Reviewer #3 (Public review):

Summary:

The author showed expression of the viral proteases 2Apro and 3Cpro of EV-D68, which cleaved specific components of the nuclear pore complex (Nup98 and POM121 by 2Apro), and 2A but not 3C expression altered nuclear import and export. Similar nucleocytoplasmic transport deficits are observed in EV-D68-infected RD cells and iPSC-derived motor neurons (diMNs). 2A inhibitor telaprevir partially rescued the nucleocytoplasmic transport deficits and suppressed neuronal cell death after infection. While it's clear that 2A can cleave NPC proteins and affect nuclear transport, the link to neurotoxicity after EV-D68 infection is less convincing.

This study opens up a very intriguing hypothesis: that EV-D68 2Apro could be directly responsible for motor neuron cell death, mediated by POM121 and possibly Nup98 cleavage, that ultimately results in paralysis known as acute flaccid myelitis. This hypothesis notably does run counter to other published data showing that human neuronal organoids derived from iPSCs can support productive EV-D68 infection for weeks without cell death and that EV-D68-infected mice can have paralysis prevented by depletion of CD8 T cells, still with EV-D68 infection of the spinal cord. However, even if 2Apro is not ultimately responsible for motor neurons dying in human infections, that does not exclude the possibility that cleavage of nups could still disrupt motor neuron function. Notably, most children with AFM have some amount of motor function return after their acute period of paralysis, but most still have some residual paralysis for years to life. It is possible that 2A pro could mediate the acute onset of weakness, while T cells killing neurons could determine the amount of long-term, residual paralysis.

Strengths:

The characterization of nuclear pore complex components that appear to be targets of both poliovirus and EV-D68 proteases is quite thorough and expansive, so this data set alone will be useful for reference to the field. And the process by which the authors narrowed their focus to EV-D68 2Apro reducing Nup98 and POM121 as consequential to both import and export of nuclear cargo but not RNA was technically impressive, thorough, and convincing. As will be detailed below, when the authors move from studying over-expressed proteases in transformed cell lines to studying actual virus infection in both transformed cell lines and iPSC-derived neurons, some of the data only indirectly support their conclusions; however, the quality of the experiments performed is still high. So even if the claim that 2Apro causes neurotoxicity is circumstantial, the data certainly are intriguing and certainly justify further study of the effects of EV-D68 2Apro on the NPC and how this impacts pathogenesis. This is a convincing start to an intriguing line of inquiry.

Weaknesses:

This study falls a bit shy of actually showing that 2Apro effects are causing motor neuron toxicity because the evidence of this is fairly indirect. At points, the authors do admit these limitations, but at other times, they claim to have shown the link directly. The following are reasons why these claims are only indirectly supported:

(1) Cleavage of Nup98 and POM121 after EV-D68 infection in RD cells and diMNs is never demonstrated.

(2) Telaprevir was able to rescue nucleocytoplasmic transport in RD cells at low concentrations (Figure 4A). It is not shown if this correlates with its antiviral effect in RD cells, or could this correlate with inhibition of 2A cleavage of Nup98 or POM121, which is never measured.

(3) Building off of the prior point, the authors' claim that the neuroprotective effect of telaprevir is independent of its antiviral effect is not well-founded. Figure 4E (neuroprotection) was done with MOI 5, and Figure 4G (virus growth) was MOI 0.5. Telaprevir neuroprotection is not shown at MOI 0.5, nor is the neuroprotective effect correlated with inhibition of 2A cleavage of Nup98 or POM121.

(4) The use of mixed virus isolates only in the diMNs is problematic because different EV-D68 isolates are known to have drastically different effects on pathogenesis in mice. Since all initial data were generated with the MO isolate, adding the additional MD isolate to the diMN experiments actually adds uncertainty to the conclusions. It is not clear if the authors infected different cultures with the different isolates and combined the data or infected all cultures with a mixture of the two isolates. If the former, then the data should be reported separately to see the effect of each individual strain, which would be interesting to EV-D68 virologists. If the latter, then there is no way to know from these data whether one of the two isolates had increased fitness over the other and exerted a dominant effect. If the MD isolate overtook the MO isolate, from which all other data in this manuscript are derived, then we have much less of an idea how much the data from the first three figures supports the final figure.

Reviewer #3 (Public review):

Summary:

The manuscript by Zhang et al. demonstrates that MORC2 undergoes liquid-liquid phase separation (LLPS) to form nuclear condensates critical for transcriptional repression. Using a combination of in vitro LLPS assays, cellular studies, NMR spectroscopy, and crystallography, the authors show that a dimeric scaffold formed by CC3 drives phase separation, while multivalent interactions between an intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) further promote condensate formation. Notably, LLPS enhances MORC2 ATPase activity in a DNA-dependent manner and contributes to transcriptional regulation, establishing a functional link between phase separation, DNA binding, and transcriptional control. Overall, the manuscript is well-organized and logically structured, offering mechanistic insights into MORC2 function, and most conclusions are supported by the presented data. Nevertheless, some of the claims are not sufficiently supported by the current data and would benefit from additional evidence to strengthen the conclusions.

The following suggestions may help strengthen the manuscript:

Major comments:

(1) The central model proposes that multivalent interactions between the IDR and IBD promote MORC2 LLPS. However, the characterization of these interactions is currently limited. It is recommended that the authors perform more systematic analyses to investigate the contribution of these interactions to LLPS, for example, by in vitro assays assessing how the IDR or IBD individually influence MORC2 phase separation.

(2) The authors mention that DNA binding can promote MORC2 LLPS. It is recommended that they generate a phase diagram to systematically assess how DNA influences phase separation.

(3) The authors use the N39A mutant as a negative control to study the effect of DNA binding on ATP hydrolysis. Given that N39A is defective in DNA binding, it could also be employed to directly test whether DNA binding influences MORC2 phase separation.

(4) Many of the cellular and in vitro LLPS experiments employ EGFP fusions. The authors should evaluate whether the EGFP tag influences MORC2 phase separation behavior.

Reviewer #3 (Public review):

Summary:

The manuscript by Stahl and colleagues reports an approach to generate ocular organoids composed of retinal and lens structures, derived from Medaka blastula cells. The authors present a comprehensive characterisation of the timeline followed by lens and retinal progenitors, showing these have distinct origins, and that they recapitulate the expression of differentiation markers found in vivo. Despite this molecular recapitulation, morphogenesis is strikingly different, with lens progenitors arising at the centre of the organoid, and subsequently translocating to the outside.

Major Comments:

- The manuscript presents a beautiful set of high-quality images showing expression of lens differentiation markers over time in the organoids. The set of experiments is very robust, with high numbers of organoids analysed and reproducible data. The mechanism by which lens specification is promoted in these organoids is, however, poorly analysed, and the reader does not get a clear understanding of what is different in these experiments, as compared to previous attempts, to support lens differentiation. There is a mention to HEPES supplementation, but no further analysis is provided, and the fact that the process is independent of ECM contradicts, as the authors point out, previous reports. The manuscript would benefit from a more detailed analysis of the mechanisms that lead to lens differentiation in this setting.

- The markers analysed to show onset of lens differentiation in the organoids seem to start being expressed, in vivo, when the lens placode starts invaginating. An analysis of earlier stages is not presented. This would be very informative, allowing to determine whether progenitors differentiate as placode and neuroepithelium first, to subsequently continue differentiating into lens and retina, respectively. Could early placodal and anterior neural plate markers be analysed in the organoids? This would provide a more complete sequence of lens vs retina differentiation in this model.

- The analysis of BMP and Fgf requirement for lens formation and differentiation is suggestive, but the source of these signals is not resolved or mentioned in the manuscript. Are BMP4 and Fgf8 expressed by the organoids? Where are they coming from?

- The fact that the lens becomes specified in the centre of the organoid is striking, but it is for me difficult to visualise how it ends up being extruded from the organoid. Did the authors try to follow this process in movies? I understand that this may be technically challenging, but it would certainly help to understand the process that leads to the final organisation of retinal and lens tissues in the organoid. There is no discussion of why the morphogenetic mechanism is so different from the in vivo situation. The manuscript would benefit from explicitly discussing this.

Significance:

This study describes a reproducible approach to differentiate ocular organoids composed of lens and retinal tissues. The characterisation of lens differentiation in this model is very detailed, and despite the morphogenetic differences, the molecular mechanisms show many similarities to the in vivo situation. The manuscript however does not highlight, in my opinion, why this model may be relevant. Clearly articulating this relevance, particularly in the discussion, will enhance the study and provide more clarity to the readers regarding the significance of the study for the field of organoid research, ocular research and regenerative studies.

Reviewer #3 (Public review):

Summary:

This perspective article by Reichmann et al. highlights the importance of moving beyond the search for a single, unified immune mechanism to explain host-Mtb interactions. Drawing from studies in immune profiling, host and bacterial genetics, the authors emphasize inconsistencies in the literature and argue for broader, more integrative models. Overall, the article is thought-provoking and well-articulated, raising a concept that is worth further exploration in the TB field.

Strengths:

Timely and relevant in the context of the rapidly expanding multi-omics datasets that provide unprecedented insights into host-Mtb interactions.

Weaknesses (Minor):

(1) Clarity on the notion of a "unified mechanism". It remains unclear whether prior studies explicitly proposed a single unifying immunological model. While inconsistencies in findings exist, they do not necessarily demonstrate that earlier work was uniformly "single-minded". Moreover, heterogeneity in TB has been recognized previously (PMIDs: 19855401, 28736436), which the authors could acknowledge.

(2) Evolutionary timeline and industrial-era framing. The evolutionary model is outdated. Ancient DNA studies place the Mtb's most recent common ancestor at ~6,000 years BP (PMIDs: 25141181; 25848958). The Industrial Revolution is cited as a driver of TB expansion, but this remains speculative without bacterial-genomics evidence and should be framed as a hypothesis. Additionally, the claim that Mtb genomes have been conserved only since the Industrial Revolution (lines 165-167) is inaccurate; conservation extends back to the MRCA (PMID: 31448322).

(3) Trained immunity and TB infection. The treatment of trained immunity is incomplete. While BCG vaccination is known to induce trained immunity (ref 59), revaccination does not provide sustained protection (ref 8), and importantly, Mtb infection itself can also impart trained immunity (PMID: 33125891). Including these nuances would strengthen the discussion.

Reviewer #3 (Public Review):

It is rare to find systems in neuroscience where a detailed mechanistic link can be made between the biophysical properties of individual neurons and observable behaviors. In this study, Medina and Margoliash examined how the intrinsic physiological properties of a subclass of neurons in HVC, the main nucleus orchestrating the production of birdsong, might have an effect on the temporal structure of a song. This builds on prior work from this lab demonstrating that intrinsic properties of these neurons are highly consistent within individual animals and more similar between animals with similar songs, by identifying specific acoustic features of the song that covary with intrinsic properties and by setting forth a detailed biophysical network model to explain the relationship.

The main experimental finding is that excitability, hyperpolarization-evoked sag, and rebound depolarization are correlated with song duration and the duration of long harmonic elements. This motivates the hypothesis that rebound depolarization acts as a coincidence detector for the offset of inhibition associated with the previous song element and excitation associated with the start of the next element, with the delay and other characteristics of the window determined primarily by Ih. The idea is then that the temporal sensitivity of coincidence detection, which is common to all HVCx neurons, sets a global tempo that relates to the temporal characteristics of a song. This model is supported by some experimental data showing variation in the temporal integration of rebound spiking and by a Hodgkin-Huxley-based computational model that demonstrates proof of principle, including the emergence of a narrow (~50 ms) post-inhibitory window when excitatory input from other principal neurons can effectively evoke spiking.

Overall, the data are convincing and the model is compelling. The manuscript plays to the strengths of zebra finch song learning and the well-characterized microcircuitry and network dynamics of HVC. Of particular note, the design for the electrophysiology experiments employed both a correlational approach exploiting the natural variation in zebra finch song and a more controlled approach comparing birds that were tutored to produce songs that differed primarily along a single acoustical dimension. The modeling is based on Hodgkin-Huxley ionic conductances that have been pharmacologically validated, and the connections and functional properties of the network are consistent with prior work. This makes for a level of mechanistic detail that will likely be fruitful for future work.

Comments on revised version:

I read through everything and I also feel that my comments have been adequately addressed.

Reviewer #3 (Public review):

Summary:

This paper by Stribling and colleagues sheds light on a decade-long P. aeruginosa outbreak of the high-risk lineage ST-621 in a US Military hospital. The origins of the outbreak date back to the late 90s and it was mainly caused by two distinct subclones SC1 and SC2. The data of this outbreak showed the emergence of antibiotic resistance to cephalosporin, carbapenems and colistin over time highlighting the emerging risk of extensively resistant infections due to P. aeruginosa and the need for ongoing surveillance.

Strengths:

This study, overall, is well constructed and clearly written. Since detailed information on floor plans of the building and transfers between facilities was available, the authors were able to show that these two subclones emerged in two separate buildings of the hospital. The authors support their conclusions with prospective environmental sampling in 2021 and 2022 and link the role of persistent environmental contamination to sustaining nosocomial transmission. Information on resistance genes in repeat isolates for the same patients allowed the authors to detect the emergence of resistance within patients. The conclusions have broader implications for infection control at other facilities. In particular, the paper highlights the value of real-time surveillance and environmental sampling in slowing nosocomial transmission of P. aeruginosa.

Weaknesses:

My major concern is that the authors used fixed thresholds and definitions to classify the origin of an infection. As such, they were not able to give uncertainty measures around transmission routes nor quantify the relative contribution of persistent environmental contamination vs patient-to-patient transmission. The latter would allow the authors to quantify the impact of certain interventions. In addition, these results represent a specific US military facility and the transmission patterns might be specific to that facility. The study also lacked any data on antibiotic use that could have been used to relate to and discuss the temporal trends of antimicrobial resistance.

Comments on revisions:

The authors have addressed my concerns adequately in the revised manuscript.

Reviewer #3 (Public review):

Summary:

Cholecystokinin (CCK) is highly expressed in auditory thalamocortical (MGB) neurons and CCK has been found to shape cortical plasticity dynamics. In order to understand how CCK shapes synaptic plasticity in the auditory thalamocortical pathway, they assessed the role of CCK signaling across multiple mechanisms of LTP induction with the auditory thalamocortical (MGB - layer IV Auditory Cortex) circuit in mice. In these physiology experiments that leverage multiple mechanisms of LTP induction and a rigorous manipulation of CCK and CCK-dependent signaling, they establish an essential role of auditory thalamocortical LTP on the co-release of CCK from auditory thalamic neurons. By carefully assessing the development of this plasticity over time and CCK expression, they go on to identify a window of time that CCK is produced throughout early and middle adulthood in auditory thalamocortical neurons to establish a window for plasticity from 3 weeks to 1.5 years in mice, with limited LTP occurring outside of this window. The authors go on to show that CCK signaling and its effect on LTP in the auditory cortex is also capable of modifying frequency discrimination accuracy in an auditory PPI task. In evaluating the impact of CCK on modulating PPI task performance, it also seems that in mice <1.5 years old CCK-dependent effects on cortical plasticity is almost saturated. While exogenous CCK can modestly improve discrimination of only very similar tones, exogenous focal delivery of CCK in older mice can significantly improve learning in a PPI task to bring their discrimination ability in line with those from young adult mice.

Strengths:

(1) The clarity of the results along with the rigor multi-angled approach provide significant support for the claim that CCK is essential for auditory thalamocortical synaptic LTP. This approach uses a combination of electrical, acoustic, and optogenetic pathway stimulation alongside conditional expression approaches, germline knockout, viral RNA downregulation and pharmacological blockade. Through the combination of these experimental configures the authors demonstrate that high-frequency stimulation-induced LTP is reliant on co-release of CCK from glutamatergic MGB terminals projecting to the auditory cortex.

(2) The careful analysis of the CCK, CCKB receptor, and LTP expression is also a strength that puts the finding into the context of mechanistic causes and potential therapies for age-dependent sensory/auditory processing changes. Similarly, not only do these data identify a fundamental biological mechanism, but they also provide support for the idea that exogenous asynchronous stimulation of the CCKBR is capable of restoring an age-dependent loss in plasticity.

(3) Although experiments to simultaneously relate LTP and behavioral change or identify a causal relationship between LTP and frequency discrimination are not made, there is convincing evidence that CCK signaling in the auditory cortex (known to determine synaptic LTP) is important for auditory processing/frequency discrimination. These experiments are key for establishing the relevance of this mechanism.

Weaknesses:

The following are weaknesses or limitations of the study that may also fall outside of the scope of this work, but which could be addressed in the future.

(1) Given the magnitude of the evoked responses, one expects that pyramidal neurons in layer IV are primarily those that undergo CCK-dependent plasticity, but the degree to which PV-interneurons and pyramidal neurons participate in this process differently is unclear.

(2) While these data support an important role for CCK in synaptic LTP in the auditory thalamocortical pathway, perhaps temporal processing of acoustic stimuli is as or more important than frequency discrimination. Given the enhanced responsivity of the system, it is unclear whether this mechanism would improve or reduce the fidelity of temporal processing in this circuit. Understanding this dynamic may also require consideration of cell type as raised in weakness #1.

(3) In Figure 1, an example of increased spontaneous and evoked firing activity of single neurons after HFS is provided. Yet it is surprising that the group data are analyzed only for the fEPSP. It seems that single neuron data would also be useful at this point to provide insight into how CCK and HFS affect temporal processing and spontaneous activity/excitability.

Reviewer #3 (Public review):

Bogdan et al. present an intriguing and timely investigation into the intrinsic dynamics of prediction error (PE)-related brain states. The manuscript is grounded in an intuitive and compelling theoretical idea: that the brain alternates between high and low PE states even at rest, potentially reflecting an intrinsic drive toward predictive minimization. The authors employ a creative analytic framework combining different prediction tasks and imaging modalities. They shared open code, which will be valuable for future work.

However, the current manuscript would benefit from further clarification and empirical grounding, especially with regard to its theoretical framing (that PE-like state fluctuations are intrinsic and help us minimize PE), interpretation of results, and broader functional significance. Below, I outline a few major comments and suggestions that I think would strengthen the contribution.

(1) Consistency in Theoretical Framing

The title, abstract, and introduction suggest inconsistent theoretical goals of the study.

The title suggests that the goal is to test whether there are intrinsic fluctuations in high and low PE states at rest. The abstract and introduction suggest that the goal is to test whether the brain intrinsically minimizes PE and whether this minimization recruits global brain networks. My comments here are that a) these are fundamentally different claims, and b) both are challenging to falsify. For one, task-like recurrence of PE states during resting might reflect the wiring and geometry of the functional organization of the brain emerging from neurobiological constraints or developmental processes (e.g., experience), but showing that mirroring exists because of the need to minimize PE requires establishing a robust relationship with behavior or showing a causal effect (e.g., that interrupting intrinsic PE state fluctuations affects prediction).

The global PE hypothesis-"PE minimization is a principle that broadly coordinates brain functions of all sorts, including abstract cognitive functions"-is more suitable for discussion rather than the main claim in the abstract, introduction, and all throughout the paper.

Given the above, I recommend that the authors clarify and align their core theoretical goals across the title, abstract, introduction, and results. If the focus is on identifying fluctuations that resemble task-defined PE states at rest, the language should reflect that more narrowly, and save broader claims about global PE minimization for the discussion. This hypothesis also needs to be contextualized within prior work. I'd like to see if there is similar evidence in the literature using animal models.

(2) Interpretation of PE-Related Fluctuations at Rest and Its Functional Relevance

It would strengthen the paper to clarify what is meant by "intrinsic" state fluctuations. Intrinsic might mean task-independent, trait-like, or spontaneously generated. Which do the authors mean here? Is the key prediction that these fluctuations will persist in the absence of a prediction task?

Regardless of the intrinsic argument, I find it challenging to interpret the results as evidence of PE fluctuations at rest. What the authors show directly is that the degree to which a subset of regions within a PE network discriminates high vs. low PE during task correlates with the magnitude of separation between high and low PE states during rest. While this is an interesting relationship, it does not establish that the resting-state brain spontaneously alternates between high and low PE states, nor that it does so in a functionally meaningful way that is related to behavior. How can we rule out brain dynamics of other processes, such as arousal, that also rise and fall with PE? I understand the authors' intention to address the reverse inference concern by testing whether "a participant's unique connectivity response to PE in the reward-processing task should match their specific patterns of resting-state fluctuation". However, I'm not fully convinced that this analysis establishes the functional role of the identified modules to PE because of the following:

Theoretically, relating the activities of the identified modules directly to behavior would demonstrate a stronger functional role.

a) Across participants: Do individuals who exhibit stronger or more distinct PE-related fluctuations at rest also perform better on tasks that require prediction or inference? This could be assessed using the HCP prediction task, though if individual variability is limited (e.g., due to ceiling effects), I would suggest exploring a dataset with a prediction task that has greater behavioral variance.

Or even more broadly, does this variability in resting state PE state fluctuations predict general cognitive abilities like WM and attention (which the HCP dataset also provides)? I appreciate the inclusion of the win-loss control, and I can see the intention to address specificity. This would test whether PE state fluctuations reflect something about general cognition, but also above and beyond these attentional or WM processes that we know are fluctuating.

b) Within participants: Do momentary increases in PE-network expression during tasks relate to better or faster prediction? In other words, is there evidence that stronger expression of PE-related states is associated with better behavioral outcomes?

(3) Apriori Hypothesis for EEG Frequency Analysis

It's unclear how to interpret the finding that fMRI fluctuations in the defined modules correlate with frontal Delta/Theta power, specifically in the 3-6 Hz range. However, in the EEG literature, this frequency band is most commonly associated with low arousal, drowsiness, and mind wandering in resting, awake adults, not uniquely with prediction error processing. An a priori hypothesis is lacking here: what specific frequency band would we expect to track spontaneous PE signals at rest, and why? Without this, it is difficult to separate a PE-based interpretation from more general arousal or vigilance fluctuations.

(4) Significance Assessment

The significance of the correlation above and all other correlation analyses should be assessed through a permutation test rather than a single parametric t-test against zero. There are a few reasons: a) EEG and fMRI time series are autocorrelated, violating the independence assumption of parametric tests;<br /> b) Standard t-tests can underestimate the true null distribution's variance, because EEG-fMRI correlations often involve shared slow drifts or noise sources, which can yield spurious correlations and inflating false positives unless tested against an appropriate null.

Building a null distribution that preserves the slow drifts, for example, would help us understand how likely it is for the two time series to be correlated when the slow drifts are still present, and how much better the current correlation is, compared to this more conservative null. You can perform this by phase randomizing one of the two time courses N times (e.g., N=1000), which maintains the autocorrelation structure while breaking any true co-occurrence in patterns between the two time series, and compute a non-parametric p-value. I suggest using this approach in all correlation analyses between two time series.

(5) Analysis choices

If I'm understanding correctly, the algorithm used to identify modules does so by assigning nodes to communities, but it does not itself restrict what edges can be formed from these modules. This makes me wonder whether the decision to focus only on connections between adjacent modules, rather than considering the full connectivity, was an analytic choice by the authors. If so, could you clarify the rationale? In particular, what justifies assuming that the gradient of PE states should be captured by edges formed only between nearby modules (as shown in Figure 2E and Figure 4), rather than by the full connectivity matrix? If this restriction is instead a by-product of the algorithm, please explain why this outcome is appropriate for detecting a global signature of PE states in both task and rest.

When assessing the correspondence across task-fMRI and rs-fMRI in section 2.2.2, why was the pattern during task calculated from selecting a pair of bilateral ROIs (resulting in a group of eight ROIs), and the resting state pattern calculated from posterior-anterior/ventral-dorsal fluctuation modules? Doesn't it make more sense to align the two measures? For example, calculating task effects on these same modules during task and rest?

Reviewer #3 (Public review):

Summary:

This manuscript presents a novel investigation into unidirectionally propagating waves observed on the surface of Pseudomonas nitroreducens bacterial biofilms. The authors explore how these waves, initially spiral in form, transition into combinations of spiral, target, and planar patterns. The study identifies the periodic extension-retraction cycles of type IV pili as the driving mechanism for wave propagation, which preferentially moves from the colony's edge to its center. Furthermore, the manuscript proposes two theoretical models-a phase-oscillator model and a continuum active solid model-to reproduce these phenomena, and demonstrates how external manipulations (e.g., water droplets, temperature, PEG) can control wave patterns and direction, often correlating with oscillation frequency gradients. The work aims to bridge the fields of active-matter physics and bacterial biophysics by providing both experimental observations and theoretical frameworks for understanding these complex biological wave phenomena.

Strengths:

The experimental discovery of unidirectionally propagating waves on bacterial biofilms is highly intriguing and represents a significant contribution to both microbiology and active-matter physics. The detailed observations of wave pattern transitions (spiral to target to planar) and their response to various environmental perturbations (water, temperature, PEG) provide valuable empirical data. The identification of type IV pili as the driving force offers a concrete biological mechanism. The observed correlation between frequency gradients and wave direction is a compelling finding with potential for broader implications in understanding biological pattern formation. This work has the potential to stimulate further research in the collective behavior of living systems and the physical principles underlying biological organization.

Weaknesses:

The manuscript attempts to link unidirectional wave propagation to non-reciprocal couplings but ultimately shows that the wave direction is determined by the gradient of the oscillation frequency. The couplings in the two theoretical models are both isotropic and thus cannot dictate the wave direction. A clear distinction should be made between non-reciprocity as a source of wave generation and non-uniformity as a controlling factor of wave direction.

The relationship between the phase oscillator model and the active solid model is unclear. Given that U and P are both dynamical variables evolving in three-dimensional space, defining the phase Φ precisely in the phase space spanned by U and P could be challenging. A graphical illustration of the definition of Φ would be beneficial. To ensure reproducibility of the numerical results, the parameter values used in the numerical simulations and an explicit definition of the elastic force in the active solid model should be provided.

The link between the theoretical models and experimental results is weak. For example, the propagation of the kink from the lower to the higher part of the surface (Figure 1e) could be addressed within the framework of the active solid model. The mechanism of transition from spiral to target waves (Figure 3a), b)) requires clarification, identifying which model parameter is crucial for inducing this transition. The wave propagation toward the lower frequency side is numerically demonstrated using the phase oscillator model, but a physical or intuitive explanation for this phenomenon is missing. Also, the wave transitions induced by the addition of water droplets and temperature rise are not linked to specific parameters in the theoretical models.

Reviewer #3 (Public review):

Summary:

The authors in this paper introduce BuzzWatch, an open-source, low-cost (200-300 Euros) platform for long-term monitoring of mosquito flight and behavior. They use a Raspberry Pi with a Noirv2 Camera set up under laboratory conditions to observe 3 different species of mosquitoes. The system captures a variety of multimodal data, like flight activity, sugar feeding, and host-seeking responses, with the help of external modules like CO2 and fructose-soaked cottons. They also release a GUI in addition to automated tracking and behaviour analysis, which doesn't run on Pi but rather on a personal laptop.

Four main use cases are demonstrated:

(1) Characterizing diel rhythms in various Aedes aegypti populations.

(2) Differentiating behaviors of native African vs. invasive human-adapted subspecies.

(3) Assessing physiological (blood-feeding) and environmental (light regime) perturbations.

(4) Testing time-of-day variation in responses to host-associated cues like CO₂ and heat.

Description (Strengths):

(1) The authors introduce a low-cost, scalable system that uses flight tracking in 2D as an alternative to 3D multi-camera systems.

(2) Due to the low pixel quality required by the system, they can record for weeks at a time, capturing long temporal and behavioral activities.

