Reviewer #1 (Public review):

Review of the revised submission:

I thank the authors for their detailed consideration of my comments and for the additional data, analyses, and clarifications they have incorporated. The new behavioral experiments, quantification of targeted manipulations, and expanded methodological details strengthen the manuscript and address many of my initial concerns. While some questions remain for future work, the authors' careful responses and the additional evidence provided help resolve the main issues I raised, and I am generally satisfied with the revisions.

Review of original submission:

Summary

In this article, Kawanabe-Kobayashi et al., aim to examine the mechanisms by which stress can modulate pain in mice. They focus on the contribution of noradrenergic neurons (NA) of the locus coeruleus (LC). The authors use acute restraint stress as a stress paradigm and found that following one hour of restraint stress mice display mechanical hypersensitivity. They show that restraint stress causes the activation of LC NA neurons and the release of NA in the spinal cord dorsal horn (SDH). They then examine the spinal mechanisms by which LC→SDH NA produces mechanical hypersensitivity. The authors provide evidence that NA can act on alphaA1Rs expressed by a class of astrocytes defined by the expression of Hes (Hes+). Furthermore, they found that NA, presumably through astrocytic release of ATP following NA action on alphaA1Rs Hes+ astrocytes, can cause an adenosine-mediated inhibition of SDH inhibitory interneurons. They propose that this disinhibition mechanism could explain how restraint stress can cause the mechanical hypersensitivity they measured in their behavioral experiments.

Strengths:

(1) Significance. Stress profoundly influences pain perception; resolving the mechanisms by which stress alters nociception in rodents may explain the well-known phenomenon of stress-induced analgesia and/or facilitate the development of therapies to mitigate the negative consequences of chronic stress on chronic pain.

(2) Novelty. The authors' findings reveal a crucial contribution of Hes+ spinal astrocytes in the modulation of pain thresholds during stress.

(3) Techniques. This study combines multiple approaches to dissect circuit, cellular, and molecular mechanisms including optical recordings of neural and astrocytic Ca2+ activity in behaving mice, intersectional genetic strategies, cell ablation, optogenetics, chemogenetics, CRISPR-based gene knockdown, slice electrophysiology, and behavior.

Weaknesses:

(1) Mouse model of stress. Although chronic stress can increase sensitivity to somatosensory stimuli and contribute to hyperalgesia and anhedonia, particularly in the context of chronic pain states, acute stress is well known to produce analgesia in humans and rodents. The experimental design used by the authors consists of a single one-hour session of restraint stress followed by 30 min to one hour of habituation and measurement of cutaneous mechanical sensitivity with von Frey filaments. This acute stress behavioral paradigm corresponds to the conditions in which the clinical phenomenon of stress-induced analgesia is observed in humans, as well as in animal models. Surprisingly, however, the authors measured that this acute stressor produced hypersensitivity rather than antinociception. This discrepancy is significant and requires further investigation.

(2) Specifically, is the hypersensitivity to mechanical stimulation also observed in response to heat or cold on a hotplate or coldplate?

(3) Using other stress models, such as a forced swim, do the authors also observe acute stress-induced hypersensitivity instead of stress-induced antinociception?

(4) Measurement of stress hormones in blood would provide an objective measure of the stress of the animals.

(5) Results:

(a) Optical recordings of Ca2+ activity in behaving rodents are particularly useful to investigate the relationship between Ca2+ dynamics and the behaviors displayed by rodents.

(b) The authors report an increase in Ca2+ events in LC NA neurons during restraint stress: Did mice display specific behaviors at the time these Ca2+ events were observed such as movements to escape or orofacial behaviors including head movements or whisking?

(c) Additionally, are similar increases in Ca2+ events in LC NA neurons observed during other stressful behavioral paradigms versus non-stressful paradigms?

(d) Neuronal ablation to reveal the function of a cell population.

(e) The proportion of LC NA neurons and LC→SDH NA neurons expressing DTR-GFP and ablated should be quantified (Figures 1G and J) to validate the methods and permit interpretation of the behavioral data (Figures 1H and K). Importantly, the nocifensive responses and behavior of these mice in other pain assays in the absence of stress (e.g., hotplate) and a few standard assays (open field, rotarod, elevated plus maze) would help determine the consequences of cell ablation on processing of nociceptive information and general behavior.

(f) Confirmation of LC NA neuron function with other methods that alter neuronal excitability or neurotransmission instead of destroying the circuit investigated, such as chemogenetics or chemogenetics, would greatly strengthen the findings. Optogenetics is used in Figure 1M, N but excitation of LC→SDH NA neuron terminals is tested instead of inhibition (to mimic ablation), and in naïve mice instead of stressed mice.

(g) Alpha1Ars. The authors noted that "Adra1a mRNA is also expressed in INs in the SDH".

(h) The authors should comprehensively indicate what other cell types present in the spinal cord and neurons projecting to the spinal cord express alpha1Ars and what is the relative expression level of alpha1Ars in these different cell types.

(i) The conditional KO of alpha1Ars specifically in Hes5+ astrocytes and not in other cell types expressing alpha1Ars should be quantified and validated (Figure 2H).

(j) Depolarization of SDH inhibitory interneurons by NA (Figure 3). The authors' bath applied NA, which presumably activates all NA receptors present in the preparation.

k) The authors' model (Figure 4H) implies that NA released by LC→SDH NA neurons leads to the inhibition of SDH inhibitory interneurons by NA. In other experiments (Figure 1L, Figure 2A), the authors used optogenetics to promote the release of endogenous NA in SDH by LC→SDH NA neurons. This approach would investigate the function of NA endogenously released by LC NA neurons at presynaptic terminals in the SDH and at physiological concentrations and would test the model more convincingly compared to the bath application of NA.

(l) As for other experiments, the proportion of Hes+ astrocytes that express hM3Dq, and the absence of expression in other cells, should be quantified and validated to interpret behavioral data.

(m) Showing that the effect of CNO is dose-dependent would strengthen the authors' findings.

(n) The proportion of SG neurons for which CNO bath application resulted in a reduction in recorded sIPSCs is not clear.

(o) A1Rs. The specific expression of Cas9 and guide RNAs, and the specific KD of A1Rs, in inhibitory interneurons but not in other cell types expressing A1Rs should be quantified and validated.

(6) Methods:

It is unclear how fiber photometry is performed using "optic cannula" during restraint stress while mice are in a 50ml falcon tube (as shown in Figure 1A).

Reviewer #1 (Public review):

Summary:

In this study, Lamberti et al. investigate how translation initiation and elongation are coordinated at the single-mRNA level in mammalian cells. The authors aim to uncover whether and how cells dynamically adjust initiation rates in response to elongation dynamics, with the overarching goal of understanding how translational homeostasis is maintained. To this end, the study combines single-molecule live-cell imaging using the SunTag system with a kinetic modeling framework grounded in the Totally Asymmetric Simple Exclusion Process (TASEP). By applying this approach to custom reporter constructs with different coding sequences, and under perturbations of the initiation/elongation factor eIF5A, the authors infer initiation and elongation rates from individual mRNAs and examine how these rates covary.

The central finding is that initiation and elongation rates are strongly correlated across a range of coding sequences, resulting in consistently low ribosome density ({less than or equal to}12% of the coding sequence occupied). This coupling is preserved under partial pharmacological inhibition of eIF5A, which slows elongation but is matched by a proportional decrease in initiation, thereby maintaining ribosome density. However, a complete genetic knockout of eIF5A disrupts this coordination, leading to reduced ribosome density, potentially due to changes in ribosome stalling resolution or degradation.

Strengths:

A key strength of this work is its methodological innovation. The authors develop and validate a TASEP-based Hidden Markov Model (HMM) to infer translation kinetics at single-mRNA resolution. This approach provides a substantial advance over previous population-level or averaged models and enables dynamic reconstruction of ribosome behavior from experimental traces. The model is carefully benchmarked against simulated data and appropriately applied. The experimental design is also strong. The authors construct matched SunTag reporters differing only in codon composition in a defined region of the coding sequence, allowing them to isolate the effects of elongation-related features while controlling for other regulatory elements. The use of both pharmacological and genetic perturbations of eIF5A adds robustness and depth to the biological conclusions. The results are compelling: across all constructs and conditions, ribosome density remains low, and initiation and elongation appear tightly coordinated, suggesting an intrinsic feedback mechanism in translational regulation. These findings challenge the classical view of translation initiation as the sole rate-limiting step and provide new insights into how cells may dynamically maintain translation efficiency and avoid ribosome collisions.

Assessment of Goals and Conclusions:

The authors successfully achieve their stated aims: they quantify translation initiation and elongation at the single-mRNA level and show that these processes are dynamically coupled to maintain low ribosome density. The modeling framework is well suited to this task, and the conclusions are supported by multiple lines of evidence, including inferred kinetic parameters, independent ribosome counts, and consistent behavior under perturbation.

Impact and Utility:

This work makes a significant conceptual and technical contribution to the field of translation biology. The modeling framework developed here opens the door to more detailed and quantitative studies of ribosome dynamics on single mRNAs and could be adapted to other imaging systems or perturbations. The discovery of initiation-elongation coupling as a general feature of translation in mammalian cells will likely influence how researchers think about translational regulation under homeostatic and stress conditions.

The data, models, and tools developed in this study will be of broad utility to the community, particularly for researchers studying translation dynamics, ribosome behavior, or the effects of codon usage and mRNA structure on protein synthesis.

Context and Interpretation:

This study contributes to a growing body of evidence that translation is not merely controlled at initiation but involves feedback between elongation and initiation. It supports the emerging view that ribosome collisions, stalling, and quality control pathways play active roles in regulating initiation rates in cis. The findings are consistent with recent studies in yeast and metazoans showing translation initiation repression following stalling events. However, the mechanistic details of this feedback remain incompletely understood and merit further investigation, particularly in physiological or stress contexts.

In summary, this is a thoughtfully executed and timely study that provides valuable insights into the dynamic regulation of translation and introduces a modeling framework with broad applicability. It will be of interest to a wide audience in molecular biology, systems biology, and quantitative imaging.

Reviewer #1 (Public review):

Summary:

Drosophila larval type II neuroblasts generate diverse types of neurons by sequentially expressing different temporal identity genes during development. Previous studies have shown that transition from early temporal identity genes (such as Chinmo and Imp) to late temporal identity genes (such as Syp and Broad) depends on the activation of the expression of EcR by Seven-up (Svp) and progression through the G1/S transition of the cell cycle. In this study, Chaya and Syed examined if the expression of Syp and EcR is regulated by cell cycle and cytokinesis by knocking down CDK1 or Pav, respectively, throughout development or at specific developmental stages. They find that knocking down CDK1 or Pav either in all type II neuroblasts throughout the development or in single type neuroblast clones after larval hatching consistently leads to failure to activate late temporal identity genes Syp and EcR. To determine whether the failure of the activation of Syp and EcR is due to impaired Svp expression, they also examined Svp expression using a Svp-lacZ reporter line. They find that Svp is expressed normally in CDK1 RNAi neuroblasts. Further, knocking down CDK1 or Pav after Svp activation still leads to loss of Syp and EcR expression. Finally, they also extended their analysis to type I neuroblasts. They find that knocking down CDK1 or Pav, either at 0 hours or at 42 hours after larval hatching, also results in loss of Syp and EcR expression in type I neuroblasts. Based on these findings, the authors conclude that cycle and cytokinesis are required for the transition from early to late late temporal identity genes in both types of neuroblasts. These findings add mechanistic details to our understanding of the temporal patterning of Drosophila larval neuroblasts.

Strengths:

The data presented in the paper are solid and largely support their conclusion. Images are of high quality. The manuscript is well-written and clear.

Weaknesses:

The authors have addressed all the weaknesses in this revision.

Reviewer #1 (Public review):

Summary:

Here, the authors aim to investigate the potential improvements of ANNs when used to explain brain data using top-down feedback connections found in the neocortex. To do so, they use a retinotopic and tonotopic organization to model each subregion of the ventral visual (V1, V2, V4, and IT) and ventral auditory (A1, Belt, A4) regions using Convolutional Gated Recurrent Units. The top-down feedback connections are inspired by the apical tree of pyramidal neurons, modeled either with a multiplicative effect (change of gain of the activation function) or a composite effect (change of gain and threshold of the activation function).

To assess the functional impact of the top-down connections, the authors compare three architectures: a brain-like architecture derived directly from brain data analysis, a reversed architecture where all feedforward connections become feedback connections and vice versa, and a random connectivity architecture. More specifically, in the brain-like model the visual regions provide feedforward input to all auditory areas, whereas auditory areas provide feedback to visual regions.

First, the authors found that top-down feedback influences audiovisual processing and that the brain-like model exhibits a visual bias in multimodal visual and auditory tasks. Second, they discovered that in the brain-like model, the composite integration of top-down feedback, similar to that found in the neocortex, leads to an inductive bias toward visual stimuli, which is not observed in the feedforward-only model. Furthermore, the authors found that the brain-like model learns to utilize relevant stimuli more quickly while ignoring distractors. Finally, by analyzing the activations of all hidden layers (brain regions), they found that the feedforward and feedback connectivity of a region could determine its functional specializations during the given tasks.

Strengths:

The study introduces a novel methodology for designing connectivity between regions in deep learning models. The authors also employ several tasks based on audiovisual stimuli to support their conclusions. Additionally, the model utilizes backpropagation of error as a learning algorithm, making it applicable across a range of tasks, from various supervised learning scenarios to reinforcement learning agents. Conversely, the presented framework offers a valuable tool for studying top-down feedback connections in cortical models. Thus, it is a very nice study that can also give inspiration to other fields (machine learning) to start exploring new architectures.

Reviewer #1 (Public review):

Summary:

Jeay-Bizot and colleagues investigate the neural correlates of the preparation of, and commitment to, a self-initiated motor action. In their introduction, they differentiate between theoretical proposals relating to the timing of such neural correlates relative to the time of a recorded motor action (e.g., a keypress). These are categorised into 'early' and 'late' timing accounts. The authors advocate for 'late' accounts based on several arguments that align well with contemporary models of decision-making in other domains (for example, evidence accumulation models applied to perceptual decisions). They also clearly describe prevalent methodological issues related to the measurement of event-related potentials (ERPs) and time-frequency power to gauge the timing of the commitment to making a motor action. These methodological insights are communicated clearly and denote potentially important limitations on the inferences that can be drawn from a large body of existing work.

To attempt to account for such methodological concerns, the authors devise an innovative experiment that includes an experimental condition whereby participants make a motor action (a right-hand keypress) to make an image disappear. They also include a condition whereby the stimulus presentation program automatically proceeds at a set time that is matched to the response timing in a previous trial. In this latter condition, no motor action is required by the participant. The authors then attempt to determine the times at which they can differentiate between these two conditions (motor action vs no motor action) based on EEG and MEG data, using event-related potential analyses, time-frequency analyses, and multivariate classifiers. They also apply analysis techniques based on comparing M/EEG amplitudes at different time windows (as used in previous work) to compare these results to those of their key analyses.

When using multivariate classifiers to discriminate between conditions, they observed very high classification performance at around -100ms from the time of the motor response or computer-initiated image transition, but lower classification performance and a lack of statistically significant effects across analyses for earlier time points. Based on this, they make the key claim that measured M/EEG responses at the earlier time points (i.e., earlier than around -100ms from the motor action) do not reliably correlate with the execution of a motor action (as opposed to no such action being prepared or made). This is argued to favour 'late' accounts of motor action commitment, aligning with the well-made theoretical arguments in favour of these accounts in the introduction. Although the exact time window related to 'late' accounts is not concretely specified, an effect that occurs around -100ms from response onset is assumed here to fall within that window.

Importantly, this claim relies on accepting the null hypothesis of zero effect for the time points preceding around -100ms based on a somewhat small sample of n=15 and some additional analyses of individual participant datasets. Although the authors argue that their classifiers are sensitive to detecting relevant effects, and the study appears well-powered to detect the (likely to be large magnitude) M/EEG signal differences occurring around the time of the response or computer-initiated image transition, there is no guarantee that the study is adequately sensitive to detect earlier differences in M/EEG signals. These earlier effects are likely to be more subtle and exhibit lower signal-to-noise ratios, but would still be relevant to the 'early' vs 'late' debate framed in the manuscript. This, along with some observed patterns in the data, may substantially reduce the confidence one may have in the key claim about the onset timing of M/EEG signal differences.

Notably, there is some indication of above-chance (above 0.5 AUC) classification performance at time points earlier than -100ms from the response, as visible in Figure 3A for the task-based EEG analyses (EEG OC dataset, blue line). While this was not statistically significantly above chance for their n=15 sample, these results do not appear to be clear evidence in favour of a zero-effect null-hypothesis. In Figures 2A-B, there are also visible differences in the ERPs across conditions, from around the time that motor action-related components have been previously observed (around -500ms from the response). The plotted standard errors in the data are large enough to indicate that the study may not have been adequately powered to differentiate between the conditions.

Although the authors acknowledge this limitation in the discussion section of their manuscript, their counter-argument is that the classifiers could reliably differentiate between conditions at time points very close to the motor response, and in the time-based analyses where substantive confounds are likely to be present, as demonstrated in a set of analyses. Based on this data, the authors imply that the study is sufficiently powered to detect effects across the range of time points used in the analyses. While it's commendable that these extra analyses were run, they do not provide convincing evidence that the study is necessarily sensitive to detecting more subtle effects that may occur at earlier time points. In other words, the ability of classifiers (or other analysis methods) to detect what are likely to be very prominent, large effects around the time of the motor response does not guarantee that such analyses will detect smaller magnitude effects at other time points.

In summary, the authors develop some very important lines of argument for why existing work may have misestimated the timing of neural signals that precede motor actions. This in itself is an important contribution to the field. However, their attempt to better estimate the timing of such signals is limited by a reliance on accepting the null hypothesis based on non-statistically significant results, and arguably a limited degree of sensitivity to detect subtle but meaningful effects.

Strengths:

This manuscript provides compelling reasons why existing studies may have misestimated the timing of the neural correlates of motor action preparation and execution. They provide additional analyses as evidence of the relevant confounds and provide simulations to back up their claims. This will be important to consider for many in the field. They also endeavoured to collect large numbers of trials per participant to also examine effects in individuals, which is commendable and arguably better aligned with contemporary theory (which pertains to how individuals make decisions to act, rather than groups of people).

The innovative control condition in their experiment may also be very useful for providing complementary evidence that can better characterise the neural correlates of motor action preparation and commitment. The method for matching image durations across active and passive conditions is particularly well thought-out and provides a nice control for a range of potential confounding factors.

Weaknesses:

There is a mismatch between the stated theoretical phenomenon of interest (commitment to making a motor action) and what is actually tested in the study (differences in neural responses when an action is prepared and made compared to when no action is required). The assumed link between these concepts could be made more explicit for readers, particularly because it is argued in the manuscript that neural correlates of motor action preparation are not necessarily correlates of motor action commitment.

As mentioned in the summary, the main issue is the strong reliance on accepting the null hypothesis of no differences between motor action and computer initiation conditions based on a lack of statistically significant results from the modest (n=15) sample. Although a larger sample will increase measurement precision at the group level, there are some EEG data processing changes that could increase the signal-to-noise ratio of the analysed data and produce more precise estimates of effects, which may improve the ability to detect more subtle effects, or at least provide more confidence in the claims of null effects.

First, it is stated in the EEG acquisition and preprocessing section that the 64-channel Biosemi EEG data were recorded with a common average reference applied. Unless some non-standard acquisition software was used (of which we are not aware exists), Biosemi systems do not actually apply this reference at recording (it is for display purposes only, but often mistaken to be the actual reference applied). As stated in the Biosemi online documentation, a reference should be subsequently applied offline; otherwise, there is a substantial decrease in the signal-to-noise ratio of the EEG data, and a large portion of ambient alternating current noise is retained in the recordings. This can be easily fixed by applying a referencing scheme (e.g., the common average reference) offline as one of the first steps of data processing. If this was, in fact, done offline, it should be clearly communicated in the manuscript.

In addition, the data is downsampled using a non-integer divisor of the original sampling rate (a 2,048 Hz dataset is downsampled to 500 Hz rather than 512 Hz). Downsampling using a non-integer divisor is not recommended and can lead to substantial artefacts in raw data as a result, as personally observed by this Reviewer in Biosemi data. Finally, although a 30 Hz low-pass filter is applied for visualisation purposes of ERPs, no such filter is applied prior to analyses, and no method is used to account for alternating current noise that is likely to be in the data. As noted above, much of the alternating current noise will be retained when an offline reference is not applied, and this is likely to further degrade the quality of the data and reduce one's ability to identify subtle patterns in EEG signals. Changes in data processing to address these issues would likely lead to more precise estimates of EEG signals (and by extension differences across conditions).

With regard to possible effects extending hundreds of milliseconds before the response, it would be helpful for the authors to more precisely clarify the time windows associated with 'early' and 'late' theories in this case. The EEG data that would be required to support 'early' theories is also not made sufficiently clear. For example, even quite early neural correlates of motor actions in this task (e.g., around -500ms from the response, or earlier) could still be taken as evidence for the 'late' theories if these correlates simply reflect the accumulation of evidence toward making a decision and associated motor action, as implied by the Leaky Stochastic Accumulator model described by the authors. In other words, even observations of neural correlates of motor action preparation that occur much earlier than the response would not constitute clear evidence against the 'late' account if this neural activity represents an antecedent to a decision and action (rather than commitment to the action), as the authors point out in the introduction.

In addition, there is some discrepancy regarding the data that is used by the classifiers to differentiate between the conditions in the EEG data and the claims about the timing of neural responses that differentiate between conditions. Unless we reviewers are mistaken, the Sliding Window section of the methods states that the AUC scores in Figure 3 are based on windows of EEG data that extend from the plotted time point until 0.5 seconds into the past. In other words, an AUC value at -100ms from the response is based on classifiers applied to data ranging from -600 to -100 milliseconds relative to the response. In this case, the range of data used by the classifiers extends much earlier than the time points indicated by Figure 3, and it is difficult to know whether the data at these earlier time points may have contributed (even in subtle ways) to the success of the classifiers. This may undermine the claim that neural responses only become differentiable from around -100ms from response onset. The spans of these windows used for classification could be made more explicit in Figure 3, and classification windows that are narrower could be included in a subset of analyses to ensure that classifiers only using data in a narrow window around the response show the high degree of classification performance in the dataset. If we are mistaken, then perhaps these details could be clarified in the method and results sections.

Reviewer #1 (Public review):

Summary:

This study reports the effects of psilocin on iPSC-derived human cortical neurons.

Strengths:

The characterization was comprehensive, involving immunohistochemistry of various markers, 5-HT2A receptors, BDNF, and TrkB, transcriptomics analyses, morphological determination, electrophysiology, and finally synaptic protein measurements. The results are in close agreement with prior work (PMID 29898390) on rat cultured cortical neurons. Nevertheless, there is value in confirming those earlier findings and furthermore to demonstrate the effects in human neurons, which are important for translation. The genetic, proteomics, and cell structure analyses used in this paper are its major strength. The study supports the value of using iPSC-derived human cortical neurons for drug development involving psychedelics-related compounds.

Weaknesses:

(1) Line 140: 5-HT2A receptor expression was found via immunocytochemistry to reside in the somatodendritic and axonal compartments. However, prior work from ex vivo tissue using electron microscopy has found predominantly 5-HT2A receptor expression in the somatodendritic compartment (PMID: 12535944). Was this antibody validated to be 5-HT2A receptor-specific? Can the authors reason why the discrepancy may arise, and if the axonal expression is specific to the cultured neurons?

