from prior reports of the reference back. If they were taking an unusual strategy, it further complicates the interpretation of these results and the implications they hold for theory.

In summary, the present observations are useful, particularly for those interested in the reference back task. For example, they might call into question verbal theories and task analyses of the reference back task that tie constructs like gate-opening to striatal mechanisms. However, given the ambiguities noted above, the broader implications for models like PBWM, or indeed, other models of working memory gating, are less clear.