(3) They also integrate external modules such as lights, CO2, and heat as a way to measure responses to a variety of stimuli.

(4) They also introduce a wiki as a guide for building replication and a help in using the GUI module.

(5) They implement both GLMM hourly and PCA of behavior data.

Limitations - Major Comments:

(1) Most experiments are only done with single replicates per colony. If the setup is claimed to be cheap and replicable, there should be clearer replicates across experiments.

(2) No external validation for the flight tracking algorithm using manual annotation or comparison with field data. The authors focus early on biological proof of principle, but the validity of the tracking algorithm is not presented. How accurate is the algorithm at classifying behaviours (e.g., vs human ground truth)? How reliable is tracking?

(3) Why develop a custom GUI instead of using established packages such as rethomics (https://rethomics.github.io/) that are already available for behavioral analysis?

(4) Why use RGB light strips when perceptual white light for humans is not relevant for mosquitoes? The choice of lighting should be based on the mosquito's visual perception. - https://pmc.ncbi.nlm.nih.gov/articles/PMC12077400/ .

(5) Why use GLMMs instead of GAMs (with explicit periodic components)? With GLMMs, you do not account for temporal structure, which is highly relevant and autocorrelated in behavioral time series data.

(6) What is the proportion of mosquitoes that stay alive throughout the experiments? How do you address dead animals in tracking? No data are available on whether all mosquitoes made it through the monitoring period. No survival data is mentioned in the paper, and in the wiki, it is not clear how it is used or how it affects the analyses - https://theomaire.github.io/buzzwatch/analyze.html#diff-cond .

(7 )The sugar feeding behavior is not manually validated.

(8) Figure 4d is difficult to understand - how did you align time? Why is ZT4 aligning with ZT0? Should you "warp" the time series to compare them (e.g., from dawn to dusk)?

(9) No video recordings are made available for demonstration or validation purposes.

Appraisal

(1) The core conclusions---that BuzzWatch can capture multiscale mosquito behavioral rhythms and quantify the effect of genetic, environmental, and physiological variation - show promise but require stronger validation.

(2) Statistical approaches (GLMM, PCA) are chosen but may not be optimal for temporal data with autocorrelation.

(3) The host-seeking module shows a differential response, which is a potentially valuable feature.

Reviewer #3 (Public review):

These findings suggest that Nup107 is involved in regulating ecdysone signaling during developmental transitions, with depletion of Nup107 disrupting hormone-regulated processes. Moreover, the rescue experiments hint that Nup107 might directly influence EcR signaling and ecdysone biosynthesis, though the precise molecular mechanism remains unclear.

Overall, the manuscript presents compelling data supporting Nup107's role in regulating developmental transitions.

Comments on revisions:

RNAi specificity: The authors now provide a more thorough discussion of off-target effects and justify their reliance on the Nup107KK RNAi line. The explanation regarding the predicted off-target for the GD line and their choice to use the KK line with a known insertion site is appropriate and adequately addresses the original concern.

NPC component specificity: The authors clarify that among the Nup107 complex members tested, only Nup107 knockdown induced developmental arrest. Their inclusion of Nup153 as a control helps to support the specificity of the phenotype, although expanding this analysis beyond a single additional Nup would further strengthen the claim.

Mechanistic clarity: The authors now distinguish between Nup107's upstream role in regulating torso and ecdysone biosynthetic genes versus direct control of EcR translocation. The clarification that EcR nuclear localization is 20E-dependent but Nup107-independent improves interpretive clarity.

The molecular mechanism linking Nup107 to torso regulation remains somewhat speculative. A deeper exploration of whether Nup107 influences transcriptional regulation through chromatin association (as the authors suggest) would strengthen the mechanistic narrative.

Conclusion:

Overall, the authors have addressed the major concerns raised in the initial review, and the revised manuscript presents a more coherent and compelling case for Nup107 as a regulator of developmental timing via the ecdysone signaling axis. While some mechanistic questions remain, the core findings are supported by the data, and the work provides novel insights into NPC function in development.

Reviewer #3 (Public review):

Gonzaga-Saavedra et al report an analysis on genomic binding of Polycomb group proteins, and of H2Aub1 and H3K27me3 domain formation in the early Drosophila embryo. Using carefully staged embryos during the nuclear cycles (NC) leading up to the cellular blastoderm stage, the authors provide compelling evidence that H3K27me3 domains at PcG target genes are only established during NC14 and do not exist in NC13. In contrast, H2Aub1 domains already start to appear during NC13. The authors show that E(z), the catalytic subunit of the H3K27 histone methyltransferase PRC2, is readily detected in interphase nuclei during the rapid nuclear divisions in pre-blastoderm embryos. In contrast, the DNA-binding proteins Pho, Cg, and GAF that are known (Pho) or have been postulated (Cg, GAF) to anchor PRC2 and PRC1 to Polycomb Response Elements (PREs) in Polycomb target genes only start to show nuclear localization from NC10 onwards with gradually increasing nuclear concentrations, reaching a maximum during NC14. These data strongly corroborate the simple, straightforward view that targeting of PRC2 and PRC1 to PREs by sequence-specific DNA-binding proteins is a prerequisite for the formation of H3K27me3 and H2Aub1 domains at Polycomb target genes.

The authors then explore the potential role of GAF/Trl in this process. They find that in embryos depleted of GAF/Trl, H3K27me3 domain formation is largely unperturbed.

The authors also depleted the pioneer factor Zelda (Zld) and found that removal of Zld results in a more complex outcome. Zelda appears to counteract the accumulation of H3K27me3 at the Polycomb targets eve and zen, but also appears to be required for effective H3K27me3 domain formation at Polycomb targets such as amos or atonal.

This is a very thorough study that reports data of superior technical quality that are highly relevant for the field. The study by Gonzaga-Saavedra et al extends and strengthens previous work from the labs of Eisen (Li et al, eLife 2014) and Zeitlinger (Chen et al, eLife 2013) to convincingly demonstrate that Polycomb domain formation in the early embryo occurs during ZGA but that such domains do not exist prior to ZGA. This should now finally put to rest earlier claims by the Iovino lab (Zenk et al, Science 2017) that H3K27me3 domains present in the zygote nucleus would be propagated and partially maintained during the rapid nuclear cleavage cycles and serve as seeds for H3K27me3 domain formation during ZGA.

The experiments analyzing H3K27me3 domain formation in embryos depleted of GAF/Trl or Zelda will be of great interest to the field.

Reviewer #3 (Public review):

Summary:

This is an interesting and clinically relevant in vitro study by Taber et al., exploring how mutations in PHD2 contribute to erythrocytosis and/or neuroendocrine tumors. PHD2 regulates HIFα degradation through prolyl-hydroxylation, a key step in the cellular oxygen-sensing pathway.

Using a time-resolved NMR-based assay, the authors systematically analyze seven patient-derived PHD2 mutants and demonstrate that all exhibit structural and/or catalytic defects. Strikingly, the P317R variant retains normal activity toward the C-terminal proline but fails to hydroxylate the N-terminal site. This provides the first direct evidence that N-terminal prolyl-hydroxylation is not dispensable, as previously thought.

The findings offer valuable mechanistic insight into PHD2-driven effects and refine our understanding of HIF regulation in hypoxia-related diseases.

Strengths:

The manuscript has several notable strengths. By applying a novel time-resolved NMR approach, the authors directly assess hydroxylation at both HIF1α ODD sites, offering a clear functional readout. This method allows them to identify the P317R variant as uniquely defective in NODD hydroxylation, despite retaining normal activity toward CODD, thereby challenging the long-held view that the N-terminal proline is biologically dispensable. The work significantly advances our understanding of PHD2 function and its role in oxygen sensing, and might help in the future interpretation and clinical management of associated erythrocytosis.

Weaknesses:

There is a lack of in vivo/ex vivo validation. This is actually required to confirm whether the observed defects in hydroxylation-especially the selective NODD impairment in P317R-are sufficient to drive disease phenotypes such as erythrocytosis.

The reliance on HRE-luciferase reporter assays may not reliably reflect the PHD2 function and highlights a limitation in the assessment of downstream hypoxic signaling.

The study clearly documents the selective defect of the P317R mutant, but the structural basis for this selectivity is not addressed through high-resolution structural analysis (e.g., cryo-EM).

Given the proposed central role of HIF2α in erythrocytosis, direct assessment of HIF2α hydroxylation by the mutants would have strengthened the conclusions.

Comments on revision:

The revised manuscript by Taber et al. addresses the key points raised during the review process in a comprehensive and appropriate manner. While some limitations remain, such as the lack of in vivo validation or direct HIF2α assessment, I agree with the authors that these are beyond the scope of the current in vitro-focused study. The authors' primary goal was to define the structural and functional defects caused by disease-associated PHD2 mutations. In this respect, the evidence they present is largely convincing and methodologically appropriate. Additional clarifications and an expanded discussion of the luciferase assay's limitations and the P317R structural context strengthen the manuscript further.

Reviewer #3 (Public review):

Summary:

In this article, Toshniwal et al. investigate the role of pyruvate metabolism in controlling cell growth. They find that elevated expression of the mitochondrial pyruvate carrier (MPC) leads to decreased cell size in the Drosophila fat body, a transformed human hepatocyte cell line (HepG2), and primary rat hepatocytes. Using genetic approaches and metabolic assays, the authors find that elevated pyruvate import into cells with forced expression of MPC increases the cellular NADH/NAD+ ratio, which drives the production of oxaloacetate via pyruvate carboxylase. Genetic, pharmacological, and metabolic approaches suggest that oxaloacetate is used to support gluconeogenesis rather than amino acid synthesis in cells over-expressing MPC. The reduction in cellular amino acids impairs protein synthesis, leading to impaired cell growth.

Strengths:

This study shows that the metabolic program of a cell, and especially its NADH/NAD+ ratio, can play a dominant role in regulating cell growth.

The combination of complementary approaches, ranging from Drosophila genetics to metabolic flux measurements in mammalian cells, strengthens the findings of the paper and shows a conservation of MPC effects across evolution.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors describe the results of a high-throughput screen for small-molecule activators of GCN2. Ultimately, they find 3 promising compounds. One of these three, compound 20 (C20), is of the most interest both for its potency and specificity. The major new finding is that this molecule appears to activate GCN2 independent of GCN1, which suggests that it works by a potentially novel mechanism. Biochemical analysis suggests that each binds in the ATP-binding pocket of GCN2, and that at least in vitro, C20 is a potent agonist. Structural modeling provides insight into how the three compounds might dock in the pocket and generates testable hypotheses as to why C20 perhaps acts through a different mechanism than other molecules.

Strengths:

Of the 3 compounds identified by the authors, C20 is the most interesting, not just for its intriguing mechanistic distinction as being GCN1-independent (shown genetically in two distinct cell lines, CHO and 293T in Figure 4, and in contrast to other GCN2 activators) but also for its potency. In in-cellulo assays, compound 21 appears as more of an ISR enhancer than an activator per se, and although compound 18 and compound 21 lead to upregulation of the ISR targets (Figure 2), that degree of upregulation is probably not significantly different from that induced by those compounds in Gcn2-/- cells. For C20, the effect appears stronger (although it is unclear whether the authors performed statistical analysis comparing the two genotypes in Figure 2D). In Figure 3, only C20 activates the ISR robustly in both CHO and 293T. Ultimately, C20 might be a tool for providing mechanistic insight into the details of GCN2 activation and regulation, and could be exploited therapeutically.

Weaknesses:

There are some limitations to the existing work. As the authors acknowledge, they do not use any of the compounds in animals; their in vivo efficacy, toxicity, and pharmacokinetics are unknown. But even in the context of the in cellulo experiments, it is puzzling that none of the three compounds, including C20, has any effects in HeLa cells when Neratinib does. It's beyond the scope of this paper to address definitively why that is, but it would at least be reassuring to know that C20 activates the ISR in a wider range of cells, including ideally some primary, non-immortalized cells. In addition, the ISR is a complex, feedback-regulated response whose output varies depending on the time point examined. The in cellulo analysis in this paper is limited to reporter assays at 18 hours and qRT-PCR assays at 4 and 8 hours. A more extensive examination of the behavior of the relevant ISR mRNAs and proteins (eIF2, ATF4, CHOP, cell viability, etc.) for C20 across a more extensive time course would give the reader a clearer sense of how this molecule affects ISR output. I also find it a bit strange that the authors describe C20 as "demonstrat(ing) weak inhibition of ... PKR"-the measured IC50 is ~4 μM, which is right around its EC50 for GCN2 activation. This raises the confounding possibility that C20 would simultaneously activate GCN2 while inhibiting PKR. While perhaps inhibition of PKR is not relevant under the conditions when GCN2 would be activated either experimentally or therapeutically, examining in cells the effects of C20 on GCN2 and PKR across a dose range would shed light on whether this cross-reactivity is likely to be of concern.

Reviewer #3 (Public review):

Summary:

The manuscript by Raiola and colleagues entitled "Quantitative computerized analysis demonstrates strongly compartmentalized tissue deformation patterns underlying mammalian heart tube formation" takes a highly quantitative approach to interrogating the earliest stages of cardiogenesis (12 hours, from early cardiac crescent to early heart tube) in a new and innovative way. The paper presents a new computational framework to help identify both regional and temporal patterns of tissue deformation at cellular resolution. The method is applied to live embryo imaging data (newly generated and from the group's previous pioneering work). In the initial setup, the new model was applied directly to raw time-lapse data, and the results were compared to actual cell tracks identified manually, showing close correlations of the model with the manual tracking. Next, they integrated spatial and temporal information from different embryos to generate a new model for tissue movement, driven by parameters such as tissue growth and anisotropy. Key findings from their model suggest that there are distinct compartments of tissue deformation patterns as the bilateral cardiac crescent develops into the linear heart tube, and that the ventricular chamber forms by a defined expansion pattern, as a 'hemi-barrel shape', with the aterial and venous poles (IFT and OFT) acting as the harnessing belts constraining the expansion of the chamber further. Lastly, the model is tested for its ability to predict future residence of cardiac crescent cells in the heart tube, which it seems to be able to do successfully based on fate tracking validation experiments.

Strengths:

The manuscript provides an exceptionally careful analysis of a critical stage during heart development - that of the earliest stages of morphogenesis, when the heart forms its first tube and chamber structures. While numerous studies have interrogated this stage of heart development, few studies have performed time-lapse imaging, and, to my knowledge, no other report has performed such in in-depth quantitative analysis and modeling of this complex process. The computational model applied to normal heart development of the myocardium (labelled by Nkx2-5) has revealed multiple new and interesting concepts, such as the distinct compartments of tissue deformation patterns and the growth trajectories of the emerging ventricle. The fact that the model operates at cellular resolution and over a nearly continuous time period of approximately 12 hours allows for unprecedented depth of the analysis in a largely unbiased manner. Going forward, one can imagine such models revealing additional information on these processes, performing analyses of subpopulations that form the heart, and maybe most importantly, applying the model to various perturbation models (genetic or otherwise). The manuscript is very well written, and the data display is accessible and transparent.

Weaknesses:

No major weaknesses are noted with the study. It would have been very exciting to see the model applied to any kind of perturbation, for example, a left-right defect model, or a model with compromised cardiac progenitor populations. However, the amount of live imaging required for such analyses renders this out of scope for the current study.

Reviewer #3 (Public review):

Summary:

This manuscript presents a comprehensive and well-executed investigation into the metabolic role of D-serine in the central nervous system. The authors provide solid evidence that D-serine competitively inhibits mitochondrial L-serine transport, thereby impairing one-carbon metabolism. This stereoselective mechanism reduces glycine and formate production, suppresses cellular proliferation, and induces apoptosis in immature neural cells and glioblastoma stem cells. Developmental analyses further reveal a physiological enantiomeric shift in serine metabolism during neurogenesis, aligning with the transition from proliferation to maturation. Overall, the study bridges developmental neurobiology, cancer metabolism, and amino acid transport, uncovering a previously unrecognized metabolic function of D-serine beyond its role in neurotransmission.

Strengths:

(1) The discovery that D-serine inhibits one-carbon metabolism by competing for mitochondrial L-serine transport-rather than through enzymatic inhibition or receptor-mediated signaling-represents a significant and previously underappreciated mechanism. This finding has broad implications for understanding metabolic regulation during neurodevelopment and offers potential relevance for targeting metabolic vulnerabilities in cancer.

(2) The authors integrate metabolomics, mitochondrial transport assays, molecular dynamics simulations, genetic and pharmacologic perturbations, transcriptomics, and both in vitro and ex vivo models. The breadth of experimental approaches, combined with the coherence of the findings across systems, provides strong support for the central conclusions and enhances the overall impact of the study.

(3) The temporal shift in D-/L-serine levels during neurodevelopment is elegantly linked to the transition from proliferative to mature neuronal states. The selective vulnerability of neural progenitors and tumor cells-contrasted with the resistance of mature neurons-highlights a biologically meaningful and potentially targetable metabolic distinction.

Weaknesses:

(1) While the authors attribute D-serine's metabolic effects to competition with mitochondrial L-serine transport, the specific identity of the transporter(s) mediating this process remains undefined. This represents a meaningful mechanistic gap, as the central conclusion depends on D-serine limiting mitochondrial L-serine availability to inhibit one-carbon metabolism.

(2) The effective concentrations of D-serine used in vitro (IC₅₀ ≈ 1-2 mM) exceed typical brain levels (~0.3 mM). While the authors acknowledge this, a more focused discussion on whether higher local D-serine concentrations could arise in specific microenvironments - such as synaptic compartments, tumor niches, or pathological states-would help contextualize the in vitro findings and strengthen their physiological relevance. For example, disruptions in D-serine clearance or altered expression of serine racemase and transporters in disease contexts could lead to localized accumulation. Moreover, differences between extracellular and intracellular D-serine pools - and the mechanisms governing their regulation - may further influence its metabolic impact in vivo.

(3) While the manuscript focuses on neural stem/progenitor cells and neural tumors, it remains unclear whether the anti-proliferative effects of D-serine are specific to neural lineages or extend to other highly proliferative non-neural cell types. A brief discussion addressing this point would help clarify the scope of D-serine's metabolic impact and whether its mechanism of action reflects a unique vulnerability in neural cells or a more general feature of proliferative metabolism. This distinction is particularly relevant for assessing the broader therapeutic potential of targeting mitochondrial L-serine transport.

Reviewer #3 (Public review):

Summary:

This manuscript presents a step towards testing the hypothesis that plasmodesmata have homology to nuclear pores. The similarities between the two structures have long been noted as both structures allow the transport of proteins and nucleic acids, and both structures are composed of curved membranes. The manuscript has identified nuclear pore proteins (NUPs) in plasmodesmal protein fractions and uses live imaging in a non-endogenous system and functional assays of a mutant to propose that this might be a bona fide association.

The conclusions the authors seek to draw are that: NUPs are present in plasmodesmal protein fractions; NUPs localise at plasmodesmata; NUPs might form a pore-gating complex at plasmodesmata, regulating non-specific (2xGFP) and specific (SHR) transport through plasmodesmata

The authors then use these conclusions to propose the possibility that phase separation mediates transport through plasmodesmata. If there is phase separation at plasmodesmata or a nuclear pore-like complex, it would revolutionise the community. However, this data is insufficient to act as a cornerstone for such a discovery.

Strengths:

The strength of the manuscript lies in the boldness and novelty of the idea.

Weaknesses:

The weaknesses lie in the lack of informative controls. The authors' own assessments of their data suggest they agree with this - in their abstract alone, they point out that the transport defects they observe might be off-target effects, and suggest there is a requirement in the future to determine whether the NUPs are bona fide PD components.

Across the proteomic and live imaging experiments, the conclusions could be stronger if they compared the NUP localisation and accumulation with ER proteins - the question of whether NUPs behave like other ER proteins is not addressed. As NUPs reside in the nuclear envelope, continuous with the ER, and the ER traverses plasmodesmata, a comparison between the NUPs and ER proteins would be extremely informative.

Regarding the proteomic identification of NUPs in plasmodesmal fractions, the authors place significant weight on their own metric for PD enrichment, the PD score. As I understand it, this a metric derived from addition of two factors: a two component enrichment score that is the difference between intensity of peptides of a given protein in the PD fraction and cell wall fraction, added to the difference between intensity of peptides of a given protein in the PD fraction and total cell fraction, and a feature score that is a factor that describes representation of protein domains contained in said given protein in the plasmodesmal fraction relative to the representation of that domain in proteins in the whole proteome. The features chosen for analysis are not indicated, and the feature factor, as I understand it, is a score common to all proteins with a given feature. While each of the factors carries a measure of meaning and information, I do not understand how adding them is mathematically or biologically meaningful.

Reviewer #3 (Public review):

Summary:

Mutations that result in consistent RAS activation constitute a major driver of cancer. Therefore, RAS is a favorable target for cancer therapy. However, since normal RAS activity is essential for the function of normal cells, a mechanism that differentiates aberrant RAS activity from normal one is required to avoid severe adverse effects. To this end, the authors designed and optimized a synthetic gene circuit that is induced by active RAS-GTP. The circuit components, such as RAS-GTP sensors, dimerization domains, and linkers. To enhance the circuit selectivity and dynamic range, the authors designed a synthetic promoter comprised of MAPK-responsive elements to regulate the expression of the RAS sensors, thus generating a feed-forward loop regulating the circuit components. Circuit outputs with respect to circuit design modification were characterized in standard model cell lines using basal RAS activity, active RAS mutants, and RAS inactivation.

This approach is interesting. The design is novel and could be implemented for other RAS-mediated applications. The data support the claims, and while this circuit may require further optimization for clinical application, it is an interesting proof of concept for targeting of aberrant RAS activity. I therefore recommend accepting this paper.

Strengths:

Novel circuit design, through optimization and characterization of the circuit components, solid data.

Weaknesses:

This manuscript could significantly benefit from testing the circuit performance in more realistic cell lines, such as patient-derived cells driven by RAS mutations, as well as in corresponding non-cancer cell lines with normal RAS activity. Furthermore, testing with therapeutic output proteins in vitro, and especially in vivo, would significantly strengthen the findings and claims.

Summary:

Given the revision made, I would recommend a minor revision that discusses the specificity limitations of this experimental setup.

Reviewer #3 (Public review):

Summary:

This manuscript reports the discovery of new compounds that selectively inhibit SMARCA4/SMARCA2 ATPase activity and have pronounced effects on uveal melanoma cell proliferation. They induce apoptosis and suppress tumor growth, with no toxicity in vivo. The report provides biological significance by demonstrating that the drugs alter chromatin accessibility at lineage specific gene enhancer regions and decrease expression of lineage specific genes, including SOX10 and SOX10 target genes.

Strengths:

The study provides compelling evidence for the therapeutic use of these compounds and does a thorough job at elucidating the mechanisms by which the drugs work. The study will likely have a high impact on the chromatin remodeling and cancer fields. The datasets will be highly useful to these communities.

Weaknesses:

The authors have addressed all my concerns.

Reviewer #3 (Public review):

This manuscript describes a careful and thorough evaluation of an evolutionary simulation model published previously. The model and this report address the question, whether heterozygote advantage (HA) by itself as a selection mechanism can explain a substantial level of allelic diversity as it is often seen in MHC immune genes. Despite decades of research on the topic of pathogen-mediated selection for MHC diversity, it remains an open question by which specific selection mechanisms this exceptional allelic diversity is maintained.

The previously published paper posits, in contrast to various previous studies, that HA is, in fact, able to maintain a level of allelic diversity as seen in many populations, just by itself, given certain conditions. The current manuscript now challenges this conclusion by highlighting that the previous model results only hold under very narrow parameter ranges.

Besides criticizing some of the conceptual points of the previous paper, the author carefully rebuilt the previously published model and replicated their results, before then evaluating the robustness of the model results to reasonable variation in different parameters. From this evaluation, it becomes clear that the previously reported results hinge strongly on a certain scaling or weighing factor that is adjusted for every parameter setting and essentially counteracts the changes induced by changing the parameters. The critical impact of this one parameter is not clearly stated in the previous paper, but raises serious doubts about the generalizability of the model to explain MHC allelic variation across diverse vertebrate species.

Given the fact that the MHC genes are among the most widely studied genes in vertebrates, and that understanding their evolution will shed light on their association with various complex diseases, the insights from this report and the general discussion of how MHC diversity evolved are of interest to at least some of the community. The manuscript is very well written and makes it easy to follow the theoretical and methodological details of the model and the arguments. I have only a few minor comments that I am detailing below. Furthermore, I would be very interested to read a response by the previous authors, especially on the relevance of this scaling/weighing factor that they introduced into their model, as it is possible that I might have missed something about its meaning.

Reviewer #3 (Public review):

Summary:

The authors have extended their previous research to develop TOPBP1 as a potential drug target for colorectal cancer by inhibiting its condensation. Utilizing an optogenetic approach, they identified the small molecule AZD2858, which inhibits TOPBP1 condensation and works synergistically with first-line chemotherapy to suppress colorectal cancer cell growth. The authors investigated the mechanism and discovered that disrupting TOPBP1 assembly inhibits the ATR/Chk1 signaling pathway, leading to increased DNA damage and apoptosis, even in drug-resistant colorectal cancer cell lines.

Comments on latest version:

This reviewer does not have further comments to the paper.

Reviewer #3 (Public review):

Summary:

In multicellular organisms, autophagosomes are formed throughout the cytosol, while late endosomes/lysosomes are relatively enriched in the perinuclear region. It is known that autophagosomes gain access to the lysosome-enriched region by microtubule-based trafficking. The mechanism by which autophagosomes move along microtubules remains incompletely understood. In this manuscript, Péter Lőrincz and colleagues investigated the mechanism driving the movement of nascent autophagosomes along microtubule towards non-centrosomal microtubule organizing center (ncMTOC) using fly fat body as a model system. The authors took an approach by examining autophagosome positioning in cells where autophagosome-lysosome fusion was inhibited by knocking down the HOPS subunit Vps16A. Despite being generated at random positions in the cytosol, autophagosomes accumulate around the nucleus when Vps16A is depleted. They then performed an RNA interference screen to identify the factors involved in autophagosome positioning. They found that the dynein-dynactin complex is required for trafficking of autophagosomes toward ncMTOC. Dynein loss leads to the peripheral relocation of autophagosomes. They further revealed that a pair of small GTPases and their effectors, Rab7-Epg5 and Rab39-ema, are required for bidirectional autophagosome transport. Knockdown of these factors in Vps16a RNAi cells causes scattering of autophagosomes throughout the cytosol.

Strengths:

The data presented in this study help us to understand the mechanism underlying the trafficking and positioning of autophagosomes.

Weaknesses:

(1) The experiments were performed in Vps16A RNAi KD cells. Vps16A knockdown blocks fusion of vesicles derived from the endolysosomal compartments such as fusion between lysosomes. The pleiotropic effect of Vps16A RNAi may complicate the interpretation.

(2) In this study, the transport of autophagosomes is investigated in fly fat cells. In fat cells, a large number of large lipid droplets accumulate and the endomembrane systems are distinct from that in other cell types. The knowledge gain from this study may not apply to other cell types.

Reviewer #3 (Public review):

Significance:

About 5% of metastatic castration-resistant prostate cancers (mCRPC) display genomic alterations in the transcriptional kinase CDK12. The mechanisms by which CDK12 alterations drive tumorigenesis in this molecularly-defined subset of mCRPC have remained elusive. In particular, some studies have suggested that CDK12 loss confers a homologous recombination deficiency (HRd) phenotype, However, clinical studies have not borne out the benefit to PARP inhibitors in patients with CDK12 alterations, despite the fact that these agents are typically active against tumors with HRd.