(2) Line 143: It would be helpful to specify the dose of psilocin tested, and describe how this dose was chosen.

(3) Figure 1: The interpretation is that the differential internalization in the axonal and somatodendritic compartments is time-dependent. However, given that only one dose is tested, it is also possible that this reflects dose dependence, with the longer time exposure leading to higher dose exposure, so these variables are related. That is, if a higher dose is given, internalization may also be observed after 10 minutes in the dendritic compartment.

(4) Figure 3 & 4: What is the 'control' here? A more appropriate control for the 24 hours after psilocin application would be 24 hours after vehicle application. Here the authors are looking at before and after, but the factor of time elapsed and perturbation via application is not controlled for.

(5) The sample size was not clearly described. In the figure legend, N = the number of neurites is provided, but it is unclear how many cells have been analyzed, and then how many of those cells belong to the same culture. These are important sample size information that should be provided. Relatedly, statistical analyses should consider that the neurites from the same cells are not independent. If the neurites indeed come from the same cells, then the sample size is much smaller and a statistical analysis considering the nested nature of the data should be used.

Comments on revisions:

The authors performed substantial experiments to check validity of the HTR2A antibody for the revision. Briefly, they found that western blot shows a single band, abolished by a blocking peptide, in neural progenitors and iPSC-derived neurons, suggesting positive results. However, they also detected immunofluorescence signals in HEK293 and HeLa cells, which do not express 5-HT2A receptors as scRNAseq analysis of these cells show complete absence of the transcript. Therefore the antibody has epitope-selective binding but also has some non-specific binding, precluding its use. The authors rightfully removed the data related to the antibody in the revised manuscript. The account is repeated here to highlight to anyone who may find the information helpful. Overall, the additional results added rigor to the study.

Reviewer #1 (Public review):

Summary:

This manuscript presents findings on the adaptation mechanisms of Saccharomyces cerevisiae under extreme stress conditions. The authors try to generalize this to adaptation to stress tolerance. A major finding is that S. cerevisiae evolves a quiescence-like state with high trehalose to adapt to freeze-thaw tolerance independent of their genetic background. The manuscript is comprehensive, and each of the conclusions is well supported by careful experiments.

Strengths:

This is excellent interdisciplinary work.

I have commented on the response of the authors, in-line, below. This is to maintain the conversation thread with the authors.

Comment 1:

Earlier papers have shown that loss of ribosomal proteins, that slow growth, leads to better stress tolerance in S. cerevisiae. Given this, isn't it expected that any adaptation that slows down growth would, overall, increase stress tolerance? Even for other systems, it has been shown that slowing down growth (by spore formation in yeast or bacteria/or dauer formation in C. elegans) is an effective strategy to combat stress and hence is a likely route to adaptation. The authors stress this as one of the primary findings. I would like the authors to explain their position, detailing how their findings are unexpected in the context of the literature.

Response:

We agree that the link between slower growth and higher stress tolerance has been well stud-ied. What is distinctive here is that repeated, near-lethal freeze-thaw selected not only for a tolerant/quiescent-like state but also for a shorter lag on re-entry. In this regime of freeze-thaw-regrowth, cells that are tolerant but slow to restart would be outcompeted by naive fast growers. Our quiescence-based selection simulations reproduce exactly this constraint. We have added this explanation to the Results to make clear that the novelty is the co-evolution of a tolerant, trehalose-rich state together with rapid regrowth under an alternating regime.

Comment to Response: I get the point. I believe that the outcome is highly dependent on how selection pressure is administered. So, generalizing this over all stresses (as done in the abstract) may not be accurate.

Comment 2:

Convergent evolution of traits: I find the results unsurprising. When selecting for a trait, if there is a major mode to adapt to that stress, most of the strains would adapt to that mode, independent of the route. According to me, finding out this major route was the objective of many of the previous reports on adaptive evolution. The surprising part in the previous papers (on adaptive evolution of bacteria or yeast) was the resampling of genes that acquired mutations in multiple replicates of an evolution experiments, providing a handle to understand the major genetic route or the molecular mechanism that guides the adaptation (for example in this case it would be - what guides the over-accumulation of trehalose). I fail to understand why the authors find the results surprising, and I would be happy to understand that from the authors. I may have missed something important.

Response:

Our surprise was precisely that we did not see the classical pattern of "phenotypic convergence + repeated mutations in the same locus/module." All independently evolved lines converged on a trehalose-rich, mechanically reinforced, quiescence-like phenotype, but population sequencing across lines did not reveal a single repeatedly hit gene or small shared pathway, even when we increased selection stringency (1-3 freeze-thaw cycles per round). We have now stated in the manuscript that this decoupling (strong phenotypic convergence, non-overlapping genetic routes) is the central inference: selection is acting on a physiologically defined state that multiple genotypes can reach.

Comment to Response: You indeed saw a case of phenotypic convergence. Converging towards trehalose-rich, mechanically reinforced, quiescent like - are phenotypes that have converged. This is what prevented lysis. The same locus need not be mutated over and over again, if the trehalose pathway is controlled by many processes (it is, and many are still unknown as I point in the next comment), many different mutations on different loci can result in the same regulation! I do not see the decoupling between phenotypic convergence and decoupling of genetic mutations as surprising or novel; molecular and cellular biology is replete with such examples where deletion(mutation) of hundreds of different genes can have the same phenotypic outcome (yeast deletion library screening, indirect effects etc). If this was a specific question unsolved in evolutionary biology, then the matter is different.

A minor point: Here I would also like to point out that the three phenotypes you measure may be linked to each other, so their independent evolution may just be a cause-effect relationship. For example Trehalose accumulation may drive the other two. This has not been deconvoluted in this manuscript.

Comment 3:

Adaptive evolution would work on phenotype, as all of selective evolution is supposed to. So, given that one of the phenotypes well-known in literature to allow free-tolerance is trehalose accumulation, I think it is not surprising that this trait is selected. For me, this is not a case of "non-genetic" adaptation as the authors point out: it is likely because perturbation of many genes can individually result in the same outcome - up-regulation of trehalose accumulation. Thereby, although the adaptation is genetic, it is not homogeneous across the evolving lines - the end result is. Do the authors check that the trait is actually a non-genetic adaptation, i.e., if they regrow the cells for a few generations without the stress, the cells fall back to being similarly only partially fit to freeze-thaw cycles? Additionally, the inability to identify a network that is conserved in the sequencing does not mean that there is no regulatory pathway. A large number of cryptic pathways may exist to alter cellular metabolic states.<br /> This is a point in continuation of point #2, and I would like to understand what I have missed.

Response:

We agree, and we have removed the wording "non-genetic adaptation." The evolved populations retain high survival even after regrowth for {greater than or equal to}25 generations without freeze-thaw, so the adaptation is clearly genetically maintained. What our data show is that there is no single genetic route to the shared phenotype; different mutations can all drive cells into the same trehalose-rich, quiescence-like, mechanochemically reinforced state. We now describe this as "genetic diversification with phenotypic convergence."

Comment to Response: While the last term does explain what is going on, isn't it an outcome that is routine in cell biology (as pointed out in my previous comment to your response)? I apologize for not understanding the punchline that is provided in the last few sentences of the abstract.

Comment 4:

To propose the convergent nature, it would be important to check for independently evolved lines and most probably more than 2 lines. It is not clear from their results section if they have multiple lines that have evolved independently.

Response:

We indeed evolved four independent lines and maintained two independent controls. We have added this information at the start of the Results so that the level of replication is immediately clear.

Comment to Response: Previous large scale studies have done hundreds of sequencing to oversample the pathway and figure out reproducible loci. With pooled sequencing (as mentioned below) and only 4 sample evolution, I am not sure that you would have the power in your study to conclude in the loci are sampled or not! If there were 10 gene LOFs that control Trehalose levels (which you can find from the published deletion screening experiment), then four of the experiments are likely to go through one of these routes; what is the likely event that you would identify the same route in two pools? It is unlikely, and therefore, sequencing of 4 pools cannot tell you if the mutation path is repeatedly sampled or not.

Comment 5:

For the genomic studies, it is not clear if the authors sequenced a pool or a single colony from the evolved strains. This is an important point, since an average sequence will miss out on many mutations and only focus on the mutations inherited from a common ancestral cell. It is also not clear from the section.

Response:

We sequenced population samples from the evolved lines. Our specific question was whether independently evolved lines would show the same high-frequency genetic solution, as is often seen in parallel evolution. Pool sequencing may under-sample rare/private variants, but it is appropriate for detecting such shared, high-frequency routes - and we do not find any. We have clarified this rationale in the Methods/Results.

Comment to Response: Please provide the average sequencing depth of each sequencing run. It is essential to understand the power of this study in identifying mutations. What coverage was used in Xgenome size?

Reviewer #1 (Public review):

In their manuscript, Papadopoli et al explore the role of ETFDH in transformation. They note that ETFDH protein levels are decreased in cancer, and that deletion of ETFDH in cancer cell lines results in increased tumorigenesis, elevated OXPHOS and glycolysis, and a reduction in lipid and amino acid oxidation. The authors attribute these effects to increased amino acid levels stimulating mTORC1 signaling and driving alterations in BCL6 and EIF4EBP1. They conclude that ETFDH1 is epigenetically silenced in a proportion of neoplasms, suggesting a tumor-suppressive function. Overall, the authors logically present clear data and perform appropriate experiments to support their hypotheses.

Reviewer #1 (Public review):

Schafer et al. tested whether the hippocampus tracks social interactions as sequences of neural states within an abstract social space defined by the dimensions of affiliation and power, using a narrative-based task in which participants engaged in dynamic social interactions. The study showed that individual social relationships were represented as distinct trajectories of hippocampal activity patterns. These neural trajectories systematically reflected trial-by-trial changes in affiliation and power between the participant and each character, suggesting that the hippocampus encodes sequences of socially relevant events and their relational structure, extending its well-established role beyond spatial representations.

A major strength of this study is the use of a richly structured, narrative-based task that allows social relationships to evolve dynamically over time. The use of representational similarity analysis provides a principled framework for linking behavioral trajectories in social space to neural pattern dynamics.

One potential limitation concerns temporal autocorrelation in the neural data, as nearby trials are inherently related both behaviorally and temporally within a continuous narrative. Although the authors carefully attempted to control for temporal distance and related confounds, fully disentangling representational similarity driven by social structure from similarity driven by temporal proximity remains challenging within a single-session task design.

While the findings of a two-dimensional representational structure is an important contribution, it remains an open question whether such a representation reflects an inherent property of how the human brain encodes social relationships, or whether it is partly driven by task constraints in which social interactions were limited to changes along two (affiliation and power) dimensions. Future studies that allow social relationships to vary along richer or higher-dimensional feature spaces will be necessary to determine the generality of low dimensional representations.

Reviewer #1 (Public review):

Summary:

The manuscript by Mengxing et al., reports an assessment of three first-order thalamic nuclei (auditory, visual, somatosensory) in a 3 x 2 factorial design to test for specificity of responses in first-order thalamic nuclei to linguistic processing particularly in the left hemisphere. The conditions are reading, speech production, and speech comprehension and their respective control conditions. The authors report the following results:

(1) BOLD-response analyses: left MGB linguistic vs non-linguistic significant; left LGN linguistic vs non-linguistic significant. There is no hemisphere x stimulus interaction.

(2) MVPA: left MGB linguistic vs. non-linguistic significant; bilateral VLN linguistic vs. non-linguistic significant; significant lateralisation in MGB (left MGB responses better classified linguistic vs. non-linguistic in contrast to right).

(3) Functional connectivity: there is, in general, connectivity between the thalamic ROIs and the respective primary cortices independent of linguistics.

Strengths:

The study has a clear and comprehensive design and addresses a timely topic. First-order thalamic nuclei and their interaction with the respective cerebral cortex area are likely key to understanding how perception works in a world where one has to compute highly dynamic stimuli often in an instant. Speech is a prime example of an ecologically important, extremely dynamic, and complex stimulus. The field of the contribution of cerebral cortex-thalamic loops is wide open, and the study presents a solid approach to address their role in different speech modalities (i.e., reading, comprehension, production).

Weaknesses:

I see two major overall weaknesses in the manuscript in its current form:

(1) Statistics:

Unfortunately, I have doubts about the solidity of the statistics. In the analyses of the BOLD responses, the authors do not find significant hemisphere x stimulus interactions. In my view, such results would pre-empt doing a post-hoc t-test. Nevertheless, the authors motivate their post-hoc t-test by 'trends' in the interaction and prior hypotheses. I see two difficulties with that. First, the origin of the prior hypotheses is somewhat unclear (see also the comment below on hypotheses), and the post-hoc t-test is not corrected for multiple comparisons. I find that it is a pity that the authors did not derive more specific hypotheses grounded in the literature to guide the statistical testing, as I think these would have been available, and the response properties of the MGB and LGN also make sense in light of them. In addition, I was wondering whether the MVPA results would also need to be corrected for the three tests, i.e., the three ROIs.

Hypotheses:

In my view, it is relatively unclear where the hypotheses precisely come from. For example, the paragraph on the hypotheses in the introduction (p. 6-7) is devoid of references. I also have the impression that the hypotheses are partly not taking into account previous reports on first-order thalamic nuclei involvement in linguistic vs. non-linguistic processing. For example, the authors test for lateralisation of linguistic vs. non-linguistic responses in all nuclei. However, from previous literature, one could derive the hypothesis that the lateralisation in MGB for speech might be there - previous work shows, for example, that speech recognition abilities consistently correlate with left MGB only (von Kriegstein et al., 2008 Curr Biol; Mihai et al., 2019 eLife). In addition, the involvement of the MGB in speech in noise processing is present in the left MGB (Mihai et al., 2021, J Neuroscience). Developmental dyslexia, which is supposed to be based on imprecise phonological processing (Ramus et al., 2004 TiCS), has alterations in left MGB (Diaz et al., 2012 PNAS; Galaburda et al., 1994 PNAS) and left MGB connections to planum temporale (Tschentscher et al., 2019 J Neurosci) as well as altered lateralisation (Müller-Axt et al., 2025 Brain). Conversely, in the LGN, I'm not aware of any studies showing lateralisation for speech. See, for example, Diaz et al., 2018, Neuroimage, where there are correlations of LGN task-dependent modulation with visual speech recognition behaviour in both LGNs. Thus, based on this literature, one could have predicted the result pattern displayed, for example, in Figure 3A at least for MGB and LGN.

In summary, the motivation for the different hypotheses needs to be carved out more and couched into previous literature that is directly relevant to the topic. The above paragraph is, of course, my view on the topic, but currently, the paper lacks different literature as references to fully understand where the hypotheses are derived from.

Reviewer #1 (Public review):

Summary:

Thach et al. report on the structure and function of trimethylamine N-oxide demethylase (TDM). They identify a novel complex assembly composed of multiple TDM monomers and obtain high-resolution structural information for the catalytic site, including an analysis of its metal composition, which leads them to propose a mechanism for the catalytic reaction.

In addition, the authors describe a novel substrate channel within the TDM complex that connects the N-terminal Zn²-dependent TMAO demethylation domain with the C-terminal tetrahydrofolate (THF)-binding domain. This continuous intramolecular tunnel appears highly optimized for shuttling formaldehyde (HCHO), based on its negative electrostatic properties and restricted width. The authors propose that this channel facilitates the safe transfer of HCHO, enabling its efficient conversion to methylenetetrahydrofolate (MTHF) at the C-terminal domain as a microbial detoxification strategy.

Strengths:

The authors provide convincing high-resolution cryo-EM structural evidence (up to 2 Å) revealing an intriguing complex composed of two full monomers and two half-domains. They further present evidence for the metal ion bound at the active site and articulate a plausible hypothesis for the catalytic cycle. Substantial effort is devoted to optimizing and characterizing enzyme activity, including detailed kinetic analyses across a range of pH values, temperatures, and substrate concentrations. Furthermore, the authors validate their structural insights through functional analysis of active-site point mutants.

In addition, the authors identify a continuous channel for formaldehyde (HCHO) passage within the structure and support this interpretation through molecular dynamics simulations. These analyses suggest an exciting mechanism of specific, dynamic, and gated channeling of HCHO. This finding is particularly appealing, as it implies the existence of a unique, completely enclosed conduit that may be of broad interest, including potential applications in bioengineering.

Weaknesses:

Although the idea of an enclosed channel for HCHO is compelling, the experimental evidence supporting enzymatic assistance in the reaction of HCHO with THF is less convincing. The linear regression analysis shown in Figure 1C demonstrates a THF concentration-dependent decrease in HCHO, but the concentrations used for THF greatly exceed its reported KD (enzyme concentration used in this assay is not reported). It has previously been shown that HCHO and THF can couple spontaneously in a non-enzymatic manner, raising the possibility that the observed effect does not require enzymatic channeling. An additional control that can rule out this possibility would help to strengthen the evidence. For example, mutating the THF binding site to prevent THF binding to the protein complex could clarify whether the observed decrease in HCHO depends on enzyme-mediated proximity effects. A mutation which would specifically disable channeling could be even more convincing (maybe at the narrowest bottleneck).

Another concern is that the observed decrease in HCHO could alternatively arise from a reduced production of HCHO due to a negative allosteric effect of THF binding on the active site. From this perspective, the interpretation would be more convincing if a clear coupled effect could be demonstrated, specifically, that removal of the product (HCHO) from the reaction equilibrium leads to an increase in the catalytic efficiency of the demethylation reaction.

While the enzyme kinetics appear to have been performed thoroughly, the description of the kinetic assays in the Methods section is very brief. Important details such as reaction buffer composition, cofactor identity and concentration (Zn²⁺), enzyme concentration, defined temperature, and precise pH are not clearly stated. Moreover, a detailed methodological description could not be found in the cited reference (6), if I am not mistaken.

The composition of the complex is intriguing but raises some questions. Based on SDS-PAGE analysis, the purified protein appears to be predominantly full-length TDM, and size-exclusion chromatography suggests an apparent molecular weight below 100 kDa. However, the cryo-EM structure reveals a substantially larger complex composed of two full-length monomers and two half-domains.

Given the lack of clear evidence for proteolytic fragments on the SDS-PAGE gel, it is unclear how the observed stoichiometry arises. This raises the possibility of higher-order assemblies or alternative oligomeric states. Did the authors attempt to pick or analyze larger particles during cryo-EM processing? Additional biophysical characterization of particle size distribution - for example, using interferometric scattering microscopy (iSCAT)-could help clarify the oligomeric state of the complex in solution.

The authors mention strict symmetry in the complex, yet C2 symmetry was enforced during refinement. While this is reasonable as an initial approach, it would strengthen the structural interpretation to relax the symmetry to C1 using the C2-refined map as a reference. This could reveal subtle asymmetries or domain-specific differences without sacrificing the overall quality of the reconstruction.

In this context, the proposed catalytic role of Zn²⁺ raises additional questions. Why is a 2:1 enzyme-to-metal stoichiometry observed, and how does this reconcile with previous reports? This point warrants discussion. Does this imply asymmetric catalysis within the complex? Would the stoichiometry change under Zn²⁺-saturating conditions, as no Zn²⁺ appears to be added to the buffers? It would be helpful to clarify whether Zn²⁺ occupancy is equivalent in both active sites when symmetry is not imposed, or whether partial occupancy is observed.

The divalent ion Zn2+ is suggested to activate water for the catalytic reaction. I am not sure if there is a need for a water molecule to explain this catalytic mechanism. Can you please elaborate on this more? As one aspect, it might be helpful to explain in more detail how Zn-OH and D220 are recovered in the last step before a new water molecule comes in.

Overall, the authors were successful in advancing our structural and functional understanding of the TDM complex. They suggest an interesting oligomeric complex composition which should be investigated with additional biophysical techniques.

Additionally, they provide an intriguing hypothesis for a new type of substrate channeling. Additional kinetic experiments focusing on HCHO and THF turnover by enzymatic proximity effects would strengthen this potentially fundamental finding. If this channeling mechanism can be supported by stronger experimental evidence, it would substantially advance our understanding and knowledge of biologic conduits and enable future efforts in the design of artificial cascade catalysis systems with high conversion rate and efficiency, as well as detoxification pathways.

Reviewer #1 (Public review):

This study by Radziun and colleagues investigates the effects of using a hand-augmentation device on mental body representations. The authors use a proprioceptive localisation task to measure metric representations of finger length before and after participants wear the device, and then before and after they learn to use the device, which extends the lengths of the fingers by 10 cm. The authors find changes between different time points, which they interpret as evidence for three distinct forms of plasticity: one related to simply wearing the device, one related to learning to use it, and an aftereffect after taking the device off. A control experiment with a similar device, which does not lengthen the fingers, showed the first and third of these forms of plasticity, but not the second.

This study takes an interesting approach to a timely and theoretically significant issue. The study appears to be appropriately designed and conducted. There are, however, some points which require clarification.

(1) The nature of the localization task is unclear. On its face, the task appears to involve localization of each landmark within the 2-dimensional surface of the touchscreen. However, the regression analysis presupposes that localization is made in a 1-dimensional space. Figure S2 shows that three lines are presented on the screen above the index, middle, and ring fingers, which I imagine the participant is meant to use as a guide. But it is at least conceivable that the perceived location or orientation of the finger might not correspond exactly to these lines. While the method can deal gracefully with proximal-distal translations of the fingers (i.e., with the intercept parameter of the regression), it isn't clear how the participant is supposed to respond if their proprioceptive perception of finger location is translated left-right or rotated relative to the lines on the screen. I also worry that presenting a long, thin line to represent each finger on the screen may not be a neutral method and may prime participants to represent the finger as long and thin.

(2) The task used here fits within a wider family of tasks in the literature using localization judgments of multiple landmarks to map body representations. I feel that some discussion of this broader set of tasks and their use to measure body representation and plasticity is notably absent from the paper. It is also striking to me that some of the present authors have themselves recently criticized the use of landmark localization methods as a measure of represented body size and shape (Peviani et al, 2024, Current Biology). It is therefore surprising to see them use this task here as a measure of represented finger length without commenting on this issue.

(3) 18 participants strikes me as a relatively small sample size for this type of study. It weakens the manuscript that the authors do not provide any justification, or even comment on, the sample size. This is especially true as participants are excluded from the entire sample, and from specific analyses, on rather post-hoc grounds.

(4) I have some concerns about the interpretation of contraction in stage 2. The authors claim that wearing the finger extended produces "a contraction",i.e., an "under-representation" (page 12). But in both experiments, regression slopes in stage 2 were not significantly different from 1 (i.e., 0.98 [SE: 0.07] in Exp 1a and 1.04 [SE: 0.09] in Experiment 1b). So how can that be interpreted as "under-representation"?

(5) I also have concerns about the interpretation of the stretch that is claimed to occur following training. In Exp 1a, regression slopes in stage 3 are on average 1.15. That is LESS than in the pretest at stage 1 (mean: 1.16). The idea of stretch only comes about because of the lower slopes in stage 2, which the authors have interpreted as reflecting contraction. So what the authors call stretch and a 2nd form of plasticity could just be the contraction from stage 2 wearing off or dissipating, since perceived finger length in stage 3 just appears to return to the baseline level seen in stage 1. While the authors describe their results in terms of three distinct forms of plasticity, these are not in fact statistically independent. The dip in regression slopes in stage 2 is interpreted as evidence for two distinct plasticity effects, which I do not find convincing.