In this study, Frank et al. reconcile these findings by showing that: (1) tumors with biallelic CDK12 alterations do not have genomic features of HRd; (2) in vitro, HR gene downregulation occurs with acute depletion of CDK12 but is far less pronounced with chronic CDK12 loss; (3) CDK12-altered cells are uniquely sensitive to genetic or pharmacologic inhibition of CDK13.

Strengths:

Overall, this is an important study that reconciles disparate experimental and clinical observations. The genomic analyses are comprehensive and conducted with a high degree of rigor and represent an important resource to the community regarding the features of this molecular subtype of mCRPC.

Weaknesses:

(1) It is generally assumed that CDK12 alterations are inactivating, but it is noteworthy that homozygous deletions are comparatively uncommon (Figure 1a). Instead many tumors show missense mutations on either one or both alleles, and many of these mutations are outside of the kinase domain (Figure 1b). It remains possible that the CDK12 alterations that occur in some tumors may retain residual CDK12 function, or may confer some other neomorphic function, and therefore may not be accurately modeled by CDK12 knockout or knockdown in vitro. This would also reconcile the observation that knockout of CDK12 is cell-essential while the human genetic data suggest that CDK12 functions as a tumor suppressor gene.

(2) It is not entirely clear whether CDK12 altered tumors may require a co-occurring mutation to prevent loss of fitness, either in vitro or in vivo (e.g. perhaps one or more of the alterations that occur as a result of the TDP may mitigate against the essentiality of CDK12 loss).

Reviewer #3 (Public review):

Summary:

Sethi and Zou present a new neural network to study the importance of epistatic interactions in pairs and groups of amino acids to the function of proteins. Their new model is validated on a small simulated data set and then applied to 10 empirical data sets. Results show that epistatic interactions in groups of amino acids can be important to predict the function of a protein, especially for sequences that are not very similar to the training data.

Strengths:

The manuscript relies on a novel neural network architecture that makes it easy to study specifically the contribution of interactions between 2, 3, 4, or more amino acids. The study of 10 different protein families shows that there is variation among protein families.

Weaknesses:

The manuscript is good overall, but could have gone a bit deeper by comparing the new architecture to standard transformers, and by investigating whether differences between protein families explain some of the differences in the importance of interactions between amino acids. Finally, the GitHub repository needs some more information to be usable.

Reviewer #3 (Public review):

In this manuscript, the authors propose a product-dependent negative-feedback mechanism of human glutamine synthetase, whereby the product glutamine facilitates filament formation, leading to reduced catalytic specificity for ammonia. Using time-resolved cryo-EM, the authors demonstrate filament formation under product-rich conditions. Multiple high-quality structures, including decameric and di-decameric assemblies, were resolved under different biochemical states and combined with MD simulations, revealing that the conformational space of the active site loop is critical for the GS catalysis. The study also includes extensive steady-state kinetic assays, supporting the view that glutamine regulates GS assembly and its catalytic activity. Overall, this is a detailed and comprehensive study. However, I would advise that a few points be addressed and clarified.

(1) In Figure 2D and Supplementary Figure 7, the extra density observed between the two decamers does not appear to have the defining features of a glutamine. A less defined density may be expected given the nature of the complex, but even though mutagenesis assays were performed to support this assignment, none of these results constitutes direct and conclusive evidence for glutamine binding at this site. I would thus suggest showing the density maps at multiple contour thresholds to allow readers to also better evaluate the various small molecules under turnover conditions that cannot be well fitted based on this density map, helping to provide a more balanced interpretation of the results.

(2) On the same point regarding the density for the enzyme under turnover conditions, more details should be provided about the symmetry expansion and classification performed, and also show the approximate ratio of reconstructions that include this density. Did you try symmetry expansion followed by focused classification, especially on the interface region?

(3) The interface between the two decamers of the model needs to be double-checked and reassigned, especially for the residues surrounding the fitted glutamine. For example, the side chain of the Lys residue shown in the attached figure is most likely modeled incorrectly.

Reviewer #3 (Public review):

Summary:

Using a specparam (1/f) analysis of task-evoked activity, the authors propose that "substantial changes traditionally attributed to theta oscillations in working memory tasks are, in fact, due to shifts in the spectral slope of aperiodic activity." This is a very bold and ambitious statement, and the field of event-related EEG would benefit from more critical assessments of the role of aperiodic changes during task events. Unfortunately, the data shown here does not support the main conclusion advanced by the authors.

Strengths:

The field of event-related EEG would benefit from more critical assessments of the role of aperiodic changes during task events. The authors perform a number of additional control analyses, including different types of baseline correction, ERP subtraction, as well as replication of the experiment with two additional datasets.

Comments on previous revisions:

The authors have completed a substantial revision based on the comments from all of the reviewers. Overall, the major claims of the initial report have been profoundly tempered.

[Editors' note: We determined that this revised version appropriately tempers some of the prior claims and addresses the concerns raised by the reviewers through two rounds of review.]

Reviewer #3 (Public review):

Summary:

The authors aimed to test whether hypoxia disrupts the migration of human cortical interneurons, a process long suspected to underlie brain injury in preterm infants but previously inaccessible for direct study. Using human forebrain assembloids and ex vivo developing brain tissue, they visualized and quantified interneuron migration under hypoxic conditions, identified molecular components of the response, and explored the effect of pharmacological intervention (specifically ADM) on restoring the migration deficits.

Strengths:

The major strength of this study lies in its use of human forebrain assembloids and ex vivo prenatal brain tissue, which provide a direct system to study interneuron migration under hypoxic conditions. The authors combine multiple approaches: long-term live imaging to directly visualize interneuron migration, bulk and single-cell transcriptomics to identify hypoxia-induced molecular responses, pharmacological rescue experiments with ADM to establish therapeutic potential, and mechanistic assays implicating the cAMP/PKA/pCREB pathway and GABA receptor expression in mediating the effect. Together, this rigorous and multifaceted strategy convincingly demonstrates that hypoxia disrupts interneuron migration and that ADM can restore this defect through defined molecular mechanisms.

Overall, the authors achieve their stated aims, and the results strongly support their conclusions. The work has a significant impact by providing the first direct evidence of hypoxia-induced interneuron migration deficits in the human context, while also nominating a candidate therapeutic avenue. Beyond the specific findings, the methodological platform - particularly the combination of assembloids and live imaging - will be broadly useful to the community for probing neurodevelopmental processes in health and disease.

Weaknesses:

The main weakness of the study lies in the extent to which forebrain assembloids recapitulate in vivo conditions, as the migration of interneurons from hSO to hCO does not fully reflect the native environment or migratory context of these cells. Nevertheless, this limitation is tempered by the fact that the work provides the first direct observation of human interneuron migration under hypoxia, representing a major advance for the field. In addition, while the transcriptomic analyses are valuable and highlight promising candidates, more in-depth exploration will be needed to fully elucidate the molecular mechanisms governing neuronal migration and maturation under hypoxic conditions.

Reviewer #3 (Public review):

Summary

This manuscript, from the developers of the novel DREADD-selective agonist DCZ (Nagai et al., 2020), utilizes a unique dataset where multiple PET scans in a large number of monkeys, including baseline scans before AAV injection, 30-120 days post-injection, and then periodically over the course of the prolonged experiments, were performed to access short- and long-term dynamics of DREADD expression in vivo, and to associate DREADD expression with the efficacy of manipulating the neuronal activity or behavior. The goal was to provide critical insights into practicality and design of multi-year studies using chemogenetics, and to elucidate factors affecting expression stability.

Strengths are systematic quantitative assessment of the effects of both excitatory and inhibitory DREADDs, quantification of both the short-term and longer-term dynamics, a wide range of functional assessment approaches (behavior, electrophysiology, imaging), and assessment of factors affecting DREADD expression levels, such as serotype, promoter, titer (concentration), tag, and DREADD type.

These finding will undoubtedly have a very significant impact on the rapidly growing, but still highly challenging field of primate chemogenetic manipulations. As such, the work represents an invaluable resource for the community.

Reviewer #3 (Public review):

Summary:

This is an exciting, comprehensive paper that demonstrates the role of GATA4 on OA-like changes in chondrocytes. The authors present elegant reverse translational experiments that justify this mechanism and demonstrate the sufficiency of GATA4 in a mouse model of osteoarthritis (DMM), where GATA4 drove cartilage degeneration and pain in a manner that was significantly worse than DMM alone. This could pave the way for new therapies for OA that account for both structural changes and pain.

Strengths:

(1) GATA4 was identified from human chondrocytes.

(2) IHC and sequencing confirmed GATA4 presence.

(3) Activation of SMADs is clearly shown in vitro with GATA4 overexpression.

(4) The role of GATA4 was functionally assessed in vivo using the mouse DMM model, where the authors uncovered that GATA4 worsens OA structure and hyperalgesia in male mice.

(5) It is interesting that GATA4 is largely known to be found in cardiac cells and to have a role in cardiac repair, metabolism, and inflammation, among other things listed by the authors in the discussion (in liver, lung, pancreas). What could this new knowledge of GATA4 mean for OA as a potentially systemically mediated disease, where cardiac disease and metabolic syndrome are often co-morbid?

Weaknesses:

I do not have further comments. Thank you for addressing the previously mentioned concerns.

Reviewer #3 (Public review):

The manuscript by Rios-Jimenez developed a software tool, BEHAV3D Tumor Profiler, to analyze 3D intravital imaging data and identify distinctive tumor cell migratory phenotypes based on the quantified 3D image data. Moreover, the heterogeneity module in this software tool can correlate the different cell migration phenotypes with variable features of the tumor microenvironment. Overall, this is a useful tool for intravital imaging data analysis and its open-source nature makes it accessible to all interested users.

Strengths:

An open-source software tool that can quantify cell migratory dynamics from intravital imaging data and identify distinctive migratory phenotypes that correlate with variable features of the tumor microenvironment.

Weaknesses:

Motility is the main tumor cell feature analyzed in the study together with some other tumor-intrinsic features, such as morphology. However, these features are insufficient to characterize and identify the heterogeneity of the tumor cell population that impacts their behaviors in the complex tumor microenvironment (TME). For instance, there are important non-tumor cell types in the TME, and the interaction dynamics of tumor cells with other cell types, e.g., fibroblasts and distinct immune cells, play a crucial role in regulating tumor behaviors. BEHAV3D-TP focuses on analysis of tumor-alone features, and cannot be applied to analyze important cell-cell interaction dynamics in 3D.

Reviewer #3 (Public review):

Summary:

This manuscript by Duan and Song interrogates the gating mechanisms and specifically force transmission in mechanosensitive NOMPC channels using steered molecular dynamics simulations. They propose that the ankyrin spring can transmit force to the gate through torsional forces adding molecular detail to the force transduction pathways in this channel.

Strengths:

Detailed, rigorous simulations coupled with a novel model for force transduction.

Weaknesses:

Experimental validation of reduced mechanosensitivity through mutagenesis of proposed ankyrin/TRP domain coupling interactions would greatly enhance the manuscript.

Reviewer #3 (Public review):

Summary:

In the submitted manuscript, the authors investigate the role of Synaptotagmins (Syt1) and (Syt7) in MR1 presentation of MtB.

Strengths:

In the first series of experiments, the authors determined that knocking down Syt1 and Sy7 in antigen-presenting cells decreases IFN-γ production following cellular infection with Mtb. These experiments are well performed and controlled.

Weaknesses:

Next, they aim to mechanistically investigate how Syt1 and Syt7 affect MtB presentation. In particular, they focus on MR1, a non-classical MHC-I molecule known to present endogenous and exogenous metabolites, including MtB metabolites.

Results from these next series of experiments are less clear. Firstly, they show that knocking down Syt1 and Sy7 does not change MtB phagocytosis as well as MR1 ER-plasma membrane translocation. Based on this, they suggest that Syt1 and Syt7 may affect MR1 trafficking in endosomal compartments. However, neither subcellular compartment analysis nor flow organelleometry clearly establishes the role of Syt1 and Syt7 in MtB trafficking.

Altogether, the notion that Synaptotagmins facilitate MR1 interaction with Mtb-containing compartments and its vesicular transport was already known. As such, the manuscript should add additional insight on where/how the interaction occurs. The reviewer is left with the notion that Syt1 and Sy7 may affect MR1 presentation, facilitating the trafficking of MR1 vesicles from endosomal compartments to either the cell surface or other endosomal compartments. The analysis is observational and additional data or discussion could address what the insight gained beyond what is already known from the literature.

Reviewer #3 (Public review):

Summary:

Thapliyal and Glauser show that hunger alters how C. elegans respond to noxious thermal stimuli. Using targeted neural ablation, mutant analysis, and live-cell functional imaging the authors demonstrate that hunger changes the properties of AWC sensory neurons, which sense noxious heat. The authors further show that effects of hunger on nociception require ASI neurons, which are known to respond to hunger and mediate effects of food deprivation on behavior. Finally, the study uses mutant analysis to implicate glutamate and specific neuropeptides in thermal nociception and in modulation of nociceptors by hunger-responsive neurons.

Strengths:

The study clearly shows a strong effect of hunger on nociception and documents a striking effect of hunger on the intrinsic properties of AWC sensory neurons, which respond to noxious heat. The study also clearly and compellingly demonstrates that ablation of hunger-responsive ASI neurons blocks effects of hunger on nociceptive AWCs. These data, which constitute the kernel of the manuscript, are striking and exciting.

Weaknesses:

The study has some weaknesses that the authors should address.

(1) Ablation of AWC neurons alters the basal sensitivity to noxious heat stimuli. This should be clearly noted in the description of the result and warrants some discussion.

(2) Throughout the study it seems that data are replotted in multiple figure panels. The authors should clearly indicate in figure legends when this occurs. Also, the authors should ensure that statistical tests requiring multiple comparisons are correctly implemented and reflect the number of times experimental data are compared to a single set of control data.

(3) How ASIs modulate AWCs remains unclear. The authors find that loss of INS-6, an insulin-like peptide provided by ASIs, partially recapitulates the effect of ASI ablation. This is observation is not further developed and instead the authors characterize other secreted factors that seem to mediate sensitization of animals to noxious heat stimuli. While it is interesting that there are multiple opposing inputs into the nociceptor circuit, the essential connection between ASIs and AWCs that underlies the foundational observations in figures 1 and 2 is not sufficiently characterized.

(4) The assertion that 'starvation reshapes AWC responses from deterministic to stochastic' is not clearly supported by the data. AWC neurons seem capable of showing different responses to thermal stimuli, and the probabilities associated with these responses change after fasting. The different kinds of responses are seen under basal and fasted conditions.

Reviewer #3 (Public review):

Summary:

In this paper, the authors developed a simple algorithm to analyse live imaging transcription data (MS2) and infer various kinetic parameters. They then applied it to analyse data from previous publications on Drosophila that measured the dynamics of reporter genes driven by various enhancers alone (sna, Kr, rho), or in an endogenous context (eve).

The authors find that the main correlate with mean gene expression levels is the activity time, that is, the time during which the gene is bursting. They also find a correlation with the variation of the off time.

Strengths:

(1) The findings are very clearly presented.

(2) The simplicity of the algorithm is nice, and the comparative analysis among the various enhancers can be helpful for the field.

Weaknesses:

(1) The algorithm is not benchmarked against previously used algorithms in the field to infer ON and OFF times, for example, those based on Hidden Markov models. A comparison would help strengthen the support for this algorithm (if it really works well) or show at which point one must be careful when interpreting this data.

(2) More broadly, the novelty of the findings and how those fit within the knowledge of the field is not super clear. A better account of previous findings that have already quantified ON, OFF times and so on, and how the current findings fit within those, would help better appreciate the significance of the work.

Reviewer #3 (Public review):

Summary:

This manuscript by Mukherjee and colleagues extended earlier studies on the coordination of the SidC and SidE effector families on the generation of a unique ubiquitin layer on the surface of the vacuoles containing the bacterial pathogen Legionella pneumophila (LCV).

Strengths:

The main strength of the manuscript is the identification of the small GTPase Rab5 as a major "carrier" of these differently modified ubiquitin and ubiquitin chains, which was nicely quantified.

Weaknesses:

(1) The results are mostly descriptive, based on mechanistic studies from earlier works.

(2) The majority of the work was dedicated to the characterization of the unique ubiquitin layer on the LCV. One important question was ignored: what is the role of Rab5 in this process? Is the GTPase activity of Rab5 required for its ubiquitination by SidC and SidE? The authors should create a Rab5 KO cell line, complement the line with different mutants of Rab5, and examine their ubiquitination and association with the LCV.

(3) The finding that Rab5 is associated with the LCV supports the notion that the LCV has characteristics of endo- or/late endosomes. The positioning of the LCV in the endocytic pathway should be discussed in the context of earlier studies (e.g.,PMID: 38739652; PMID: 11067875; PMID: 11067875).

Reviewer #3 (Public review):

Summary:

This is a very nice and interesting paper to read about motif conservation in protein sequences and mainly in IDRs regions using the ESM2 language model. The topic of the paper is timely, with strong biological significance. The paper can be of great interest to the scientific community in the field of protein phase transitions and future applications using the ESM models. The ability of ESM2 to identify conserved motifs is crucial for disease prediction, as these regions may serve as potential drug targets. Therefore, I find these findings highly significant, and the authors strongly support them throughout the paper. The work motivates the scientific community towards further motif exploration related to diseases.

Strengths:

(1) Revealing conserved regions in IDRs by the ESM-2 language model.

(2) Identification of functionally significant residues within protein sequences, especially in IDRs.

(3) Findings supported by useful analyses.

Weaknesses:

(1) Lack of examples demonstrating the potential biological functions of these conserved regions

(2) Very limited discussion of potential future work and of limitations.

Reviewer #3 (Public review):

Summary & Strengths:

This review by Yu-Tung Li sheds new light on the processes involved in leukocyte extravasation, with a focus on the interaction between leukocytes and the extracellular matrix. In doing so, it presents a fresh perspective on the topic of leukocyte extravasation, which has been extensively covered in numerous excellent reviews. Notably, the role of the extracellular matrix in leukocyte extravasation has received relatively little attention until recently, with a few exceptions, such as a study focusing on the central nervous system (J Inflamm 21, 53 (2024) doi.org/10.1186/s12950-024-00426-6) and another on transmigration hotspots (J Cell Sci (2025) 138 (11): jcs263862 doi.org/10.1242/jcs.263862). This review synthesizes the substantial knowledge accumulated over the past two decades in a novel and compelling manner.

The author dedicates two sections to discussing the relevant barriers, namely, endothelial cell-cell junctions and the basement membrane. The following three paragraphs address how leukocytes interact with and transmigrate through endothelial junctions, the mechanisms supporting extravasation, and how minimal plasma leakage is achieved during this process. The subsequent question of whether the extravasation process affects leukocyte differentiation and properties is original and thought-provoking, having received limited consideration thus far. The consequences of the interaction between leukocytes and the extracellular matrix, particularly regarding efferocytosis, macrophage polarization, and the outcome of inflammation, are explored in the subsequent three chapters. The review concludes by examining tissue-specific states of macrophage identity.

Weaknesses:

Firstly, the first ten sections provide a comprehensive overview of the topic, presenting logical and well-formulated arguments that are easily accessible to a general audience. In stark contrast, the final section (Chapter 11) fails to connect coherently with the preceding review and is nearly incomprehensible without prior knowledge of the author's recent publication in Cell. Mol. Life Sci. CMLS 772 82, 14 (2024). This chapter requires significantly more background information for the general reader, including an introduction to the Macrophage Identity Kinetics Archive (MIKA), which is not even introduced in this review, its basis (meta-analysis of published scRNA-seq data), its significance (identification of major populations), and the reasons behind the revision of the proposed macrophage states and their further development. Secondly, while the attempt to integrate a vast amount of information into fewer figures is commendable, it results in figures that resemble a complex puzzle. The author may consider increasing the number of figures and providing additional, larger "zoom-in" panels, particularly for the topics of clot formation at transmigration hotspots and the interaction between ECM/ECM fragments and integrins. Specifically, the color coding (purple for leukocyte α6-integrins, blue for interacting laminins, also blue for EC α6 integrins, and red for interacting 5-1-1 laminins) is confusing, and the structures are small and difficult to recognize.

Reviewer #3 (Public Review):

Summary:

In this article, Barnett examines a pressing question regarding citing behavior of authors during the peer review process. In particular, the author studies the interaction between reviewers and authors, focusing on the odds of acceptance, and how this may be affected by whether or not the authors cited the reviewers' prior work, whether the reviewer requested such citations be added, and whether the authors complied/how that affected the reviewer decision-making.

Strengths:

The author uses a clever analytical design, examining four journals that use the same open peer review system, in which the identities of the authors and reviewers are both available and linkable to structured data. Categorical information about the approval is also available as structured data. This design allows a large scale investigation of this question.

Weaknesses:

My concerns pertain to the interpretability of the data as presented and the overly terse writing style.

Regarding interpretability, it is often unclear what subset of the data are being used both in the prose and figures. For example, the descriptive statistics show many more Version 1 articles than Version 2+. How are the data subset among the different possible methods?

Likewise, the methods indicate that a matching procedure was used comparing two reviewers for the same manuscript in order to control for potential confounds. However, the number of reviews is less than double the number of Version 1 articles, making it unclear which data were used in the final analysis. The methods also state that data were stratified by version. This raises a question about which articles/reviews were included in each of the analyses. I suggest spending more space describing how the data are subset and stratified. This should include any conditional subsetting as in the analysis on the 441 reviews where the reviewer was not cited in Version 1 but requested a citation for Version 2. Each of the figures and tables, as well as statistics provided in the text should provide this information, which would make this paper much more accessible to the reader. [Note from editor: Please see "Editorial feedback" for more on this]

Finally, I would caution against imputing motivations to the reviewers, despite the important findings provided here. This is because the data as presented suggest a more nuanced interpretation is warranted. First, the author observes similar patterns of accept/reject decisions whether the suggested citation is a citation to the reviewer or not (Figs 3 and 4). Second, much of the observed reviewer behavior disappears or has much lower effect sizes depending on whether "Accept with Reservations" is considered an Accept or a Reject. This is acknowledged in the results text, but largely left out of the discussion. The conditional analysis on the 441 reviews mentioned above does support a more cautious version of the conclusion drawn here, especially when considered alongside the specific comments left by reviewers that were mentioned in the results and information in Table S.3. However, I recommend toning the language down to match the strength of the data.

Reviewer #5 (Public review):

Summary:

In the research article, "Functional genomics reveals strain-specific genetic requirements conferring hypoxic growth in Mycobacterium intracellulare" Tateshi et al focussed their research on pulmonary disease caused by Mycobacterium avium-intracellulare complex which has recently become a major health concern. The authors were interested in identifying the genetic requirements necessary for growth/survival within host and used hypoxia and biofilm conditions that partly replicate some of the stress conditions experienced by bacteria in vivo. An important finding of this analysis was the observation that genes involved in gluconeogenesis, type VII secretion system and cysteine desulphurase were crucial for the clinical isolates during standard culture while the same were necessary during hypoxia in the ATCC type strain.

Strength of the study:

Transposon mutagenesis has been a powerful genetic tool to identify essential genes/pathways necessary for bacteria under various in vitro stress conditions and for in vivo survival. The authors extended the TnSeq methodology not only to the ATCC strain but also to the recently clinical isolates to identify the differences between the two categories of bacterial strains. Using this approach they dissected the similarities and differences in the genetic requirement for bacterial survival between ATCC type strains and clinical isolates. They observed that the clinical strains performed much better in terms of growth during hypoxia than the type strain. These in vitro findings were further extended to mouse infection models and similar outcomes were observed in vivo further emphasising the relevance of hypoxic adaptation crucial for the clinical strains which could be explored as potential drug targets.

Weakness:

The authors have performed extensive TnSeq analysis but fail to present the data coherently. The data could have been well presented both in Figures and text. In my view this is one of the major weakness of the study.

Reviewer #3 (Public review):

Summary

This study aimed to investigate whether the differences observed in the organization of visual brain networks between blind and sighted adults result from a reorganization of an early functional architecture due to blindness, or whether the early architecture is immature at birth and requires visual experience to develop functional connections. This question was investigated through the comparison of 3 groups of subjects with resting-state functional MRI (rs-fMRI). Based on convincing analyses, the study suggests that: 1) secondary visual cortices showed higher connectivity to prefrontal cortical regions (PFC) than to non-visual sensory areas (S1/M1 and A1) in infants like in blind adults, in contrast to sighted adults; 2) the V1 connectivity pattern of infants lies between that of sighted adults (showing stronger functional connectivity with non-visual sensory areas than with PFC) and that of blind adults (showing stronger functional connectivity with PFC than with non-visual sensory areas); 3) the laterality of the connectivity patterns of infants resembled those of sighted adults more than those of blind adults, but infants showed a less differentiated fronto-occipital connectivity pattern than adults.

Strengths

The question investigated in this article is important for understanding the mechanisms of plasticity during typical and impaired development, and the approach considered, which compares different groups of subjects including, neonates/infants and blind adults, is highly original.

Overall, the presented analyses are solid and well detailed, and the results and discussion are convincing.

Weaknesses

While it is informative to compare the "initial" state (close to birth) and the "final" states in blind and sighted adults to study the impact of post-natal and visual experience, this study does not analyze the chronology of this development and when the specialization of functional connections is completed. This would require investigating the evolution of functional connectivity of the visual system as a function of visual experience and thus as a function of age, at least during toddlerhood given the early and intense maturation of the visual system after birth. This could be achieved by analyzing different developmental periods using open databases such as the Baby Connectome Project.

The rationale for grouping full-term neonates and preterm infants (scanned at term-equivalent age) is not understandable when seeking to perform comparisons with adults. Even if the study results do not show differences between full-terms and preterms in terms of functional connectivity differences between regions and of connectivity patterns, preterms group had different neurodevelopment and post-natal (including visual) experiences (even a few weeks might have an impact). And actually they show reduced connectivity strength systematically for all regions compared with full-terms (Sup Fig 7). Considering a more homogeneous group of neonates would have strengthen the study design.

The rationale for presenting results on the connectivity of secondary visual cortices before the one of primary cortices (V1) could be clarified.

The authors acknowledge the methodological difficulties for defining regions of interest (ROIs) in infants in a similar way as adults. Since the brain development is not homogeneous and synchronous across brain regions (in particular with the frontal and parietal lobes showing a delayed growth), this poses major problems for registration. This raises the question of whether the study findings could be biased by differences in ROI positioning across groups.

Reviewer #3 (Public review):

Summary:

The authors generated knockout mice for Atad2, a conserved bromodomain-containing factor expressed during spermatogenesis. In Atad2 KO mice, HIRA, a chaperone for histone variant H3.3, was upregulated in round spermatids, accompanied by an apparent increase in H3.3 levels. Furthermore, the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis were partially disrupted in the absence of ATAD2, possibly due to delayed histone removal. Despite these abnormalities, Atad2 KO male mice were able to produce offspring normally.

Strengths:

The manuscript addresses the biological role of ATAD2 in spermatogenesis using a knockout mouse model, providing a valuable in vivo framework to study chromatin regulation during male germ cell development. The observed redistribution of H3.3 in round spermatids is clearly presented and suggests a previously unappreciated role of ATAD2 in histone variant dynamics. The authors also document defects in the sequential incorporation and removal of TH2B and PRM1 during spermiogenesis, providing phenotypic insight into chromatin transitions in late spermatogenic stages. Overall, the study presents a solid foundation for further mechanistic investigation into ATAD2 function.

Weaknesses:

While the manuscript reports the gross phenotype of Atad2 KO mice, the findings remain largely superficial and do not convincingly demonstrate how ATAD2 deficiency affects chromatin dynamics. Moreover, the phenotype appears too mild to elucidate the functional significance of ATAD2 during spermatogenesis.

(1) Figures 4-5: The analyses of differential gene expression and chromatin organization should be more comprehensive. First, Venn diagrams comparing the sets of significantly differentially expressed genes between this study and previous work should be shown for each developmental stage. Second, given the established role of H3.3 in MSCI, the effect of Atad2 knockout on sex chromosome gene expression should be analyzed. Third, integrated analysis of RNA-seq and ATAC-seq data is needed to evaluate how ATAD2 loss affects gene expression. Finally, H3.3 ChIP-seq should be performed to directly assess changes in H3.3 distribution following Atad2 knockout.

(2) Figure 3: The altered distribution of H3.3 is compelling. This raises the possibility that histone marks associated with H3.3 may also be affected, although this has not been investigated. It would therefore be important to examine the distribution of histone modifications typically associated with H3.3. If any alterations are observed, ChIP-seq analyses should be performed to explore them further.

(3) Figure 7: While the authors suggest that pre-PRM2 processing is impaired in Atad2 KO, no direct evidence is provided. It is essential to conduct acid-urea polyacrylamide gel electrophoresis (AU-PAGE) followed by western blotting, or a comparable experiment, to substantiate this claim.

(4) HIRA and ATAD2: Does the upregulation of HIRA fully account for the phenotypes observed in Atad2 KO? If so, would overexpression of HIRA alone be sufficient to phenocopy the Atad2 KO phenotype? Alternatively, would partial reduction of HIRA (e.g., through heterozygous deletion) in the Atad2 KO background be sufficient to rescue the phenotype?

(5) The mechanism by which ATAD2 regulates HIRA turnover on chromatin and the deposition of H3.3 remains unclear from the manuscript and warrants further investigation.

Reviewer #3 (Public review):

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

The more concrete contributions, however, are not as strong. In particular, evidence for the paper's most striking claims is weak. Quoting the abstract, these claims are (1) "the elasticity of control [is] a distinct cognitive construct guiding adaptive behavior" and (2) "overestimation of elasticity is associated with elevated psychopathology involving an impaired sense of control."

Main issues

I'll highlight the key points.

- The task cannot distinguish elasticity inference from general learning processes

- Participants were explicitly instructed about elasticity, with labeled examples

- The psychopathology claims rely on an invalid interpretation of CCA, and are contradicted by simple correlations (elasticity bias and the sense of agency scale is r=0.03)

Distinct construct

Starting with claim 1, there are three subclaims here. (1A) People's behavior is sensitive to differences in elasticity; (1B) there are mental processes specific to elasticity inference, i.e., not falling out of general learning mechanisms; and, implicitly, (1C) people infer elasticity naturally as they go about their daily lives. The results clearly support 1A. However, 1B and 1C are not well supported.

(1B) The data cannot support the "distinct cognitive construct" claim because the task is too simple to dissociate elasticity inference from more general learning processes (also raised by Reviewer 1). The key behavioral signature for elasticity inference (vs. generic controllability inference) is the transfer across ticket numbers, illustrated in Fig 4. However, this pattern is also predicted by a standard Bayesian learner equipped with an intuitive causal model of the task. Each ticket gives you another chance to board and the agent infers the probability that each attempt succeeds. Crucially, this logic is not at all specific to elasticity or even control. An identical model could be applied to inferring the bias of a coin from observations of whether any of N tosses were heads-a task that is formally identical to this one (at least, the intuitive model of the task; see first minor comment).

Importantly, this point cannot be addressed by showing that the author's model fits data better than this or any other specific Bayesian model. It is not a question of whether one particular updating rule explains data better than another. Rather, it is a question of whether the task can distinguish between biases in *elasticity* inference versus biases in probabilistic inference more generally. The present task cannot make this distinction because it does not make separate measurements of the two types of inference. To provide compelling evidence that elasticity inference is a "distinct cognitive construct", one would need to show that there are reliable individual differences in elasticity inference that generalize across contexts but do not generalize to computationally similar types of probabilistic inference (e.g. the coin flipping example).

(1C) The implicit claim that people infer elasticity outside of the experimental task is undermined by the experimental design. The authors explicitly tell people about the two notions of control as part of the training phase: "To reinforce participants' understanding of how elasticity and controllability were manifested in each planet, [participants] were informed of the planet type they had visited after every 15 trips."

In the revisions, the authors seem to go back and forth on whether they are claiming that people infer elasticity without instruction (I won't quote it here). I'll just note that the examples they provide in the most recent rebuttal are all cases in which one never receives explicit labels about elasticity. If people only infer elasticity when it is explicitly labeled, I struggle to see its relevance for understanding human cognition and behavior.

Psychopathology

Finally, I turn to claim 2, that "overestimation of elasticity is associated with elevated psychopathology involving an impaired sense of control." The CCA analysis is in principle unable to support this claim. As the authors correctly note in their latest rebuttal, the CCA does show that "there is a relationship between psychopathology traits and task parameters". The lesion analysis further shows that "elasticity bias specifically contributes to this relationship" (and similarly for the Sense of Agency scale). Crucially, however, this does *not* imply that there is a relationship between those two variables. The most direct test of that relationship is the simple correlation, which the authors report only in a supplemental figure: there is no relationship (r=0.03). Although it is of course possible that there is a relationship that is obscured by confounding variables, the paper provides no evidence-statistical or otherwise-that such a relationship exists.

Minor comments

The statistical structure of the task is inconsistent with the framing. In the framing, participants can make either one or two second boarding attempts (jumps) by purchasing extra tickets. The additional attempt(s) will thus succeed with probability p for one ticket and 2p - p^2 for two tickets; the p^2 captures the fact that you only take the second attempt if you fail on the first. A consequence of this is buying more tickets has diminishing returns. In contrast, in the task, participants always jumped twice after purchasing two tickets, and the probability of success with two tickets was exactly double that with one ticket. Thus, if participants are applying an intuitive causal model to the task, the researcher could infer "biases" in elasticity inference that are probably better characterized as effective use of prior information (encoded in the causal model).

The model is heuristically defined and does not reflect Bayesian updating. For example, it over-estimates maximum control by not using losses with less than 3 tickets (intuitively, the inference here depends on what your beliefs about elasticity). Including forced three-ticket trials at the beginning of each round makes this less of an issue; but if you want to remove those trials, you might need to adjust the model. The need to introduce the modified model with kappa is likely another symptom of the heuristic nature of the model updating equations.

Reviewer #3 (Public review):

Summary:

Developing consistent and reliable biomarkers is critically important for developing new pharmacological therapies in autism spectrum disorders (ASDs). Altered sensory perception is one of the hallmarks of autism and has been recently added to DSM-5 as one of the core symptoms of autism. Touch is one of the fundamental sensory modalities, yet it is currently understudied. Furthermore, there seems to be a discrepancy between different studies from different groups focusing on tactile discrimination. It is not clear if this discrepancy can be explained by different experimental setups, inconsistent terminology, or the heterogeneity of sensory processing alterations in ASDs. The authors aim to investigate the interplay between tactile discrimination and cognitive processes during perceptual decisions. They have developed a forepaw-based 2-alternative choice task for mice and investigated tactile perception and learning in Fmr1-/y mice

Strengths:

There are several strengths of this task: translational relevance to human psychophysical protocols, including controlled vibrotactile stimulation. In addition to the experimental setup, there are also several interesting findings: Fmr1-/y mice demonstrated choice consistency bias, which may result in impaired perceptual learning, and enhanced tactile discrimination in low-salience conditions, as well as attentional deficits with increased cognitive load. The increase in the error rates for low salience stimuli is interesting. These observations, together with the behavioral design, may have a promising translational potential and, if confirmed in humans, may be potentially used as biomarkers in ASD.

Weaknesses:

Some weaknesses are related to the lack of the original raster plots and density plots of licks under different conditions, learning rate vs time, and evaluation of the learning rate at different stages of learning. Overall, these data would help to answer the question of whether there are differences in learning strategies or neural circuit compensation in Fmr1-/y mice. It is also not clear if reversal learning is impaired in Fmr1-/y mice.

Reviewer #3 (Public review):

Summary:

The manuscript by Shaikh and Assisi addresses a timely and important question related to the neural circuit mechanisms underlying spatial representations during navigation. Concretely, they present a model of the medial entorhinal cortex (MEC) with biophysically detailed conductance-based stellate cells that can perform path integration and reveal two potential mechanisms underlying two forms of predictive coding by grid cells in the MEC. One mechanism uses HCN channels to explain predictive coding in MEC layer II grid cells equivalent to ~5% of the diameter of a grid field, and the other uses asymmetric connections between interneurons and stellate cells, resulting in a ~25% predictive bias of layer III grid cells. The methods and model are technically sound, and the model is expected to be useful for computational neuroscientists studying the neural mechanisms of spatial navigation.

Strengths:

One strength of the model is its use of conductance-based neuron models of stellate cells and interneurons, adding important biophysical constraints and details to existing continuous attractor network models of grid cells. The model fills a gap in the literature by providing mechanisms for predictive coding constrained by biophysical properties of stellate cells and simplified network topology.

Weaknesses:

A weakness of the model is that the neural network is relatively small (five sheets with 71 × 71 neurons each), and the 2-D toroidal topology is further simplified to a 1-D ring attractor consisting of three rings with 192 neurons each. The model incorporates biophysical detail at the single-neuron level, but not at the network level. For example, it includes only stellate cells and a generic interneuron type, and does not implement data-driven connectivity patterns.

The restricted network size and the limited experimental knowledge about connectivity among stellate cells, principal cells, and different interneuron types in the MEC could be addressed in more detail. Moreover, the manuscript lacks a thorough discussion of assumptions common to most continuous attractor network (CAN) models of grid cells, such as the use of "hand-crafted" connections between direction-sensitive conjunctive grid cells and network cells to drive attractor shifts. Including such a discussion would strengthen the manuscript. This is especially relevant given the authors' explicit claim that they have revealed two mechanisms underlying the emergence of a predictive code in the MEC. In this reviewer's view, the work demonstrates a potential mechanism, but one that requires experimental verification. The significance of the model would thus be increased by providing more experimentally testable predictions of the model.

Reviewer #3 (Public review):

Summary:

This study provides the Drosophila community with a large collection of new split-Gal4 descending neuron genetic lines. They extend previous efforts to characterize and identify genetic lines for this important class of neurons by providing images of descending neurons and a metric for genetic lines based on specificity and consistency. Their discussion highlights several applications of this collection, for example, to understand the function of new descending neurons through optogenetic and/or physiological characterization. They also helpfully discuss caveats, encouraging users of this collection to validate expression patterns and to be careful when interpreting optogenetic experimental results, considering potential off-target labeling in the lines. Overall, members of the Drosophila community interested in understanding the function of descending neurons and their role in behavior will find this a helpful resource.

Strengths:

(1) The authors extend the previous genetic access of descending neurons in Drosophila to over 800 split-Gal4 lines and 190 cell types (nearly half of the known population of descending neurons). The authors update and at times correct the previous identification of descending neurons from a previous, large-scale analysis. The authors extend and, at times, correct previous efforts at characterizing these neurons.

(2) Clear images of descending neurons labeled by new genetic lines are presented in the main figure papers for reference.

(3) This study classifies lines labeling descending neurons using a quality score to indicate specificity and consistency. They provide this for the entire set of genetic lines, a valuable assessment for researchers interested in targeting these neurons for optogenetic or physiological characterization.

Weaknesses:

Although this paper represents a substantial effort and useful contribution to the Drosophila community, a few weaknesses, primarily regarding the specificity and reliability of genetic lines, remain:

(1) The authors state that optogenetic activation of DN types using the new split-GAL4 lines is expected to reliably activate the target neurons with virtually no off-target effects in the rest of the central nervous system. More data supporting this conclusion, including both qualitative and quantitative anatomical evidence, would strengthen this claim.

(2) The authors do recommend that researchers using these lines examine expression patterns themselves to evaluate line cleanliness and consistency, but some analysis by the authors would be useful, for example, providing guidelines for best practices to perform this evaluation.

(3) Changes in expression patterns after several generations are noted by the authors, weakening confidence somewhat in the long-term usefulness of this collection of genetic lines.

Reviewer #3 (Public review):

Summary:

The authors were trying to validate SARS-CoV-2 Mac1 as a drug discovery target and by extension other viral macrodomains.

Strengths:

The medicinal chemistry and structure based optimization is exemplary. Macrodomains and ADPribosyl hydrolases have the reputation for being undruggable, yet the authors managed to optimize hits from a fragment screen using structure based approaches and fragment linking to make a 20nM inhibitor as a tool compound to validate the target.<br /> In addition, the in vivo work is also a strength. The ability to reduce the viral count at a rate comparable to nirmatrelvir is impressive. Tracking the cytokine expression levels also supports much of the genetic data and mechanism of action for macrodomains.

Weaknesses:

The main compound AVI-4206, while being very potent and selective is not appreciably orally bioavailable. The fact that they have to use high doses of the compound IP to see in vivo effects may lead to questions regarding off target effects. The authors acknowledge this and point it out as a potential avenue for further optimization.

The cellular models are not as predictive of antiviral activity as one would expect. However, the authors had enough chutzpah to test the compound in vivo knowing that cellular models might not be an accurate representation of a living system with a fully functional immune system all of which is most likely needed in an antiviral response to test the importance of Mac1 as a target.

Comments on revisions:

All previous suggestions were addressed. I am satisfied with the author's modifications.

Reviewer #3 (Public review):

Summary:

Mirkovic et al explore the cause underlying development of aneuploidy during aging. This paper provides a compelling insight into the basis of chromosome missegregation in aged cells, tying this phenomenon to the established Nuclear Pore Complex architecture remodeling that occurs with aging across a large span of diverse organisms. The authors first establish that aged mother cells exhibit aberrant error correction during mitosis. As extrachromosomal rDNA circles (ERCs) are known to increase with age and lead to NPC dysfunction that can result in leakage of unspliced pre-mRNAs, Mirkovic et al search for intron-containing genes in yeast that may be underlying chromosome missegregation, identifying three genes in the aurora B-dependent error correction pathway: MCM21, NBL1, and GLC7. Interestingly, intron-less mutants in these genes suppress chromosome loss in aged cells, with a significant impact observed when all three introns were deleted (3x∆i). The 3x∆i mutant also suppresses the increased chromosome loss resulting from nuclear basket destabilization in a mlp1∆ mutant. The authors then directly test if aged cells do exhibit aberrant mRNA export, using RNA FISH to identify that old cells indeed leak intron-containing pre-mRNA into the cytoplasm, as well as a reporter assay to demonstrate translation of leaked pre-mRNA, and that this is suppressed in cells producing less ERCs. Mutants causing increased pre-mRNA leakage are sufficient to induce chromosome missegregation, which is suppressed by the 3x∆i.

Strengths:

The finding that deleting the introns of 3 genes in the Aurora B pathway can suppress age-related chromosome missegregation is highly compelling. Additionally, the rationale behind the various experiments in this paper is well-reasoned and clearly explained.

Weaknesses:

My main concerns have been thoroughly addressed by the authors.

Reviewer #3 (Public review):

Summary:

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

Strengths:

A key strength of the study is its rigorous assessment of the similarity in evolutionary trajectories between humans and macaques. This cross-species comparison is particularly compelling, as it quantitatively establishes a shared pattern of viral evolution using a sophisticated inference method. The finding that similar selective pressures operate in both species adds robustness to the study's conclusions and suggests broader biological relevance. In the revised version, the Authors included a simple but clear explanation of the statistical method for inferring the model's parameters in the main text. Moreover, I find the potential implications of the methodology absent in the original submission very interesting.

Conclusions:

Overall, the study presents a compelling analysis of HIV-1 evolution and its parallels in SHIV-infected macaques.

Reviewer #3 (Public review):

Summary:

Gazal et al present convincing evidence supporting a new model of MPS formation where a gap-and-patch MPS pattern coalesces laterally to give rise to a lattice covering the entire axon shaft.

Strengths:

(1) This is a very interesting study that supports a change in paradigm in the model of MPS lattice formation.

(2) Knowledge on MPS organization is mainly derived from studies using rat hippocampal neurons. In the current manuscript, Gazal et al use human IPS-derived motor neurons, a highly relevant neuron type, to further the current knowledge on MPS biology.

(3) The quality of the images provided, specifically of those involving super-resolution, is of a high standard. This adequately supports the conclusions of the authors.

Weaknesses:

(1) The main concern raised by the manuscript is the assumption that staudosporine-induced gap and patch formation recapitulates the physiological assembly of gaps and patches of betaII-spectrin.

(2) One technical challenge that limits a more compelling support of the new model of MPS formation is that fixed neurons are imaged, which precludes the observation of patch coalescence.

Reviewer #3 (Public review):

Summary:

Mou and Ji investigated neuro-computational mechanisms behind observational spatial learning in rats and reported several signs of functional coupling between the ACC and CA1 at the single neuron level. Using multi-site tetrode recording, they found that ACC cells encoding a path in a maze were activated while a rat observed another rat taking that path. This activation was also correlated with the activation of CA1 cells encoding the same path and facilitated their replay during sharp-wave ripples (SWRs) before the recording rat ran on the maze by itself. These activity patterns were associated with correct path choice during self-running and were absent in control conditions where the recording rat did not learn the correct choice through observations. Based on these findings, the authors argue that ACC cells capture the critical information during observation to organize hippocampal cell activity for subsequent spatial decisions.

Strengths:

The authors used multiple outcome measures to build a strong case for path-specific spike coordination between ACC and CA1 cells. The analyses were conducted carefully, and proper control measures were used to establish the statistical significance of the detected effects. The authors also demonstrated tight correlations between the spike coordination patterns and the successful use of observed information for future decisions.

Weaknesses:

(1) As evidence for the activation of path information in the ACC during observation, the authors showed positive correlations between firing rates during observation and those during self-running. This argument will be solidified if the authors use a decoding approach to demonstrate the activation of path-selective ACC ensemble activity patterns during observation. This approach will also open the door to uncovering how the activation of ACC path representation is related to the moment-to-moment position of the demonstrator rat and whether it is coupled with the timing of SWRs.

(2) The authors argued that the ACC biases the content of awake replay in CA1 during SWRs in the observation period. The reviewer wonders if a similar bias also occurs during SWRs in the self-run period (i.e., water consumption after the correct choice). This analysis will help test whether the biased replay occurs due to the need to convert observed information into future choices.

(3) Although the authors demonstrated the necessity of the ACC for the task, it remains to be determined whether firing coordination between the ACC and CA1 during observation is necessary for the correct path choice during self-runs. Some discussion on this point, along with future direction, would be beneficial for readers.

Comments on revisions:

The authors fully addressed my recommendations. I do not have any further comments.

Reviewer #3 (Public review):

Summary:

The authors present a method to address class imbalance in T cell receptor (TCR)-epitope binding datasets by generating synthetic positive binding examples using generative models, specifically BERT-based architectures and Restricted Boltzmann Machines (RBMs). They hypothesize that improving class balance can enhance model performance in predicting TCR-peptide binding.

Strengths:

(1) Interesting biological as well as technical topic.

(2) Solid technical foundations.

Weaknesses:

(1) Fundamental Biological Oversight:

While the computational strategy of augmenting positive samples via generative models is technically interesting, the manuscript falls short in addressing key biological considerations. Specifically, the authors simulate and evaluate only CDR3β-peptide binding interactions. However, antigen recognition by T cells involves both the α- and β-chains of the TCR. The omission of CDR3α undermines the biological realism and limits the generalizability of the findings.

(2) Validation of Simulated Data:

The central claim of the manuscript is that simulated positive examples improve predictive performance. However, there is no rigorous validation of the biological plausibility or realism of the generated TCR sequences. Without independent evaluation (e.g., testing whether synthetic TCR-peptide pairs are truly binding), it remains unclear whether the performance gains are biologically meaningful or merely reflect artifacts of the generation process.

(3) Risk of Bias and Overfitting:

Training and evaluating models with generated data introduces a risk of circularity and bias. The observed improvements may not reflect better generalization to real-world TCR-epitope interactions but could instead arise from overfitting to synthetic patterns. Additional testing on independent, biologically validated datasets would help clarify this point.

Reviewer #3 (Public review):

Summary:

In this manuscript, Guin et al. use a CRISPR KO screen of ~1000 candidates in two human cell lines, along with high-throughput image analysis, to demonstrate that orderly progression through mitosis shapes centromere organization. They identify ~50 genes that perturb centromere clustering when depleted in both RPE1 and HCT116 cells and validate many of these hits using RNAi. They then use auxin-mediated acute depletion of four factors (NCAPH2, KI67, SPC24, and NUF2) to demonstrate that their effects on centromere clustering require passage through mitosis. They further suggest that the lack of these factors during mitosis leads to the disorganization of centromeres on the mitotic spindle, and these effects persist in the subsequent interphase. Overall, the manuscript is clear, well-written, the experiments performed are appropriate, and the data are interpreted accurately. In my opinion, the main strength of this manuscript is the discovery of several hits associated with altered centromere organization. These hits will serve as a solid foundation for future work investigating genome organization in human cells. On the other hand, how the changes in centromere organization relate to other aspects of interphase genome architecture (A/B compartments, chromosome territories, etc) remains unclear and represents the main shortcoming of this manuscript.

Comments:

(1) Given the authors' suggestion that disorderly mitotic progression underlies the changes in centromere clustering in the subsequent interphase, I think it would be beneficial to showcase examples of disorderly mitosis in the AID samples and perhaps even quantify the misalignment on the metaphase plate.

(2) I don't quite agree with the description that centromeres cluster into chromocenters (p4 para 2, p17 para 1, and other instances in the manuscript). To the best of my knowledge, chromocenters primarily consist of clustered pericentromeric heterochromatin, while the centromeres are studded on the chromocenter surface. This has been beautifully demonstrated in mouse cells (Guenatri et al., JCB, 2004), but it is true in other systems like flies and plants as well.

Reviewer #3 (Public review):

Summary:

The authors present a technically impressive dataset showing that repeated excitation or restraint stress internalises somatodendritic α2A adrenergic autoreceptors (α2A ARs) in locus coeruleus (LC) neurons. Loss of these receptors weakens GIRK-dependent autoinhibition, raises neuronal excitability, and is accompanied by higher MAO A, DOPEGAL, AEP, and tau N368 levels. The work combines rigorous whole-cell electrophysiology with barbadin-based trafficking assays, qPCR, Western blotting, and immunohistochemistry. The final schematic is appealing and, in principle, could explain early LC hyperactivity followed by degeneration in ageing and Alzheimer's disease.

Strengths:

- Multi-level approach - The study integrates electrophysiology, pharmacology, mRNA quantification, and protein-level analysis.

-Use of barbadin to block β-arrestin/AP-2-dependent internalisation is both technically precise and mechanistically informative

-Well-executed electrophysiology

-translation relevance

-converges to a model that peers discussed (scientists can only discuss models - not data!)

Weaknesses:

Nevertheless, the manuscript currently reads as a sequence of discrete experiments rather than a single causal chain.

Reviewer #3 (Public review):

The manuscript investigated the kinetics of molecule transport across interfaces in phase-separated mixtures. Through the development of a theoretical approach for a binary mixture in a sharp interface limit, the authors found that interface resistance leads to a slowdown in interfacial movement. Subsequently, they extended this approach to multiple molecular species (incorporating both labeled and unlabeled molecules) and continuous transport models. Finally, they proposed experimental settings in vitro and commented on the necessary optical resolution to detect signatures of interfacial kinetics associated with resistance.

The investigation of transport kinetics across biomolecular condensate interfaces holds significant relevance for understanding cellular function and dysfunction mechanisms; thus, the topic is important and timely. However, the current manuscript presentation requires improvement. Firstly, the inclusion of numerous equations in the main text substantially compromises readability, and relocation of a part of the formulae and derivations to the Appendix would be more appropriate. Secondly, the manuscript would benefit from more comprehensive comparisons with existing theoretical studies on molecular transport kinetics. The text should also be written to be more approachable for a general readership. Modifications and sufficient responses to the specific points outlined below are recommended.

(1) The authors introduced a theoretical framework to study the kinetics of molecules across an interface between two coexisting liquid phases and found that interface resistance leads to a slowdown in interfacial movement in a binary mixture and a decelerated molecule exchange between labeled and unlabeled molecules across the phase boundary. However, these findings appear rather expected. The work would be strengthened by a more thorough discussion of the kinetics of molecule transport across interfaces (such as the physical origin of the interface resistance and its specific impact on transport kinetics).

(2) The formulae in the manuscript should be checked and corrected. Notably, Equation 10 contains "\phi_2\ln\phi_2" while Eq. 11b shows "n^{-1}\ln\phi_2", suggesting a missing factor of "n^{-1}". Similarly, Equation 18 obtained from Equation 11: the logarithmic term in Eq.11a is "n^{-1}\ln phi_1-\ln(1-\phi)" but the pre-exponential factor in Equation 18a is just "\phi_1/(1-\phi*)", where is "n^{-1}"? Additionally, there is a unit inconsistency in Equation 36, where the unit of \rho (s/m) does not match that of the right-hand side expression (s/m^2).

(3) The authors stated that the numerical solutions are obtained using a custom finite difference scheme implemented in MATLAB in the Appendix. The description of numerical methods is insufficiently detailed and needs to be expanded, including specific equations or models used to obtain specific figures, the introduction of initial and boundary conditions, the choices of parameters and their reasons in terms of the biology.

(4) The authors claimed that their framework naturally extends to multiple molecular species, but only showed the situation of labeled and unlabeled molecules across a phase boundary. How about three or more molecular species? Does this framework still work? This should be added to strengthen the manuscript and confirm the framework's general applicability.

Reviewer #3 (Public review):

Summary:

In this delightful study, the authors use local indentation of the cell surface combined with out-of-focus microscopy to measure the rates of pressure spread in the cell and to argue that the results can be explained with the poroelastic model. Osmotic shock that decreases cytoskeletal mesh size supports this notion. Experiments with water injection and water suction further support it, and also, together with a mechanical model and elegant measurements of decreasing fluorescence in the cell 'flashed' by external flow, demonstrate that the membrane is permeable, and that steady flow and pressure gradient can exist in a cell with water source/sink in different locations. Use of blebs as indicators of the internal pressure further supports the notion of differential cytoplasmic pressure.

Strengths:

The study is very imaginative, interesting, novel and important.

Weaknesses: I have two broad critical comments:

(1) I sense that the authors are correct that the best explanation of their results is the passive poroelastic model. Yet, to be thorough, they have to try to explain the experiments with other models and show why their explanation is parsimonious. For example, one potential explanation could be some mechanosensitive mechanism that does not involve cytoplasmic flow; another could be viscoelastic cytoskeletal mesh, again not involving poroelasticity. I can imagine more possibilities. Basically, be more thorough in the critical evaluation of your results. Besides, discuss potential effect of significant heterogeneity of the cell.

(2) The study is rich in biophysics but a bit light on chemical/genetic perturbations. It could be good to use low levels of chemical inhibitors for, for example, Arp2/3, PI3K, myosin etc, and see the effect and try to interpret it. Another interesting question - how adhesive strength affects the results. A different interesting avenue - one can perturb aquaporins. Etc. At least one perturbation experiment would be good.