(6) The distinction between plasticity at stage 3 (which appears specific to augmentation) and plasticity at stage 4 (which does not appear specific, as it also occurs in Experiment 1b) feels strained. This feels like a very subtle distinction, and the theoretical significance of it is not convincingly developed.

(7) The reporting of statistics is not always consistent. For example, 95%CIs are presented for regression slopes in stages 1, 3, and 4, but not for stage 2. Statistics are performed on regression slopes, except for one t-test on page 7 comparing lengths in cm. Estimates of effect size would be nice additions to statistical tests.

(8) Minor point: On page 4, the authors write, "These included sorting colored blocks, stacking a Jenga tower, and sorting pegs into holes; the latter task required fine-grained manipulation and was used as our outcome measure of motor learning." This suggests that peg sorting was the outcome measure, but in Figure 1D, Jenga is presented as the outcome measure.

Reviewer #1 (Public review):

Summary:

Ewing sarcoma is an aggressive pediatric cancer driven by the EWS-FLI oncogene. Ewing sarcoma cells are addicted to this chimeric transcription factor, which represents a strong therapeutic vulnerability. Unfortunately, targeting EWS-FLI has proven to be very difficult and better understanding how this chimeric transcription factor works is critical to achieving this goal. Towards this perspective, the group had previously identified a DBD-𝛼4 helix (DBD) in FLI that appears to be necessary to mediate EWS-FLI transcriptomic activity. Here, the authors used multi-omic approaches, including CUT&tag, RNAseq, and MicroC to investigate the impact of this DBD domain. Importantly, these experiments were performed in the A673 Ewing sarcoma model where endogenous EWS-FLI was silenced, and EWS-FLI-DBD proficient or deficient isoforms were re-expressed (isogenic context). They found that the DBD domain is key to mediate EWS-FLI cis activity (at msat) and to generate the formation of specific TADs. Furthermore, cells expressing DBD deficient EWS-FLI display very poor colony forming capacity, highlighting that targeting this domain may lead to therapeutic perspectives.

Strengths:

The group has strong expertise in Ewing sarcoma genetics and epigenetics and also in using and analyzing this model (Theisen et al., 2019; Boone et al., 2021; Showpnil et al., 2022).

They aim at better understanding how EWS-FLI mediated its oncogenic activity, which is critical to eventually identifying novel therapies against this aggressive cancer.

They use the most recent state-of-the-art omics methods to investigate transcriptome, epigenetics, and genome conformation methods. In particular, Micro-C enables achieving up to 1kb resolved 3D chromatin structures, making it possible to investigate a large number of TADs and sub-TADs structures where EWS-FLI1 mediates its oncogenic activity.

They performed all their experiments in an Ewing sarcoma genetic background (A673 cells) which circumvents bias from previously reported approaches when working in non-orthologous cell models using similar approaches.

Weaknesses:

The main weakness stems from the poor reproducibility of the Micro-C data. Indeed, the distances and clustering observed between replicates appear to be similar to, or even greater than, those observed between biological conditions. For instance, in Figure 1B, we do not observe any clear clustering among DBD1, DBD2, DBD+1, and DBD+2. Although no further experiments were performed, the authors tempered their claims by rephrasing aspects related to this issue and the reviewer also acknowledged that the transcriptomic data are convincing and support their findings.

Regarding DBD stability and the cycloheximide experiments requested to rule out any half-life bias of DBD (as higher stability of the re-expressed DBD+ could also partially explain the results independently of a 3D conformational change), the reviewer acknowledged that the WB, RNA-seq data and agar assays presented by the authors appear reproducible across experiments.

Reviewer #1 (Public review):

Summary:

This study by Howe and colleagues investigates the role of the posterolateral cortical amygdala (plCoA) in mediating innate responses to odors, specifically attraction and aversion. By combining optogenetic stimulation, single-cell RNA sequencing, and spatial analysis, the authors identify a topographically organized circuit within plCoA that governs these behaviors. They show that specific glutamatergic neurons in the anterior and posterior regions of plCoA are responsible for driving attraction and avoidance, respectively, and that these neurons project to distinct downstream regions, including the medial amygdala and nucleus accumbens, to control these responses.

Strengths:

The major strength of the study is the thoroughness of the experimental approach, which combines advanced techniques in neural manipulation and mapping with high-resolution molecular profiling. The identification of a topographically organized circuit in plCoA and the connection between molecularly defined populations and distinct behaviors is a notable contribution to understanding the neural basis of innate motivational responses. Additionally, the use of fucntional manipulations adds depth to the findings, offering valuable insights into the functionality of specific neuronal populations.

Weaknesses:

Previously described weaknesses in the study's methods and interpretation were fully addressed during revision. Locomotor behavior of the mice during head-fixed imaging experiments was added and analysis of the correlation of locomotion with neural activity was also added.

This work provides significant insights into the neural circuits underlying innate behaviors and opens new avenues for further research. The findings are particularly relevant for understanding the neural basis of motivational behaviors in response to sensory stimuli, and the methods used could be valuable for researchers studying similar circuits in other brain regions. If the authors address the methodological issues raised, this work could have a substantial impact on the field, contributing to both basic neuroscience and translational research on the neural control of behavior.

Reviewer #1 (Public review):

Summary:

This study set out to investigate potential pharmacological drug-drug interactions between the two most common antimalarial classes, the artemisinins and quinolines. There is strong rationale for this aim, because drugs from these classes are already widely-used in Artemisinin Combination Therapies (ACTs) in the clinic, and drug combinations are an important consideration in the development of new medicines. Furthermore, whilst there is ample literature proposing many diverse mechanisms of action and resistance for the artemisinins and quinolines, it is generally accepted that the mechanisms for both classes involve heme metabolism in the parasite, and that artemisinin activity is dependent on activation by reduced heme. The study was designed to measure drug-drug interactions associated with a short pulse exposure (4 h) that is reminiscent of the short duration of artemisinin exposure obtained after in vivo dosing. Clear antagonism was observed between dihydroartemisinin (DHA) and chloroquine, which became even more extensive in chloroquine-resistant parasites. Antagonism was also observed in this assay for the more clinically-relevant ACT partner drugs piperaquine and amodiaquine, but not for other ACT partners mefloquine and lumefantrine, which don't share the 4-aminoquinoline structure or mode of action. Interestingly, chloroquine induced an artemisinin resistance phenotype in the standard in vitro Ring-stage Survival Assay, whereas this effect was not as extensive for piperaquine.

The authors also utilised a heme-reactive probe to demonstrate that the 4-aminoquinolines can inhibit heme-mediated activation of the probe within parasites, which suggests that the mechanism of antagonism involves the inactivation of heme, rendering it unable to activate the artemisinins. Measurement of protein ubiquitination showed reduced DHA-induced protein damage in the presence of chloroquine, which is also consistent with decreased heme-mediated activation, and/or with decreased DHA activity more generally.

Overall, the study clearly demonstrates a mechanistic antagonism between DHA and 4-aminoquinoline antimalarials in vitro. It is interesting that this combination is successfully used to treat millions of malaria cases every year, which may raise questions about the clinical relevance of this finding. However, the conclusions in this paper are supported by multiple lines of evidence and the data is clearly and transparently presented, leaving no doubt that DHA activity is compromised by the presence of chloroquine in vitro. It is perhaps fortunate the that the clinical dosing regimens of 4-aminoquinoline-based ACTs have been sufficient to maintain clinical efficacy despite the non-optimal combination. Nevertheless, optimisation of antimalarial combinations and dosing regimens is becoming more important in the current era of increasing resistance to artemisinins and 4-aminoquinolines. Therefore, these findings should be considered when proposing new treatment regimens (including Triple-ACTs) and the assays described in this study should be performed on new drug combinations that are proposed for new or existing antimalarial medicines.

Strengths:

This manuscript is clearly written and the data presented is clear and complete. The key conclusions are supported by multiple lines of evidence, and most findings are replicated with multiple drugs within a class, and across multiple parasite strains, thus providing more confidence in the generalisability of these findings across the 4-aminoquinoline and peroxide drug classes.

A key strength of this study was the focus on short pulse exposures to DHA (4 h in trophs and 3 h in rings), which is relevant to the in vivo exposure of artemisinins. Artemisinin resistance has had a significant impact on treatment outcomes in South-East Asia, and is now emerging in Africa, but is not detected using a 'standard' 48 or 72 h in vitro growth inhibition assay. It is only in the RSA (a short pulse of 3-6 h treatment of early ring stage parasites) that the resistance phenotype can be detected in vitro. Therefore, assays based on this short pulse exposure provide the most relevant approach to determine whether drug-drug interactions are likely to have a clinically-relevant impact on DHA activity. These assays clearly showed antagonism between DHA and 4-aminoquinolines (chloroquine, piperaquine, amodiaquine and ferroquine) in trophozoite stages. Interestingly, whilst chloroquine clearly induced an artemisinin-resistant phenotype in the RSA, piperaquine only had a minor impact on the early ring stage activity of DHA, which may be fortunate considering that piperaquine is a currently recommended DHA partner drug in ACTs, whereas chloroquine is not.

The evaluation of additional drug combinations at the end of this paper is a valuable addition, which increases the potential impact of this work. The finding of antagonism between piperaquine and OZ439 in trophozoites is consistent with the general interactions observed between peroxides and 4-aminoquinolines, and it may be interesting to see whether piperaquine impacts the ring-stage activity of OZ439.

The evaluation of reactive heme in parasites using a fluorescent sensor, combined with the measurement of K48-linked ubiquitin, further support the findings of this study, providing independent read-outs for the chloroquine-induced antagonism.<br /> The in-depth discussion of the interpretation and implications of the results are an additional strength of this manuscript. Whilst the discussion section is rather lengthy, there are important caveats to the interpretation of some of these results, and clear relevance to the future management of malaria that require these detailed explanations.

Overall, this is a high quality manuscript describing an important study that has implications for the selection of antimalarial combinations for new and existing malaria medicines.

Weaknesses:

This study is an in vitro study of parasite cultures, and therefore caution should be taken when applying these findings to decisions about clinical combinations. The drug concentrations and exposure durations in these assays are intended to represent clinically relevant exposures, although it is recognised that the in vitro system is somewhat simplified and there may be additional factors that influence in vivo activity. This limitation is reasonably well acknowledged in the manuscript.

It is also important to recognise that the majority of the key findings regarding antagonism are based on trophozoite-stage parasites, and one must show caution when generalising these findings to other stages or scenarios. For example, piperaquine showed clear antagonism in trophozoite stages, but minimal impact in ring stages under these assay conditions.

A key limitation is the interpretation of the mechanistic studies that implicate heme-mediated artemisinin activation as the mechanism underpinning antagonism by chloroquine. This study did not directly measure the activation of artemisinins. The data obtained from the activation of the fluorescent probe are generally supportive of chloroquine suppressing the heme-mediated activation of artemisinins, and I think this is the most likely explanation, but there are significant caveats to consider. Primarily, the inconsistency between the fluorescence profile in the chemical reactions and the cell-based assay raise questions about the accuracy of this readout. In the chemical reaction, mefloquine and chloroquine showed identical inhibition of fluorescence, whereas piperaquine had minimal impact. On the contrary, in the cell, chloroquine and piperaquine had similar impacts on fluorescence, but mefloquine had minimal impact. This inconsistency indicates that the cellular fluorescence based on this sensor does not give a simple direct readout of the reactivity of ferrous heme, and therefore, these results should be interpreted with caution. Indeed, the correlation between fluorescence and antagonism for the tested drugs is a correlation, not causation. There could be several reasons for the disconnect between the chemical and biological results, either via additional mechanisms that quench fluorescence, or the presence of biomolecules that alter the oxidation state or coordination chemistry of heme or other potential catalysts of this sensor. It is possible that another factor that influences the H-FluNox fluorescence in cells also influences the DHA activity in cells, leading to the correlation with activity. It should be noted that H-FluNox is not a chemical analogue of artemisinins. It's activation relies on Fenton-like chemistry, but with a N-O rather that O-O bond, and it possesses very different steric and electronic substituents around the reactive centre, which are known to alter reactivity to different iron sources. Despite these limitations, the authors have provided reasonable justification for the use of this probe to directly visualise heme reactivity in cells, and the results are still informative.

Another interesting finding that was not elaborated by the authors is the impact of chloroquine in the DHA dose-response curves from the ring stage assays. Detection of artemisinin resistance in the RSA generally focuses on the % survival at high DHA concentrations (700 nM) as there is minimal shift in the IC50 (see Fig 2), however, chloroquine clearly induces a shift in the IC50 (~5-fold), where the whole curve is shifted to the right, whereas the increase in % survival is relatively small. This different profile suggests that the mechanism of chloroquine-induced antagonism may be different to the mechanism of artemisinin resistance. Current evidence regarding the mechanism of artemisinin resistance generally points towards decreased heme-mediated drug activation due to a decrease in hemoglobin uptake, which should be analogous to the decrease in heme-mediated drug activation caused by chloroquine. However, these different dose response curves suggest different mechanisms are primarily responsible. Additional mechanisms have been proposed for artemisinin resistance, involving redox or heat stress responses, proteostatic responses, mitochondrial function, dormancy and PI3K signalling among others. Whilst the H-FluNox probe generally supports the idea that chloroquine suppresses heme-mediated DHA activation, it remains plausible that chloroquine could induce these, or other, cellular responses that suppress DHA activity.

Impact:

This study has important implications for the selection of drugs to form combinations for the treatment of malaria. The overall findings of antagonism between peroxide antimalarials and 4-aminoquinolines in the trophozoite stage are robust, and the this carries across to the ring stage for chloroquine.

The manuscript also provides a plausible mechanism to explain the antagonism, although future work will be required to further explore the details of this mechanism and to rule out alternative factors that may contribute.

Overall, this is an important contribution to the field and provides a clear justification for the evaluation of potential drug combinations in relevant in vitro assays before clinical testing.

Reviewer #1 (Public review):

Summary:

Mitochondria encode a small set of proteins that are made inside the organelle by specialized ribosomes. When this mitochondrial translation system fails, oxidative phosphorylation is impaired, an outcome that is particularly harmful to energy-demanding tissues such as the heart. In this manuscript, the authors use a targeted CRISPR/Cas9 screen in cultured cells grown on galactose (a condition that forces reliance on oxidative phosphorylation) to identify genes required for mitochondrial activity. They highlight EOLA1, previously studied mainly in inflammatory contexts, as a top candidate.

Strengths:

The authors present data suggesting that EOLA1 is imported into mitochondria via an N-terminal targeting sequence and resides in the mitochondrial matrix. Loss of EOLA1 reduces oxygen consumption and is associated with altered mitochondrial ultrastructure. Mechanistically, affinity purification suggests interaction with mitochondrial elongation factors TUFM (mtEF-Tu), and RNA immunoprecipitation experiments enrich 12S mt-rRNA, consistent with a relationship to the small ribosomal subunit. Multiple assays, including sucrose-gradient profiling, reduced abundance of selected mtDNA-encoded proteins, and a click-chemistry labeling approach, support the conclusion that mitochondrial protein synthesis is decreased in EOLA1-deficient cells. Finally, whole-body Eola1 knockout mice show echocardiographic findings consistent with dilated cardiomyopathy and reduced levels of representative mitochondrially encoded proteins in cardiac tissue.

How to interpret the work:

The data support a role for EOLA1 in maintaining mitochondrial gene expression and oxidative phosphorylation capacity, and they plausibly implicate mitochondrial translation.

Weaknesses:

The main caveat is that the study does not yet establish how EOLA1 acts, whether it directly modulates translation elongation through TUFM, whether it is primarily required for mitoribosome biogenesis/rRNA stability, or whether it influences translation indirectly through mitochondrial stress pathways. The in vivo phenotype is intriguing, but without tissue-specific deletion/rescue and deeper cardiac pathology/mitochondrial functional measurements, it remains uncertain how directly the heart phenotype reflects a cardiomyocyte-autonomous defect in mitochondrial translation.

Reviewer #1 (Public review):

Summary:

Du, Daniel X. et al studied the interaction of the ultrashort electron and laser pulses inside a scanning electron microscopy (SEM), aiming to build a foundation for pulsed laser phase plate electron microscopy, in which the contrast of cryo samples can be significantly increased. The author modified a commercial SEM to accommodate optics to introduce a laser beam inside the instrument to overlap with the electron beam and performed multiple experiments aimed to characterize the electron-light interaction, particularly reaching an extremely high phase shift of >400 rad. Moreover, the authors built a theoretical model for this interaction and estimated the laser beam parameters needed to reach 90 degrees phase shift in transmission electron microscopy (TEM).

Strengths:

The conclusion on the interaction of the electron pulses and laser pulses is well described and supported by the experiment.

The presented instrument can serve as a great tool for studying fundamental interactions of electrons with extremely intense light pulses.

Weaknesses:

The authors motivate the project by using the pulsed electron beam with a phase shift for improving the contrast in cryo-EM, and while they indicate the low current in UEM, they do not discuss the limitations of the laser beam properties.

Such, even for 1 ps electron pulses with the repetition rate of 100 GHz (duty cycle of 10%), they will need to use 100 GHz laser pulses with pulse energies of at least ~1 uJ a second (the lowest pulse energy reported in the simulations in Figure 4), which would mean that ~10 kW of optical power needs to enter the electron microscope and be dumped somewhere after leaving the instrument. This significantly complicates the system and, in my view, makes it harder to use a pulsed laser phase plate in cryo-EM due to either low acquisition rate at lower repetition rates or extreme difficulties to operate multi kW ultrafast laser system.

I would also expect the unscattered electron beam diameter to be <1 micron, which would significantly change the plot in 4b for the 300 keV electron beam.

Adding experimental parameters for a typical cryo-EM experiment with the pulsed phase plate, including the repetition rate, electron pulse duration, number of electrons per pulse, electron beam size, and the parameters of the laser beam (wavelength, laser pulse duration, pulse energy), will help readers better understand technical requirements for the proposed cryo-EM experiments.

Reviewer #2 (Public review):

Zhang et al. have developed an advanced three-dimensional culture system of human endometrial cells, termed a receptive endometrial assembloid, that models the uterine lining during the crucial window of implantation (WOI). During this mid-secretory phase of the menstrual cycle, the endometrium becomes receptive to an embryo, undergoing distinctive changes. In this work, endometrial cells (epithelial glands, stromal cells, and immune cells from patient samples) were grown into spheroid assembloids and treated with a sequence of hormones to mimic the natural cycle. Notably, the authors added pregnancy-related factors (such as hCG and placental lactogen) on top of estrogen and progesterone, pushing the tissue construct into a highly differentiated, receptive state. The resulting WOI assembloid closely resembles a natural receptive endometrium in both structure and function. The cultures form characteristic surface structures like pinopodes and exhibit abundant motile cilia on the epithelial cells, both known hallmarks of the mid-secretory phase. The assembloids also show signs of stromal cell decidualization and an epithelial mesenchymal transition, like process at the implantation interface, reflecting how real endometrial cells prepare for possible embryo invasion.

Although the WOI assembloid represents an important step forward, it still has limitations: the supportive stromal and immune cell populations decrease over time in culture, so only early-passage assembloids retain full complexity. Additionally, the differences between the WOI assembloid and a conventional secretory-phase organoid are more quantitative than absolute; both respond to hormones and develop secretory features, but the WOI assembloid achieves a higher degree of differentiation due to the addition of "pregnancy" signals. Overall, while it's a reinforced model (not an exact replica of the natural endometrium), it provides a valuable in vitro system for implantation studies and testing potential interventions, with opportunities to improve its long-term stability and biological fidelity in the future.

[Editors' note: the authors have responded to the previous round of recommendations.]

Reviewer #1 (Public review):

Summary:

This paper presents maRQup a Python pipeline for automating the quantitative analysis of preclinical cancer immunotherapy experiments using bioluminescent imaging in mice. maRQup processes images to quantify tumor burden over time and across anatomical regions, enabling large-scale analysis of over 1,000 mice. The study uses this tool to compare different CAR-T cell constructs and doses, identifying differences in initial tumor control and relapse rates, particularly noting that CD19.CD28 CAR-T cells show faster initial killing but higher relapse compared to CD19.4-1BB CAR-T cells. Furthermore, maRQup facilitates the spatiotemporal analysis of tumor dynamics, revealing differences in growth patterns based on anatomical location, such as the snout exhibiting more resistance to treatment than bone marrow.

Strengths:

(1) The maRQup pipeline enables the automatic processing of a large dataset of over 1,000 mice, providing investigators with a rapid and efficient method for analyzing extensive bioluminescent tumor image data.

(2) Through image processing steps like tail removal and vertical scaling, maRQup normalizes mouse dimensions to facilitate the alignment of anatomical regions across images. This process enables the reliable demarcation of nine distinct anatomical regions within each mouse image, serving as a basis for spatiotemporal analysis of tumor burden within these consistent regions by quantifying average radiance per pixel.

Weaknesses:

(1) While the pipeline aims to standardize images for regional assessment, the reliance on scaling primarily along the vertical axis after tail removal may introduce limitations to the quantitative robustness of the anatomically defined regions. This approach does not account for potential non-linear growth across dimensions in animals of different ages or sizes, which could result in relative stretching or shrinking of subjects compared to an average reference.

(2) Furthermore, despite excluding severely slanted images, the pipeline does not fully normalize for variations in animal pose during image acquisition (e.g., tucked body, leaning). This pose variability not only impacts the precise relative positioning of internal anatomical regions, potentially making their definition based on relative image coordinates more qualitative than truly quantitative for precise regional analysis, but it also means that the bioluminescent light signal from the tumor will not propagate equally to the camera as photons will travel differentially through the tissue. This differing light path through tissues due to variable positioning can introduce large variability in the measured radiance that was not accounted for in the analysis algorithm. Achieving more robust anatomical and quantitative normalization might require methods that control animal posture using a rigid structure during imaging.

Comments on revisions:

(1) Clarification of 2D Analysis. We strongly recommend that the authors explicitly define maRQup as a 2D spatiotemporal analysis technique. Since optical imaging quantification is inherently dependent on tissue type and signal depth, characterizing this as a 3D or volumetric method without tomographic correction is inaccurate. Please precede "spatiotemporal" with "2D" throughout the text to ensure precision regarding the method's capabilities.

(2) Data Validation and Scaling in Supplemental Figure g currently lacks the units necessary to support the assertion.

Non-Uniform Growth: The authors' method implies that mouse growth is linear and uniform in all directions (isotropic). However, murine growth is not akin to the inflation of a balloon; animals elongate and widen at different rates. The current scaling does not account for these physiological non-linearities.

Pose Variability: The scaling approach appears to neglect significant variability in animal positioning. Even under anesthesia, animal pose is rarely identical across subjects or time points.

Requirement for Evidence: Without quantitative data, there appears to be significant differences between the individual images and the merged image. If the authors assert that this is a "classical setting" where mouse positioning is 100% consistent and growth curves are identical in multiple dimensions, please provide specific references that validate these assumptions. Otherwise, the scaling must be corrected to account for anisotropic growth and pose differences or stated that scaling was only based on one dimension.

(3) Methodology of Spatial Regions The manuscript does not currently indicate how the nine distinct spatial regions were determined. Please expand the methods section to include the specific segmentation algorithms or anatomical criteria used to define these regions, as this is critical for reproducibility.