Comments on revisions: I am satisfied with the revisions

Reviewer #3 (Public review):

Summary:

In their article "Range geography and temperature variability explain cross-continental convergence in range and phenology shifts in a model insect taxon" the authors rigorously investigate the spatial and temporal trends in the occurrence of odonate species and their potential drivers. Specifically, they examine whether species shift their geographic ranges poleward or alter their phenology to cope with changing conditions. Leveraging opportunistic observations of European and North American odonates, they find that species showing significant range shifts also exhibited shifts to earlier emergence. Considering a broad range of potential predictors, their results reveal that geographical factors, but not functional traits, are associated with these shifts.

Strengths:

The article addresses an important topic in ecology and conservation that is particularly timely in the face of reports of substantial insects declines in North America and Europe over the past decades. Through data integration the authors leverage the rich natural history record for odonates, broadening the taxonomic scope of analyses of temporal trends in phenology and distribution. The combination of phenological and range shifts in one framework presents an elegant way to reconcile previous findings and informs about the drivers of biodiversity loss.

Weaknesses:

To better understand whether species shifting both their ranges and phenology are more successful, or as stated here are 'clear winners', and hence whether those that do neither are more vulnerable would require integrating population trends alongside the discussed response. The ~10% species that have not shifted their distribution or phenology might have not declined in abundance, if they have rapidly adapted to local changes in climatic conditions (i.e. they might show a plastic response). These species might be the real 'winners', while species that have recently shifted their ranges or phenology may eventually reach hard limits. The authors are discussing this limitation but might want to adapt their wording, given the potential for misinterpretation. The finding that species with more northern ranges showed lesser northward shifts would speak to the fact that some species have already reached such a geographical range limit.

Achievements and impact:

The results support broad differences in the response of odonate species to climate change, and the prediction that range geography and temperature seasonality are more important predictors of these changes than functional traits. Simultaneously addressing range and phenological shifts highlights that most species exhibit coupled responses but also identifies a significant portion of species that do not respond in these ways that are of critical conservation concern. These results are important for improving forecasts of species' responses to climate change and identifying species of particularly conservation concern. Although not exhaustive regarding abundance trends, the study presents an important step towards a general framework for investigating the drivers of multifaceted species responses.

Reviewer #3 (Public review):

Summary:

Using three strains of mice that are founders of the Diversity Outbred Population of mice, this paper attempts to identify key genetic drivers of obesity and metabolic dysfunction. Through a series of in-depth phenotyping experiments, the authors describe substantial differences in the propensity of these strains to develop obesity and complications associated with obesity. The key here was the careful selection of these strains, as they mostly spanned the spectrum of minor susceptibility (C57BL/6J), major susceptibility (NZO/HILtJ), and complete resistance to diet-induced obesity (CAST/EiJ). This was done in the setting of both a normal diet and a high-fat diet. These studies identified that one of the most transcriptionally activated tissues in this setting across the strains was adipose tissue. Furthermore, a critical pathway in adipose tissue that inferred protection against obesity in the CAST strain was related to immune infiltration. Subsequently, the authors extended their studies into this phenotype using their existing access to the vast array of genetic information from the DO datasets. From this analysis, it was identified that a key region on Chr19 had a significant influence on this phenotype, and subsequent work investigated the potentially causal genes. Overall, this study encompasses an impressive amount of in vivo and genetic work and identifies some new gene regulators associated with obesity complications, which warrant further investigation.

Strengths:

This study engages multiple mouse lines with diet intervention, as well as powerful genetic mapping tools to isolate genetic drivers of various obesity related phenotypes. The animal studies are thorough and well performed, and they also include detailed omics analysis of several tissues. Subsequent genetic mapping uses some of the world's most powerful preclinical genetic approaches, and findings identify some novel genes associated with obesity.

Weaknesses:

These mouse lines and hybrid genetic screens in this paper have been used for some years now to map similar phenotypes, so in that sense, the approach is not overly novel. Moreover, the most compelling and exciting part of the study, in this reviewer's opinion, is the DO mapping of the immune phenotype in adipose tissue. In some ways, the authors could have potentially come to this same conclusion without the need to perform the mouse studies in the three different strains (other than the nice storytelling of finding the phenotype initially in CAST). Likewise, with this being the most novel aspect of the study, it was a shame that the genes identified at Chr19 were not investigated in more detail in the manuscript, other than just some associative outcomes in mice and humans. It would have been pleasing to see some attempt to validate one of these genes in a mouse model, linking it to either obesity or immune phenotypes in WAT.

Reviewer #3 (Public review):

Summary:

This work aims to understand how cells repair damage to the plasma membrane (PM). This is important, as failure to do so will result in cell lysis and death. Therefore, this is an important fundamental question with broad implications for all eukaryotic cells. Despite this importance, there are relatively few proteins known to contribute to this repair process. This study expands the number of experimentally validated PM from 8 to 80. Further, they use precise laser-induced damage of the PM/cell wall and use live-cell imaging to track the recruitment of repair proteins to these damage sites. They focus on repair proteins that are involved in either exocytosis or clathrin-mediated endocytosis (CME) to understand how these membrane remodeling processes contribute to PM repair. Through these experiments, they find that while exocytosis and CME both occur at the sites of PM damage, exocytosis predominates in the early stages of repairs, while CME predominates in the later stages of repairs. Lastly, they propose that CME is responsible for diverting repair proteins localized to the growing bud cell to the site of PM damage.

Strengths:

The manuscript is very well written, and the experiments presented flow logically. The use of laser-induced damage and live-cell imaging to validate the proteome-wide screen using SDS-induced damage strengthens the role of the identified candidates in PM/cell wall repair.

Weaknesses:

(1) Could the authors estimate the fraction of their candidates that are associated with cell wall repair versus plasma membrane repair? Understanding how many of these proteins may be associated with the repair of the cell wall or PM may be useful for thinking about how these results are relevant to systems that do or do not have a cell wall. Perhaps this is already in their GO analysis, but I don't see it mentioned in the manuscript.

(2) Do the authors identify actin cable-associated proteins or formin regulators associated with sites of PM damage? Prior work from the senior author (reference 26) shows that the formin Bnr1 relocalizes to sites of PM damage, so it would be interesting if Bnr1 and its regulators (e.g., Bud14, Smy1, etc) are recruited to these sites as well. These may play a role in directing PM repair proteins (see more below).

(3) Do the authors suspect that actin cables play a role in the relocalization of material from the bud tip to PM damage sites? They mention that TMD proteins are secretory vesicle cargo (lines 134-143) and that Myo2 localizes to damage sites. Together, this suggests a possible role for cable-based transport of repair proteins. While this may be the focus of future work, some additional discussion of the role of cables would strengthen their proposed mechanism (steps 3 and 4 in Figure 7).

(4) Lines 248-249: I find the rationale for using an inducible Gal promoter here unclear. Some clarification is needed.

Reviewer #3 (Public review):

Summary:

Ioakeimidis and colleagues studied microstructural abnormalities in N=56 Huntington's disease (HD) patients compared to N=57 normative controls. The authors used a powerful MRI Connectom scanner and applied the SANDI model to estimate the soma size, neurite size, soma density, and extracellular fraction in key subcortical nuclei related to HD. In the striatum, they found decreased soma density and increased soma size, which also seemed to become more pronounced in advanced HD individuals in the final exploratory analyses. The authors conducted important analyses to find whether the SANDI measures correlate with clinical scores (i.e., QMotor) and whether the variance of the striatal volume is explained by the SANDI measures. They found a relationship between SANDI measures for both.

Strengths:

The study is both innovative and of high interest for the HD community. The authors provide a rich pool of statistical analyses and results that anticipate the questions that may emerge in the HD research community. Statistics are carefully chosen and image processing is done with state-of-the-art methods and tools. The sample size gives sufficient credibility to the findings. Altogether, I think this study sets a milestone in the attempts of the HD community to understand neuropathological processes with non-invasive methods, and extends the current knowledge of microstructural anomalies identified in HD with diffusion MRI. More importantly, the newly identified anomalies in soma size and soma density open new avenues for studying these biological effects further and perhaps developing these biomarkers for use in clinical trials.

Weaknesses:

(1) An important question is whether the SANDI measures, which require an expensive scanner and elaborate processing, are better biomarkers than the more traditional DTI measures. Can the authors compare the effect size of FA/MD with SANDI measures? In some of the plots and tables, FA/MD seem to have comparable, if not higher, correlations with QMotor or CAP scores. On the same vein, it is unclear whether DTI measures were included in hierarchical stepwise regression. I wonder if the stepwise models may have picked up FA/MD instead of SANDI measures if they are given a chance. Overall, I hope the authors can discuss their findings also in this light of cost vs. benefit of adopting SANDI in future studies, which is an important topic for clinical trials.

(2) Similar to the above point, it is very important to consider how strong the biomarking signal is from SANDI measures compared to the good old striatal volume. Some plots seem to indicate that volumes still have the highest correlation with QMotor and the highest effect size in group comparisons. It would be helpful for the community to know where the new SANDI measures stand compared to the most typically used volumes in terms of effect size.

(3) The diffusion measures are inevitably correlated to some degree. Please provide a correlation matrix in the supplementary material, including all DWI measures, to enable readers to better understand how similar SANDI measures are to each other or vs. other DTI measures. Perhaps adding volumes to this correlation matrix may also be a good future reference.

(4) ISS stages:

a) The online ISS calculator requires cut-offs derived from the longitudinal Freesurfer pipeline, while the authors do not have longitudinal data. Thus, the ISS classification might be inaccurate to some degree if the authors used the FS cross-sectional pipeline. Please review this issue and see if updated cut-offs should be used to classify participants.

b) Were there really no participants with ISS 0 among the 56 HD individuals? Please clarify in the manuscript.

(5) A note on terminology that might be confusing to some readers. According to the creators of ISS, the ISS stages are created for research only; they are not used or applied in the clinic. On the other hand, the terms "premanifest" and "manifest" have a clinical meaning, typically based on the diagnostic confidence level. The assignment of ISS0-1 to premanifest and ISS2-3 to manifest may create some non-trivial confusion, if not opposition, in some segments of the HD community. The authors can keep their current terminology, but will need to at least clarify to the reader that this assignment is speculative, does not fully match the clinically-based categories, and should not be confused with similarly named groups in the previous literature.

Reviewer #3 (Public review):

Summary:

The melibiose permease from Salmonella enterica serovar Typhimurium (MelBSt) is a member of the Major Facilitator Superfamily (MFS). It catalyzes the symport of a galactopyranoside with Na⁺, H⁺, or Li⁺, and serves as a prototype model system for investigating cation-coupled transport mechanisms. In cation-coupled symporters, a coupling cation typically moves down its electrochemical gradient to drive the uphill transport of a primary substrate; however, the precise role and molecular contribution of the cation in substrate binding and translocation remain unclear. In a prior study, the authors showed that the binding affinity for melibiose is increased in the presence of Na+ by about 8-fold, but the molecular basis for the cooperative mechanism remains unclear. The objective of this study was to better understand the allosteric coupling between the Na+ and melibiose binding sites. To verify the sugar-recognition specific determinants, the authors solved the outward-facing crystal structures of a uniport mutant D59C with four sugar ligands containing different numbers of monosaccharide units (α-NPG, melibiose, raffinose, or α-MG). The structure with α-NPG bound has improved resolution (2.7 Å) compared to a previously published structure and to those with other sugars. These structures show that the specificity is clearly directed toward the galactosyl moiety. However, the increased affinity for α-NPG involves its hydrophobic phenyl group, positioned at 4 Å-distance from the phenyl group of Tyr26 forms a strong stacking interaction. Moreover, a water molecule bound to OH-4 in the structure with α-NPG was proposed to contribute to the sugar recognition and appears on the pathway between the two specificity-determining pockets. Next, the authors analyzed by hydrogen-to-deuterium exchange coupled to mass spectrometry (HDX-MS) the changes in structural dynamics of the transporter induced by melibiose, Na+, or both. The data support the conclusion that the binding of the coupling cation at a remote location stabilizes the sugar-binding residues to switch to a higher-affinity state. Therefore, the coupling cation in this symporter was proposed to be an allosteric activator.

Strengths:

(1) The manuscript is generally well written.

(2) This study builds on the authors' accumulated knowledge of the melibiose permease and integrates structural and HDX-MS analyses to better understand the communication between the sodium ion and sugar binding sites. A high sequence coverage was obtained for the HDX-MS data (86-87%), which is high for a membrane protein.

Weaknesses:

(1) I am not sure that the resolution of the structure (2.7 Å) is sufficiently high to unambiguously establish the presence of a water molecule bound to OH-4 of the α-NPG sugar. In Figure 2, the density for water 1 is not obvious to me, although it is indeed plausible that water mediates the interaction between OH4/OH6 and the residues Q372 and T373.

(2) Site-directed mutagenesis could help strengthen the conclusions of the authors. Would the mutation(s) of Q372 and/or T373 support the water hypothesis by decreasing the affinity for sugars? Mutations of Thr 121, Arg 295, combined with functional and/or HDX-MS analyses, may also help support some of the claims of the authors regarding the allosteric communication between the two substrate-binding sites.

(3) The main conclusion of the authors is that the binding of the coupling cation stabilizes those dynamic sidechains in the sugar-binding pocket, leading to a high-affinity state. This is visible when comparing panels c and a from Figure S5. However, there is both increased protection (blue, near the sugar) and decreased protection in other areas (red). The latter was less commented, could the increased flexibility in these red regions facilitate the transition between inward- and outward-facing conformations? The HDX changes induced by the different ligands were compared to the apo form (see Figure S5). It might be worth it for data presentation to also analyze the deuterium uptake difference by comparing the conditions sodium ion+melibiose vs melibiose alone. It would make the effect of Na+ on the structural dynamics of the melibiose-bound transporter more visible. Similarly, the deuterium uptake difference between sodium ion+melibiose vs sodium ion alone could be analyzed too, in order to plot the effect of melibiose on the Na+-bound transporter.

(4) For non-specialists, it would be beneficial to better introduce and explain the choice of using D59C for the structural analyses.

(5) In Figure 5a, deuterium changes are plotted as a function of peptide ID number. It is hardly informative without making it clearer which regions it corresponds to. Only one peptide is indicated (213-226), I would recommend indicating more of them in areas where deuterium changes are substantial.

(6) From prior work of the authors, melibiose binding also substantially increases the affinity of the sodium ion. Can the authors interpret this observation based on the HDX data?

Reviewer #3 (Public review):

Summary:

Kern et al. critically assess the sensitivity of temporally delayed linear modelling (TDLM), a relatively new method used to detect memory replay in humans via MEG. While TDLM has recently gained traction and been used to report many exciting links between replay and behavior in humans, Kern et al. were unable to detect replay during a post-learning rest period. To determine whether this null result reflected an actual absence of replay or sensitivity of the method, the authors ran a simulation: synthetic replay events were inserted into a control dataset, and TDLM was used to decode them, varying both replay density and its correlation with behavior. The results revealed that TDLM could only reliably detect replay at unrealistically (not-physiological) high replay densities, and the authors were unable to induce strong behavior correlations. These findings highlight important limitations of TDLM, particularly for detecting replay over extended, minutes-long time periods.

Strengths:

Overall, I think this is an extremely important paper, given the growing use of TDLM to report exciting relationships between replay and behavior in humans. I found the text clear, the results compelling, and the critique of TDLM quite fair: it is not that this method can never be applied, but just that it has limits in its sensitivity to detect replay during minutes-long periods. Further, I greatly appreciated the authors' efforts to describe ways to improve TDLM: developing better decoders and applying them to smaller time windows.

The power of this paper comes from the simulation, whereby the authors inserted replay events and attempted to detect them using TDLM. Regarding their first study, there are many alternative explanations or possible analysis strategies that the authors do not discuss; however, none of these are relevant if, under conditions where it is synthetically inserted, replay cannot be detected.

Additionally, the authors are relatively clear about which parameters they chose, why they chose them, and how well they match previous literature (they seem well matched).

Finally, I found the application of TDLM to a baseline period particularly important, as it demonstrated that there are fluctuations in sequenceness in control conditions (where no replay would be expected); it is important to contrast/calculate the difference between control (pre-resting state) and target (post-resting state) sequenceness values.

Weaknesses:

While I found this paper compelling, I was left with a series of questions.

(1) I am still left wondering why other studies were able to detect replay using this method. My takeaway from this paper is that large time windows lead to high significance thresholds/required replay density, making it extremely challenging to detect replay at physiological levels during resting periods. While it is true that some previous studies applying TDLM used smaller time windows (e.g., Kern's previous paper detected replay in 1500ms windows), others, including Liu et al. (2019), successfully detected replay during a 5-minute resting period. Why do the authors believe others have nevertheless been able to detect replay during multi-minute time windows?

For example, some studies using TDLM report evidence of sequenceness as a contrast between evidence of forwards (f) versus backwards (b) sequenceness; sequenceness was defined as ZfΔt - ZbΔt (where Z refers to the sequence alignment coefficient for a transition matrix at a specific time lag). This use case is not discussed in the present paper, despite its prevalence in the literature. If the same logic were applied to the data in this study, would significant sequenceness have been uncovered? Whether it would or not, I believe this point is important for understanding methodological differences between this paper and others.

(2) Relatedly, while the authors note that smaller time windows are necessary for TDLM to succeed, a more precise description of the appropriate window size would greatly improve the utility of this paper. As it stands, the discussion feels incomplete without this information, as providing explicit guidance on optimal window sizes would help future researchers apply TDLM effectively. Under what window size range can physiological levels of replay actually be detected using TDLM? Or, is there some scaling factor that should be considered, in terms of window size and significance threshold/replay density? If the authors are unable to provide a concrete recommendation, they could add information about time windows used in previous studies (perhaps, is 1500ms as used in their previous paper a good recommendation?).

(3) In their simulation, the authors define a replay event as a single transition from one item to another (example: A to B). However, in rodents, replay often traverses more than a single transition (example: A to B to C, even to D and E). Observing multistep sequences increases confidence that true replay is present. How does sequence length impact the authors' conclusions? Similarly, can the authors comment on how the length of the inserted events impacts TDLM sensitivity, if at all?

For example, regarding sequence length, is it possible that TDLM would detect multiple parts of a longer sequence independently, meaning that the high density needed to detect replay is actually not quite so dense? (example: if 20 four-step sequences (A to B to C to D to E) were sampled by TDLM such that it recorded each transition separately, that would lead to a density of 80 events/min).

Reviewer #3 (Public review):

Summary:

Borghi and colleagues present results from 4 experiments aimed at investigating the effects of dual γtACS and iTBS stimulation of the precuneus on behavioral and neural markers of memory formation. In their first experiment (n = 20), they find that a 3-minute offline (i.e., prior to task completion) stimulation that combines both techniques leads to superior memory recall performance in an associative memory task immediately after learning associations between pictures of faces, names, and occupation, as well as after a 15-minute delay, compared to iTBS alone (+ tACS sham) or no stimulation (sham for both iTBS and tACS). Performance in a second task probing short-term memory was unaffected by the stimulation condition. In a second experiment (n = 10), they show that these effects persist over 24 hours and up to a full week after initial stimulation. A third (n = 14) and fourth (n = 16) experiment were conducted to investigate neural effects of the stimulation protocol. The authors report that, once again, only combined iTBS and γtACS increases gamma oscillatory activity and neural excitability (as measured by concurrent TMS-EEG) specific to the stimulated area at the precuneus compared to a control region, as well as precuneus-hippocampus functional connectivity (measured by resting state MRI), which seemed to be associated with structural white matter integrity of the bilateral middle longitudinal fasciculus (measured by DTI).

Strengths:

Combining non-invasive brain stimulation techniques is a novel, potentially very powerful method to maximize the effects of these kinds of interventions that are usually well-tolerated and thus accepted by patients and healthy participants. It is also very impressive that the stimulation-induced improvements in memory performance resulted from a short (3 min) intervention protocol. If the effects reported here turn out to be as clinically meaningful and generalizable across populations as implied, this approach could represent a promising avenue for treatment of impaired memory functions in many conditions.

Methodologically, this study is expertly done! I don't see any serious issues with the technical setup in any of the experiments. It is also very commendable that the authors conceptually replicated the behavioral effects of experiment 1 in experiment 2 and then conducted two additional experiments to probe the neural mechanisms associated with these effects. This certainly increases the value of the study and the confidence in the results considerably.

The authors used a within-subject approach in their experiments, which increases statistical power and allows for stronger inferences about the tested effects. They also used to individualize stimulation locations and intensities, which should further optimize the signal-to-noise ratio.

Reviewer #3 (Public review):

Summary:

In the manuscript by Shen, Yeung, and colleagues, the authors generate an improved and expanded Mosaic analysis by gRNA-induced crossing-over (MAGIC) toolkit for use in making mosaic clones in Drosophila. This is a clever method by which mitotic clones can be induced in dividing cells by using CRISPR/Cas9 to generate double-strand breaks at specific locations that induce crossing over at those locations. This is conceptually similar to previous mosaic methods in flies that utilized FRT sites that had been inserted near centromeres along with heat-shock inducible FLPase. The advantage of the MAGIC system is that it can be used along with chromosomes lacking FRT sites already introduced, such as those found in many deficiency collections or in EMS mutant lines. It may also be simpler to implement than FRT-based mosaic systems. There are two flavors of the MAGIC system: nMAGIC and pMAGIC. In nMAGIC, the main constituents are a transgene insertion that contains gRNAs that target DNA near the centromere, along with a fluorescent marker. In pMAGIC, the main constituents are a transgenic insertion that contains gRNAs that target DNA near the centromere, along with ubiquitous expression of GAL80. As such, nMAGIC can be used to generate clones that are not labelled, whereas pMAGIC (along with a GAL4 line and UAS-marker) can be used much like MARCM to positively label a clone of cells. This manuscript introduces MAGIC transgenic reagents that allow all 4 chromosomes to be targeted. They demonstrate its use in a variety of tissues, including with mutants not compatible with current FLP/FRT methods, and also show it works well in tissues that prove challenging for FLP/FRT mosaic analyses (such as motor neurons). They further demonstrate that it can be used to generate mosaic clones in non-melanogaster hybrid tissues. Overall, this work represents a valuable improvement to the MAGIC method that should promote even more widespread adoption of this powerful genetic technique.

Strengths:

(1) Improves the design of the gRNA-marker by updating the gRNA backbone and also the markers used. GAL80 now includes a DE region that reduces the perdurance of the protein and thus better labeling of pMAGIC clones. The data presented to demonstrate these improvements is rigorous and of high quality.

(2) Introduces a toolkit that now covers all chromosome arms in Drosophila. In addition, the efficiency of 3 target different sites is characterized for each chromosome arm (e.g., 3 different gRNA-Marker combinations), which demonstrate differences in efficiency. This could be useful to titrate how many clones an experimenter might want (e.g., lower efficiency combinations might prove advantageous).

(3) The manuscript is well written and easy to follow. The authors achieved their aims of creating and demonstrating MAGIC reagents suitable for mosaic analysis of any Drosophila chromosome arm.

(4) The MAGIC method is a valuable addition to the Drosophila genetics toolkit, and the new reagents described in this manuscript should allow it to become more widely adopted.

Weaknesses:

(1) The MAGIC method might not be well known to most readers, and the manuscript could have benefited from schematics introducing the technique.

(2) Traditional mosaic analyses using the FLP/FRT system have strongly utilized heat-shock FLPase for inducible temporal control over mitotic clones, as well as a way to titrate how many clones are induced (e.g., shorter heat shocks will induce fewer clones). This has proven highly valuable, especially for developmental studies. A heat-shock Cas9 is available, and it would have been beneficial to determine the efficiency of inducing MAGIC clones using this Cas9 source.

Reviewer #3 (Public review):

Leshem et al have generated a transcriptional cell atlas of the human outflow tract at two developmental timepoints and its adult valvular derivatives. This carefully performed study provides a useful resource for the study of known genes implicated in outflow tract defects and potentially also for discovering new disease genes. The authors reveal neural crest and mesodermal contributions to different outflow tract components and show that GATA6, known to play a role in arterial valve development, controls a set of genes expressed in endocardium-derived cells during valve development. Interestingly, the results suggest lineage persistence of expression of certain genes through to the adult timepoint, a main new finding of this study.

The following points should be addressed to reinforce the conclusions and emphasize the novel features of this study.

(1) It would be helpful to clarify how these new findings confirm or diverge from what is known from analysis of neural crest and mesodermal lineage contributions to different cell populations in the mouse heart. Did the authors identify any human-specific populations of cells, such as the LGR5 population reported by Sahara et al?

(2) The authors should clarify in the introduction and results that they consider the endocardium to be on the SHF trajectory as indicated in Figure S4C. Please add a reference for this point.

(3) The GATA6 results are interesting and support this experimental approach. The paper would be reinforced if the authors could provide any functional validation (in addition to their GATA6 genomic occupancy data) that the designated target genes are regulated by GATA6. This might involve looking at mutant mouse embryos or cultured cells. Do the authors consider that GATA6 may regulate the endocardial to mesenchymal transition during the early stages of valve development? Or the valve interstitial cell versus fibroblast fate choice?

(4) Do the new findings reveal whether human valves have a direct SHF to VIC trajectory (ie, without transiting through endocardium) as has been recently shown in the murine non-coronary valve leaflet? Relevant to this point, Figure 5E appears to show contributions to a single adult aortic valve leaflet - this should be explained, or corrected.

Reviewer #3 (Public review):

Summary:

In this manuscript, Sumegi et al. use calcium imaging in head-fixed mice to test whether new place fields tend to emerge due to events that resemble behavioral time scale plasticity (BTSP) or other mechanisms. An impressive dataset was amassed (163 sessions from 45 mice with 500-1000 neurons per sample) to study spontaneous emergence of new place fields in area CA1 that had the signature of BTSP. The authors observed that place fields could emerge due to BTSP and non-BTSP-like mechanisms. Interestingly, when non-BTSP mechanisms seemed to generate a place field, this tended to occur on a trial with a spontaneous reset in neural coding (a remapping event). Novelty seemed to upregulate non-BTSP events relative to BTSP events. Finally, large calcium transients (presumed plateau potentials) were not sufficient to generate a place field.

Strengths:

I found this manuscript to be exceptionally well written, well powered, and timely given the outstanding debate and confusion surrounding whether all place fields must arise from BTSP event. Working at the same institute, Albert Lee (e.g. Epszstein et al., 2011 - which should be cited) and Jeff Magee (e.g. Bittner et al., 2017) showed contradictory results for how place fields arise. These accounts have not fully been put toe-to-toe and reconciled in the literature. This manuscript addresses this gap and shows that both accounts are correct - place fields can emerge due to a pre-existing map and due to BTSP.

Weaknesses:

I find only three significant areas for improvement in the present study:

First, can it be concluded that non-BTSP events occur exclusively due to a global remapping event, as stated in the manuscript "these PFF surges included a high fraction of both non-BTSP- and BTSP-like PFF events, and were associated with global remapping of the CA1 representation"? Global remapping has a precise definition that involves quantifying the stability of all place fields recorded. Without a color scale bar in Figure 3D (which should be added), we cannot know whether the overall representations were independent before and after the spontaneous reset. It would be good to know if some neurons are able to maintain place coding (more often than expected by chance), suggestive of a partial-remapping phenomenon.

Second, BTSP has a flip side that involves weakening of existing place fields when a novel field emerges. Was this observed in the present study? Presumably place fields can disappear due to this bidirectional-BTSP or due to global remapping. For a full comparison of the two phenomena, the disappearance of place fields must also be assessed.