Reviewer #1 (Public review):

Summary:

This study presents a technically sophisticated intravital two-photon calcium imaging approach to characterize meningeal macrophage Ca²⁺ dynamics in awake mice. The development of a Pf4Cre:GCaMP6s reporter line and the integration of event-based Ca²⁺ analysis represent clear methodological strengths. The findings reveal niche-specific Ca²⁺ signaling patterns and heterogeneous macrophage responses to cortical spreading depolarization (CSD), with potential relevance to migraine and neuroinflammatory conditions. Despite these strengths, several conceptual, technical, and interpretational issues limit the impact and mechanistic depth of the study. Addressing the points below would substantially strengthen the manuscript.

Strengths:

The use of chronic two-photon Ca²⁺ imaging in awake, behaving mice represents a major technical strength, minimizing confounds introduced by anesthesia. The development of a Pf4Cre:GCaMP6s reporter line, combined with high-resolution intravital imaging, enables long-term and subcellular analysis of macrophage Ca²⁺ dynamics in the meninges.

The comparison between perivascular and non-perivascular macrophages reveals clear niche-dependent differences in Ca²⁺ signaling properties. The identification of macrophage Ca²⁺ activity temporally coupled to dural vasomotion is particularly intriguing and highlights a potential macrophage-vascular functional unit in the dura.

By linking macrophage Ca²⁺ responses to CSD and implicating CGRP/RAMP1 signaling in a subset of these responses, the study connects meningeal macrophage activity to clinically relevant neuroimmune pathways involved in migraine and other neurological disorders.

Weaknesses:

The manuscript relies heavily on Pf4Cre-driven GCaMP6s expression to selectively image meningeal macrophages. Although prior studies are cited to support Pf4 specificity, Pf4 is not an exclusively macrophage-restricted marker, and developmental recombination cannot be excluded. The authors should provide direct validation of reporter specificity in the adult meninges (e.g., co-labeling with established macrophage markers and exclusion of other Pf4-expressing lineages). At minimum, the limitations of Pf4Cre-based labeling should be discussed more explicitly, particularly regarding how off-target expression might affect Ca²⁺ signal interpretation.

The manuscript offers an extensive characterization of Ca²⁺ event features (frequency spectra, propagation patterns, synchrony), but the biological significance of these signals is largely speculative. There is no direct link established between Ca²⁺ activity patterns and macrophage function (e.g., activation state, motility, cytokine release, or interaction with other meningeal components). The discussion frequently implies functional specialization based on Ca²⁺ dynamics without experimental validation. To strengthen the conceptual impact, a clearer framing of the study as a foundational descriptive resource, rather than a functional dissection, would improve alignment between data and conclusions.

The GLM analysis revealing coupling between dural perivascular macrophage Ca²⁺ activity and vasomotion is technically sophisticated and intriguing. However, the directionality of this relationship remains unresolved. The current data do not distinguish whether macrophages actively regulate vasomotion, respond to mechanical or hemodynamic changes, or are co-modulated by neural activity. Statements suggesting that macrophages may "mediate" vasomotion are therefore premature. The authors should reframe these conclusions more cautiously, emphasizing correlation rather than causation, and expand the discussion to explicitly outline experimental strategies required to establish causality (e.g., macrophage-specific Ca²⁺ manipulation).

The authors conclude that synchronous Ca²⁺ events across macrophages are driven by extrinsic signals rather than intercellular communication, based primarily on distance-time analyses. This conclusion is not sufficiently supported, as spatial independence alone does not exclude paracrine signaling, vascular cues, or network-level coordination. No perturbation experiments are presented to test alternative mechanisms. The authors can either provide additional experimental evidence or rephrase the conclusion to acknowledge that the source of synchrony remains unresolved.

A major and potentially important finding is that the dominant macrophage response to CSD is a persistent decrease in Ca²⁺ activity, which is independent of CGRP/RAMP1 signaling. However, this phenomenon is not mechanistically explored. It remains unclear whether Ca²⁺ suppression reflects macrophage inhibition, altered viability, homeostatic resetting, or an anti-inflammatory program. Minimally, the discussion should be more deeply engaged with possible interpretations and implications of this finding.

The pharmacological blockade of RAMP1 supports a role for CGRP signaling in persistent Ca²⁺ increases after CSD, but the experiments are based on a relatively small number of cells and animals. The limited sample size constrains confidence in the generality of the conclusions. Pharmacological inhibition alone does not establish cell-autonomous effects in macrophages. The authors should acknowledge these limitations more explicitly and avoid overextension of the conclusions.

Reviewer #1 (Public review):

Summary:

In this study, the authors' aim was to determine whether hepatic palmitoylation is a physiologically relevant regulator of systemic metabolism. The data demonstrate that loss of DHHC7 in hepatocytes disrupts Gαi palmitoylation, enhances cAMP-PKA-CREB signaling, and drives transcriptional upregulation and secretion of Prg4. The KO mice display increased body weight, fat mass, and plasma cholesterol, but at 12 weeks on HFD, do not exhibit insulin resistance. The potential mechanism underlying the metabolic phenotype was examined by assessing adipocyte signaling and by exploring whether Prg4 acts through GPR146. Through this pathway, the authors intend to link DHHC7-dependent palmitoylation to the regulation of hepatokines that exert systemic metabolic effects.

Strengths:

(1) Hepatic palmitoylation in systemic metabolic regulation is largely unexplored. The authors demonstrate the role of DHHC7 in vivo using a successful liver-specific knockout mouse model that causes HFD-dependent obesity without insulin resistance.

(2) Several studies were performed on chow and HFD, as well as male and female mice.

(3) Plasma proteomics identified Prg4 as a circulating factor elevated in KO mice. Prg4 overexpression phenocopied the KO mice.

(4) There is solid mechanistic data supporting the hypothesis that hepatic DHHC7 loss selectively increases Prg4 secretion as a hepatokine.

(5) There is convincing evidence for the DHHC7 mechanism in liver: DHHC7 controls cAMP-PKA-CREB via Gαi palmitoylation. The authors recognize that the palmitoylation change is causative rather than correlated, and this needs to be more fully explored in the future.

(6) Strong in vitro data support that Prg4 acts through adipocyte GPR146 via its SMB domain

Weaknesses:

(1) The assessment of liver and adipose tissue responses to DHH7 loss is insufficient to support claims that it alters systemic lipolysis. In this new mouse model, liver histology is necessary, especially given the cholesterol increase in the KO. As this is a newly established mouse line, common assessments of the liver during HFD feeding would be important for interpreting the phenotype.

(2) The data show DHH7 loss causes adipose tissue dysfunction and alterations in lipid metabolism. Beyond that, I suggest not stating more regarding the phenotype of the DHH7 mice for this work. A thorough analysis would be needed to determine which factor drives the obesity and changes in energy balance in the mice. For example, the KO mice had lower oxygen consumption (but no change in CO2 production, which is also usually similarly altered), suggesting a CNS component could drive obesity. However, since the data are not normalized for lean mass and there is no information about locomotor activity, this analysis is incomplete. RER may be informative if available. A broad conservative description of the KO phenotype would be more accurate since Pgr4 has many paracrine targets and likely has autocrine signaling in the liver.

(3) Most references to lipolysis or lipolysis flux systemically would be inaccurate. To suggest a suppression of lipolysis, serum NEFA would need to be measured, and in vivo or in vitro lipolysis assays performed to test the effect of DHH7 loss or the specificity of PGR4 action on adipocytes in vivo. To demonstrate adipose tissue dysfunction, analysis of lipogenesis markers, canonical markers for insulin sensitivity, and mitochondrial dysfunction should be performed/measured.

(4) Line 179: The experiment was performed in brown adipocytes to show that Prg4 does not affect p-CREB Figure S8 under the heading: "DHHC7 controls hepatic PKA-CREB activity through Gαi palmitoylation to regulate Prg4 transcription." Unless repeated using liver lysate, the conclusions stated in the text throughout the paper should be revised.

(5) It appears that the serum and liver proteomics were only assessed for factors that increased in KO mice? Were proteins that were significantly decreased analyzed?

(6) The beige adipocyte culture method is unclear. The methods do not describe the fat pad used, and the protocol suggests the cells would be differentiated into mature white adipocytes. If they are beige cells, a reference for the method, gene expression, and cell images could support that claim.

(7) The use of tamoxifen can confound adipocyte studies, as it increases beigeing and weight gain even after a brief initiation period. Both groups were treated with Tam, but another way to induce Cre would be ideal.

(8) Evidence for the lack of the glucose phenotype is incomplete. One reason could be due to the IP route of glucose administration, which has a large impact on glucose handling during a GTT. To confirm the absence of a glucose tolerance phenotype, an OGTT should be performed, as it is more physiological. In addition, the mice should be fed for 16 weeks. Prg4 affects immune cells, changing how adipose tissue expands, and 12 weeks of HFD feeding is often not long enough to see the effects of adipose tissue inflammation spilling over into the system.

(9) There may be liver-adipose tissue crosstalk in KO mice, but this was not fully assessed in this study and would be difficult to determine in any setting, given the diverse cell types that are targets of Pdg4. The crosstalk claim is unnecessary to share the basic premises; there is the DHH7 mechanism/phenotype and the Pgr4 mechanism/phenotype, and while there is no Pgr4 adipose direct mechanism, the paper can be successfully reframed.

(10) Although the DHH7 loss on the chow diet did not result in a phenotype, did the Pgr4 increase in the KO mice on chow? This would determine whether either i) the expression of Pgr4 is dependent on HFD/obesity, or ii) circulating Pgr4 has effects only in an HFD condition. The receptors may also change on HFD, especially in adipocytes.

Impact:

This work would significantly contribute to the study of liver metabolism, provided it includes data describing the liver. The role of Pgr4 in adipocytes and other cell types is of substantial value to the field of metabolism. By reframing the paper and conducting some key experiments, its quality and impact can be increased.

Reviewer #1 (Public review):

Summary:

This manuscript by Lin et al. presents a timely, technically strong study that builds patient-specific midbrain-like organoids (MLOs) from hiPSCs carrying clinically relevant GBA1 mutations (L444P/P415R and L444P/RecNcil). The authors comprehensively characterize nGD phenotypes (GCase deficiency, GluCer/GluSph accumulation, altered transcriptome, impaired dopaminergic differentiation), perform CRISPR correction to produce an isogenic line, and test three therapeutic modalities (SapC-DOPS-fGCase nanoparticles, AAV9-GBA1, and SRT with GZ452). The model and multi-arm therapeutic evaluation are important advances with clear translational value.

My overall recommendation is that the work undergo a major revision to address the experimental and interpretive gaps listed below.

Strengths:

(1) Human, patient-specific midbrain model: Use of clinically relevant compound heterozygous GBA1 alleles (L444P/P415R and L444P/RecNcil) makes the model highly relevant to human nGD and captures patient genetic context that mouse models often miss.

(2) Robust multi-level phenotyping: Biochemical (GCase activity), lipidomic (GluCer/GluSph by UHPLC-MS/MS), molecular (bulk RNA-seq), and histological (TH/FOXA2, LAMP1, LC3) characterization are thorough and complementary.

(3) Use of isogenic CRISPR correction: Generating an isogenic line (WT/P415R) and demonstrating partial rescue strengthens causal inference that the GBA1 mutation drives many observed phenotypes.

(4) Parallel therapeutic testing in the same human platform: Comparing enzyme delivery (SapC-DOPS-fGCase), gene therapy (AAV9-GBA1), and substrate reduction (GZ452) within the same MLO system is an elegant demonstration of the platform's utility for preclinical evaluation.

(5) Good methodological transparency: Detailed protocols for MLO generation, editing, lipidomics, and assays allow reproducibility

Weaknesses:

(1) Limited genetic and biological replication

(a) Single primary disease line for core mechanistic claims. Most mechanistic data derive from GD2-1260 (L444P/P415R); GD2-10-257 (L444P/RecNcil) appears mainly in therapeutic experiments. Relying primarily on one patient line risks conflating patient-specific variation with general nGD mechanisms.

(b) Unclear biological replicate strategy. It is not always explicit how many independent differentiations and organoid batches were used (biological replicates vs. technical fields of view).

(c) A significant disadvantage of employing brain organoids is the heterogeneity during induction and potential low reproducibility. In this study, it is unclear how many independent differentiation batches were evaluated and, for each test (for example, immunofluorescent stain and bulk RNA-seq), how many organoids from each group were used. Please add a statement accordingly and show replicates to verify consistency in the supplementary data.

(d) Isogenic correction is partial. The corrected line is WT/P415R (single-allele correction); residual P415R complicates the interpretation of "full" rescue and leaves open whether the remaining pathology is due to incomplete correction or clonal/epigenetic effects.

(e) The authors tested week 3, 4, 8, 15, and 28 old organoids in different settings. However, systematic markers of maturation should be analyzed, and different maturation stages should be compared, for example, comparing week 8 organoids to week 28 organoids, with immunofluorescent marker staining and bulk RNAseq.

(f) The manuscript frequently refers to Wnt signaling dysregulation as a major finding. However, experimental validation is limited to transcriptomic data. Functional tests, such as the use of Wnt agonist/inhibitor, are needed to support this claim (see below).

(g) Suggested fixes/experiments

Add at least one more independent disease hiPSC line (or show expanded analysis from GD2-10-257) for key mechanistic endpoints (lipid accumulation, transcriptomics, DA markers)

Generate and analyze a fully corrected isogenic WT/WT clone (or a P415R-only line) if feasible; at minimum, acknowledge this limitation more explicitly and soften claims.

Report and increase independent differentiations (N = biological replicates) and present per-differentiation summary statistics.

(2) Mechanistic validation is insufficient

(a) RNA-seq pathways (Wnt, mTOR, lysosome) are not functionally probed. The manuscript shows pathway enrichment and some protein markers (p-4E-BP1) but lacks perturbation/rescue experiments to link these pathways causally to the DA phenotype.

(b) Autophagy analysis lacks flux assays. LC3-II and LAMP1 are informative, but without flux assays (e.g., bafilomycin A1 or chloroquine), one cannot distinguish increased autophagosome formation from decreased clearance.

(c) Dopaminergic dysfunction is superficially assessed. Dopamine in the medium and TH protein are shown, but no neuronal electrophysiology, synaptic marker co-localization, or viability measures are provided to demonstrate functional recovery after therapy.

(d) Suggested fixes/experiments

Perform targeted functional assays:

(i) Wnt reporter assays (TOP/FOP flash) and/or treat organoids with Wnt agonists/antagonists to test whether Wnt modulation rescues DA differentiation.

(ii)Test mTOR pathway causality using mTOR inhibitors (e.g., rapamycin) or 4E-BP1 perturbation and assay effects on DA markers and autophagy.

Include autophagy flux assessment (LC3 turnover with bafilomycin), and measure cathepsin activity where relevant.

Add at least one functional neuronal readout: calcium imaging, MEA recordings, or synaptic marker quantification (e.g., SYN1, PSD95) together with TH colocalization.

(3) Therapeutic evaluation needs greater depth and standardization

(a) Short windows and limited durability data. SapC-DOPS and AAV9 experiments range from 48 hours to 3 weeks; longer follow-up is needed to assess durability and whether biochemical rescue translates into restored neuronal function.

(b) Dose-response and biodistribution are under-characterized. AAV injection sites/volumes are described, but transduction efficiency, vg copies per organoid, cell-type tropism quantification, and SapC-DOPS penetration/distribution are not rigorously quantified.

(c) Specificity controls are missing. For SapC-DOPS, inclusion of a non-functional enzyme control (or heat-inactivated fGCase) would rule out non-specific nanoparticle effects. For AAV, assessment of off-target expression and potential cytotoxicity is needed.

(d) Comparative efficacy lacking. It remains unclear which modality is most effective in the long term and in which cellular compartments.

(e) Suggested fixes/experiments

Extend follow-up (e.g., 6+ weeks) after AAV/SapC dosing and evaluate DA markers, electrophysiology, and lipid levels over time.

Quantify AAV transduction by qPCR for vector genomes and by cell-type quantification of GFP+ cells (neurons vs astrocytes vs progenitors).

Include SapC-DOPS control nanoparticles loaded with an inert protein and/or fluorescent cargo quantitation to show distribution and uptake kinetics.

Provide head-to-head comparative graphs (activity, lipid clearance, DA restoration, and durability) with statistical tests.

(4) Model limitations not fully accounted for in interpretation

(a) Absence of microglia and vasculature limits recapitulation of neuroinflammatory responses and drug penetration, both of which are important in nGD. These absences could explain incomplete phenotypic rescues and must be emphasized when drawing conclusions about therapeutic translation.

(b) Developmental vs degenerative phenotype conflation. Many phenotypes appear during differentiation (patterning defects). The manuscript sometimes interprets these as degenerative mechanisms; the distinction must be clarified.

(c) Suggested fixes

Tone down the language throughout (Abstract/Results/Discussion) to avoid overstatement that MLOs fully recapitulate nGD neuropathology.

Add plans or pilot data (if available) for microglia incorporation or vascularization to indicate how future work will address these gaps.

(5) Statistical and presentation issues

(a) Missing or unclear sample sizes (n). For organoid-level assays, report the number of organoids and the number of independent differentiations.

(b) Statistical assumptions not justified. Tests assume normality; where sample sizes are small, consider non-parametric tests and report exact p-values.

(c) Quantification scope. Many image quantifications appear to be from selected fields of view, which are then averaged across organoids and differentiations.

(d) RNA-seq QC and deposition. Provide mapping rates, batch correction details, and ensure the GEO accession is active. Include these in Methods/Supplement.

(e) Suggested fixes

Add a table summarizing biological replicates, technical replicates, and statistical tests used for each figure panel.

Recompute statistics where appropriate (non-parametric if N is small) and report effect sizes and confidence intervals.

(6) Minor comments and clarifications

(a) The authors should validate midbrain identity further with additional regional markers (EN1, OTX2) and show absence/low expression of forebrain markers (FOXG1) across replicates.

(b) Extracellular dopamine ELISA should be complemented with intracellular dopamine or TH+ neuron counts normalized per organoid or per total neurons.

(c) For CRISPR editing: the authors should report off-target analysis (GUIDE-seq or targeted sequencing of predicted off-targets) or at least in-silico off-target score and sequencing coverage of the edited locus.

(d) It should be clarified as to whether lipidomics normalization is to total protein per organoid or per cell, and include representative LC-MS chromatograms or method QC.

(e) Figure legends should be improved in order to state the number of organoids, the number of differentiations, and the exact statistical tests used (including multiple-comparison corrections).

(f) In the title, the authors state "reveal disease mechanisms", but the studies mainly exhibit functional changes. They should consider toning down the statement.

(7) Recommendations

This reviewer recommends a major revision. The manuscript presents substantial novelty and strong potential impact but requires additional experimental validation and clearer, more conservative interpretation. Key items to address are:

(a) Strengthening genetic and biological replication (additional lines or replicate differentiations).

(b) Adding functional mechanistic validation for major pathways (Wnt/mTOR/autophagy) and providing autophagy flux data.

(c) Including at least one neuronal functional readout (calcium imaging/MEA/patch) to demonstrate functional rescue.

(d) Deepening therapeutic characterization (dose, biodistribution, durability) and including specificity controls.

(e) Improving statistical reporting and explicitly stating biological replicate structure.

Reviewer #1 (Public review):

Summary:

This study uses data from a recent RVFV serosurvey among transhumant cattle in The Gambia to inform the development of an RVFV transmission model. The model incorporates several hypotheses that capture the seasonal nature of both vector-borne RVFV transmission and cattle migration. These natural phenomena are driven by contrasting wet and dry seasons in The Gambia's two main ecoregions and are purported to drive cyclical source-sink transmission dynamics. Although the Sahel is hypothesized to be unsuitable for year-long RVFV transmission, findings suggest that cattle returning from the Gambia River to the Sahel at the beginning of the wet season could drive repeated RVFV introductions and ensuing seasonal outbreaks. Upon review, the authors have removed an additional analysis evaluating the potential impacts of cattle movement bans on transmission dynamics, which was poorly supported by the methodological approach.

Strengths:

Like most infectious diseases in animal systems in low- and middle-income countries, the transmission dynamics of RVFV in cattle in The Gambia are poorly understood. This study harnesses important data on RVFV seroepidemiology to develop and parameterize a novel transmission model, providing plausible estimates of several epidemiological parameters and transmission dynamic patterns.

This study is well written and easy to follow.

The authors consider both deterministic and stochastic formulations of their model, demonstrating potential impacts of random events (e.g. extinctions) and providing confidence regarding model robustness.

The authors use well-established Bayesian estimation techniques for model fitting and confront their transmission model with a seroepidemiological model to assess model fit.

Elasticity analyses help to understand the relative importance of competing demographic and epidemiological drivers of transmission in this system.

Weaknesses:

The model does not include an impact of infection on cattle birth rates, but the authors justify that this parameter should have limited impact on dynamics given predicted low-level circulation patterns, as opposed to explosive outbreaks, in this region.

The importance of the LVFV positivity decay rate is highlighted but loss of immunity is not considered in the SIR model. The authors do discuss uncertainty regarding model structure and a need for future data collection to begin to answer this question.

The model's structure, including homogenous mixing within each ecoregion and step-change seasonality, allows for estimation of generalized transmission rates at a macro scale. However, it greatly simplifies the movement process itself and assumes that transhumant cattle movement is the only mechanism for RVF reintroduction into the Sahel region. The authors discuss that integration of more finely-scaled movement and contact data may help to address this limitation in future work.

This model seems well-suited to be exploited in future work to explore for e.g. impacts of cattle vaccination, and potential differential efficiency when targeting T herds relative to M or L.

Comments on revisions:

I thank the authors for thoughtfully and thoroughly addressing my concerns. I have no further comments.

Reviewer #1 (Public review):

Summary:

In this work by Mohite et al., they have used transcriptomic and metabolic profiling of H. armigera, muscle development, and S. frugiperda to link energy trehalose metabolism and muscle development. They further used several different bioinformatics tools for network analysis to converge upon transcriptional control as a potential mechanism of metabolite-regulated transcriptional programming for muscle development. The authors have also done rescue experiments where trehalose was provided externally by feeding, which rescues the phenotype. Though the study is exciting, there are several concerns and gaps that lead to the current results as purely speculative. It is difficult to perform any genetic experiments in non-model insects; the authors seem to suggest a similar mechanism could also be applicable in systems like Drosophila; it might be possible to perform experiments to fill some missing mechanistic details.

A few specific comments below:

The authors used N-(phenylthio) phthalimide (NPP), a trehalose-6-phosphate phosphatase (TPP) inhibitor. They also find several genes, including enzymes of trehalose metabolism, that change. Further, several myogenic genes are downregulated in bulk RNA sequencing. The major caveat of this experiment is that the NPP treatment leads to reduced muscle development, and so the proportion of the samples from the muscles in bulk RNA sequencing will be relatively lower, which might have led to the results. So, a confirmatory experiment has to be performed where the muscle tissues are dissected and sequenced, or some of the interesting targets could be validated by qRT-PCR. Further to overcome the off-target effects of NPP, trehalose rescue experiments could be useful.

Even the reduction in the levels of ADP, NAD, NADH, and NMN, all of which are essential for efficient energy production and utilization, could be due to the loss of muscles, which perform predominantly metabolic functions due to their mitochondria-rich environment. So it becomes difficult to judge if the levels of these energy molecules' reduction are due to a cause or effect.

The authors have used this transcriptomic data for pathway enrichment analysis, which led to the E2F family of transcription factors and a reduction in the level of when trehalose metabolism is perturbed. EMSA experiments, though, confirm a possibility of the E2F interaction with the HaTPS/TPP promoter, but it lacks proper controls and competition to test the actual specificity of this interaction. Several transcription factors have DNA-binding domains and could bind any given DNA weakly, and the specificity is ideally known only from competitive and non-competitive inhibition studies.

The work seems to have connected the trehalose metabolism with gene expression changes, though this is an interesting idea, there are no experiments that are conclusive in the current version of the manuscript. If the authors can search for domains in the E2F family of transcription factors that can bind to the metabolite, then, if not, a chip-seq is essential to conclusively suggest the role of E2F in regulating gene expression tuned by the metabolites.

Some of the above concerns are partially addressed in experiments where silencing of E2F/Dp shows similar phenotypes as with NPP and dsRNA. It is also notable that silencing any key transcription factor can have several indirect effects, and delayed pupation and lethality could not be definitely linked to trehalose-dependent regulation.

Trehalose rescue experiments that rescue phenotype and gene expression are interesting. But is it possible that the fed trehalose is metabolized in the gut and might not reach the target tissue? In which case, the role of trehalose in directly regulating transcription factors becomes questionable. So, a confirmatory experiment is needed to demonstrate that the fed trehalose reaches the target tissues. This could possibly be done by measuring the trehalose levels in muscles post-rescue feeding. Also, rescue experiments need to be done with appropriate control sugars.

No experiments are performed with non-target control dsRNA. All the experiments are done with an empty vector. But an appropriate control should be a non-target control.

Reviewer #1 (Public review):

Summary:

This study evaluates the feasibility of using crispant founder mice, first-generation animals directly edited by CRISPR/Cas9, for initial phenotypic assessments. The authors target seven genes known to produce visible recessive traits to test whether mosaicism in founder animals prevents meaningful phenotype-genotype interpretation. Remarkably, they observe clear null phenotypes in founders for six of the seven genes, with high editing efficiencies. These results demonstrate that crispant mice can, under specific conditions, display recessive phenotypes that are readily interpretable. However, this conclusion should be moderated, as the study addresses only one biological context, visible Mendelian traits, and may not generalize to quantitative, subtle, or late-onset phenotypes. The report also examines attempts at multiplex CRISPR targeting, which reduce viability, underscoring limits for concurrent gene disruptions. Finally, the detailed description of diverse alleles generated by CRISPR provides valuable insight into how allelic series can be exploited to investigate protein function.

Strengths:

(1) The manuscript provides a comprehensive and technically rigorous description of CRISPR/Cas9‑induced mutations across several loci. The accompanying genotyping, sequencing, and analytical approaches are sound, complementary, and well-detailed, providing a resource that will be valuable to researchers using genome editing beyond the specific application of genetic screening.

(2) By documenting a wide diversity of alleles and mutation types, the study contributes to understanding how allelic series generated by CRISPR can be leveraged for dissecting protein function, a perspective that has been less systematically presented in prior literature and could be compared to targeted strategies such as those described by Cassidy et al. (2022, DOI: [10.1016/bs.mie.2022.03.053]) or other relevant studies addressing CRISPR-based allelic series generation.

(3) The work demonstrates technically solid editing and validation workflows, setting a methodological reference point for similar projects across species or trait categories.

Weaknesses:

(1) There is a disconnect between the abstract/introduction and the discussion. While both the abstract and introduction focus on the potential use of crispant founders for phenotypic assessment in the context of genetic screening, with the introduction notably emphasizing this framework through a detailed section on ENU-based screens, the discussion devotes relatively little attention to this aspect. Instead, it primarily examines CRISPR mutagenesis outcomes, mutation detection, and allele characterization. Overall, the study's aims are not clearly or explicitly defined, which contributes to the lack of alignment across sections.

(2) Important limitations of the approach are not sufficiently discussed. For instance, the paper does not address how applicable the findings are beyond visible Mendelian traits, such as for quantitative, late-onset, or more subtle phenotypes, including behavioral ones, or how to interpret wild-type appearing founders. There is little consideration of appropriate experimental controls (e.g., wild-type or mock-edited animals) or of how many animals might be required to robustly establish genotype-phenotype associations.

(3) The conclusion that this strategy will "dramatically reduce time, resources, and animal numbers" is not quantitatively supported by the data presented and should be expressed more cautiously.

repairing a remington portable model 1<br /> by [[Just My Typewriter]] on YouTube <br /> accessed on 2026-02-11T14:47:34

Keep moving forward in your typewriter repair career

Reviewer #1 (Public review):

Summary:

Alveolar macrophages (AMs) are key sentinel cells in the lungs, representing the first line of defense against infections. There is growing interest within the scientific community in the metabolic and epigenetic reprogramming of innate immune cells following an initial stress, which alters their response upon exposure to a heterologous challenge. In this study, the authors show that exposure to extracellular ATP can shape AM functions by activating the P2X7 receptor. This activation triggers the relocation of the potassium channel TWIK2 to the cell surface, placing macrophages in a heightened state of responsiveness. This leads to the activation of the NLRP3 inflammasome and, upon bacterial internalization, to the translocation of TWIK2 to the phagosomal membrane, enhancing bacterial killing through pH modulation. Through these findings, the authors propose a mechanism by which ATP acts as a danger signal to boost the antimicrobial capacity of AMs.

Strengths:

This is a fundamental study in a field of great interest to the scientific community. A growing body of evidence has highlighted the importance of metabolic and epigenetic reprogramming in innate immune cells, which can have long-term effects on their responses to various inflammatory contexts. Exploring the role of ATP in this process represents an important and timely question in basic research. The study combines both in vitro and in vivo investigations and proposes a mechanistic hypothesis to explain the observed phenotype.

Weaknesses:

The authors have revised the manuscript to address the comments raised during the first round of review. However, several figures, figure legends, and methodological sections still require additional adjustments and clarification.

The interpretation of CFU from lysates as 'killing' is unclear; lysate CFUs typically reflect intracellular surviving bacteria and are confounded by differences in uptake. Please include an uptake control (early time point) or time-course to distinguish phagocytosis from intracellular killing. Also, clarify how bacterial burden was calculated (supernatant vs cell-associated vs total). Supernatant alone may not capture adherent bacteria. The normalization as 'fold killing' (mean negative control / sample) is non-standard; please report absolute CFU (log scale) and specify the exact definition of killing/survival.

The Methods section is largely incomplete and requires substantial revision. For instance, the authors report quantification of cytokine concentrations, yet no information is provided regarding how these measurements were performed. It is unclear whether cytokines were measured in BALF by ELISA, or assessed at the mRNA level by qPCR from total lung lysates, or by another method. This information must be clearly specified. In addition, the rationale for selecting the measured cytokines should be justified. While the choice of IL-1β and IL-6 is relatively straightforward, the focus on IL-18 requires explicit justification.

Similarly, the methodology used to quantify immune cell populations presented in Figure 2 is not described. It is not stated how immune cells were isolated and identified (e.g. flow cytometry from lung tissue). No information is provided regarding tissue digestion, cell isolation procedures, or gating strategy (presumably by flow cytometry). These details are essential and should be included, together with the corresponding gating strategy and absolute cell numbers.

Moreover, immune cell quantification would be expected in the context of the challenge experiment as well. Reporting unchanged percentages of lung immune cells following ATP exposure does not support the conclusion of a training effect, particularly one that is specific to alveolar macrophages (AMs). In addition, AMs are not considered recruited immune cells; this should be corrected in the figure legend and throughout the manuscript where applicable.

There are inconsistencies throughout the manuscript. For example, the authors report n = 5 for the survival curves in the figure legend, whereas n = 7 is stated in the Methods section. This discrepancy is unclear and should be clarified.

Supplementary Fig. 1 contains major conceptual errors. The volcano plot represents ATAC-seq peaks (differentially accessible chromatin regions), yet the figure, legend, and color scale repeatedly refer to 'genes' and 'differentially expressed genes'. This conflates chromatin accessibility with gene expression and is misleading. Peaks are secondarily annotated to nearby genes, which should be clearly described as an annotation step rather than the unit of analysis. The figure should be revised to explicitly present peak-level statistics (DARs), with gene names shown only as optional annotations. Additionally, the use of simultaneous P < 0.05 and Q < 0.05 thresholds is non-standard, and the absence of down-regulated regions in the plot requires explanation.

In Figure 7, trained WT and Nlrp3⁻/⁻ mice display similar levels of bacterial clearance. How should this result be interpreted?

Overall, while the study addresses an interesting biological question, the manuscript would benefit from substantial revision prior to publication. In particular, clarifications and improvements regarding the methodology, data presentation, and interpretation are required to strengthen the rigor and reproducibility of the conclusions.

Reviewer #1 (Public review):

Summary

The authors set out to define the genomic distribution and potential functional associations of acetylation of histone H3 lysine 115 (H3K115ac), a poorly characterized modification located in the globular domain of histone H3. Using native ChIP-seq and complementary genomic approaches in mouse embryonic stem cells and during differentiation to neural progenitor cells, they report that H3K115ac is enriched at CpG island promoters, active enhancers, and CTCF binding sites, where it preferentially localizes to regions containing fragile or subnucleosomal particles. These observations suggest that H3K115ac marks destabilized nucleosomes at key regulatory elements and may serve as an informative indicator of chromatin accessibility and regulatory activity.

Strengths

A major strength of this study is its focus on a histone post-translational modification in the globular domain, an area that has received far less attention than histone tail modifications despite strong evidence from structural and in vitro studies that such marks can directly influence nucleosome stability. The authors employ a wide range of complementary genomic analyses-including paired-end ChIP-seq, fragment size-resolved analyses, contour (V-) plots, and sucrose gradient fractionation-to consistently support the association of H3K115ac with fragile nucleosomes across promoters, enhancers, and architectural elements. The revised manuscript is careful in its interpretation and provides a coherent and internally consistent picture of how H3K115ac differs from other acetylation marks such as H3K27ac and H3K122ac. The datasets generated will be valuable to the chromatin community as a resource for further exploration of nucleosome dynamics at regulatory elements.

Weaknesses

The conclusions are largely correlative. While the authors provide strong evidence for the localization of H3K115ac to fragile nucleosomes, the work does not directly test whether this modification causally contributes to nucleosome destabilization or regulatory function in vivo. Questions regarding the enzymes responsible for depositing or removing H3K115ac and its direct functional consequences therefore remain open.

Overall assessment and impact

Overall, the authors largely achieve their stated aims by providing a detailed and well-supported characterization of H3K115ac distribution in mammalian chromatin and its association with fragile nucleosomes at regulatory elements. While mechanistic insight remains to be established, the study introduces a compelling new perspective on globular-domain histone acetylation and highlights H3K115ac as a potentially useful marker for identifying functionally important regulatory regions. The work is likely to stimulate further mechanistic studies and will be of broad interest to researchers studying chromatin structure, transcriptional regulation, and genome organization.

Reviewer #1 (Public Review):

This study by Ryu et al, provides compelling evidence to demonstrate the distributions of Oxt and Oxtr in the murine brain using an advanced RNAscope technique. Detailed information on the distributions was provided, revealing differences in Oxt and Oxtr expressions between males and females. This study will provide a new platform for investigators to study previously unknown roles of brain-region specific Oxt and Oxtr neurons and signaling in animal behaviors and metabolism, and others.

Reviewer #1 (Public Review):

This study extends a previous study by the same group on the generalization of odor discrimination from one nostril to the other. In their earlier study, the group showed that learning to discriminate between two enantiomers does not generalize across nostrils. This was surprising given the Mainland & Sobel 2001 study that found that detecting androstenone in people who do not detect it can generalize across the two nostrils. In this study, they confirmed their previous results and reported that, unlike enantiomers, learning to discriminate odor mixtures generalizes across nostrils, generalizes to other odor mixtures, and is persistent over at least two weeks. This interesting and important result extends our knowledge of this phenomenon and will likely steer more research. It may also help develop new training protocols for people with impairments in their sense of smell.

The main weakness of this study is its scope, as it does not provide substantial insight into why the results differ for enantiomers and why training on odor mixtures generalizes to other odor mixtures.

Reviewer #1 (Public Review):

The authors tested the hypothesis that at high elevations avian eggs will be adapted to prevent desiccation that might arise from loss of water to surrounding drier air. They used a combination of gas diffusion experiments and scanning electron microscopy to examine water vapour conductance rates and eggshell structure, including thickness, pore size, and pore density among 197 bird species distributed along an elevational gradient in the Andes. While there was a correlation between water vapour conductance and elevation among species, a decrease in water vapour conductance with elevation was not associated with eggshell thickness, pore size, and pore density, suggesting the variation in the structure of the eggshells is unlikely to do with among species differences in water loss along elevational gradients. This study is very interesting and timely, especially with increasing water vapour pressure due to climate warming. It is a very well-written study and easy to read. However, I have some concerns about the conclusions drawn from the results.

There are more than twice as many species in low and medium-elevation sites compared to high-elevation sites, so the amount of variation in low and medium-elevation should be expected to be higher by default. The argument for a wider range of variation in low-elevation species will be stronger if the comparison was a similar sample size. Moreover, the pattern clearly breaks down within families. Note also that for Low and medium elevation there is no difference in the amount of variation in conductance residuals possibly because the sample sizes are similar. The seemingly strong positive correlation between eggshell conductance and egg mass may be driven by the five high and two medium-elevation species with large eggs. There seem to be hardly any high-elevation species with egg mass greater than 12g whereas species in low elevation egg size seem to be as high as 80g (Figure 2a). Since larger eggs (and thus eggs of larger birds) lose more water compared to smaller eggs, the correlation between water vapour conductance and elevation may be more strongly associated with body size distribution along elevational gradients rather than egg structure and function.

Authors argue that the observed variation in the relationship between water vapour conductance and elevation among and within bird families suggests potential differences in the adaptive response to common selective pressures in terms of eggshell thickness and pore density, and size. The evidence for this is generally weak from the data analyses because the decrease in water vapour conductance with elevation was not consistent across taxonomic groups nor were differences associated with specific patterns in eggshell thickness and pore density, and size.

It is not clear how the authors expected the relationship between water vapour conductance and elevation to differ among taxonomic groups and there was no attempt to explain the biological implication of these differences among taxonomic groups based on the specific traits of the species or their families. This missing piece of information is crucial to justify the argument that differences among taxonomic groups may be due to differences in adaptive response.

Reviewer #1 (Public Review):

This study aims to develop a new system to analyze genetic determinants of neutrophil function by large-scale genetic screens. For that, the authors use a genetically-engineered ER-Hoxb8 neutrophil progenitor line that expresses Cas9 to perform CRISPR screens and to identify genes required for neutrophil survival and differentiation.

A main strength of this study is that the authors develop a pooled CRISPR sgRNA library applicable to neutrophils and show potential determinants of neutrophil differentiation in vitro using this screening methodology.

A main weakness of this study is that identified candidates associated with neutrophil differentiation, as those indicated in Fig. 4A, were not validated in vivo using neutrophil-specific K.O. models or further characterized in vitro (e.g. transcriptional or epigenetic changes during maturation when compared to non-targeting sgRNA controls).

As secondary strengths, the authors provide evidence of efficient gene editing in Cas9+ER-Hoxb8 neutrophils both in vivo and in vitro and provide evidence of the specificity of this methodology using a Cas9+ER-Hoxb8 immortalized cell line that differentiates into macrophages.

In terms of methodology, this study provides a useful tool to explore gene regulatory networks in neutrophils in large-scale genetic screens. However, it falls short in identifying and validating the true potential of this kind of methodology in the biology of the neutrophil.

Moreover, the technical advances in the field are only incremental as several studies, including those using CRISPR/Cas9 technology in Hoxb-8 immortalized neutrophil progenitor cell lines have been already performed.

Reviewer #4 (Public review):

I maintain that the images in Figure 12 (new Figure 14) do not support the authors' interpretation that 2-cell embryos resulted from in vitro fertilization (IVF) of Amrc-/- rescued sperm. They are clearly not normal 2-cell embryos and instead look very much like fragmented eggs that can be seen occasionally following in vitro fertilization procedures even when that is done with wild type eggs and sperm. The only portion of current Figure 14 that has normal looking 2-cell embryos is in panel 14A4, where wild type B6D2 sperm were used. Even in that panel, there are some fragmented eggs that the authors identify as 2-cell embryos.

The authors offer the explanation that CD1 eggs fertilized by B6D2F1 hybrid male sperm do not develop beyond the 2-cell stage, citing a 2008 paper published in Biology of Reproduction by Fernandez-Goonzalez et al. I read through that paper very carefully and even had a colleague read through it in case I missed something, but that paper says nothing at all about strain incompatibilities, much less 2-cell arrest due to them. The only crosses done in that paper are CD1 eggs x CD1 sperm and B6D2 eggs x B6D2 sperm, all by intracytoplasmic sperm injection and not standard in vitro fertilization. [Note that the paper does mention performing in vitro fertilization but says nothing about how it was done or what mouse strains were used.] I even searched the literature for information regarding incompatibility between these strains and could find nothing relevant. But even if the authors are correct and there happens to be a strain incompatibility and 2-cell arrest is expected, what the authors are calling 2-cell embryos are clearly not.

A second explanation offered by the authors is that they used collagenase to remove the cumulus cells and that this may have affected the appearance of the embryos. This technique is actually used to remove both the cumulus cells and the zona pellucida and has been described as a gentler way to do so than other standard methods (hyaluronidase treatment followed by acid Tyrodes to remove the zona pellucida) (Yamatoya et al., Reprod Med Biol 2011, DOI 10.1007/s12522-011-0075-8). I think it is highly relevant to the current study that the method they used to remove cumulus cells also dissolves the zona, either partially or completely. Given that many of the eggs, fragmented eggs, and 2-cell embryos (from the WT sperm) in Figure 14A are lacking a zona pellucida, it seems very likely that many of the eggs were either zona-free or had partial zona dissolution from the start. In fact, the authors state in the Methods section that "Cumulus-free and zona-free eggs were collected..." for how IVF was done. Partial zona dissolution is standard in some protocols for performing IVF using frozen mouse sperm, which usually have much lower motility and overall efficacy than fresh sperm. In any case, it would improve transparency if the manuscript made clear somewhere other than buried in the Methods that the IVF procedure was done on eggs with partially or fully removed zonas, to allow proper interpretation.

In the rebuttal, the authors go on to state: "To provide additional functional evidence, we complemented the IVF experiments with ICSI using rescued Armc2-/- sperm and B6D2 oocytes, which allowed embryos to develop to the blastocyst stage. In these experiments, 25% of injected oocytes reached the blastocyst stage with rescued sperm compared to 13% for untreated Armc2-/- sperm (Supplementary Fig. 9) These results support the functional competence of rescued sperm and demonstrate partial recovery of fertilization ability following Armc2 mRNA electroporation."

Their conclusion that the data support partial recovery of fertilization ability following Armc2 mRNA electroporation in my opinion has no basis. This experiment was done only once, and no information is provided regarding how many eggs underwent ICSI or how many reached the blastocyst stage. The authors claim that the rescued sperm were better than the Armc2-/- sperm in producing blastocysts, but this is based on a simple percentage report of 25% vs 13% without any statistical analysis, even on the results from the single experiment presented.

Overall, the paper shows rescue of some sperm motility by the new method they use, and the new title is therefore appropriate. The authors have also dealt reasonably with many of the original concerns regarding documenting that their methodology was effective in producing protein (at least the GFP marker) in spermatogenic cells. In my view the authors have, however, not shown any indication of functional recovery over what is already known for the knockout sperm, that ICSI can support blastocyst stage embryo development. They also have not, in my view, justified the claims at the end of the abstract "These motile sperm were able to produce embryos by IVF..." and that "...mRNA electroporation can restore...partially fertilizing ability..."

Reviewer #1 (Public Review):

The heterogeneity within the neutrophil population is becoming clear. However, it was not clear if neutrophil progenitors are also heterogenous. Because neutrophils are short-lived, it is technically challenging to tackle the question. This study used a system to isolate and expand clonal neutrophil progenitors (granulocyte-monocyte progenitors; GMPs) to achieve molecular and functional profiling. In the study, transcriptional profiling was performed by RNAseq and ATACseq. Functional assays were performed ex vivo to examine phagocytosis, ROS production, NET formation, and neutrophil swarming using Candida albicans, as well as C. glabrata and C. auris. The strengths of this study include the use of the neutrophil clone system to track GMPs developing into neutrophils. The clone-based approach made it possible to evaluate the functions of multiple neutrophil subpopulations. Limitations of this study include the dependency on ex vivo approaches and the modest degree of heterogeneity within presented neutrophils. Nevertheless, the finding - the heterogeneity of neutrophils can be traced back to the GMP stage - is significant.

Reviewer #1 (Public review):

Summary:

In their study the authors investigated the F. graminearum homologue of the Drosophila Misato-Like Protein DML1 for a function in secondary metabolism and sensitivity to fungicides.

Strengths:

Generally, the topic of the study is interesting and timely and the manuscript is well written, albeit in some cases details on methods or controls are missing.

Weaknesses:

However, a major problem I see is with the core result of the study, the decrease of the DON content associated with deletion of FgDML1: Although some growth data are shown in figure 6 - indicating a severe growth defect - the DON production presented in figure 3 is not related to biomass. Also, the method and conditions for measuring DON are not described. Consequently, it could well be concluded that the decreased amount of DON detected is simply due to a decreased growth and specific DON production of the mutant remains more or less the same.

To alleviate this concern, it is crucial to show the details on the DON measurement and growth conditions and to relate the biomass formation on the same conditions to the DON amount detected. Only then a conclusion as to an altered production in the mutant strains can be drawn.

Comments to the revised manuscript:

The authors carefully revised the manuscript and provided explanations for methods in several cases. However, there are still some problems - probably due to misunderstanding - that need revision.

(1) A major problem of the first version of the manuscript was the lack of appropriate description of biomass analysis and the consideration of the respective results for evaluation of production of DON and other metabolites. Although the authors provide some explanation in the response to reviews, I could not find a corresponding explanation or description in the manuscript. It is not sufficient to explain the problem to me, but a detailed explanation and description of the method has to be provided in the manuscript along with the definition of one "unit of mycelium". It is still not entirely clear to me what such a "unit of mycelium" is.

Please clarify this and any other uncertainties that were commented on by me and other reviewers in the manuscript, not only in the response to reviews. Also adjust the reference list accordingly.

(2) Another problem was, that the authors considered FgDML1 a regulator of DON production. As mentioned by me and reviewer 3, FgDML1 is crucial to numerous functions in F. graminearum and its lack causes a plethora of problems for fungal physiology. Hence, although it is clear that the lack of FgDML1 causes alterations in DON production, it is not appropriate to designate this factor as a "regulator".<br /> It seems to me that the authors are afraid that if FgDML1 would not be a "regulator" that this would decrease the value of their study, which is not the case. This is a matter of correct wording. Therefore, please revise the wording accordingly, starting with the title:

...FgDML1 impacts DON toxin biosynthesis...

Moreover, for sure the manuscript might benefit from more detailed description of the whole cascade leading from FgDML1 to DON biosynthesis and production of the other metabolites that change upon deletion. Such explanation can help the reader grasp the relevance of FgDML for regulatory processes as well as on more general versus specific effects.

Reviewer #2 (Public review):

This paper proposes two changes to classic RSA, a popular method to probe neural representation in neuroimaging experiments: computing RSA at row/column level of RDM, and using linear mixed modeling to compute second level statistics, using the individual row/columns to estimate a random effect of stimulus. The benefit of the new method is demonstrated using simulations and a re-analysis of a prior fMRI dataset on object perception and memory encoding.