Finally, it would be good to know if place fields differ according to how they are born. For example, are there differences in reliability, width, peak rate, out of field firing, etc for those that arise due BTSP vs non-BTSP.

Comments on revisions:

The authors have mostly addressed my feedback. Compelling evidence for a fundamental observation.

Reviewer #3 (Public review):

Summary:

The authors tackle an important problem: defining the topological changes that occur during tumorigenesis. To study this, they use an established stepwise cell model of breast cancer. A strength of their study is a careful, robust differential analysis of topological features across each cell state, which is presented clearly and rigorously. They define changes in compartmentalization, TAD structure, and chromatin looping. Intriguingly, when the authors integrate differential gene expression with chromatin looping, they see that most differentially regulated genes are not involved in loop changes, suggesting that changes in promoter or enhancer chromatin marks may play a bigger role in regulating transcription than differential loops. The differential topology analysis and its integration with transcription is very well done- one of the best versions of this I have read in the 3D genome field! However, the paper is framed largely as a cancer biology study, and it teaches us much less about this. I am worried that some of the trends for each topologic feature are not going to be consistent across the pre-malignant-malignant-metastatic spectrum and would like the authors to soften some of their claims a bit regarding how this clarifies our understanding of cancer evolution.

Weaknesses:

Major Concerns:

(1) The integration of gene expression and chromatin loops is intriguing. The authors' differential analysis, however, omits consideration of genes that are on and simply further upregulated versus genes that transition on/off or off/on. It would be nice to see the authors break out looping patterns for these two different patterns of regulation, as it may be instructive regarding the rules for how EP loops govern transcription.

(2) Given the paucity of differential loops at the majority of genes whose expression changes, the authors should examine chromatin subcompartments, as these may associate more with differential transcription.

(3) The authors could push their TAD analysis further by integrating it with transcription. Can they look at genes and their enhancers that span these altered boundaries to see if these shifts impact transcription?

(4) The progression of cancer critically goes from a benign -> pre-malignant -> malignant -> metastatic series of steps. The AT1 line is described as 'premalignant' and thus the authors' series omits a malignant line. While I think adding such a sample is an unreasonable request at this point (as it would have had to have been studied in 'batch' with these other samples), the authors should acknowledge that they omit this step and spend some time discussing the genetic, morphologic, and phenotypic features for their 3 conditions. The images in Figure 1S aren't particularly useful- they don't tell the reader that these cells are malignant/benign. The karyotypic data are intriguing but not fully analyzed, so it is hard to know what true phenotype these cells represent. For example, malignant means DCIS/invasive carcinoma - so then what does this pre-malignant cell model represent? The described alteration in the AT1 line is a Ras oncogene, so in some sense, the transition to this line really is just +/- Ras. The authors could spend some time thinking about the effects of Ras specifically on the 3D genome.

Reviewer #3 (Public review):

Summary:

This paper seeks to identify underlying mechanisms contributing to memory deficits observed in Alzheimer's disease (AD) mouse models. By understanding these mechanisms, they hope to uncover insights into subtle cognitive changes early in AD to inform interventions for early-stage decline.

Strengths:

The paper provides a comprehensive exploration of memory deficits in an AD mouse model, covering early and late stages of the disease. The experimental design was robust, confirming age-dependent increases in Aβ plaque accumulation in the AD model mice and using multiple behavior tasks that collectively highlighted difficulties in maintaining multiple competing memory cues, with deficits most pronounced in older mice.

In the fear acquisition, extinction, and reinstatement task, AD model mice exhibited a significantly higher fear response after acquisition compared to controls, as well as a greater drop in fear response during reinstatement. These findings suggest that AD mice struggle to retain the fear memory associated with the conditioned stimulus, with the group differences being more pronounced in the older mice.

In the reversal Barnes maze task, the AD model mice displayed a tendency to explore the maze perimeter rather than the two potential target holes, indicating a failure to integrate multiple memory cues into their strategy. This contrasted with the control mice, which used the more confirmatory strategy of focusing on the two target holes. Despite this, the AD mice were quicker to reach the target hole, suggesting that their impairments were specific to memory retrieval rather than basic task performance.

The authors strengthened their findings by analyzing their data with a leading computational model, which describes how animals balance competing memories. They found that AD mice showed somewhat of a contradiction: a tendency to both treat trials as more alike than they are (lower α) and similar stimuli as more distinct than they are (lower σx) compared to controls.

Weaknesses:

While conceptually solid, the model struggles to fit the data and to support the key hypothesis about AD mice's inability to retain competing memories. These issues are evident in Figure 3:

(1) The model misses trends in the data, including the gradual learning of fear in all groups during acquisition, the absence of a fear response at the start of the experiment, and the faster return of fear during reinstatement compared to the gradual learning of fear during acquisition. It also underestimates the increase in fear at the start of day 2 of extinction, particularly in controls.

(2) The model explains the higher fear response in controls during reinstatement largely through a stronger association to the context formed during the unsignaled shock phase, rather than to any memory of the conditioned stimulus from acquisition (as seen in Figure 3C). In the experiment, however, this memory does seem to be important for explaining the higher fear response in controls during reinstatement (as seen in Author Response Figure 3). The model does show a necessary condition for memory retrieval, which is that controls rely more on the latent causes from acquisition. But this alone is not sufficient, since the associations within that cause may have been overwritten during extinction. The Rescorla-Wagner model illustrates this point: it too uses the latent cause from acquisition (as it only ever uses a single cause across phases) but does not retain the original stimulus-shock memory, updating and overwriting it continuously. Similarly, the latent cause model may reuse a cause from acquisition without preserving its original stimulus-shock association.

These issues lead to potential overinterpretation of the model parameters. The differences in α and σx are being used to make claims about cognitive processes (e.g., overgeneralization vs. over differentiation), but the model itself does not appear to capture these processes accurately.

The authors could benefit from a model that better matches the data and captures the retention and retrieval of fear memories across phases. While they explored alternatives, including the Rescorla-Wagner model and a latent state model, these showed no meaningful improvement in fit. This highlights a broader issue: these models are well-motivated but may not fully capture observed behavior.

Conclusion:

Overall, the data support the authors' hypothesis that AD model mice struggle to retain competing memories, with the effect becoming more pronounced with age. While I believe the right computational model could highlight these differences, the current models fall short in doing so.

Reviewer #3 (Public review):

Summary:

Kamal L. Nahas et al. demonstrated that pUL16, pUL21, pUL34, VP16, and pUS3 are involved in the egress of the capsids from the nucleous, since mutant viruses ΔpUL16, ΔpUL21, ΔUL34, ΔVP16, and ΔUS3 HSV-1 show nuclear egress attenuation determined by measuring the nuclear:cytoplasmic ratio of the capsids, the dfParental, or the mutants. Then, they showed that gM-mCherry+ endomembrane association and capsid clustering were different in pUL11, pUL51, gE, gK, and VP16 mutants. Furthermore, the 3D view of cytoplasmic budding events suggests an envelopment mechanism where capsid budding into spherical/ellipsoidal vesicles drives the envelopment.

Strengths:

The authors employed both structured illumination microscopy and cellular ultrastructure analysis to examine the same infected cells, using cryo-soft-X-ray tomography to capture images. This combination, set here for the first time, enabled the authors to obtain holistic data regarding a biological process, as a viral assembly. Using this approach, the researchers studied various stages of HSV-1 assembly. For this, they constructed a dual-fluorescently labelled recombinant virus, consisting of eYFP-tagged capsids and mCherry-tagged envelopes, allowing for the independent identification of both unenveloped and enveloped particles. They then constructed nine mutants, each targeting a single viral protein known to be involved in nuclear egress and envelopment in the cytoplasm, using this dual-fluorescent as the parental one. The experimental setting, both the microscopic and the virological, is robust and well-controlled. The manuscript is well-written, and the data generated is robust and consistent with previous observations made in the field.

I congratulate the authors. The work is robust, and I personally highlight the way they managed to include others' results merged among their own, providing a complete view of the story.

Comments on the latest version:

I reviewed the responses and the updated manuscript, and I agree with the reviewer's #1 words: "The manuscript was already strong, but with the addition of the summary table and the separated images, it is now excellent."

Reviewer #3 (Public review):

Summary:

The authors seek to determine the underlying traits that support the exceptional capacity of Aspergillus oryzae to secrete enzymes and heterologous proteins. To do so, they leverage the availability of multiple domesticated isolates of A. oryzae along with other Aspergillus species to perform comparative imaging and genomic analysis.

Strengths:

The strength of this study lies in the use of multifaceted approaches to identify significant differences in hyphal morphology that correlate with enzyme secretion, which is then followed by the use of genomics to identify candidate functions that underlie these differences.

Weaknesses:

The authors addressed all suggestions satisfactorily.

Reviewer #3 (Public review):

The authors have satisfactorily addressed my inquiries. However, I had to look quite hard to find where they responded to my final comment regarding the potential role of Arpc2 post-fusion during myofiber growth and/or maintenance, which I eventually located on page 7. I would appreciate it if the authors could state this point more explicitly, perhaps by adding a sentence such as "However, we cannot rule out the possibility that Arpc2 may also play a role in....." to improve clarity of communication.

While I understood from the original version that this issue falls beyond the immediate scope of the study, I believe it is important to adopt a more cautious and rigorous interpretative framework, especially given the widespread use of this experimental approach. In particular, when a gene could potentially have additional roles in myofibers, it may be helpful to explicitly acknowledge that possibility. Even if Arpc2 may not necessarily be one of them, such roles cannot be fully excluded without direct testing.

Reviewer #3 (Public review):

Mondal et al. use computational modeling to investigate how activity-dependent shifts in voltage-dependent (in)activation curves can complement changes in ion channel conductance to support homeostatic plasticity. While it is well established that the voltage-dependent properties of ion channels influence neuronal excitability, their potential role in homeostatic regulation, alongside conductance changes, has remained largely unexplored. The results presented here demonstrate that activity-dependent regulation of voltage dependence can interact with conductance plasticity to enable neurons to attain and maintain target activity patterns, in this case, intrinsic bursting. Notably, the timescale of these voltage-dependent shifts influences the final steady-state configuration of the model, shaping both channel parameters and activity features such as burst period and duration. A major conclusion of the study is that altering this timescale can seamlessly modulate a neuron's intrinsic properties, which the authors suggest may be a mechanism for adaptation to perturbations.

While this conclusion is largely well-supported, additional analyses could help clarify its scope. For instance, the effects of timescale alterations are clearly demonstrated when the model transitions from an initial state that does not meet the target activity pattern to a new stable state. However, Fig. 6 and the accompanying discussion appear to suggest that changing the timescale alone is sufficient to shift neuronal activity more generally. It would be helpful to clarify that this effect primarily applies during periods of adaptation, such as neurodevelopment or in response to perturbations, and not necessarily once the system has reached a stable, steady state. As currently presented, the simulations do not test whether modifying the timescale can influence activity after the model has stabilized. In such conditions, changes in timescale are unlikely to affect network dynamics unless they somehow alter the stability of the solution, which is not shown here. That said, it seems plausible that real neurons experience ongoing small perturbations which, in conjunction with changes in timescale, could allow gradual shifts toward new solutions. This possibility is not discussed but could be a fruitful direction for future work.

Editor's note: The authors have adequately addressed the concerns raised in the public reviews above, as well as the previous recommendations, and revised the manuscript where necessary.

Reviewer #3 (Public review):

This study is a part of the ongoing series of rigorous work from this group exploring neural coding deficits in the auditory nerve, and dissociating the effects of cochlear synaptopathy from other age-related deficits. They have previously shown no evidence of phase-locking deficits in the remaining auditory nerve fibers in quiet-aged gerbils. Here, they study the effects of aging on the perception and neural coding of temporal fine structure cues in the same Mongolian gerbil model.

They measure TFS coding in the auditory nerve using the TFS1 task which uses a combination of harmonic and tone-shifted inharmonic tones which differ primarily in their TFS cues (and not the envelope). They then follow this up with a behavioral paradigm using the TFS1 task in these gerbils. They test young normal hearing gerbils, aged gerbils, and young gerbils with cochlear synaptopathy induced using the neurotoxin ouabain to mimic synapse losses seen with age.

In the behavioral paradigm, they find that aging is associated with decreased performance compared to the young gerbils, whereas young gerbils with similar levels of synapse loss do not show these deficits. When looking at the auditory nerve responses, they find no differences in neural coding of TFS cues across any of the groups. However, aged gerbils show an increase in the representation of periodicity envelope cues (around f0) compared to young gerbils or those with induced synapse loss. The authors hence conclude that synapse loss by itself doesn't seem to be important for distinguishing TFS cues, and rather the behavioral deficits with age are likely having to do with the misrepresented envelope cues instead.

The manuscript is well written, and the data presented are robust. Some of the points below will need to be considered while interpreting the results of the study, in its current form. These considerations are addressable if deemed necessary, with some additional analysis in future versions of the manuscript.

Spontaneous rates - Figure S2 shows no differences in median spontaneous rates across groups. But taking the median glosses over some of the nuances there. Ouabain (in the Bourien study) famously affects low spont rates first, and at a higher degree than median or high spont rates. It seems to be the case (qualitatively) in figure S2 as well, with almost no units in the low spont region in the ouabain group, compared to the other groups. Looking at distributions within each spont rate category and comparing differences across the groups might reveal some of the underlying causes for these changes. Given that overall, the study reports that low-SR fibers had a higher ENV/TFS log-z-ratio, the distribution of these fibers across groups may reveal specific effects of TFS coding by group.

[Update: The revised manuscript has addressed these issues]

Threshold shifts - It is unclear from the current version if the older gerbils have changes in hearing thresholds, and whether those changes may be affecting behavioral thresholds. The behavioral stimuli appear to have been presented at a fixed sound level for both young and aged gerbils, similar to the single unit recordings. Hence, age-related differences in behavior may have been due to changes in relative sensation level. Approaches such as using hearing thresholds as covariates in the analysis will help explore if older gerbils still show behavioral deficits.

[Update: The issue of threshold shifts with aging gerbils is still unresolved in my opinion. From the revised manuscript, it appears that aged gerbils have a 36dB shift in thresholds. While the revised manuscript provides convincing evidence that these threshold shifts do not affect the auditory nerve tuning properties, the behavioral paradigm was still presented at the same sound level for young and aged animals. But a potential 36 dB change in sensation level may affect behavioral results. The authors may consider adding thresholds as covariates in analyses or present any evidence that behavioral thresholds are plateaued along that 30dB range].

Task learning in aged gerbils - It is unclear if the aged gerbils really learn the task well in two of the three TFS1 test conditions. The d' of 1 which is usually used as the criterion for learning was not reached in even the easiest condition for aged gerbils in all but one condition for the aged gerbils (Fig. 5H) and in that condition, there doesn't seem to be any age-related deficits in behavioral performance (Fig. 6B). Hence dissociating the inability to learn the task from the inability to perceive TFS 1 cues in those animals becomes challenging.

[Update: The revised manuscript sufficiently addresses these issues, with the caveat of hearing threshold changes affecting behavioral thresholds mentioned above].

Increased representation of periodicity envelope in the AN - the mechanisms for increased representation of periodicity envelope cues is unclear. The authors point to some potential central mechanisms but given that these are recordings from the auditory nerve what central mechanisms these may be is unclear. If the authors are suggesting some form of efferent modulation only at the f0 frequency, no evidence for this is presented. It appears more likely that the enhancement may be due to outer hair cell dysfunction (widened tuning, distorted tonotopy). Given this increased envelope coding, the potential change in sensation level for the behavior (from the comment above), and no change in neural coding of TFS cues across any of the groups, a simpler interpretation may be -TFS coding is not affected in remaining auditory nerve fibers after age-related or ouabain induced synapse loss, but behavioral performance is affected by altered outer hair cell dysfunction with age.

[Update: The revised manuscript has addressed these issues]

Emerging evidence seems to suggest that cochlear synaptopathy and/or TFS encoding abilities might be reflected in listening effort rather than behavioral performance. Measuring some proxy of listening effort in these gerbils (like reaction time) to see if that has changed with synapse loss, especially in the young animals with induced synaptopathy, would make an interesting addition to explore perceptual deficits of TFS coding with synapse loss.

[Update: The revised manuscript has addressed these issues]

Reviewer #3 (Public review):

Summary:

Submitted to the Tools and Resources series, this study reports on the use of a single-domain antibody targeting the nucleoporin Nup84 to probe and track NPCs in budding yeast. The authors demonstrate their ability to rapidly label or pull down NPCs by inducing the expression of a tagged version of the nanobody (Figure 1).

Strengths:

This tool's main strength is its versatility as an inexpensive, easy-to-set-up alternative to metabolic labelling or optical switching. This same rationale could, in principle, be applied to the study of other multiprotein complexes using similar strategies, provided that single-chain antibodies are available.

Weaknesses:

This approach has no inherent weaknesses, but it would be useful for the authors to verify that their pulse labelling strategy can also be used to detect assembly intermediates, structural variants, or damaged NPCs.

Overall, the data clearly show that Nup84 nanobodies are a valuable tool for imaging NPC dynamics and investigating their interactomes through affinity purification.

Reviewer #4 (Public review):

The manuscript reports on a large-scale study correlating genomic architecture with splicing complexity over almost 1,500 species. We still know relatively little about alternative splicing functional consequences and evolution, and thus, the study is relevant and timely. The methodology relies on annotations from NCBI for high-quality genomes and a main metric proposed by the authors and named Alternative Splicing Ratio (ASR). It quantifies the level of redundancy of each coding nucleotide in the annotated isoforms.

According to the authors' response to the first reviewers' comments, the present version of the manuscript seems to be a profoundly revised version compared to the original submission. I did not have access to the reviewers' comments.

Although the study addresses an important question and the authors have visibly made an important effort to make their claims more statistically robust, I have a number of major concerns regarding the methodology and its presentation.

(1) A large part of the manuscript is speculative and vague. For instance, the Discussion is very long (almost longer than the Results section) and the items discussed are sometimes not in direct connection with the present work. I would suggest merging the last 2 paragraphs, for instance, since the before last paragraph is essentially a review of the literature without direct connection to the present work.

(2) The Methods section lacks clarity and precision. A large part is devoted to explaining the biases in the data without any reference or quantification. The definition of ASR is very confusing. It is first defined in equation 2, with a different name, and then again in the next subsection from a different perspective on lines 512-518. Why build matrices of co-occurrences if these are, in practice, never used? It seems the authors exploit only the trace. A major revision, if I understood correctly, was the correction/normalisation of the ASR metric. This normalisation is not explained. The authors argue that they will write another paper about it, I do not think this is acceptable for the publication of the present manuscript. Furthermore, there is no information about the technical details of the implementation: which packages did the authors use?

(3) Could the authors motivate why they do not directly focus on the MC permutation test? They motivate the use of permutations because the data contains extreme outliers and are non normal in most cases. Hence, it seems the Welch's ANOVA is not adapted. "To further validate our findings, we also conducted<br /> 148 a Monte Carlo permutation test, which supported the conclusions (see Methods)." Where is the comparison shown? I did not see any report of the results for the non-permuted version of the Welch's ANOVA.

(4) What are the assumptions for the Phylogenetic Generalized Least Squares? Which evolution model was chosen and why? What is the impact of changing the model? Could the authors define more precisely (e.g. with equations) what is lambda? Is it estimated or fixed?

(5) I think the authors could improve their account of recent literature on the topic. For instance, the paper https://doi.org/10.7554/eLife.93629.3, published in the same journal last year, should be discussed. It perfectly fits in the scope of the subsection "Evidence for the adaptive role of alternative splicing". Methods and findings reported in https://doi.org/10.1186/s13059-021-02441-9 and https://www.genome.org/cgi/doi/10.1101/gr.274696.120 directly concern the assessment of AS evolutionary conservation across long evolutionary times and/or across many species. These aspects are mentioned in the introduction on p.3. but without pointing to such works. Can we really qualify a work published in 2011 as "recent" (line 348-350)?

The generated data and codes are available on Zenodo, which is a good point for reproducibility and knowledge sharing with the community.

Reviewer #3 (Public review):

Summary:

Su et al. sought to understand how the opportunistic pathogen Staphylococcus aureus responds to multiple selection pressures during infection. Specifically, the authors were interested in how the host environment and antibiotic exposure impact the evolution of both virulence and antibiotic resistance in S. aureus. To accomplish this, the authors performed an evolution experiment where S. aureus was fed to Caenorhabditis elegans as a model system to study the host environment and then either subjected to the antibiotic oxacillin or not. Additionally, the authors investigated the difference in evolution between an antibiotic-resistant strain, MRSA, and an isogenic susceptible strain, MSSA. They found that MRSA strains evolved in both antibiotic and host conditions became more virulent, and that strains evolved outside these conditions lost virulence. Looking at the strains evolved in just antibiotic conditions, the authors found that S. aureus maintained its ability to lyse blood cells. Mutations in codY, gdpP, and pbpA were found to be associated with increased virulence. Additionally, these mutations identified in these experiments were found in S. aureus strains isolated from human infections.

Strengths:

The data are well-presented, thorough, and are an important addition to the understanding of how certain pathogens might adapt to different selective pressures in complex environments.

Weaknesses:

There are a few clarifications that could be made to better understand and contextualize the results. Primarily, when comparing the number of mutations and selection across conditions in an evolution experiment, information about population sizes is important to be able to calculate the mutation supply and number of generations throughout the experiment. These calculations can be difficult in vivo, but since several steps in the methodology require plating and regrowth, those population sizes could be determined. There was also no mention of how the authors controlled the inoculation density of bacteria introduced to each host. This would need to be known to calculate the generation time within the host. These caveats should be addressed in the manuscript.

Another concern is the number of generations the populations of S. aureus spent either with relaxed selection in rich media or under antibiotic pressure in between the host exposure periods. It is probable then that the majority of mutations were selected for in these intervening periods between host infection. Again, a more detailed understanding of population sizes would contribute to the understanding of which phase of the experiment contributed to the mutation profile observed.

Reviewer #3 (Public review):

Summary:

This study aimed to investigate pseudouridylation across various RNA species in multiple bacterial strains using an optimized BID-seq approach. It examined both conserved and divergent modification patterns, the potential functional roles of pseudouridylation, and its dynamic regulation across different growth conditions.

Strengths:

The authors optimized the BID-seq method and applied this important technique to bacterial systems, identifying multiple pseudouridylation sites across different species. They investigated the distribution of these modifications, associated sequence motifs, their dynamics across growth phases, and potential functional roles. These data are of great interest to researchers focused on understanding the significance of RNA modifications, particularly mRNA modifications, in bacteria.

Weaknesses:

(1) The reliability of BID-seq data is questionable due to a lack of experimental validations.

(2) The manuscript is not well-written, and the presented work shows a major lack of scientific rigor, as several key pieces of information are missing.

(3) The manuscript's organization requires significant improvement, and numerous instances of missing or inconsistent information make it difficult to understand the key objectives and conclusions of the study.

(4) The rationale for selecting specific bacterial species is not clearly explained, and the manuscript lacks a systematic comparison of pseudouridylation among these species.

Reviewer #3 (Public review):

Summary:

This is a well-done study. It shows, in a comprehensive manner, that Sp5 and Sp8 play essential roles in maintaining the complicated positive feedback circuitry needed for specification of neuromesodermal competent progenitors (NMCs) in caudal mesodermal development in murine embryos.

Strengths:

The developmental genetics, transcriptomic, and genomic survey of TF binding are all satisfactory and make a compelling story. The CRISPR deletion of the Wnt3a downstream enhancer clearly demonstrates that it plays an important role in the positive feedback circuit.

Weaknesses:

My only concerns are some of the language surrounding the mechanistic interpretation of the Wnt3a downstream enhancer and the relationship between TCF and TLE binding.

Reviewer #3 (Public review):

Summary:

It has been a long time since I enjoyed reviewing a paper as much as this one. In it, the authors generate an unprecedented view of the aboral organ of a 5-day-old ctenophore. They proceed to derive numerous insights by reconstructing the populations and connections of cell types, with up to 150 connections from the main Q1-4 neuron.

Strengths:

The strengths of the analysis are the sophisticated imaging methods used, the labor-intensive reconstruction of individual neurons and organelles, and especially the mapping of synapses. The synaptic connections to and from the main coordinating neurons allow the authors to create a polarized network diagram for these components of the aboral organ. These connections give insight into the potential functions of the major neurons. This also gives some unexpected results, particularly the lack of connections from the balancer system to the coordinating system.

Weaknesses:

There were no significant weaknesses in the paper - only a slate of interesting unanswered questions to motivate future studies.

Reviewer #3 (Public review):

Summary:

The authors build on a recent computational model of planning, the "value-guided construal" framework by Ho et al. (2022), which proposes that people plan by constructing simple models of a task, such as by attending to a subset of obstacles in a maze. They analyze both published experimental data and new experimental data from a task in which participants report attention to objects in mazes. The authors find that attention to objects is affected by spatial proximity to other objects (i.e., attentional overspill) as well as whether relevant objects are lateralized to the same hemifield. To account for these results, the authors propose a "spotlight-VGC" model, in which, after calculating attention scores based on the original VGC model, attention to objects is enhanced based on distance. They find that this model better explains participant responses when objects are lateralized to different hemifields. These results demonstrate complex interactions between filtering of task-relevant information and more classical signatures of attentional selection.

Strengths:

(1) The paper builds on existing modeling work in a novel manner and integrates classic results on attention into the computational framework.

(2) The authors report new and extensive analyses of existing data that shed light on additional sources of systematic variability in responses related to attentional spillover effects

(3) They collect new data using new stimuli in the original paradigm that directly test predictions related to the lateralization of task-relevant information, including eye tracking data that allows them to control for possible confounds.

(4) The extended model (spotlight-VGC) provides a formal account of these new results.

Weaknesses:

(1) The spotlight-VGC model has a free parameter - the "width" of the attentional spotlight. This seems to have been fixed to be 3 squares. It would be good if the authors could describe a more principled procedure for selecting the width so that others can use the model in other contexts.

(2) Have the authors considered other ways in which factors such as attentional spillover and lateralization could be incorporated into the model? The spotlight-VGC model, as presented, involves first computing VGC predictions and only afterwards computing spillover. This seems psychologically implausible, since it supposes that the "optimal" representation is first formed and then it gets corrupted. Is there a way to integrate these biases directly into the VGC framework, perhaps as a prior on construals? The authors gesture towards this when they talk about "inductive biases", but this is not formalized.

(3) Can the authors rule out that the lateralization effects are the result of memory biases since the main measure used is a self-report of attention?

Reviewer #3 (Public review):

Summary:

Zhu et al. set out to elucidate how the moral emotions of guilt and shame emerge from specific cognitive antecedents - harm and responsibility - and how these emotions subsequently drive compensatory behavior. Consistent with their prediction derived from functionalist theories of emotion, their behavioral findings indicate that guilt is more influenced by harm, whereas shame is more influenced by responsibility. In line with previous research, their results also demonstrate that guilt has a stronger facilitating effect on compensatory behavior than shame. Furthermore, computational modeling and neuroimaging results suggest that individuals integrate harm and responsibility information into a composite representation of the individual's share of the harm caused. Brain areas such as the striatum, insula, temporoparietal junction, lateral prefrontal cortex, and cingulate cortex were implicated in distinct stages of the processing of guilt and/or shame. In general, this work makes an important contribution to the field of moral emotions. Its impact could be further enhanced by clarifying methodological details, offering a more nuanced interpretation of the findings, and discussing their potential practical implications in greater depth.