The author's claim that tRSA is a promising approach to perform more complete modeling of cogneuro data, and to conceptualize representation at the single trial/event level (cf Discussion section on P42), is appealing.

In their revised manuscript, the authors have addressed some previous concerns, now referencing more literature aiming to improve RSA and its associated statistical inferences, and providing more guidance on methodological considerations in the Discussion. However, I wish the authors had more extensively edited the Introduction to better contextualize the work and clarify the specific settings in which they see the method as being beneficial over classic RSA. For example, some of the limitations of cRSA mentioned on page 6, e.g. related to presenting the same stimuli to multiple subjects, seem to be quite specific to settings where the researcher expects differential responses across subjects to fundamentally alter the interpretation, rather than something that will just average out by repeatedly offering the same stimulus, or combining data across subjects. It's not clear to me how the switch from 'matrix-level' to 'row-level' analysis in tRSA necessarily addresses this problem. I would be very helpful if the authors would more explicitly outline what problem the row-level aspect of tRSA is solving; what problem statistical inference via LMM is solving; and walk the reader through a very specific use case (perhaps a toy version of the real-data experiment which is now at the end of the paper). Explaining the utility of tRSA for experimental settings in which assessing representational strength for a single-events is crucial would clarify the contribution of this new method better.

A few weaknesses mentioned in my previous review were not adequately addressed. To demonstrate the utility of the method on real neural recordings, only a single dataset is used with a quite complicated experimental design; it's not clear if there is any benefit of using tRSA on a simpler real dataset. Moreover, the cells of an RDM/RSM reflect pairwise comparisons between response patterns. Because the response patterns are repeatedly compared, the cells of this matrix are not independent of one another. While the authors show examples that failure to meet independence assumptions do not affect results in their specific dataset, it does not get acknowledged as a problem at a more fundamental level. Finally, while the paper now states that 'simulations and example tRSA code' are publicly available, the link points to the lab's general github page containing many lab repositories, in which I could not identify a specific repository related to this paper. This is disappointing given that the main goal of this manuscript is to provide a new method that they encourage others to use; a clear pointer to available code is only a minimal requirement to achieve that goal. A dedicated repository, including documentation, READMEs and tutorials/demo's to run simulations, compare methods, etc. would greatly enhance the paper's contribution.

Reviewer #1 (Public review):

In this manuscript, Dillard and colleagues integrate cross-species genomic data with a systems approach to identify potential driver genes underlying human GWAS loci and establish the cell type(s) within which these genes act and potentially drive disease.

Specifically, they utilize a large single cell RNA-seq (scRNA-seq) dataset from an osteogenic cell culture model - bone marrow-derived stromal cells cultured under osteogenic conditions (BMSC-OBs) - from a genetically diverse outbred mouse population called the Diversity Outbred (DO) stock to discover network driver genes that likely underlie human bone mineral density (BMD) GWAS loci. The DO mice segregate over 40M single nucleotide variants, many of which affect gene expression levels, therefore making this an ideal population for systems genetic and co-expression analyses.

The current study builds on previous published work from the same group that used co-expression analysis to identify co-expressed "modules" of genes that were enriched for BMD GWAS associations. In this study, the authors utilized a much larger scRNA-seq dataset from 80 DO BMSC-OBs, inferred co-expression based on Bayesian networks for each identified mesenchymal cell type, focused on networks with dynamic expression trajectories that are most likely driving differentiation of BMSC-OBs, and then prioritized genes ("differentiation driver genes" or DDGs) in these osteogenic differentation networks that had known expression or splicing QTLs (eQTL/sQTLs) in any GTEx tissue that co-localized with human BMD GWAS loci. The systems analysis is impressive, the experimental methods are described in detail, and the experiments appear to be carefully done. The computational analysis of the single cell data is comprehensive and thorough, and the evidence presented in support of the identified DDGs, including Tpx2 and Fgfrl1, is for the most part convincing. Some limitations in the data resources and methods hamper enthusiasm somewhat and are discussed below.

Overall, while this study will no doubt be valuable to the BMD community, the cross-species data integration and analytical framework may be more valuable and generally applicable to the study of other diseases, especially for diseases with robust human GWAS data but for which robust human genomic data in relevant cell types is lacking.

Specific strengths of the study include the large scRNA-seq dataset on BMSC-OBs from 80 DO mice, the clustering analysis to identify specific cell types and sub-types, the comparison of cell type frequencies across the DO mice, and the CELLECT analysis to prioritize cell clusters that are enriched for BMD heritability (Figure 1). The network analysis pipeline outlined in Figure 2 is also a strength, as is the pseudotime trajectory analysis (results in Figure 3).

Potential drawbacks of the authors' approach include their focus on genes that were previously identified as having an eQTL or sQTL in any GTEx tissue. The authors rightly point out that the GTEx database does not contain data for bone tissue, but reason that eQTLs can be shared across many tissues - this assumption is valid for many cis-eQTLs, but it could also exclude many genes as potential DDGs with effects that are specific to bone/osteoblasts. Indeed, the authors show that important BMD driver genes have cell-type specific eQTLs. Another issue concerns potential model overfitting in the iterativeWGCNA analysis of mesenchymal cell type-specific co-expression, which identified an average of 76 co-expression modules per cell cluster (range 26-153). Based on the limited number of genes that are detected as expressed in a given cell due to sparse per cell read depth (400-6200 reads/cell) and drop outs, it's surprising that as many as 153 co-expression modules could be distinguished within any cell cluster. I would suspect some degree of model overfitting is responsible for these results.

Overall, though, these concerns are minor relative to the many strengths of the study design and results. Indeed, I expect the analytical framework employed by the authors here will be valuable to -- and replicated by -- researchers in other disease areas.

Comments on revisions:

Thank you for addressing my concerns. This is an impressive study and manuscript that you should be proud of.

Reviewer #1 (Public review):

Summary:

In this fMRI study, the authors wished to assess neural mechanisms supporting flexible temporal construals. For this, human participants learned a story consisting of fifteen events. During fMRI, events were shown to them, and participants were instructed to consider the event from "an internal" or from "an external" perspective. The authors found distinct patterns of brain activity in the posterior parietal cortex (PPC) and anterior hippocampus for the internal and the external viewpoint. Specifically, activation in the posterior parietal cortex positively correlated with distance during the external-perspective task, but negatively during the internal-perspective task. The anterior hippocampus positively correlated with distance in both perspectives. The authors conclude that allocentric sequences are stored in the hippocampus, whereas egocentric sequences are supported by the parietal cortex.

Strengths:

The research topic is fascinating, and very few labs in the world are asking the question of how time is represented in the human brain. Working hypotheses have been recently formulated, and the work tackles them from the perspective of construals theory.

Weaknesses:

Although the work uses two distinct psychological tasks, the authors do not elaborate on the cognitive operationalization the tasks entail, nor the implication of the task design for the observed neural activation.

Reviewer #1 (Public review):

In this study, the authors provide an integrated proteogenomics pipeline to enable the discovery of novel peptides in an Ewing sarcoma cell line (A673). To identify novel full-length resolved isoforms, they performed long-read RNA sequencing (Oxford Nanopore Technology). Then, to increase the chance of detecting Ewing-specific neopeptides, the authors combined two approaches: a multi-protease digestion and a multi-dimensional proteomics approach.

Given the importance of novel isoforms and cryptic sites in neoantigen discovery and its putative applications in immunotherapy, this method and resource paper are of interest for the Ewing community and potentially for a broader cancer audience. The originality of this paper relies mostly on this optimized method to discover novel peptides (long-read sequencing with multiprotease, multi-dimensional trapped ion mobility spectrometry parallel accumulation-serial fragmentation mass spectrometry). Although, to my knowledge, no study combining long-read sequencing and proteomics methods has been published on Ewing Sarcoma, this study appears limited by a few aspects:

(1) The study is restricted to the analysis of a single cell line (A673). The authors should consider extending the analysis to other Ewing cell lines.

(2) The characterization of the 1121 non-canonical transcripts can be improved. How many are just splice variants of known genes, and how many are bona fide neogenes? In this respect, the definition of what the authors call neogene is quite unclear. Is a transcript with a new exon reported as a neogene? Is a transcript with a new start site reported as a neogene? It should be clearly indicated which categories of Figure 4B are reported on Figure 4D. A general flow chart would be very useful to help follow the analysis process.

(3) Similarly, the authors detect 3216 A673 specific proteins with no match in SwissProt. This number decreases to 72 "putative non-canonical proteoforms with unique peptides after BLASTp" against Uniprot. Again, a flow chart would conveniently enable one to follow the step-by-step analysis.

(4) Finally, only 17 spectral matches are suggested to be derived from non-canonical proteoforms. It would be important to compare the spectrum of these detected peptides with that of synthetic peptides. Such an analysis would enable us to assess the number of reliably detected proteoforms that can be expected in an Ewing sarcoma cell line.

(5) It is very unclear what the authors want to highlight in Supplementary Figure 5. Is it that non-canonical transcripts are broadly expressed in normal tissue? Which again raises the question of definitions of neogenes, non-canonical... Apparently, this figure shows that these non-canonical transcripts contain a large part of canonical sequences, which account for the strong signal in many normal tissues. A similar heatmap could be presented, including only the non-canonical sequences of the non-canonical transcripts. This figure should also include Ewing sarcoma samples.

Reviewer #1 (Public review):

Summary:

This manuscript investigates how herbivorous insects, specifically whiteflies and planthoppers, utilize salivary effectors to overcome plant immunity by targeting the RLP4 receptor.

Strengths:

The authors present a strong case for the independent evolution of these effectors and provide compelling evidence for their functional roles.

Reviewer #1 (Public review):

Summary:

In this manuscript, Seegren and colleagues demonstrate that in a mouse model of neonatal E. coli meningitis, loss of endothelial toll-like receptor 4 (TLR4) leads to a marked decrease in transcriptional dysregulation across multiple leptomeningeal cell types, a decrease in vascular permeability, and a decrease in macrophage abundance. In contrast, loss of macrophage TLR4 had less pronounced effects. Using cultured wild-type and TLR4-knockout endothelial cells, the authors further demonstrate that TLR4-NF-κB signaling leads to reversible internalization of the tight junction protein claudin-5, establishing a potential mechanism of increased vascular permeability. Finally, the authors use RNA-sequencing of wild-type and TLR4-knockout endothelial cells to define the TLR4-dependent cell-autonomous transcriptional response to E. coli.

Strengths:

(1) The authors address an important, well-motivated hypothesis related to the cellular and molecular mechanisms of leptomeningeal inflammation.

(2) The authors use model systems (mouse conditional knockouts and cultured endothelial cells) that are appropriate to address their hypotheses. The data are of high quality.

Weaknesses:

(1) The authors perform single-nucleus RNA-seq on dissected leptomeninges from control and E. coli-infected mice across three genotypes (WT, Tlr4MKO, and Tlr4ECKO). A major discovery from this experiment, as summarized by the authors, is: "Tlr4ECKO mice exhibited a global attenuation of infection-induced transcriptional responses across all major leptomeningeal cell types, as judged by the positions of cell clusters in the UMAP." This conclusion could be considerably strengthened by improving the qualitative and quantitative analysis.

(2) The authors interpret E. coli infection-induced increases in leptomeningeal sulfo-NHS-biotin as evidence of compromised BBB integrity (i.e., extravasation from the vasculature) (Results, page 7), but another possible route in this context is sulfo-NHS-biotin entry from the dura across a compromised arachnoid barrier. The complete rescue in Tlr4ECKOs is strongly suggestive that the vascular route dominates, but it would strengthen the work if the authors could assess arachnoid barrier fidelity (e.g. via immunohistochemistry). At a minimum, authors should mention that the sulfo-NHS-biotin signal in this context may represent both vascular and arachnoid barrier extravasation.

(3) The authors state that "deletion of TLR4 prevented both NF-κB nuclear translocation and Cldn5 internalization in response to E. coli (Figure 4A-D)" (Results, page 9). In Figures 4C and D, however, there is no indicator of a statistical test directly comparing the two genotypes. A comparison of within-genotype P-values should not be used to support a genotype difference (PMID: 34726155).

(4) In the first paragraph of the Results, the authors summarize the meningeal layers as (1) pia, (2) subarachnoid space, (3) arachnoid, and (4) dura, and then state "The second and third layers constitute the leptomeninges." This definition of leptomeninges seems to omit the pia, which is widely considered part of the leptomeninges (PMID: 37776854).

(5) The Cdh5-CreER/+;Tlr4 fl/- mouse lacks TLR4 in all endothelial cells (i.e., in peripheral organs as well as CNS/leptomeninges), and, as the authors note, the periphery is exposed to E. coli. It would be helpful if the authors could comment in the Discussion on the possibility that peripheral effects (e.g., peripheral endothelial cytokine production, changes to blood composition as a result of changes to peripheral endothelial permeability) may contribute to the observed leptomeningeal phenotypes.

Reviewer #1 (Public review):

Summary:

In brief, this manuscript addresses a very interesting topic, namely, the impact of the Mediterranean diet on the development of cancer. Using one mouse model and three tumor cell lines, the data show that a Mediterranean diet is sufficient to promote an anti-tumor response mediated by the microbiota, metabolites, and the immune system. Mechanistically, the Mediterranean diet promotes the expansion of Bacteroides thetaiotaomicron (B. theta for short), which converts tryptophan into 3-IAA. Both B. theta and the metabolite are sufficient to phenocopy the effect of the Mediterranean diet on cancer growth in vivo. The manuscript also shows that this effect is mediated by CD8 T cells and suggests, by way of in vitro assays, that 3-IAA sustains the functionality of CD8 T cells, preserving their exhaustion and blocking the ISR pathway.

Strengths:

The conclusions of this manuscript are potentially interesting and of potential clinical relevance.

Weaknesses:

For a full technical evaluation of the strength of the data, I am missing important technical and experimental details (e.g., number of independent experiments, statistics), and found some legends with potential labelling inaccuracies.

Reviewer #1 (Public review):

Summary:

In this manuscript, Zhang et al. demonstrate that depletion of the 18S rRNA m6A methyltransferase Mettl5 compromises translation fidelity and consequently increases neoantigen generation, thereby uncovering an unexpected role for Mettl5 in tumor immunity. Mettl5-KO tumors exhibit enhanced CD8⁺ T-cell infiltration and show improved responses to immune checkpoint blockade. Mechanistically, loss of Mettl5 perturbs the local structure of 18S rRNA and disrupts the ribosome's ability to perform accurate translation. Subsequent ribosome profiling and mass spectrometry analyses provide compelling evidence that Mettl5 functions as a previously unrecognized regulator of translation to participate in tumor immune evasion.

Strengths:

This study presents a comprehensive set of experimental data supporting a mechanistic link between rRNA modification, translation fidelity, and neoantigen generation. The observed synergistic effect of Mettl5 depletion and anti-PD-1 therapy highlights the potential translational relevance of targeting rRNA modifications in cancer immunotherapy.

Weaknesses:

(1) In light of the principal function of Mettl5, which is to methylate 18S rRNA within the small ribosomal subunit, the authors focus primarily on translation fidelity, largely associated with elongation, but provide limited exploration of potential effects on translation initiation. Loss of Mettl5 may alter the initiation landscape, potentially promoting alternative or noncanonical initiation events (e.g., initiation at CUG codons), which could also contribute to the observed neoantigen repertoire changes. Further investigation into initiation-level alterations would strengthen the mechanistic interpretation.

(2) Given the broad involvement of rRNA methyltransferases in ribosome function, the authors should incorporate a parallel analysis using another enzyme (e.g., Zcchc4 or Nsun5) as a negative control. Such an experiment is essential to demonstrate that the tumor immunity phenotype observed is specific to Mettl5 rather than a general consequence of perturbing rRNA modification.

Reviewer #1 (Public review):

This is an excellent paper from Dr. Yokoyama and colleagues. The experiments are technically demanding, given the very low cell numbers and the challenges of working with implantation sites at gestational days 6.5, 10.5, and 14.5. Overall, the impact of TGF-β receptor II deficiency in the NK lineage on uterine trNK cell numbers and litter size is convincing, and the authors' conclusions are well supported by the data. Less convincing, however, is the claim that the decrease in trNK cells is compensated by an increase in cNK cells; rather, the absence of TGF-β receptor II appears to result in an overall reduction of NK/ILC1 cells.

Major Points:

(1) Figure 1A and B

Although a trend is evident, it does not appear that the absolute number of cNK cells at day 14 is significantly changed from day 6.5?

(2) Figure 2E

The authors state, "This reduction of uterine trNK cells was accompanied by a concomitant increase in the absolute number and frequency of CD49b+Eomes+ cNK cells within the pregnant uterus of TGF-βRIINcr1Δ dams (Figure 2 D, E). The number of cNK cells appears relatively low (visually ~1,000-1,300), and although the difference is statistically significant, its physiological relevance is unclear. More importantly, this modest increase does not correlate with the marked decrease in trNK and ILC1 populations, as cNK cells do not appear to accumulate. In my opinion, the conclusion "Collectively, these findings indicate that a TGF-β-driven differentiation pathway directs the conversion of peripheral cNK cells into uterine trNK cells during murine pregnancy" should be slightly toned down.

(3) Figures 2-4

It is unclear whether the littermate controls are floxed mice or floxhet-Ncr1iCre mice? This distinction is important, as Ncr1iCre expression itself could potentially lead to a phenotype.

Reviewer #1 (Public review):

The manuscript titled "The distinct role of human PIT in attention control" by Huang et al. investigates the role of the human posterior inferotemporal cortex (hPIT) in spatial attention. Using fMRI experiments and resting-state connectivity analyses, the authors present compelling evidence that hPIT is not merely an object-processing area, but also functions as an attentional priority map, integrating both top-down and bottom-up attentional processes. This challenges the traditional view that attentional control is localized primarily in frontoparietal networks.

The manuscript is strong and of high potential interest to the cognitive neuroscience community. Below, I raise questions and suggestions to help with the reliability, methodology, and interpretation of the findings.

(1) The authors argue that hPIT satisfies the criteria for a priority map, but a clearer justification would strengthen this claim. For example, how does hPIT meet all four widely recognized criteria, such as spatial selectivity, attentional modulation, feature invariance, and input integration, when compared to classical regions such as LIP or FEF? A more systematic summary of how hPIT meets these benchmarks would be helpful. Additionally, to what extent are the observed attentional modulations in hPIT independent of general task difficulty or behavioral performance?

(2) The authors report that hPIT modulation is invariant to stimulus category, but there appear to be subtle category-related effects in the data. Were the face, scene, and scrambled images matched not only in terms of luminance and spatial frequency, but also in terms of factors such as semantic familiarity and emotional salience? This may influence attentional engagement and bias interpretation.

(3) The result that attentional load modulates hPIT is important and adds depth to the main conclusions. However, some clarifications would help with the interpretation. For example, were there observable individual differences in the strength of attentional modulation? How consistent were these effects across participants?

(4) The resting-state data reveal strong connections between hPIT and both dorsal and ventral attention networks. However, the analysis is correlational. Are there any complementary insights from task-based functional connectivity or latency analyses that support a directional flow of information involving hPIT? In addition, do the authors interpret hPIT primarily as a convergence hub receiving input from both DAN and VAN, or as a potential control node capable of influencing activity in these networks? Also, were there any notable differences between hemispheres in either the connectivity patterns or attentional modulation?

(5) A few additional questions arise regarding the anatomical characteristics of hPIT: How consistent were its location and size across participants? Were there any cases where hPIT could not be reliably defined? Given the proximity of hPIT to FFA and LOp, how was overlap avoided in ROI definition? Were the functional boundaries confirmed using independent contrasts?

Comments on revisions:

The authors have successfully addressed my previous questions and concerns. The public comments above reflect my views on the initial submission and, in my opinion, will remain helpful for general readers. Given this, I do not have additional public comments and will keep my previous public review unchanged.

Reviewer #1 (Public review):

Summary:

The article investigates how the Japanese macaque makes gait transitions between quadruped and biped gaits. It presents a compelling neuromechanical simulation that replicates the transition and an interesting analysis based on an inverted pendulum that can explain why some transition strategies are successful and others are not.

Strengths:

I enjoyed reading this article. I think it presents an interesting study and elegant modeling approaches (musculoskeletal + inverted pendulum). The study is well conducted, and the results are interesting. I particularly liked how the success of gait transitions could be predicted based on the inverted pendulum and its saddle node stability. I think it makes a useful and interesting contribution to the state of the art.

Weaknesses:

The article is already in great shape, but could be improved a bit by:

(1) Strengthening the comparison to animal data. In particular, videos of the real animal should be included + snapshots of their gaits (quadruped, biped, and transitions).

(2) Exploring and testing a broader range of conditions. I think it would be very interesting to test gaits and gait transitions on up and down slopes (both with the musculoskeletal model and with the inverted pendulum model). This could be used to make predictions on how the real animal adapts to those conditions. Ideally, this should be tested on the animal as well. I think this could increase (even more) the impact of this work.

(3) Better explaining several aspects of the PSO optimization.

(4) (Ideally) performing a sensitivity analysis on the optimized parameters (e.g. variations of +-5, 10, 20%) in order to determine their respective importance and how much their instantiated values have influenced the results.

(5) Running a spell checker, as there are quite a few typos.

Reviewer #1 (Public review):

Summary:

Hoverflies are known for a striking sexual dimorphism in eye morphology and early visual system physiology. Surprisingly, the male and female flight behaviors show only subtle differences. Nicholas et al. investigate the sensori-motor transformation of sexually dimorphic visual information to flight steering commands via descending neurons. The authors combined intra- and extracellular recordings, neuroanatomy, and behavioral analysis. They convincingly demonstrate that descending neurons show sexual dimorphisms - in particular at high optic flow velocities - while wing steering responses seem relatively monomorphic. The study highlights a very interesting discrepancy between neuronal and behavioral response properties.

More specifically, the authors focused on two types of descending neurons that receive inputs from well-characterized wide-field sensitive tangential cells: OFS DN1, which receives inputs from so-called HS cells, and OFS DN2, which receives input from a set of VS cells. Their likely counterparts in Drosophila connect to the neck, wing, and haltere neuropils. The authors characterized the visual response properties of these two neuronal classes in both male and female hoverflies and identified several interesting differences. They then presented the same set of stimuli, tracked wing beat amplitude, and analyzed the sum and the difference of right and left wing beat amplitude as a readout of lift or thrust, and yaw turning, respectively. Behavioral responses showed little to no sexual dimorphism, despite the observed neuronal differences.

Strengths:

I find the question very interesting and the results both convincing and intriguing. A fundamental goal in neuroscience is to link neuronal responses and behavior. The current study highlights that the transformations - even at the level of descending neurons to motoneurons - are complex and less straightforward than one might expect.

Weaknesses:

The authors investigated two types of descending neurons, but it was not clear to me how many other descending neurons are thought to be involved in wing steering responses to wide-field motion. I would suggest providing a more in-depth overview of what is known about hoverflies and Drosophila, since the conclusions drawn from the study would be different if these two types were the only descending neurons involved, as opposed to representing a subset of the neurons conveying visual information to the wing neuropil.

Both neuronal classes have counterparts in Drosophila that also innervate neck motor regions. The authors filled the hoverfly DNs in intracellular recordings to characterize their arborization in the ventral nerve cord. In my opinion, these anatomical data could be further exploited and discussed a bit more: is the innervation in hoverflies also consistent with connecting to the neck and haltere motor regions? Are there any obvious differences and similarities to the Drosophila neurons mentioned by the authors? If the arborization also supports a role in neck movements, the authors could discuss whether they would expect any sexual dimorphism in head movements.