Strengths:

First, this work conceptualizes guilt and shame as processes unfolding across distinct stages (cognitive appraisal, emotional experience, and behavioral response) and investigates the psychological and neural characteristics associated with their transitions from one stage to the next.

Second, the well-designed experiment effectively manipulates harm and responsibility - two critical antecedents of guilt and shame.

Third, the findings deepen our understanding of the mechanisms underlying guilt and shame beyond what has been established in previous research.

Weaknesses:

(1) Over the course of the task, participants may gradually become aware of their high error rate in the dot estimation task. This could lead them to discount their own judgments and become inclined to rely on the choices of other deciders. It is unclear whether participants in the experiment had the opportunity to observe or inquire about others' choices. This point is important, as the compensatory decision-making process may differ depending on whether choices are made independently or influenced by external input.

(2) Given the inherent complexity of human decision-making, it is crucial to acknowledge that, although the authors compared eight candidate models, other plausible alternatives may exist. As such, caution is warranted when interpreting the computational modeling results.

(3) I do not agree with the authors' claim that "computational modeling results indicated that individuals integrate harm and responsibility in the form of a quotient" (i.e., harm/responsibility). Rather, the findings appear to suggest that individuals may form a composite representation of the harm attributable to each individual (i.e., harm/the number of people involved). The explanation of the modeling results ought to be precise.

(4) Many studies have reported positive associations between trait gratitude, social value orientation, and altruistic behavior. It would be helpful if the authors could provide an explanation about why this study failed to replicate these associations.

(5) As the authors noted, guilt and shame are closely linked to various psychiatric disorders. It would be valuable to discuss whether this study has any implications for understanding or even informing the treatment of these disorders.

Reviewer #3 (Public review):

This study is a follow-up to a recent study of synaptic development based on a powerful data set that combines anterograde labeling, immunofluorescence labeling of synaptic proteins, and STORM imaging (Cell Reports, 2023). Specifically, they use anti-Vglut2 label to determine the size of the presynaptic structure (which they describe as the vesicle pool size), anti-Bassoon to label active zones with the resolution to count them, and anti-Homer to identify postsynaptic densities. Their previous study compared the detailed synaptic structure across the development of synapses made with contra-projecting vs. ipsi-projecting RGCs and compared this developmental profile with a mouse model with reduced retinal waves. In this study, they produce a new detailed analysis on the same data set in which they classify synapses into "multi-active zone" vs. "single-active zone" synapses and assess the number and spacing of these synapses. The authors use measurements to make conclusions about the role of retinal waves in the generation of same-eye synaptic clusters. The authors interpret these results as providing insight into how neural activity drives synapse maturation, the strength of their conclusions is not directly tested by their analysis.

Strengths:

This is a fantastic data set for describing the structural details of synapse development in a part of the brain undergoing activity-dependent synaptic rearrangements. The fact that they can differentiate the eye of origin is what makes this data set unique over previous structural work. The addition of example images from the EM dataset provides confidence in their categorization scheme.

Weaknesses:

Though the descriptions of single vs multi-active zone synapses are important and represent a significant advance, the authors continue to make unsupported conclusions regarding the biological processes driving these changes. Although this revision includes additional information about the populations tested and the tests conducted, the authors do not address the issue raised by previous reviews. Specifically, they provide no assessment of what effect size represents a biologically meaningful result. For example, a more appropriate title is "The distribution of eye-specific single vs multi-active zone is altered in mice with reduced spontaneous activity" rather than concluding that this difference in clustering is somehow related to synaptic competition. Of course, the authors are free to speculate, but many of the conclusions of the paper are not supported by their results.

Reviewer #3 (Public review):

Summary:

The present manuscript investigates and proposes different mechanisms for the effects of two therapeutic approaches - cognitive distancing technique and use of antidepressants - on subjective ratings of happiness, confidence, and task engagement, and on the influence of such subjective experiences on choice behavior. Both approaches were found to link to changes in affective state dynamics in a choice task, specifically reduced drift (cognitive distancing) and increased baseline (antidepressant use). Results also suggest that cognitive distancing may reduce the weighing of recent expected values in the happiness model, while antidepressant use may reduce forgetting of choices and outcomes.

Strengths:

This is a timely topic and a significant contribution to ongoing efforts to improve our mechanistic understanding of psychopathology and devise effective novel interventions. The relevance of the manuscript's central question is clear, and the links to previous literature and the broader field of computational psychiatry are well established. The modelling approaches are thoughtful and rigorously tested, with appropriate model checks and persuasive evidence that modelling complements the theoretical argument and empirical findings.

Weaknesses:

Some vagueness and lack of clarity in theoretical mechanisms and interpretation of results leave outstanding questions regarding (a) the specific links drawn between affective biases, therapies aimed at mitigating them, and mental health function, and (b) the structure and assumptions of the modelling, and how they support the manuscript's central claims. Broadly, I do not fully understand the distinction between how choice behavior vs. affect are impacted separately or together by cognitive distancing. Clarification on this point is needed, possibly through a more explicit proposal of a mechanism (or several alternative mechanisms?) in the introduction and more explicit interpretation of the modelling results in the context of the cyclical choice-affect mechanism.

(1) Theoretical framework and proposed mechanisms

The link between affective biases and negative thinking patterns is a bit unclear. The authors seem to make a causal claim that "affective biases are precipitated and maintained by negative thinking patterns", but it is unclear what precisely these negative patterns are; earlier in the same paragraph, they state that affective biases "cause low mood" and possibly shift choices toward those that maintain low mood. So the directionality of the mechanism here is unclear - possibly explaining a bit more of the cyclic nature of this mechanism, and maybe clarifying what "negative thinking patterns" refer to will be helpful.

More generally, this link between affect and choices, especially given the modelling results later on, should be clarified further. What is the mechanism by which these two impact each other? How do the models of choice and affect ratings in the RL task test this mechanism? I'm not quite sure the paper answers these questions clearly right now.

The authors also seem to implicitly make the claim that symptoms of mental ill-health are at least in part related to choice behavior. I find this a persuasive claim generally; however, it is understated and undersupported in the introduction, to the point where a reader may need to rely on significant prior knowledge to understand why mitigating the impact of affective biases on choice behavior would make sense as the target of therapeutic interventions. This is a core tenet of the paper, and it would be beneficial to clarify this earlier on.

It would be helpful to interpret a bit more clearly the findings from 3.4. on decreased drift in all three subjective assessments in the cognitive distancing group. What is the proposed mechanism for this? The discussion mentions that "attenuated declines [...] over time, [add] to our previously reported findings that this psychotherapeutic technique alters aspects of reward learning" - but this is vague and I do not understand, if an explanation for how this happens is offered, what that explanation is. Given the strong correlation of the drift with fatigue, is the explanation that cognitive distancing mitigates affect drift under fatigue? Or is this merely reporting the result without an interpretation around potential mechanisms?

(Relatedly, aside from possibly explaining the drift parameter, do the fatigue ratings link with choice behavior in any way? Is it possible that the cognitive distancing was helping participants improve choices under fatigue?)

(2) Task Structure and Modelling

It is unclear what counted as a "rewarding" vs. "unrewarding" trial in the model. From my understanding of the task description, participants obtained positive or no reward (no losses), and verbal feedback, Correct/Incorrect. But given the probabilistic nature of the task, it follows that even some correct choices likely had unrewarding results. Was the verbal feedback still "Correct" in those cases, but with no points shown? I did not see any discussion on whether it is the #points earned or the verbal feedback that is considered a reward in the model. I am assuming the former, but based on previous literature, likely both play a role; so it would be interesting - and possibly necessary to strengthen the paper's argument - to see a model that assigns value to positive/negative feedback and earned points separately.

From a theory perspective, it's interesting that the authors chose to assume separate learning rates for rewarding and non-rewarding trials. Why not, for example, separate reward sensitivity parameters? E.g., rather than a scaling parameter on the PE, a parameter modifying the r term inside the PE equation to, perhaps, assign different values to positive and zero points? (While I think overall the math works out similarly at the fitting time, this type of model should be less flexible on scaling the expected value and more flexible on scaling the actual #points / the subjective experience of the obtained verbal feedback, which seems more in line with the theoretical argument made in the introduction). The introduction explicitly states that negative biases "may cause low mood by making outcomes appear less rewarding" - which in modelling equations seems more likely to translate to different reward-perception biases, and not different learning rates. Alternatively, one might incorporate a perseveration parameter (e.g., similar to Collins et al. 2014) that would also accomplish a negative bias. Either of these two mechanisms seems perhaps worth testing out in a model - especially in a model that defines more clearly what rewarding vs. unrewarding may mean to the participant.

If I understand correctly, the affect ratings models assume that the Q-value and the PE independently impact rating (so they have different weights, w2 and w3), but there is no parameter allowing for different impact for perceived rewarding and unrewarding outcomes? (I may be misreading equations 4-5, but if not, Q-value and PE impact the model via static rather than dynamic parameters.) Given the joint RL-affect fit, this seems to carry the assumption that any perceptual processing differences leading to different subjective perceptions of reward associated with each outcome only impact choice behavior, but not affect? (whereas affect is more broadly impacted, if I'm understanding this correctly, just by the magnitude of the values and PEs?) This is an interesting assumption, and the authors seem to have tested it a bit more in the Supplementary material, as shown in Figure S4. I'm wondering why this was excluded from the main text - it seems like the more flexible model found some potentially interesting differences which may be worth including, especially as they might shed additional insight into the influence of cognitive distancing on the cyclical choice-affect mechanisms proposed.

Minor comments:

If fatigue ratings were strongly associated with drift in the best-fitting model (as per page 13), I wonder if it would make sense to use those fatigue ratings as a proxy rather than allow the parameter to vary freely? (This does not in any way detract from the winning model's explanatory power, but if a parameter seems to be strongly explained by a variable we have empirical data for, it's not clear what extra benefit is earned by having that parameter in the model).

Reviewer #3 (Public review):

Summary:

This report describes the development and initial applications of the ARM (Automated Reproducible Mechano-stimulator), a programmable tool that delivers various mechanical stimuli to a select target (most frequently, a rodent hindpaw). Comparisons to traditional testing methods (e.g., experimenter application of stimuli) reveal that the ARM reduces variability in the anatomical targeting, height, velocity, and total time of stimulus application. Given that the ARM can be controlled remotely, this device was also used to assess effects of experimenter presence on reflexive responses to mechanical stimulation. Although not every experimenter had notable sex-dependent effects on animal behavior, use of the ARM never had this effect (for obvious reasons!). Lastly, the ARM was used to stimulate rodent hindpaws while measuring neuronal activity in the basolateral nucleus of the amygdala (BLA), a brain region that is associated with the negative affect of pain. This device, and similar automated devices, will undoubtedly reduce experimenter-related variability in reflexive mechanical behavior tests; this may increase experimental reproducibility between laboratories who are able to invest in this type of technology.

Strengths:

Clear examples of variability in experimenter stimulus application are provided and then contrasted with uniform stimulus application that is inherent to the ARM.

The ARM is able to quickly oscillate between delivery of various mechanical stimuli; this is advantageous for experimental efficiency.

New additions to the ARM and PAWS platforms have been methodically tested to ensure reproducibility and reliability.

Reviewer #3 (Public review):

Summary:

The authors have identified novel dRTA causing SLC4A1 mutations and studied the resulting kAE1 proteins to determine how they cause dRTA. Based on a previous study on mice expressing the dRTA kAE1 R607H variant, the authors hypothesize that kAE1 variants cause an increase in intracellular pH, which disrupts autophagic and degradative flux pathways. The authors clone these new kAE1 variants and study their transport function and subcellular localization in mIMCD cells. The authors show increased abundance of LC3B II in mIMCD cells expressing some of the kAE1 variants, as well as reduced autophagic flux using eGFP-RFP-LC3. These data, as well as the abundance of autophagosomes, serve as the key evidence that these kAE1 mutants disrupt autophagy. Furthermore, the authors demonstrate that decreasing the intracellular pH abrogates the expression of LC3B II in mIMCD cells expressing mutant SLC4A1. Lastly, the authors argue that mitochondrial function, and specifically ATP synthesis, is suppressed in mIMCD cells expressing dRTA variants and that mitochondria are less abundant in AICs from the kidney of R607H kAE1 mice. While the manuscript does reveal some interesting new results about novel dRTA causing kAE1 mutations, the quality of the data to support the hypothesis that these mutations cause a reduction in autophagic flux can be improved. In particular, the precise method of how the western blots and the immunofluorescence data were quantified, with included controls, would enhance the quality of the data and offer more supportive evidence of the authors' conclusions.

Strengths:

The authors cloned novel dRTA causing kAE1 mutants into expression vectors to study the subcellular localization and transport properties of the variants. The immunofluorescence images are generally of high quality, and the authors do well to include multiple samples for all of their western blots.

Weaknesses:

Inconsistent results are reported for some of the variants. For example, R295H causes intracellular alkalinization but also has no effect on intracellular pH when measured by BCECF. The authors also appear to have performed these in vitro studies on mIMCD cells that were not polarized, and therefore, the localization of kAE1 to the basolateral membrane seems unlikely, based upon images included in the manuscript. Additionally, there is no in vivo work to demonstrate that these kAE1 variants alter intracellular pH, including the R607H mouse, which is available to the authors. The western blots are of varying quality, and it is often unclear which of the bands are being quantified. For example, LAMP1 is reported at 100kDa, the authors show three bands, and it is unclear which one(s) are used to quantify protein abundance. Strikingly, the authors report a nonsensical value for their quantification of LCRB II in Figure 2, where the ratio of LCRB II to total LCRB (I + II) is greater than one. The control experiments with starvation and bafilomyocin are not supportive and significantly reduce enthusiasm for the authors' findings regarding autophagy. There are labeling errors between the manuscript and the figures, which suggest a lack of vigilance in the drafting process.

Reviewer #3 (Public review):

Summary:

The response to lysosomal damage is a fast-moving and timely field. Besides repair and degradation pathways, increasing interest has been focusing on damaged-induced signaling. The authors conducted both transcriptomics and proteomics to characterize the cellular response to lysosomal damage. They identify a signaling pathway leading to activation of NFkappaB. Based on this and supported by Western blot and microscopy data, the authors nicely show that TAB2/3 and TAK1 are activated at damaged lysosomes and kick off the pathway to alter gene expression, which induces cytokines and protect from cell death. TAB2/3 activation is proposed to occur through K63 ubiquitin chain formation. Generally, this is a careful and well conducted study that nicely delineates the pathway under lysosomal stress. The "omics" data serves a valuable resource for the field. More work should be invested into how TAB2/3 are activated at the damaged lysosomes, also to increase novelty in light of previous reports.

Strengths:

Generally, this is a careful and well-conducted study that nicely delineates how the NFkB pathway is activated under lysosomal stress and modulates cell behavior. The "omics" data serves as a valuable resource for the field.

Weaknesses:

While activation of TAB2/3 by K63-linked Ub chains is convincing, more work needs to be done on how they are recruited by distinct damage types to probe relevance for different pathophysiological conditions."

Comments on revisions:

The authors have addressed much of my criticism. Specifically, they have put (with new experiments) the data on the TAB2/3-TAK1 pathway in perspective to the previously reported LUBAC-mediated activation of NFkB. They also addressed the question about the significance of K63-linked chains for TAB2/3 activation with new complementation experiments (a K63-specific NZF mutant failed to rescue).

The third point (types of damage as triggers) raises more questions, though. The authors find that, in contrast to LLOMe, GPN or DC661-induced damage does not activate TAK1 (consistent with lower damage levels). However, the authors still observe K63 ubiquitylation. This goes along with their finding that TAB2 is recruited in the absence of any ubiquitylation (blocked by TAK-243). It argues that TAB2 is recruited by an unknown cue (that may be damage-specific) and then activated by K63. The authors need to clarify whether TAB2 is or is not recruited in the GPN/DC661 conditions (in which K63 occurs, but TAK1 is not activated). The point about the effects of other damage types was also raised by reviewer #1 and should be solved. The fact that TAB2 is recruited independently of K63 should also be visualized in the model. The manuscript will then be an important contribution to the field.

Reviewer #3 (Public review):

Summary:

This study by Bushey et al. adapts and evaluates two newly developed red-shifted optogenetic inhibitors, A1ACR1 and HfACR1, collectively referred to as RubyACRs, for neuronal silencing in Drosophila melanogaster. Traditional optogenetic inhibitors such as GtACR1 and GtACR2 are activated by green (~515 nm) and blue (~470 nm) light, respectively, which poses several limitations in Drosophila. Specifically, shorter-wavelength light suffers from reduced tissue penetration and increased absorption, and is visible to flies, potentially confounding behavioral assays, particularly those involving visual processing. In contrast, RubyACRs are activated by red light (~610-660 nm), which penetrates the cuticle more effectively and thus can be more potent in manipulating fly behavior. In the current manuscript, the authors first demonstrate that both A1ACR1 and HfACR1 can be robustly expressed in fly neurons and are properly trafficked to the plasma membrane. Upon red-light stimulation, both opsins produce strong and sustained hyperpolarization in larval motor neurons, outperforming GtACR1 in both magnitude and temporal dynamics. Next, using two-photon calcium imaging in the visual system, the authors further demonstrate that activation of RubyACRs significantly reduces GCaMP6s signal, indicating that they can reliably inhibit neuronal activity. Importantly, unlike reported in some mammalian studies, RubyACRs do not appear to trigger paradoxical depolarization at axon terminals in the fly visual system, as no evidence of aberrant depolarization is observed in motion-detecting Mi1 neurons.

In the second part of the manuscript, the authors characterize the effects of RubyACRs on fly behavior (walking, learning, and courtship song). Using the inhibition of genetically labelled neurons that regulate these behaviors, the authors demonstrate that stimulation of RubyACRs leads to potent suppression of locomotion, courtship song, or dopamine-dependent associative learning.

Strengths:

Altogether, the experiments conducted in this manuscript demonstrate that RubyACRs are powerful tools for optogenetic inhibition in Drosophila, with advantages in spectral compatibility, behavioral specificity, and potential applications in vivo two-photon calcium imaging.

Weaknesses:

The manuscript is strong, but it can be further improved with a few additional analyses and minor revisions. Especially, a more detailed evaluation of RubyACRs with two-photon excitation will help clarify to what extent these opsins can be simultaneously used together with green GECIs, such as GCaMPs.

Reviewer #3 (Public review):

Summary:

In this manuscript titled "Mycobacterial Metallophosphatase MmpE Acts as a Nucleomodulin to Regulate Host Gene Expression and Promote Intracellular Survival", Chen et al describe biochemical characterisation, localisation and potential functions of the gene using a genetic approach in M. bovis BCG and perform macrophage and mice infections to understand the roles of this potentially secreted protein in the host cell nucleus. The findings demonstrate the role of a secreted phosphatase of M. bovis BCG in shaping the transcriptional profile of infected macrophages, potentially through nuclear localisation and direct binding to transcriptional start sites, thereby regulating the inflammatory response to infection.

Strengths:

The authors demonstrate using a transient transfection method that MmpE when expressed as a GFP-tagged protein in HEK293T cells, exhibits nuclear localisation. The authors identify two NLS motifs that together are required for nuclear localisation of the protein. A deletion of the gene in M. bovis BCG results in poorer survival compared to the wild-type parent strain, which is also killed by macrophages. Relative to the WT strain-infected macrophages, macrophages infected with the ∆mmpE strain exhibited differential gene expression. Overexpression of the gene in HEK293T led to occupancy of the transcription start site of several genes, including the Vitamin D Receptor. Expression of VDR in THP1 macrophages was lower in the case of ∆mmpE infection compared to WT infection. This data supports the utility of the overexpression system in identifying potential target loci of MmpE using the HEK293T transfection model. The authors also demonstrate that the protein is a phosphatase, and the phosphatase activity of the protein is partially required for bacterial survival but not for the regulation of the VDR gene expression.

Weaknesses:

(1) While the motifs can most certainly behave as NLSs, the overexpression of a mycobacterial protein in HEK293T cells can also result in artefacts of nuclear localisation. This is not unprecedented. Therefore, to prove that the protein is indeed secreted from BCG, and is able to elicit transcriptional changes during infection, I recommend that the authors (i) establish that the protein is indeed secreted into the host cell nucleus, and (ii) the NLS mutation prevents its localisation to the nucleus without disrupting its secretion.

Demonstration that the protein is secreted: Supplementary Figure 3 - Immunoblotting should be performed for a cytosolic protein, also to rule out detection of proteins from lysis of dead cells. Also, for detecting proteins in the secreted fraction, it would be better to use Sauton's media without detergent, and grow the cultures without agitation or with gentle agitation. The method used by the authors is not a recommended protocol for obtaining the secreted fraction of mycobacteria.

Demonstration that the protein localises to the host cell nucleus upon infection: Perform an infection followed by immunofluorescence to demonstrate that the endogenous protein of BCG can translocate to the host cell nucleus. This should be done for an NLS1-2 mutant expressing cell also.

(2) In the RNA-seq analysis, the directionality of change of each of the reported pathways is not apparent in the way the data have been presented. For example, are genes in the cytokine-cytokine receptor interaction or TNF signalling pathway expressed more, or less in the ∆mmpE strain?

(3) Several of these pathways are affected as a result of infection, while others are not induced by BCG infection. For example, BCG infection does not, on its own, produce changes in IL1β levels. As the authors did not compare the uninfected macrophages as a control, it is difficult to interpret whether ∆mmpE induced higher expression than the WT strain, or simply did not induce a gene while the WT strain suppressed expression of a gene. This is particularly important because the strain is attenuated. Does the attenuation have anything to do with the ability of the protein to induce lysosomal pathway genes? Does induction of this pathway lead to attenuation of the strain? Similarly, for pathways that seem to be downregulated in the ∆mmpE strain compared to the WT strain, these might have been induced upon infection with the WT strain but not sufficiently by the ∆mmpE strain due to its attenuation/ lower bacterial burden.

(4) CHIP-seq should be performed in THP1 macrophages, and not in HEK293T. Overexpression of a nuclear-localised protein in a non-relevant line is likely to lead to several transcriptional changes that do not inform us of the role of the gene as a transcriptional regulator during infection.

(5) I would not expect to see such large inflammatory reactions persisting 56 days post-infection with M. bovis BCG. Is this something peculiar for an intratracheal infection with 1x107 bacilli? For images of animal tissue, the authors should provide images of the entire lung lobe with the zoomed-in image indicated as an inset.

(6) For the qRT-PCR based validation, infections should be performed with the MmpE-complemented strain in the same experiments as those for the WT and ∆mmpE strain so that they can be on the same graph, in the main manuscript file. Supplementary Figure 4 has three complementary strains. Again, the absence of the uninfected, WT, and ∆mmpE infected condition makes interpretation of these data very difficult.

(7) The abstract mentions that MmpE represses the PI3K-Akt-mTOR pathway, which arrests phagosome maturation. There is not enough data in this manuscript in support of this claim. Supplementary Figure 5 does provide qRT-PCR validation of genes of this pathway, but the data do not indicate that higher expression of these pathways, whether by VDR repression or otherwise, is driving the growth restriction of the ∆mmpE strain.

(8) The relevance of the NLS and the phosphatase activity is not completely clear in the CFU assays and in the gene expression data. Firstly, there needs to be immunoblot data provided for the expression and secretion of the NLS-deficient and phosphatase mutants. Secondly, CFU data in Figure 3A, C, and E must consistently include both the WT and ∆mmpE strain.

Reviewer #3 (Public review):

Summary:

In this manuscript, the authors examine the processing stages involved in perceptual decision-making using a new approach to analysing EEG data, combined with a critical stimulus manipulation. This new EEG analysis method enables single-trial estimates of the timing and amplitude of transient changes in EEG time-series, recurrent across trials in a behavioural task. The authors find evidence for three events between stimulus onset and the response in a two-spatial-interval visual discrimination task. By analysing the timing and amplitude of these events in relation to behaviour and the stimulus manipulation, the authors interpret these events as related to separable processing stages for stimulus encoding, attention orientation, and decision (deliberation). This is largely consistent with previous findings from both event-related potentials (across trials) and single-trial estimates using decoding techniques and neural network approaches.

Strengths:

This work is not only important for the conceptual advance, but also in promoting this new analysis technique, which will likely prove useful in future research. For the broader picture, this work is an excellent example of the utility of neural measures for mental chronometry.

Weaknesses:

The manuscript would benefit from some conceptual clarifications, which are important for readers to understand this manuscript as a stand-alone work. This includes clearer definitions of Piéron's and Fechner's laws, and a fuller description of the EEG analysis technique. The manuscript, broadly, but the introduction especially, may be improved by clearly delineating the multiple aims of this project: examining the processes for decision-making, obtaining single-trial estimates of meaningful EEG-events, and whether central parietal positivity reflects ramping activity or steps averaged across trials. A fuller discussion of the limitations of the work, in particular, the absence of motor contributions to reaction time, would also be appreciated.

At times, the novelty of the work is perhaps overstated. Rather, readers may appreciate a more comprehensive discussion of the distinctions between the current work and previous techniques to gauge single-trial estimates of decision-related activity, as well as previous findings concerning distinct processing stages in decision-making. Moreover, a discussion of how the events described in this study might generalise to different decision-making tasks in different contexts (for example, in auditory perception, or even value-based decision-making) would also be appreciated.

Reviewer #3 (Public review):

Summary:

This manuscript presents a well-designed and insightful behavioural study examining human adaptation to room acoustics, building on prior work by Brandewie & Zahorik. The psychophysical results are convincing and add incremental but meaningful knowledge to our understanding of reverberation learning. However, I find the transcranial magnetic stimulation (TMS) component to be over-interpreted. The TMS protocol, while interesting, lacks sufficient anatomical specificity and mechanistic explanation to support the strong claims made regarding a unique role of the dorsolateral prefrontal cortex (dlPFC) in this learning process. More cautious interpretation is warranted, especially given the modest statistical effects, the fact that the main TMS result of interest is a null result, the imprecise targeting of dlPFC (which is not validated), and the lack of knowledge about the timescale of TMS effects in relation to the behavioural task. I recommend revising the manuscript to shift emphasis toward the stronger behavioural findings and to present a more measured and transparent discussion of the TMS results and their limitations.

Strengths:

(1) Well-designed acoustical stimuli and psychophysical task.

(2) Comparisons across room combinations are well conducted.

(3) The virtual acoustic environment is impressive and applied well here.

(4) A timely study with interesting behavioural results.

Weaknesses:

(1) Lack of hypotheses, particularly for TMS.

(2) Lack of evidence for targeting TMS in [brain] space and time.

(3) The most interesting effect of TMS is a null result compared to a weak statistical effect for "meta adaptation"

Reviewer #3 (Public review):

Summary:

The authors review published literature and propose that a visual cortical region in the mouse that is widely considered to contain multiple visual areas should be considered a single visual area.

Strengths:

The authors point out that relatively new data showing reversals of visual-field sign within known, single visual areas of some species require that a visual field sign change by itself should not be considered evidence for a border between visual areas.

Weaknesses:

The existing data are not consistent with the authors' proposal to consolidate multiple mouse areas into a single "V2". This is because the existing definition of a single area is that it cannot have redundant representations of the visual field. The authors ignore this requirement, as well as the data and definitions found in published manuscripts, and make an inaccurate claim that "higher order visual areas in the mouse do not have overlapping representations of the visual field". For quantification of the extent of overlap of representations between 11 mouse visual areas, see Figure 6G of Garrett et al. 2014. [Garrett, M.E., Nauhaus, I., Marshel, J.H., and Callaway, E.M. (2014). Topography and areal organization of mouse visual cortex. The Journal of neuroscience 34, 12587-12600. 10.1523/JNEUROSCI.1124-14.2014.