Reviewer #1 (Public review):

Summary:

The dysgranular retrosplenial cortex (RSD) and hippocampus both encode information related to an animal's navigation through space. Here, the authors study the different ways in which these two brain regions represent spatial information when animals navigate through interconnected rooms. Most importantly, they find that the RSD contains a small fraction of neurons that encode properties of interconnected rooms by firing in different head directions within each room. This direction is shifted by 180 degrees in 2-room environments, and by 90 degrees in 4-room environments. While it cannot be definitively proven that this encoding is not just related to the presence of exits (doors) in each room, this is a noteworthy finding and will motivate further study in more complex and well-controlled environments to understand this coding scheme in the RSD. The recordings and analyses used to identify these multi-directional cells are mostly solid. Additional conclusions regarding the rotational symmetry across rooms seen in the RSD neurons that do not encode direction (representing the majority of RSD neurons) remain incomplete, given the evidence presented thus far. The differences between RSD and hippocampus encoding of space are clear and consistent with prior observations.

Strengths:

(1) Use of tetrode recordings from the RSD to identify multi-direction cells that only encode one direction in each room, but shift the preferred direction by either 180 or 90 degrees depending on the number of rooms in the environment.

(2) Solid controls to show that this multi-direction encoding is stable over time and across some environmental manipulations.

(3) Convincing evidence that these multi-direction cells can co-exist with single-direction head direction cells in the RSD (as both cell types can be simultaneously recorded).

(4) Convincing evidence for clear differences between directional and spatial encoding in the RSD versus hippocampus, consistent with prior observations.

Weaknesses:

(1) The paper mostly uses the term "retrosplenial cortex", but it is important to clarify that the study is only focused on the dysgranular retrosplenial cortex (RSD; Brodmann Area 30) and not the granular retrosplenial cortex (Brodmann Area 29). These are two distinct regions (despite the similar names), each with distinct connectivity and distinct behavioral encoding and function, so it is important to clarify in the abstract and title that the present study is solely about the RSD to prevent confusion in the literature.

(2) The proportion of each observed cell type is not clearly stated, although it is clear that the multi-directional cells are in the minority. Having the proportion of well-isolated neurons in distinct sessions that encode each type of information (e.g., multi vs single direction encoding) would greatly aid the interpretation of the result and help the field know how common each cell type is in the RSD.

(3) The authors state that "MDCs [multi-directional cells] never exhibited multidirectional activity within a single room" - but many of the single room examples from the 4-room environment (shown in Figures 2E and 2F) reveal multi-peaked directional encoding. This suggests that the multi-direction encoding may be more compatible with encoding some property of the number of exits rather than relative room orientations.

(4) The spatial rotation analyses of non-directional cell analyses are considered incomplete. This is impacted by the slower speed at the doors and hence altered firing rates (as evidenced in spatial rate plots). The population rate is not relevant as the correlational analyses are done on a single cell level. Since some cells fire more with increasing speed and others fire less, that will necessarily result in a population rate map that minimizes firing rate differences near the doorway, where the animals move more slowly. But on a single cell level, that reduced speed is having a big effect, as evidenced by individual rate map examples, and the rooms will need to be rotated to obtain a higher correlation by overlapping the doorway regions. This does not necessarily say anything about spatial coding across the two or four interconnected rooms being rotationally symmetric, and it would appear difficult to draw any conclusions related to spatial encoding from those analyses.

Reviewer #1 (Public review):

Summary:

This manuscript presents a tunable Bessel-beam two-photon fluorescence microscopy (tBessel-TPFM) platform that enables high-speed volumetric imaging with stable axial focus. The work is technically strong and broadly significant, as it substantially improves the flexibility and practicality of Bessel-beam-based two-photon microscopy. The demonstrations are generally strong and bridge a wide range of neuroimaging applications, namely vascular dynamics, neurovascular coupling, optogenetic perturbation, and microglial responses. These convincingly show that the approach enables biological measurements that are difficult or impractical with existing methods.

The evidence supporting the technical and biological claims is generally strong. The optical design is carefully motivated, clearly described, and validated through a combination of simulations and experimental characterization. The biological applications are diverse and well chosen to highlight the strengths of the proposed method, and the data are of high quality, with appropriate controls and comparative measurements where relevant.

Strengths:

(1) The optical innovation addresses a well-recognized limitation of existing Bessel-TPFM implementations, namely axial focus drift during tuning, and does so using a relatively simple, light-efficient, and cost-effective design.

(2) The manuscript provides convincing experimental evidence for this being a versatile platform to map flow dynamics across diverse vessel sizes and orientations in both healthy and pathological states.

(3) Biological demonstrations are comprehensive and span multiple domains such as hemodynamics, neurovascular coupling, and neuroimmune responses.

(4) Quantitative analyses of blood flow across vessel sizes and orientations, including kilohertz line scanning, are particularly compelling and clearly beyond the reach of standard Gaussian TPFM.

(5) Particular advantages are that higher blood slow speeds become measurable up to 23mm/sec (20x more than conventional frame scanning), and that simultaneous (Bessel-)imaging and (Gaussian-)perturbation are possible because of the stable axial focus.

Weaknesses:

(1) At present, the paper does not properly position the new Bessel-beam method against previous work, and fails to compare it to alternative fast volumetric imaging methods without Bessel beams.

(2) The cost-effectiveness of the proposed method is not well described or supported by evidence; it would be useful to include more detail or remove this claim.

(3) Some biological conclusions, e.g., regarding novel features of microglial dynamics (i.e., the observed two-wave responses and coordinated extension-retraction), are based on relatively limited sample size and would benefit from clearer discussion of variability across animals and fields of view.

(4) The use of neural network-based denoising for microglial imaging is reasonable but introduces potential concerns about trustworthiness; additional clarification of validation or failure modes would strengthen confidence in these results.

To conclude, most of the authors' claims are well supported by the data. The central conclusion, namely that tBessel-TPFM provides tunable volumetric imaging enabling experiments not feasible with existing two-photon approaches, is justified. Some biological interpretations would benefit from a more cautious framing, but they do not undermine the main technical and methodological contributions of the study. This is a strong and technically rigorous manuscript that makes a substantial methodological advance with clear relevance to neuroscience and intravital imaging. Minor clarifications and a slightly more measured discussion of certain biological findings are recommended.

Reviewer #1 (Public review):

Summary:

The study investigates the Drosophila non-visual light receptor rhodopsin7 with regard to its role in light information processing and resulting consequences for behavioral patterns and circadian clock function. Using behavioral, in situ staining, and receptor activation assays together with different fly mutants, the authors show that rhodopsin7 is an important determinant of activity under and response to darkness, which likely signals via a pathway distinct from other, visual Drosophila rhodopsins. Based on phylogenetic analysis, the authors further discuss a potentially conserved functional role of non-visual photoreceptors like rhodopsin7 and the mammalian melanopsin light information processing and circadian clock modulation.

Strengths:

The manuscript follows a very clear structure with all investigations logically building onto each other. Background information and methodology are provided in appropriate detail so that readers can fully understand why and how experiments were conducted. It is further praiseworthy that the authors provide the details that allow also non-experts in the field to fully understand their approaches. Experimental work was conducted in a highly standardized manner, and also considered potential "side-aspects" like the consequences of temperature cycles and changed photoperiods. The detailed and clear description of the obtained results makes them very convincing, with (almost) all observable patterns being addressed.

By highlighting the evolutionary old phylogenetic position of rhodopsin7 and its conservation across numerous clades, the authors provide strong reasoning for the relevance of their work, also pointing out the similarities to the mammalian melanopsin. The postulated hypothesis regarding protein structure and functioning, as well as the role in light information processing and behavioral and circadian clock modulation are well based on the authors' observations, and speculative aspects are correctly pointed out.

Weaknesses:

Where the manuscript still has potential for improvement is the discussion, which in its current form does seem slightly self-contained and does not fully integrate the findings of previous studies on Drosophila rhodopsin7. As the introduction specifically points out that previous findings have been contradictory, this seems like a missed opportunity. Further details on this are provided in the recommendations below.

Similarly, the manuscript currently lacks a discussion of the possible relevance of rhodopsin7 (and other non-visual light receptors in other organisms) in the context of a species' environment and lifestyle, i.e., what is the relevance/benefit of having rhodopsin7 in the fly's everyday life? While this clearly involves speculation, when done carefully, it can elevate the paper's relevance from a primarily academic to a societal one.

An additional point concerns the title and abstract, which postulate rhodopsin7 roles in contrast vision as well as motion and brightness perception. Contrast remains poorly defined in the text, leaving it ambiguous whether it refers to bright/dark contrasts, e.g., along edges, or the temporal contrast that results from dark pulses (startle response). While the latter seems to apply here, the former is likely more intuitive. Thus, this aspect should be rephrased (also in the title) or properly clarified early on. Regarding motion detection, this is backed up by the optomotor response results, but the findings stand somewhat isolated from the other results, lacking a clear connection aside from general visual processing. Lastly, brightness perception is mentioned in the abstract, but never again, possibly due to inconsistent phrasing throughout the manuscript.

Reviewer #1 (Public review):

Summary:

Using a computational modeling approach based on the Drift and Diffusion Model (DDM) introduced by Ratcliff and McKoon in 2008, the article by Shevlin and colleagues investigates whether there are differences between neutral and negative emotional states in:

(1) The timings of the integration in food choices of the perceived healthiness and tastiness of food options in individuals with bulimia nervosa (BN) and healthy participants (2) The weighting of the perceived healthiness and tastiness of these options.

Strengths:

By looking at the mechanistic part of the decision process, the approach has potential to improve the understanding of pathological food choices.

Weaknesses:

I thank the authors for revising their manuscript.

I still notice that the authors did not go through their manuscript to look for wordings refering to a prediction interpretation of their results while I already highlighted the inappropriateness of this wording in my two first rounds of reviews: e.g. there is still "we used zero-inflated negative binomial models to predict the three-month frequency" and I can find other statements like this. The design of their study does not allow such claims.

The authors answered my major concern regarding the experimental induction towards a negative or a neutral state before running the food decision task. My concern is: BN patients already seemed to be already in a high negative state before undergoing the neutral induction, while these patients are in a lower negative state before undergoing the negative induction. It is therefore not surprising that patients seem to report a similar level of negative state after the two inductions (according to the figure of the authors' previous article). Of note is that the additional analysis the authors ran within the BN group only provides a significant result: this result shows that there has been an induction but does not rule out that patients were in the exact same magnitude of negative state to perform the task as the figure in their previously published article suggests it. The major issue is to show that:

(1) As compared to the neutral induction, there has been a higher variation in negative state after as compared to before the negative induction.

(2) The magnitude of the negative state after the negative induction is higher than the magnitude of the negative state after the neutral induction.

The first point shows that the induction worked. The second point shows that the participants are in two distinct states. Without showing the second point, it may be possible that one induction increases the negative state of participants to the same level as the one of the second induction that has not increased anything.

Within this context, how is it possible to associate, in patients, a difference in the DDM between the two sessions to a negative state (which is one of the main focus of the article) rather than to another parameter that has not been captured? A similar situation would be in an experiment studying the consequence of stress, a stressfull induction over relaxed participants attending the lab has high chances to raise the level of stress of those participants to the same level as the one that the same participants would experience after a neutral induction when these participants attend the lab with an already high level of stress. In that case, would it be approrpiate to claim that a difference at a task performed after the induction would be related to stress while the participants would be at the same level of stress when performing the task despite the fact that the induction worked ?

In the experiment performed by the authors, the additional analysis to perform would be a paired sample t-test (or the appropriate non-parametric test) to check whether the magnitude of negative state of BN patients was different between the negative and neutral conditions after the induction only. If not, associating the difference at the DDM with negative states in BN is highly misleading.

I read carefully the authors' answer related to mixed models: they claim that mixed models take into account correlations within their repeated data. The specification of the structure of the covariance matrix allows to control only partly for that. I notice that the authors did not specify the structure of that matrix: the article they refer to to justify the appropriatness of their analyses is not adapted. The specification of the structure of the covariance matrix needs to address, in a mixed model, the difference in handling 4 repeated data per participants that cannot be paired as compared to 4 repeated data that can be paired (two per session with one before and one after the neutral or negative priming sessions, if I count right). Of note is that a covariance structure that is left free of constraint for the fit of the model does not capture appropriately the pairing of the data: it has all chances to capture the covariance in a different way. And a covariance structure that has constraints has more chances to lead to a model that cannot be estimated because of an absence of convergence of the algorithms.

By the way, a single two-sample t-test (or a Mann-Whitney test if appropriate), and not a set of multiple paired-sample t-test as the authors suggest, would answer the goal of the authors to test for what they call the three-way interaction in their comment. This test would be performed between the two groups of participants (BN/controls) with the computation for each participant separately: (assessment after neutral induction-assessment before neutral induction)-(assessment after negative induction-assessment before negative induction). This analysis answers points 1, 2 and 4 they raise together with my point of controlling for the paired data. I would have agreed with their choice of a mixed model if they had an unbalanced dataset within each participant.

Reviewer #1 (Public review):

Summary:

This useful study provides incomplete evidence of an association between atovaquone-proguanil use (as well as toxoplasmosis seropositivity) and reduced Alzheimer's dementia risk. The study reinforces findings that VZ vaccine lowers AD risk and suggests that this vaccine may be an effect modifier of A-P's protective effect. Strengths of the study include two extremely large cohorts, including a massive validation cohort in the US. Statistical analyses are sound, and the effect sizes are significant and meaningful. The CI curves are certainly impressive.

Weaknesses include the inability to control for potentially important confounding variables. In my view, the findings are intriguing but remain correlative / hypothesis generating rather than causative. Significant mechanistic work needs to be done to link interventions which limit the impact of Toxoplasmosis and VZV reactivation on AD.

Weaknesses:

Major:

(1) Most of the individuals in the study received A-P for malaria prophylaxis as it is not first line for Toxo treatment. Many (probably most) of these individuals were likely to be Toxo negative (~15% seropositive in the US), thereby eliminating a potential benefit of the drug in most people in the cohort. Finally, A-P is not a first line treatment for Toxo because of lower efficacy.

(2) A-P exposure may be a marker of subtle demographic features not captured in the dataset such as wealth allowing for global travel and/or genetic predisposition to AD. This raises my suspicion of correlative rather than casual relationships between A-P exposure and AD reduction. The size of the cohort does not eliminate this issue, but rather narrows confidence intervals around potentially misleading odds ratios which have not been adjusted for the multitude of other variables driving incident AD.

(3) The relationship between herpes virus reactivation and Toxo reactivation seems speculative.

(4) A direct effect on A-P on AD lesions independent on infection is not considered as a hypothesis. Given the limitations above and effects on metabolic pathways, it probably should be. The Toxo hypothesis would be more convincing if the authors could demonstrate an enhanced effect of the drug in Toxo positive individuals without no effect in Toxo negative individuals.

Minor:

(5) "Clinically meaningful" should be eliminated from the discussion given that this is correlative evidence.

Reviewer #1 (Public review):

The current manuscript investigates a regulatory axis containing Prmt1, which methylates RNA binding proteins and alters intron splicing outcomes and expression of matrix genes. Authors test the effects of deficient Prmt1, Sfpq, and various other factors, using a combination of bioinformatic analyses and wet-lab validation approaches. Authors show that intron retention often triggers NMD, contributing to aberrant gene expression regulation and craniofacial development. The revised manuscript introduces several complementary experiments that help to strengthen conclusions. For example, authors directly investigate NMD-mediated transcript turnover to better understand how retention contributes to expression changes in genes of interest, and they assess several additional factors downstream of Prmt1 to justify a centralized interested in the PRMT1/SFPQ axis.

Weaknesses:

However, some points remain unaddressed or unexplored, which could bolster conclusions. For example, the transcriptome data from knockdown experiments indicate robust exon skipping, suggesting that analysis of these patterns in parallel with intron retention could provide additional insights into the responsive gene programs. Given that SFPQ is known to have multiple regulatory roles, a more thorough investigation of its possible mechanisms of action during craniofacial development would allow for definitive conclusions about the isolated impact of SFPQ-dependent splicing. Although authors employ CUT&Tag analysis of Pol II binding at the promoters and across the gene body, at the current scope, no change in Pol II association (i.e., absence of transcriptional repression) does not directly indicate a lack of transcriptional regulation by other means (pause release, elongation rate or processivity, transcription termination, etc.). Without a more thorough investigation of these mechanisms, this confounds definitive claims about their relative contributions to the gene expression landscape.

Reviewer #1 (Public review):

Summary

The authors determine the phylogenetic relation of the roughly two dozen wtf elements of 21 S. pombe isolates and show that none of them in the original S. pombe are essential for robust mitotic growth. It would be interesting to test their meiotic function by simply crossing each deletion mutant with the parent and analyzing spores for non-Mendelian inheritance. If this has been reported already, that information should be added to the MS. If not, I suggest the authors do these simple experiments and add this information.

Strengths:

The most interesting data (Fig. 4) show that one recombinant (wtfC4) between wtf18 and wtf23 produces in mitotic growth a poison counteracted by its own antidote but not by the parental antidotes. Again, it would be interesting to test this recombinant in a more natural setting - meiosis between it and each of the parents.

Weaknesses:

Some minor rewriting is needed.

Comments on Revision:

(1) The parameter for "maximum growth rate" in Figure 2D needs to be defined and put on the graph.

(2) On page 8, line 182, the authors should consider testing the hybrid wtf in meiosis using strain 975 of Leupold, which is h+, or another standard h+ strain. I don't think the antidote allele is needed; rather, it seems to me it would counter the lethality of the poison protein and should be omitted to test drive of the hybrid wtf. This is a simple experiment and would add considerably to the paper.

Joint Public Review:

While DNA sequence divergence, differential expression and differential methylation analysis have been conducted between humans and the great apes to study changes that "make us human", the role of lncRNAs and their impact on the human genome and biology has not been fully explored. In this study the authors computationally predict HSlncRNAs as well as their DNA Binding sites using a method they have developed previously and then examine these predicted regions with different types of enrichment analyses. Broadly the analysis are straightforward and after identifying these regions/HSlncRNAs they examined their effects using different external datasets.

Comments on the latest version from Reviewer #2:

I think this is as good as it is going to get, and I do appreciate that the authors are still engaging in good faith after all these rounds of revision, so I am happy to stop here! I do think the paper is significantly improved from the last time around, and the conclusions have been tempered significantly.

Reviewer #1 (Public review):

Summary:

The present study evaluates the role of visual experience in shaping functional correlations between human extrastriate visual cortex and frontal regions. The authors used fMRI to assess "resting-state" temporal correlations in three groups: sighted adults, congenitally blind adults, and neonates. Previous research has already demonstrated differences in functional correlations between visual and frontal regions in sighted compared to early blind individuals. The novel contribution of the current study lies in the inclusion of an infant dataset, which allows for an assessment of the developmental origins of these differences.

The main results of the study reveal that correlations between prefrontal and visual regions are more prominent in the blind and infant groups, with the blind group exhibiting greater lateralization. Conversely, correlations between visual and somato-motor cortices are more prominent in sighted adults. Based on these data, the authors conclude that visual experience shapes these cortical networks through activity-dependent plasticity. This study provides novel insights into the impact of visual experience on the development of temporal correlations in the brain.

Strengths:

The dissociations in functional correlations observed among the sighted adult, congenitally blind, and neonate groups provide strong support for the main conclusion regarding postnatal experience-driven shaping of visual-frontal connectivity.

The neonatal data offers a unique and valuable developmental anchor for interpreting divergence between blind and sighted adults. This is a major advance over prior studies limited to adult comparisons.

Convergence with prior findings in the blind and sighted adult groups reinforces the reliability and external validity of the present results.

The split-half reliability analysis in the infant and adult data increases confidence in the robustness of the reported group differences.

Weaknesses:

The methodology cannot determine whether group differences in correlations reflect direct changes in communication between visual and frontal regions or indirect effects mediated by other structures.

The cross-sectional design cannot reveal the timecourse over which visual experience shapes connectivity between infancy and adulthood.

Whether the infant resting-state patterns imply similar functional capacity to blind adults (e.g., cross-modal task responses) remains untested.

Comments on revisions:

The authors have done a fantastic job addressing my remaining questions.

Reviewer #1 (Public review):

Summary:

Lesser et al provide a comprehensive description of Drosophila wing proprioceptive sensory neurons at the electron microscopy resolution. This "tour-de-force", provides a strong foundation for future structural and functional research aimed at understanding wing motor control in Drosophila with implications to understanding wing control across other insects.

Strengths:

(1) Authors leverage previous research that described many of the fly wing proprioceptors, and combine this knowledge with EM connectome data such that they now provide a near-complete morphological description of all wing proprioceptors.

(2) Authors cleverly leverage genetic tools and EM connectome data to tie the location of proprioceptors on the wings with axonal projections in the connectome. This enables them to both align with previous literature as well as make some novel claims.

(3) In addition to providing a full description of wing proprioceptors, authors also identified a novel population of sensors on the wing tegula that make direct connections with the B1 wing motor neurons implicating the role of tegula in wing movements that was previously underappreciated.

(4) Despite being the most comprehensive description so far, it is reassuring that authors clearly state the missing elements in the discussion.

Weaknesses:

(1) Authors do their main analysis on data from FANC connectome but provide corresponding IDs for sensory neurons in the MANC connectome. I wonder how the connectivity matrix compares across FANC and MANC if the authors perform similar analysis as they have done in Fig. 2. This could be a valuable addition and potentially also pick up any sexual dimorphism.

(2) Authors speculate about presence of gap junctions based on density of mitochondria. I'm not convinced about this given mitochondrial densities could reflect other things that correlate with energy demands in sub-compartments.

Overall, I consider this an exceptional analysis which will be extremely valuable to the community.

Reviewer #1 (Public review):

The authors show experimentally that, in 2D, bacteria swim up a chemotactic gradient much more effectively when they are in the presence of lateral walls. Systematic experiments identify an optimum for chemotaxis for a channel width of ~8µm, a value close to the average radius of the circle trajectories of the unconfined bacteria in 2D. These chiral circles impose that the bacteria swim preferentially along the right-side wall, which indeed yields chemotaxis in the presence of a chemotactic gradient. These observations are backed by numerical simulations and a geometrical analysis.

Reviewer #1 (Public review):

Summary:

This is a careful and comprehensive study demonstrating that effector-dependent conformational switching of the MT lattice from compacted to expanded deploys the alpha tubulin C-terminal tails so as to enhance their ability to bind interactors.

Strengths:

The authors use 3 different sensors for the exposure of the alpha CTTs. They show that all 3 sensors report exposure of the alpha CTTs when the lattice is expanded by GMPCPP, or KIF1C, or a hydrolysis-deficient tubulin. They demonstrate that expansion-dependent exposure of the alpha CTTs works in tissue culture cells as well as in vitro.

Appraisal:

The authors have gone to considerable lengths to test their hypothesis that microtubule expansion favours deployment of the alpha tubulin C-terminal tail, allowing its interactors, including detyrosinase enzymes, to bind. There is a real prospect that this will change thinking in the field. One very interesting possibility, touched on by the authors, is that the requirement for MAP7 to engage kinesin with the MT might include a direct effect of MAP7 on lattice expansion.

Impact:

The possibility that the interactions of MAPS and motors with a particular MT or region feed forward to determine its future interaction patterns is made much more real. Genuinely exciting.