Reviewer #3 (Public review):

Summary:

The authors use calcium recordings from STN to measure STN activity during spontaneous movement and in a multi-stage avoidance paradigm. They also use optogenetic excitation, optogenetic inhibition, and lesion approaches to increase or decrease the activity of STN during the avoidance paradigm. The paper reports a large amount of data and makes many claims, some seem well supported to this Reviewer, others not so much.

Strengths:

Well-supported claims include data showing that during spontaneous movements, especially contraversive ones, STN calcium activity is increased using bulk photometry measurements. Single-cell measures back this claim but also show that it is only a modest minority of STN cells that respond strongly, with most showing no response during movement, and a similar number showing smaller inhibitions during movement.

Similar data during cued active avoidance procedures show that STN calcium activity sharply increases in response to auditory cues, and during cued movements to avoid a footshock. Optogenetic and lesion experiments are consistent with an important role for STN in generating cue-evoked avoidance. And a strength of these results is that multiple bi-directional approaches were used.

Weaknesses:

I found the experimental design and presentation convoluted and the results over-interpreted.

(1) I really don't understand or accept this idea that delayed movement is necessarily indicative of cautious movements. Is the distribution of responses multi-modal in a way that might support this idea, or do the authors simply take a normal distribution and assert that the slower responses represent 'caution'? Even if responses are multi-modal and clearly distinguished by 'type', why should readers think this that delayed responses imply cautious responding instead of say: habituation or sensitization to cue/shock, variability in attention, motivation, or stress; or merely uncertainty which seems plausible given what I understand of the task design where the same mice are repeatedly tested in changing conditions. This relates to a major claim (i.e., in the work's title).

(2) Related to the last, I'm struggling to understand the rationale for dividing cells into 'types' based the their physiological responses in some experiments (e.g., Figure 7).

(3) The description and discussion of orienting head movements were not well supported, but were much discussed in the avoidance datasets. The initial speed peaks to cue seem to be the supporting data upon which these claims rest, but nothing here suggests head movement or orientation responses.

(4) Similar to the last, the authors note in several places, including abstract, the importance of STN in response timing, i.e., particularly when there must be careful or precise timing, but I don't think their data or task design provides a strong basis for this claim.

(5) I think that other reports show that STN calcium activity is recruited by inescapable foot shock as well. What do these authors see? Is shock, independent of movement, contributing to sharp signals during escapes?

(6) In particular, and related to the last point, the following work is very relevant and should be cited: https://elifesciences.org/reviewed-preprints/104643#tab-content. Note that the focus of this other paper is on a subset of VGLUT2+ Tac1 neurons in paraSTN, but using VGLUT2-Cre to target STN will target both STN and paraSTN.

(7) In multiple other instances, claims that were more tangential to the main claims were made without clearly supporting data or statistics. E.g., claim that STN activation is related to translational more than rotational movement; claim that GCaMP and movement responses to auditory cues were small; claims that 'some animals' responded differently without showing individual data.

(8) In several figures, the number of subjects used was not described. This is necessary. Also necessary is some assessment of the variability across subjects. The only measure of error shown in many figures relates to trial-to-trial or event variability, which is minimal because, in many cases, it appears that hundreds of trials may have been averaged per animal, but this doesn't provide a strong view of biological variability. When bar/line plots are used to display data, I recommend showing individual animals where feasible.

(9) Can the authors consider the extent to which calcium imaging may be better suited to identify increases compared to decreases and how this may affect the results, particularly related to the GRIN data when similar numbers of cells show responses in both directions (e.g., Figure 3)?

(10) Raw example traces are not provided.

(11) The timeline of the spontaneous movement and avoidance sessions was not clear, nor was the number of events or sessions per animal nor how this was set. It is not clear if there was pre-training or habituation, if many or variable sessions were combined per animal, or what the time gaps between sessions were, or if or how any of these parameters might influence interpretation of the results.

(12) It is not clear if or how the spread of expression outside of the target STN was evaluated, and if or how many mice were excluded due to spread or fiber placements.

Reviewer #3 (Public review):

Summary:

The authors recorded brain responses while participants viewed images and captions. The images and captions were taken from the COCO dataset, so each image has a corresponding caption, and each caption has a corresponding image. This enabled the authors to extract features from either the presented stimulus or the corresponding stimulus in the other modality. The authors trained linear decoders to take brain responses and predict stimulus features. "Modality-specific" decoders were trained on brain responses to either images or captions, while "modality-agnostic" decoders were trained on brain responses to both stimulus modalities. The decoders were evaluated on brain responses while the participants viewed and imagined new stimuli, and prediction performance was quantified using pairwise accuracy. The authors reported the following results:

(1) Decoders trained on brain responses to both images and captions can predict new brain responses to either modality.

(2) Decoders trained on brain responses to both images and captions outperform decoders trained on brain responses to a single modality.

(3) Many cortical regions represent the same concepts in vision and language.

(4) Decoders trained on brain responses to both images and captions can decode brain responses to imagined scenes.

Strengths:

This is an interesting study that addresses important questions about modality-agnostic representations. Previous work has shown that decoders trained on brain responses to one modality can be used to decode brain responses to another modality. The authors build on these findings by collecting a new multimodal dataset and training decoders on brain responses to both modalities.

To my knowledge, SemReps-8K is the first dataset of brain responses to vision and language where each stimulus item has a corresponding stimulus item in the other modality. This means that brain responses to a stimulus item can be modeled using visual features of the image, linguistic features of the caption, or multimodal features derived from both the image and the caption. The authors also employed a multimodal one-back matching task, which forces the participants to activate modality-agnostic representations. Overall, SemReps-8K is a valuable resource that will help researchers answer more questions about modality-agnostic representations.

The analyses are also very comprehensive. The authors trained decoders on brain responses to images, captions, and both modalities, and they tested the decoders on brain responses to images, captions, and imagined scenes. They extracted stimulus features using a range of visual, linguistic, and multimodal models. The modeling framework appears rigorous, and the results offer new insights into the relationship between vision, language, and imagery. In particular, the authors found that decoders trained on brain responses to both images and captions were more effective at decoding brain responses to imagined scenes than decoders trained on brain responses to either modality in isolation. The authors also found that imagined scenes can be decoded from a broad network of cortical regions.

Weaknesses:

The characterization of "modality-agnostic" and "modality-specific" decoders seems a bit contradictory. There are three major choices when fitting a decoder: the modality of the training stimuli, the modality of the testing stimuli, and the model used to extract stimulus features. However, the authors characterize their decoders based on only the first choice-"modality-specific" decoders were trained on brain responses to either images or captions, while "modality-agnostic" decoders were trained on brain responses to both stimulus modalities. I think that this leads to some instances where the conclusions are inconsistent with the methods and results.

First, the authors suggest that "modality-specific decoders are not explicitly encouraged to pick up on modality-agnostic features during training" (line 137) while "modality-agnostic decoders may be more likely to leverage representations that are modality-agnostic" (line 140). However, whether a decoder is required to learn modality-agnostic representations depends on both the training responses and the stimulus features. Consider the case where the stimuli are represented using linguistic features of the captions. When you train a "modality-specific" decoder on image responses, the decoder is forced to rely on modality-agnostic information that is shared between the image responses and the caption features. On the other hand, when you train a "modality-agnostic" decoder on both image responses and caption responses, the decoder has access to the modality-specific information that is shared by the caption responses and the caption features, so it is not explicitly required to learn modality-agnostic features. As a result, while the authors show that "modality-agnostic" decoders outperform "modality-specific" decoders in most conditions, I am not convinced that this is because they are forced to learn more modality-agnostic features.

Second, the authors claim that "modality-specific decoders can be applied only in the modality that they were trained on, while "modality-agnostic decoders can be applied to decode stimuli from multiple modalities, even without knowing a priori the modality the stimulus was presented in" (line 47). While "modality-agnostic" decoders do outperform "modality-specific" decoders in the cross-modality conditions, it is important to note that "modality-specific" decoders still perform better than expected by chance (figure 5). It is also important to note that knowing about the input modality still improves decoding performance even for "modality-agnostic" decoders, since it determines the optimal feature space-it is better to decode brain responses to images using decoders trained on image features, and it is better to decode brain responses to captions using decoders trained on caption features.

Reviewer #3 (Public review):

Summary

This paper investigates how disinformation affects reward learning processes in the context of a two-armed bandit task, where feedback is provided by agents with varying reliability (with lying probability explicitly instructed). They find that people learn more from credible sources, but also deviate systematically from optimal Bayesian learning: They learned from uninformative random feedback, learned more from positive feedback, and updated too quickly from fully credible feedback (especially following low-credibility feedback). Overall, this study highlights how misinformation could distort basic reward learning processes, without appeal to higher order social constructs like identity.

Strengths

• The experimental design is simple and well-controlled; in particular, it isolates basic learning processes by abstracting away from social context
• Modeling and statistics meet or exceed standards of rigor
• Limitations are acknowledged where appropriate, especially those regarding external validity
• The comparison model, Bayes with biased credibility estimates, is strong; deviations are much more compelling than e.g. a purely optimal model
• The conclusions are of substantial interest from both a theoretical and applied perspective

Weaknesses

The authors have addressed most of my concerns with the initial submission. However, in my view, evidence for the conclusion that less credible feedback yields a stronger positivity bias remains weak. This is due to two issues.

Absolute or relative positivity bias?

The conclusion of greater positivity bias for lower credible feedback (Fig 5) hinges on the specific way in which positivity bias is defined. Specifically, we only see the effect when normalizing the difference in sensitivity to positive vs. negative feedback by the sum. I appreciate that the authors present both and add the caveat whenever they mention the conclusion. However, without an argument that the relative definition is more appropriate, the fact of the matter is that the evidence is equivocal.

There is also a good reason to think that the absolute definition is more appropriate. As expected, participants learn more from credible feedback. Thus, normalizing by average learning (as in the relative definition) amounts to dividing the absolute difference by increasingly large numbers for more credible feedback. If there is a fixed absolute positivity bias (or something that looks like it), the relative bias will necessarily be lower for more credible feedback. In fact, the authors own results demonstrate this phenomenon (see below). A reduction in relative bias thus provides weak evidence for the claim.

It is interesting that the discovery study shows evidence of a drop in absolute bias. However, for me, this just raises questions. Why is there a difference? Was one a just a fluke? If so, which one?

Positivity bias or perseveration?

Positivity bias and perseveration will both predict a stronger relationship between positive (vs. negative) feedback and future choice. They can thus be confused for each other when inferred from choice data. This potentially calls into question all the results on positivity bias.

The authors clearly identify this concern in the text and go to considerable lengths to rule it out. However, the new results (in revision 1) show that a perseveration-only model can in fact account for the qualitative pattern in the human data (the CA parameters). This contradicts the current conclusion:

Critically, however, these analyses also confirmed that perseveration cannot account for our main finding of increased positivity bias, relative to the overall extent of CA, for low-credibility feedback.

Figure 24c shows that the credibility-CA model does in fact show stronger positivity bias for less credible feedback. The model distribution for credibility 1 is visibly lower than for credibilities 0.5 and 0.75.

The authors need to be clear that it is the magnitude of the effect that the perseveration-only model cannot account for. Furthermore, they should additionally clarify that this is true only for models fit to data; it is possible that the credibility-CA model could capture the full size of the effect with different parameters (which could fit best if the model was implemented slightly differently).

The authors could make the new analyses somewhat stronger by using parameters optimized to capture just the pattern in CA parameters (for example by MSE). This would show that the models are in principle incapable of capturing the effect. However, this would be a marginal improvement because the conclusion would still rest on a quantitative difference that depends on specific modeling assumptions.

New simulations clearly demonstrate the confound in relative bias

Figure 24 also speaks to the relative vs. absolute question. The model without positivity bias shows a slightly stronger absolute "positivity bias" for the most credible feedback, but a weaker relative bias. This is exactly in line with the logic laid out above. In standard bandit tasks, perseveration can be quite well-captured by a fixed absolute positivity bias, which is roughly what we see in the simulations (I'm not sure what to make of the slight increase; perhaps a useful lead for the authors). However, when we divide by average credit assignment, we now see a reduction. This clearly demonstrates that a reduction in relative bias can emerge without any true differences in positivity bias.

Given everything above, I think it is unlikely that the present data can provide even "solid" evidence for the claim that positivity bias is greater with less credible feedback. This confound could be quickly ruled out, however, by a study in which feedback is sometimes provided in the absence of a choice. This would empirically isolate positivity bias from choice-related effects, including perseveration.

Reviewer #3 (Public review):

This manuscript investigates computational mechanisms underlying increased risk-taking behavior in adolescent patients with suicidal thoughts and behaviors. Using a well-established gambling task that incorporates momentary mood ratings and previously established computational modeling approaches, the authors identify particular aspects of choice behavior (which they term approach bias) and mood responsivity (to certain rewards) that differ as a function of suicidality. The authors replicate their findings on both clinical and large-scale non-clinical samples.

The main problem, however, is that the results do not seem to support a specific conclusion with regard to suicidality. The S+ and S- groups differ substantially in the severity of symptoms, as can be seen by all symptom questionnaires and the baseline and mean mood, where S- is closer to HC than it is to S+. The main analyses control for illness duration and medication but not for symptom severity. The supplementary analysis in Figure S11 is insufficient as it mistakes the absence of evidence (i.e., p > 0.05) for evidence of absence. Therefore, the results do not adequately deconfound suicidality from general symptom severity.

The second main issue is that the relationship between an increased approach bias and decreased mood response to CR is conceptually unclear. In this respect, it would be natural to test whether mood responses influence subsequent gambling choices. This could be done either within the model by having mood moderate the approach bias or outside the model using model-agnostic analyses.

Additionally, there is a conceptual inconsistency between the choice and mood findings that partly results from the analytic strategy. The approach bias is implemented in choice as a categorical value-independent effect, whereas the mood responses always scale linearly with the magnitude of outcomes. One way to make the models more conceptually related would be to include a categorical value-independent mood response to choosing to gamble/not to gamble.

The manuscript requires editing to improve clarity and precision. The use of terms such as "mood" and "approach motivation" is often inaccurate or not sufficiently specific. There are also many grammatical errors throughout the text.

Claims of clinical relevance should be toned down, given that the findings are based on noisy parameter estimates whose clinical utility for the treatment of an individual patient is doubtful at best.

Reviewer #3 (Public review):

Chen et al. identify endophilin A1 as a novel component of the inhibitory postsynaptic scaffold. Their data show impaired evoked inhibitory synaptic transmission in CA1 neurons of mice lacking endophilin A1, and an increased susceptibility to seizures. Endophilin can interact with the postsynaptic scaffold protein gephyrin and promotes assembly of the inhibitory postsynaptic element. Endophilin A1 is known to play a role in presynaptic terminals and in dendritic spines, but a role for endophilin A1 at inhibitory postsynaptic densities has not yet been described, providing a valuable addition to the field.

To investigate the role of endophilin A1 at inhibitory postsynapses, the authors used a broad array of experimental approaches, including tests of seizure susceptibility, electrophysiology, biochemistry, neuronal culture and image analysis. The authors have addressed the remaining concerns in their revision. Taken together, their results expand the synaptic role of endophilin-A1 to include the inhibitory post synaptic element.

Reviewer #3 (Public review):

This study provides insights into the growth kinetics of a diverse collection of Streptococcus pneumoniae, identifying capsule and lineage differences. It was not able to identify any specific loci from the GWAS that were associated with the growth features. It does provide a useful study linking phenotypic data with large scale genomic population data.

In the revised version, the authors have addressed the points raised by the reviewers. The authors have provided additional detail in the Introduction and Methods that both improves the general accessibility for the broad readership of eLife, and the ability of other researchers to reproduce the approaches used in this study. They have expanded the Results and Discussion text in some sections to provide greater clarity and accuracy in reporting their data.

The inclusion of a Data Availability statement was a useful addition and will help ensure the manuscript adheres to eLife's publishing policies.

Reviewer #3 (Public review):

Summary:

The authors aimed to develop Channelrhodopsins (ChRs), light-gated ion channels, with high potency and blue action spectra for use in multicolor (multiplex) optogenetics applications. To achieve this, they performed a bioinformatics analysis to identify ChR homologues in several protist species, focusing on ChRs from ancyromonads, which exhibited the highest photocurrents and the most blue-shifted action spectra among the tested candidates. Within the ancyromonad clade, the authors identified two new anion-conducting ChRs and one cation-conducting ChR. These were characterized in detail using a combination of manual and automated patch-clamp electrophysiology, absorption spectroscopy, and flash photolysis. The authors also explored sequence features that may explain the blue-shifted action spectra and differences in ion selectivity among closely related ChRs.

Strengths:

A key strength of this study is the high-quality experimental data, which were obtained using well-established techniques such as manual patch-clamp and absorption spectroscopy, complemented by modern automated patch-clamp approaches. These data convincingly support most of the claims. The newly characterized ChRs expand the optogenetics toolkit and will be of significant interest to researchers working with microbial rhodopsins, those developing new optogenetic tools, as well as neuro- and cardioscientists employing optogenetic methods.

Weaknesses:

This study does not exhibit major methodological weaknesses.

Reviewer #3 (Public review):

Summary:

This manuscript from Mudgett et al. explores the relative roles of PID and NPY1 in auxin-dependent floral initiation in Arabidopsis. Micro vectorial auxin flows directed by PIN1 are essential to flower initiation, and loss of PIN1 or two of its regulators, PID and NPY1 (in a yucca-deficient background) phenocopies the pinformed phenotype. This group has previously shown that PID-PIN1 interactions and function are dosage-dependent. The authors pick up this thread by demonstrating that a heterozygote containing a CRISPR deletion of one copy of PIN1 can restore quasi-wild type floral initiation to pid.

The authors then show that overexpression of NPY1 is sufficient to more or less restore wild-type floral initiation to the pid mutant. The authors claim that this result demonstrates that NPY1 functions downstream of PID, as this ectopic abundance of NPY1 resulted in phosphorylation of PIN1 at sites that differ from sites of action of PID. The authors pursue evidence that PID action via NPY1 is analogous to the mode of action by which phot1/2 act on NPH3 in seedling phototropism. Such a model is supported by the evidence presented herein that the C terminus of NPY1, which has abundant Ser/Thr content, is phosphorylated, and that the deletion of this domain prevents overexpression compensation of the pinformed phenotype.<br /> While the results presented support evidence in the literature that PID acts on NPY1 to regulate PIN1 function, it is also possible that NPY1 overexpression results in limited expansion of phosphorylation targets observed with other AGC kinases. And if the phot model is any indication, there may be other PID targets that modulate PIN1-dependent floral initiation.

However, overexpression of the NPY1 C-terminal deletion construct resulted in phosphorylation of both PIN1 and PIN2 and agravitropic root growth similar to what is observed in pin2 mutants. This suggests that direct PID phosphorylation of PINs and action via NPY1 can be distinguished by phosphorylation sites and by growth phenotypes.

Strengths:

A very important effort that places NPY1 downstream of PID in floral initiation.

Weaknesses:

As PID has been shown to act on sites that regulate PIN protein polarity as well as PIN protein function, it would be useful if the authors consider how their results would fit/not fit with a model where combinatorial function of NPY1 and PID regulate PIN1 in a manner similar to the way that PID appears to function combinatorially with D6PK on PIN3.

Reviewer #3 (Public review):

Summary:

The study explores a molecular mechanism by which C. elegans detects low-quality food through neuron-digestive crosstalk, offering new insights into food quality control systems. Liu and colleagues demonstrated that NSY-1, expressed in AWC neurons, is a key regulator for sensing Staphylococcus saprophyticus (SS), inducing avoidance behavior and shutting down the digestive system via intestinal BCF-1. They further revealed that INS-23, an insulin peptide, interacts with the DAF-2 receptor in the gut to modulate SS digestion. The study uncovers a food quality control system connecting neural and intestinal responses, enabling C. elegans to adapt to environmental challenges.

Strengths:

The study employs a genetic screening approach to identify nsy-1 as a critical regulator in detecting food quality and initiating adaptive responses in C. elegans. The use of RNA-seq analysis is particularly noteworthy, as it reveals distinct regulatory pathways involved in food sensing (Figure 4) and digestion of Staphylococcus saprophyticus (Figure 5). The strategic application of both positive and negative data mining enhances the depth of analysis. Importantly, the discovery that C. elegans halts digestion in response to harmful food and employs avoidance behavior highlights a physiological adaptation mechanism.

Weaknesses:

Major weaknesses have been addressed.

Reviewer #3 (Public review):

Hawes et al. combined behavioral, optical imaging, and activity manipulation techniques to investigate the role of striatal patch SPNs in locomotion regulation. Using Sepw1-Cre transgenic mice, they found that patch SPNs encode locomotion deceleration in a light-dark box procedure through optical imaging techniques. Moreover, genetic ablation of patch SPNs increased locomotion speed, while chemogenetic activation of these neurons decreased it. The authors concluded that a subtype of patch striatonigral neurons modulates locomotion speed based on external environmental cues.

In the revision, the authors have largely addressed my concerns with additional explanation and discussion, although some of the key experiments to strengthen the authors' claim by identifying the function of specific cell populations remain to be conducted due to technical challenges. Nevertheless, the current results remain valuable and interesting to a wide audience in the field.

Reviewer #3 (Public review):

Summary:

The authors present a novel method to measure passive joint torques - torques due to internal forces other than active muscle contraction - in the fruit fly: genetically inactivating all motor neurons in intact limb acted upon by a gravitational load results in a change in limb configuration; evaluating the moment equilibrium condition about the limb joints then yields a direct estimate of the passive joint torques. Deactivating all motor neurons in an intact standing fly provided two further conclusions: First, because deactivation causes the fly to drop to the floor, the passive joint torques are deemed insufficient to maintain rotational equilibrium against the body weight; using a multi-body-dynamics simulation, the authors estimate that the passive torques would need to be about 40-80 times higher to maintain a typical posture without active muscle action. Second, a delay between the motor neuron inactivation and the onset of the "free fall" motivates the authors to invoke a simple exponential decay model, which is then used to derive a time constant for muscle deactivation, in robust agreement with direct electro-physiological recordings.

Strengths:

The experimental design that permits determination of passive joint torques is elegant, effective, novel, and altogether excellent; it permits measurements previously impossible. A careful error analysis is presented, and a spectrum of technically challenging methods, including multi-body dynamics and e-phys, is deployed to further interpret and contextualise the results.

Weaknesses:

(1) Passive torques are measured, but only some short speculative statements, largely based on previous work, are offered on their functional significance; some of these claims are not well supported by experimental evidence or theoretical arguments. Passive forces are judged as "large" compared to the weight force of the limb, but the arguably more relevant force is the force limb muscles can generate, which, even in equilibrium conditions, is already about two orders of magnitude larger. The conclusion that passive forces are dynamically irrelevant seems natural, but contrasts with the assertion that "passive forces [...] will have a strong influence on limb kinematics". As a result, the functional significance of passive joint torques in the fruit fly, if any, remains unclear, and this ambiguity represents a missed opportunity. We now know the magnitude of passive joint torques - do they matter and for what? Are they helpful, for example, to maintain robust neuronal control, or a mechanical constraint that negatively impacts performance, e.g., because they present a sink for muscle work?

(2) The work is framed with a scaling argument, but the assumptions that underpin the associated claims are not explicit and can thus not be evaluated. This is problematic because at least some arguments appear to contradict textbook scaling theory or everyday experience. For example, active forces are assumed to scale with limb volume, when every textbook would have them scale with area instead; and the asserted scaling of passive forces involves some hidden assumptions that demand more explicit discussion to alert the reader to associated limitations. Passive forces are said to be important only in small animals, but a quick self-experiment confirms that they are sufficient to stabilize human fingers or ankles against gravity, systems orders of magnitude larger than an insect limb, in seeming contradiction with the alleged dominance of scale. Throughout the manuscript, there are such and similar inaccuracies or ambiguities in the mechanical framing and interpretation, making it hard to fairly evaluate some claims, and rendering others likely incorrect.

Reviewer #3 (Public review):

Summary:

In this manuscript Pinon et al. describe the development of a 3D model of human vasculature within a microchip to study Neisseria meningitidis (Nm)- host interactions and validate it through its comparison to the current gold-standard model consisting of human skin engrafted onto a mouse. There is a pressing need for robust biomimetic models with which to study Nm-host interactions because Nm is a human-specific pathogen for which research has been primarily limited to simple 2D human cell culture assays. Their investigation relies primarily on data derived from microscopy and its quantitative analysis, which support the authors' goal of validating their Vessel-on-Chip (VOC) as a useful tool for studying vascular infections by Nm, and by extension, other pathogens associated with blood vessels.

Strengths:<br /> • Introduces a novel human in vitro system that promotes control of experimental variables and permits greater quantitative analysis than previous models<br /> • The VOC model is validated by direct comparison to the state-of-the-art human skin graft on mouse model<br /> • The authors make significant efforts to quantify, model, and statistically analyze their data<br /> • The laser ablation approach permits defining custom vascular architecture<br /> • The VOC model permits the addition and/or alteration of cell types and microbes added to the model<br /> • The VOC model permits the establishment of an endothelium developed by shear stress and active infusion of reagents into the system

Weaknesses:<br /> • The work presented here is mostly descriptive, with little new information that is learned about the biology of Nm or endothelial cells. However, the goal of this study was to establish the VOC model, and the validation presented here is necessary for follow-on studies on Nm pathogenesis and host response.<br /> • The VOC model contains one cell type, human umbilical cord vascular endothelial cells (HUVECs), while true vasculature contains a number of other cell types that associate with and affect the endothelium, such as smooth muscle cells, pericytes, and components of the immune system. These and other shortcomings of the VOC model as it currently stands warrant additional discussion.

Impact:<br /> The VOC model presented by Pinon et al. is an exciting advancement in the set of tools available to study human pathogens interacting with the vasculature. This manuscript focuses on validating the model, and as such sets the foundation for impactful research in the future. Of particular value is the photoablation technique that permits the custom design of vascular architecture without the use of artificial scaffolding structures described in previously published works.

Reviewer #3 (Public review):

Summary:

This paper investigates changes in brain oscillations in V1 in response to experimentally manipulating visual stimulus features (size, contrast at optimal size) and examines whether these effects are of perceptual relevance. The results reveal prominent stimulus-related theta oscillations in V1 that match in frequency the rhythms of behavioural performance (response speed in detecting targets in the visual display). Phase analyses relate these fluctuations of detection performance more formally to opposite theta phase angles in V1.

Strengths:

The non-human primate model provides unique findings on how brain oscillations relate to rhythms in perception (in two rhesus monkeys) that align well with findings from human studies (as occurring in the theta band). However, theta rhythms in humans are typically associated with fronto-parietal activity in the domain of spatial orienting, attentional sampling, while here the focus is on V1. Importantly, microsaccade-controls seem to speak against a spatial orienting/ attentional sampling mechanism to explain the observed effects (at least regarding overt attention).

Weaknesses:

This study provides interesting clues on perceptually relevant brain oscillations. Despite the microsaccade-control, I believe it remains an open question whether the V1 rhythmicity is of pure V1 origin, or driven by top-down input, as it is conceivable that specific stimuli capture attention differently (and hence induce specific covert attentional (re)orienting patterns). For perceptually relevant (yet beta) rhythmicity over occipital areas that are top-down generated, see e.g., Veniero et al., 2019.