Reviewer #1 (Public review):

Summary:

This manuscript uses primarily simulation tools to probe the pathway of cholesterol transport with the smoothened (SMO) protein. The pathway to the protein and within SMO is clearly discovered and interactions deemed important are tested experimentally to validate the model predictions.

Strengths:

The authors have clearly demonstrated how cholesterol might go from the membrane through SMO for the inner and outer leaflets of a symmetrical membrane model. The free energy profiles, structural conformations and cholesterol-residue interactions are clearly described.

Weaknesses:

None. I find the revised manuscript strong and the work should be published.

Reviewer #1 (Public review):

Willeke et al. hypothesize that macaque V4, like other visual areas, may exhibit a topographic functional organization. One challenge to studying the functional (tuning) organization of V4 is that neurons in V4 are selective for complex visual stimuli that are hard to parameterize. Thus, the authors leverage an approach comprising digital twins and most exciting stimuli (MEIs) that they have pioneered. This data-driven, deep-learning framework can effectively handle the difficulty of parametrizing relevant stimuli. They verify that the model-synthesized MEIs indeed drive V4 neurons more effectively than matched natural image controls. They then performed psychophysics experiments (on humans) along with the application of contrastive learning to illustrate that anatomically neighboring neurons often care about similar stimuli. Importantly, the weaknesses of the approach are clearly appreciated and discussed.

Comments:

(1) The correlation between predictions and data is 0.43. I'd agree with the authors that this is "reliable" and would recommend that they discuss how the fact that performance is not saturated influences the results.

(2) Modeling V4 using a CNN and claiming that the identified functional groups look like those found in artificial vision systems may be a bit circular.

(3) No architecture other than ResNet-50 was tested. This might be a major drawback, since the MEIs could very well be reflections of the architecture and also the statistics of the dataset, rather than intrinsic biological properties. Do the authors find the same result with different architectures as the basis of the goal-driven model?

(4) The closed-loop analysis seems to be using a much smaller sample of the recorded neurons - "resulting in n=55 neurons for the analysis of the closed-loop paradigm".

(5) A discussion on adversarial machine learning and the adversarial training that was used is lacking.

Reviewer #1 (Public review):

In this study, Ursu, Centeno, and Leblois record from the cerebellum of zebra finches and analyze neurons for auditory and song-related activity. The paper covers a lot of ground, ranging from lesions of the deep nuclei to song and white noise playback inside and outside of singing, and some level of survey of response types across cerebellar lobules, to provide foundational information on cerebellar relationships with song. There are a number of interesting observations in the study, to me most notably, the lack of responsivity of song-related activity in lobule IV to distorted auditory feedback. This observation is interesting in light of the perennial idea that the cerebellum may participate in rapid error corrections in other somatic control domains. If such a role were relevant for song, it stands to reason that some alteration of activity could be found there. Of course, on the other hand, zebra finches do not show rapid corrections during DAF, so perhaps the null result does not resolve much. Nevertheless, these data are important steps forward in establishing the involvement or lack of involvement in a broader set of brain structures beyond the song control system typically studied. While the study presents some interesting and important inroads, in my opinion, there was a general lack of 'polish' to the study that led to ambiguity in the report and confusing displays. This detracted from rigorous reporting of the findings.

Reviewer #1 (Public review):

Summary:

In this study, the authors investigated the detailed structural mechanism of activation of ABHD5 upon interaction with lipid structures (bilayer and LD). The authors used an elaborate multiscale computational workflow, incorporating coarse-grained, all-atom, and enhanced-sampling molecular dynamics simulations, to propose a structural mechanism for the interaction and activation of ABHD5, as well as its specific interaction with TAG in LD. The authors then corroborated these observations with experimental studies involving hydrogen-deuterium exchange coupled with mass spectrometry of wild-type ABHD5 to assess the structural and conformational changes in ABHD5 upon binding, as well as mutagenesis with cell-based and in vitro assays monitoring membrane association, defining specific interactions that infer ABHD5 to localize LD.

Strengths:

The manuscript is well-written, and the data are reported in high-quality figures. The experimental design and data analysis are rigorous and support the conclusion. One major strength is the multiscale computational work that reveals a mechanism for the insertion of ABHD5 into lipid bilayers and LD involving the insertion of the N-term portion and the lid helix motif. The design of the computational workflow was very elaborate, and the undertaking was quite extensive, with multiple strategies to (GC, all-atom MD and GaMD). The authors then elegantly generate a hypothesis from these observations to experimentally corroborate the proposed mechanism. Particularly, the HDX-MS data support the engagement of the two regions upon binding, and the fluorescence microscopy data show the role of specific residues in localization/specificity to LD.

Weaknesses:

The following limitation is noted. Central to this manuscript is the model, as observed computationally, that initial lipid interaction by the N-term insertion is followed by the insertion of lid-helix in the membrane, which undergoes a conformational switch in the process. However, HDX-MS reveals that, in the unbound form, the lid helix region displays a bimodal isotopic envelope, revealing two species, one with low uptake, suggesting a structured species and one with high uptake, suggesting a less structured species. It is unclear from the manuscript whether the authors think the bimodality fits EX1 regime kinetics or not. Regardless, the model of unbound ABHD5 shows a lid-helix region devoid of secondary structure (Figure 5A), which is more consistent with the unprotected species. The authors also mention that previous modeling had pointed to the high flexibility of the insertion domain. Upon binding, the lid-helix region seems to be ordered from computational observations and loses bimodality by HDX-MS with a deuterium uptake consistent with the protected species of the bimodal envelop in the unbound form. The authors fall short of interpreting or even discussing what the bimodality of the lid-helix represents in the unbound form. What does the protected species in the bimodal envelope represent? Is it a transition representing lid-helix formation and unfolding? Does it imply that interaction and insertion into the lipid structures are governed by conformational selection? This issue should be at the very least acknowledged and discussed, or optimally investigated by performing more integrative studies of the HDX-MS data with the extensive computational data at hand, using existing protection factor calculations or HDX-guided ensemble refinement methods.

Reviewer #1 (Public review):

Summary:

The goal of the study was to address the question of the degree to which social position in a group is a stable trait that persists across conditions. Reinwald et al. use a custom-built cage system with automated tracking and continuous testing for social dominance that does not require intervention by the experimenter. Remixing of individuals from different groups revealed that social position was rather stable and not really predictable from other measures that were taken. The authors conclude that social position is multifaceted but dependent on characteristics like personality traits.

Strengths:

(1) Reductionistic, highly controlled setting that allows for the control of many confounding variables.

(2) Very interesting and important question.

(3) Confirms the emergence of inter-individual behavior-driven differences in inbred mice in a shared environment.

(4) Innovative paradigm and experimental setup.

(5) Fresh perspective on an old question that makes the best use of modern technology.

(6) Intelligent use of behavioral and cognitive covariables to generate a non-social context.

(7) Bold and almost provocative conclusion, inviting discussion and further elaboration.

Weaknesses:

(1) Reductionistic, highly controlled setting that blends out much of the complexity of social behavior in a community.

(2) The motivation to enter the test tube is not "trait" (or at least not solely a trait) but the basic need to reach food and water; chasing behavior would be less dependent on this stimulus.

(3) Dominance is only one aspect of sociality, social structure is reduced to rank. The information that might lie in the chasing behavior is not optimally used to explain social behavior beyond the rank measure.

(4) Focus on rank bears the risk of overgeneralization for readers not familiar with the context.

(5) Conclusion only valid for the reductionistic setting, in which environment, social and non-social changes only within narrow limits, and in which the mouse population does not face challenges

(6) Animals are not naive at the beginning of the experiment, but are already several weeks old.

In summary, this is a wonderful study, but not one that is easy to interpret. The bold conclusion is valid only within the constraints of the study, but nevertheless points in an important direction. The paradigm is clever and could be used for many interesting follow-ups.

To define social position as a personality trait will elicit strong opposition and much debate; the nuances of the paper might be lost on many readers and call for the (re)-consideration of many concepts that are touched. I find this attitude a strength of the paper, but the approach bears the risk of misunderstanding.

Reviewer #1 (Public review):

Summary:

This manuscript uses serological data to quantify the effects of imprinting on subsequent influenza antibody responses. While this is an admirable goal, the HI dataset sounds impressive, and the authors developed a number of models, the manuscript came off as very dense and technical. One of the biggest pitfalls is that it is not easy to understand the lessons learned. The two Results section headers make clear statements - there was an imprinting signal in the HI titers, but much of this signal could also be seen in an imprinting-free simulation - and then the Discussion states a number of limitations. This is fine, but it leaves the reader wondering exactly how large an error would be introduced by ignoring imprinting effects altogether; alternatively, if imprinting is purposefully added, what would the expected effect size be? The comments below will provide some concrete steps to help clarify these points.

Major comments:

(1) Lines 107-133: The first Results section is a dense slog of information, and the reader is never given a good overview of what the imprinting coefficients exactly are. As the paper currently stands, if you do not start by reading the Methods, you will take away very little. I suggest adding a schematic for any of your models, showing what HI titers would be expected with/without imprinting effects. or age effects, or both, to tie in your modeling coefficients with quantities that all readers are familiar with.

(1.1) Clarify what the imprinting coefficient (y-axis in Figure 1A) looks like in this schematic.

(1.2) Another aspect that I missed: In addition to stating which models were best by BIC, what is the absolute effect size in the HI titers? During my initial reading, I had hoped that Figure 3 would answer this question, but it turned out to be just an overview of the dataset. I strongly suggest having such a figure to show the imprinting effect inferred by different models. What would the expected effect be if you kept someone's birth year constant but tuned their age? What if you kept their age at collection constant but tuned their birth year?

(1.3) It would also help to explain in your schematic what the x-axis labels (H1, H2, H1/H3) would look like in these scenarios, and what imprinting relative to H3 means.

(2) As mentioned above, it was hard to understand the takeaway messages, such as:

(2.1) A similar question would be: If you model antibody titers without imprinting, how far off would you be from the actual measurements (2x off, 4x off...)? If you add the imprinting effect, how much closer do you get?

(2.2) Are there specific age groups that require imprinting to be taken into consideration, since otherwise HI analyses will be markedly off?

(2.3) Are there age groups where imprinting can be safely ignored?

(3) HI titers against multiple H1 and H3 variants were measured, but it is unclear how these are used, and why titers against a single variant each season would not have worked equally well.

Reviewer #1 (Public review):

Summary:

This study employed a saccade-shifting sequential working memory paradigm, manipulating whether a saccade occurred after each memory array to directly compare retinotopic and transsaccadic working memory for both spatial location and color. Across four participant groups (young and older healthy adults, and patients with Parkinson's disease and Alzheimer's disease), the authors found a consistent saccade-related cost specifically for spatial memory - but not for color - regardless of differences in memory precision. Using computational modeling, they demonstrate that data from healthy participants are best explained by a complex saccade-based updating model that incorporates distractor interference. Applying this model to the patient groups further elucidates the sources of spatial memory deficits in PD and AD. The authors then extend the model to explain copying deficits in these patient groups, providing evidence for the ecological validity of the proposed saccade-updating retinotopic mechanism.

Strengths:

Overall, the manuscript is well written, and the experimental design is both novel and appropriate for addressing the authors' key research questions. I found the study to be particularly comprehensive: it first characterizes saccade-related costs in healthy young adults, then replicates these findings in healthy older adults, demonstrating how this "remapping" cost in spatial working memory is age-independent. After establishing and validating the best-fitting model using data from both healthy groups, the authors apply this model to clinical populations to identify potential mechanisms underlying their spatial memory impairments. The computational modeling results offer a clearer framework for interpreting ambiguities between allocentric and retinotopic spatial representations, providing valuable insight into how the brain represents and updates visual information across saccades. Moreover, the findings from the older adult and patient groups highlight factors that may contribute to spatial working memory deficits in aging and neurological disease, underscoring the broader translational significance of this work.

Comments on revisions:

The authors have addressed my earlier concerns.

Reviewer #2 (Public review):

Summary:

The authors of this paper note that although polyphosphate (polyP) is found throughout biology, the biological roles of polyP have been under-explored, especially in multicellular organisms. The authors created transgenic Drosophila that expressed a yeast enzyme that degrades polyP, targeting the enzyme to different subcellular compartments (cytosol, mitochondria, ER, and nucleus, terming these altered flies Cyto-FLYX, Mito-FLYX, etc.). The authors show the localization of polyP in various wild-type fruit fly cell types and demonstrate that the targeting vectors did indeed result in expression of the polyP degrading enzyme in the cells of the flies. They then go on to examine the effects of polyP depletion using just one of these targeting systems (the Cyto-FLYX). The primary findings from depletion of cytosolic polyP levels in these flies is that it accelerates eclosion and also appears to participate in hemolymph clotting. Perhaps surprisingly, the flies seemed otherwise healthy and appeared to have little other noticeable defects. The authors use transcriptomics to try to identify pathways altered by the cyto-FLYX construct degrading cytosolic polyP, and it seems likely that their findings in this regard will provide avenues for future investigation. And finally, although the authors found that eclosion is accelerated in pupae of Drosophila expressing the Cyto-FLYX construct, the reason why this happens remains unexplained.

Strengths:

The authors capitalize on the work of other investigators who had previously shown that expression of recombinant yeast exopolyphosphatase could be targeted to specific subcellular compartments to locally deplete polyP, and they also use a recombinant polyP binding protein (PPBD) developed by others to localize polyP. They combine this with the considerable power of Drosophila genetics to explore the roles of polyP by depleting it in specific compartments and cell types to tease out novel biological roles for polyP in a whole organism. This is a substantial advance.

Weaknesses:

Page 4 of Results (paragraph 1): I'm a bit concerned about the specificity of PPBD as a probe for polyP. The authors show that the fusion partner (GST) isn't responsible for the signal, but I don't think they directly demonstrate that PPBD is binding only to polyP. Could it also bind to other anionic substances? A useful control might be to digest the permeabilized cells and tissues with polyphosphatase prior to PPBD staining, and show that the staining is lost.

In the hemolymph clotting experiments, the authors collected 2 ul of hemolymph and then added 1 ul of their test substance (water or a polyP solution). They state that they added either 0.8 or 1.6 nmol polyP in these experiments (the description in the Results differs from that of the Methods). I calculate this will give a polyP concentration of 0.3 or 0.6 mM. This is an extraordinarily high polyP concentration, and is much in excess of the polyP concentrations used in most of the experiments testing the effects of polyP on clotting of mammalian plasma. Why did the authors choose this high polyP concentration? Did they try lower concentrations? It seems possible that too high a polyP concentration would actually have less clotting activity than the optimal polyP concentration.

In the revised version of the manuscript, the authors have productively responded to the previous criticisms. Their new data show stronger controls regarding the specificity of PPBD with regard to its interaction with polyP. The authors also have repeated their hemolymph clotting experiments with lower polyP concentrations, which are likely to be more physiological.

Reviewer #1 (Public review):

Summary:

This paper introduces a dual-pathway model for reconstructing naturalistic speech from intracranial ECoG data. It integrates an acoustic pathway (LSTM + HiFi-GAN for spectral detail) and a linguistic pathway (Transformer + Parler-TTS for linguistic content). Output from the two components are later merged via CosyVoice2.0 voice cloning. Using only 20 minutes of ECoG data per participant, the model achieves high acoustic fidelity and linguistic intelligibility.

Strengths:

(1) The proposed dual-pathway framework effectively integrates the strengths of neural-to-acoustic and neural-to-text decoding and aligns well with established neurobiological models of dual-stream processing in speech and language.

(2) The integrated approach achieves robust speech reconstruction using only 20 minutes of ECoG data per subject, demonstrating the efficiency of the proposed method.

(3) The use of multiple evaluation metrics (MOS, mel-spectrogram R², WER, PER) spanning acoustic, linguistic (phoneme and word), and perceptual dimensions, together with comparisons against noise-degraded baselines, adds strong quantitative rigor to the study.

Comments on revisions:

I thank the authors for their thorough efforts in addressing my previous concerns. I believe this revised version is significantly strengthened, and I have no further concerns.

Reviewer #1 (Public review):

Summary:

Chen et al. engineered and characterized a suite of next-generation GECIs for the Drosophila NMJ that allow for the visualization of calcium dynamics within the presynaptic compartment, at presynaptic active zones, and in the postsynaptic compartment. These GECIs include ratiometric presynaptic Scar8m (targeted to synaptic vesicles), ratiometric active zone localized Bar8f (targeted to the scaffold molecule BRP), and postsynaptic SynapGCaMP8m. The authors demonstrate that these new indicators are a large improvement on the widely used GCaMP6 and GCaMP7 series GECIs, with increased speed and sensitivity. They show that presynaptic Scar8m accurately captures presynaptic calcium dynamics with superior sensitivity to the GCaMP6 and GCaMP7 series and with similar kinetics to chemical dyes. The active-zone targeted Bar8f sensor was assessed for the ability to detect release-site specific nanodomain changes, but the authors concluded that this sensor is still too slow to accurately do so. Lastly, the use of postsynaptic SynapGCaMP8m was shown to enable the detection of quantal events with similar resolution to electrophysiological recordings. Finally, the authors developed a Python-based analysis software, CaFire, that enables automated quantification of evoked and spontaneous calcium signals. These tools will greatly expand our ability to detect activity at individual synapses without the need for chemical dyes or electrophysiology.

Strengths:

In this study, the authors rigorously compare their newly engineered GECIs to those previously used at the Drosophila NMJ, highlighting improvements in localization, speed, and sensitivity. These comparisons appropriately substantiate the authors claim that their GECIs are superior to the ones currently in use.

The authors demonstrate the ability of Scar8m to capture subtle changes in presynaptic calcium resulting from differences between MN-Ib and MN-Is terminals and from the induction of presynaptic homeostatic potentiation (PHP), rivaling the sensitivity of chemical dyes.

The improved postsynaptic SynapGCaMP8m is shown to approach the resolution of electrophysiology in resolving quantal events.

The authors created a publicly available pipeline that streamlines and standardizes analysis of calcium imaging data.

Reviewer #1 (Public review):

Summary:

This study presents a system for delivering precisely controlled cutaneous stimuli to freely moving mice by coupling markerless real-time tracking to transdermal optogenetic stimulation, using the tracking signal to direct a laser via galvanometer mirrors. The principal claims are that the system achieves sub-mm targeting accuracy with a latency of <100 ms. Due to the nature of mouse gait, this enables accurate targeting of forepaws even when mice are moving.

Strengths:

The study is of high quality and the evidence for the claims is convincing. There is increasing focus in neurobiology in studying neural function in freely moving animals, engaged in natural behaviour. However, a substantial challenge is how to deliver controlled stimuli to sense organs under such conditions. The system presented here constitutes notable progress towards such experiments in the somatosensory system and is, in my view, a highly significant development that will be of interest to a broad readership.

My comments on the original submission have been fully addressed.

Reviewer #1 (Public review):

Summary:

The study by Druker et al. shows that siRNA depletion of PHD1, but not PHD2, increases H3T3 phosphorylation in cells arrested in prometaphase. Additionally, the expression of wild-type RepoMan, but not the RepoMan P604A mutant, restored normal H3T3 phosphorylation localization in cells arrested in prometaphase. Furthermore, the study demonstrates that expression of the RepoMan P604A mutant leads to defects in chromosome alignment and segregation, resulting in increased cell death. These data support a role for PHD1-mediated prolyl hydroxylation in controlling progression through mitosis. This occurs, at least in part, by hydroxylating RepoMan at P604, which regulates its interaction with PP2A during chromosome alignment.

Strengths:

The data support most of the conclusions made.

Comments on revisions:

Actually, I am still concerned that PHD1 binds to RepoMan endogenously and directly. Furthermore, the authors have not yet provided genetic evidence demonstrating that PHD1 controls progression through mitosis by catalyzing the hydroxylation of RepoMan.

Reviewer #1 (Public review):

Summary:

In their paper entitled "Alpha-Band Phase Modulates Perceptual Sensitivity by Changing Internal Noise and Sensory Tuning," Pilipenko et al. investigate how pre-stimulus alpha phase influences near-threshold visual perception. The authors aim to clarify whether alpha phase primarily shifts the criterion, multiplicatively amplifies signals, or changes the effective variance and tuning of sensory evidence. Six observers completed many thousands of trials in a double-pass Gabor-in-noise detection task while an EEG was recorded. The authors combine signal detection theory, phase-resolved analyses, and reverse correlation to test mechanistic predictions. The experimental design and analysis pipeline provide a clear conceptual scaffold, with SDT-based schematic models that make the empirical results accessible even for readers who are not specialists in classification-image methods.

Strengths:

The study presents a coherent and well-executed investigation with several notable strengths. First, the main behavioral and EEG results in Figure 2 demonstrate robust pre-stimulus coupling between alpha phase and d′ across a substantial portion of the pre-stimulus interval, with little evidence that the criterion is modulated to a comparable extent. The inverse phasic relationship between hit and false-alarm rates maps clearly onto the variance-reduction account, and the response-consistency analysis offers an intuitive behavioral complement: when two identical stimuli are both presented at the participant's optimal phase, responses are more consistent than when one or both occur at suboptimal phases. The frontal-occipital phase-difference result suggests a coordinated rather than purely local phase mechanism, supporting the central claim that alpha phase is linked to changes in sensitivity that behave like changes in internal variability rather than simple gain or criterion shifts. Supplementary analyses showing that alpha power has only a limited relationship with d′ and confidence reassure readers that the main effects are genuinely phase-linked rather than a recasting of amplitude differences.

Second, the reverse-correlation results in Figure 3 extend this story in a satisfying way. The classification images and their Gaussian fits show that at the optimal phase, the weighting of stimulus energy is more sharply concentrated around target-relevant spatial frequencies and orientations, and the bootstrapped parameter distributions indicate that the suboptimal phase is best described by broader tuning and a modest change in gain rather than a pure criterion account. The authors' interpretation that optimal-phase perception reflects both reduced effective internal noise and sharpened sensory tuning is reasonable and well-supported. Overall, the data and figures largely achieve the stated aims, and the work is likely to have an impact both by clarifying the interpretation of alpha-phase effects and by illustrating a useful analytic framework that other groups can adopt.

Weaknesses:

The weaknesses are limited and relate primarily to framing and presentation rather than to the substance of the work. First, because contrast was titrated to maintain moderate performance (d′ between 1.2 and 1.8), the phase-linked changes in sensitivity appear modest in absolute terms, which could benefit from explicit contextualization. Second, a coding error resulted in unequal numbers of double-pass stimulus pairs across participants, which affects the interpretability of the response-consistency results. Third, several methodological details could be stated more explicitly to enhance transparency, including stimulus timing specifications, electrode selection criteria, and the purpose of phase alignment in group averaging. Finally, some mechanistic interpretations in the Discussion could be phrased more conservatively to clearly distinguish between measurement and inference, particularly regarding the relationship between reduced internal noise and sharpened tuning, and the physiological implementation of the frontal-occipital phase relationship.

Reviewer #1 (Public review):

Summary:

King and colleagues generated a mouse with a point mutation in IL21R and investigated the influence on IL-21-mediated T and B cell activation and differentiation. They found that mutant mice show a reduced T and B cell response, with CD4 T cell differentiation into T follicular helper cells being primarily affected.

Strengths:

The authors combined in vitro and in vivo analysis, including bone-marrow chimeric mice.

Weaknesses:

The effect of the IL21R EINS mutant does not specifically affect STAT1, as clearly shown in Figure 1 H, I. Particularly at lower doses of IL21, which may be more relevant in vivo, the effects are very similar. A second key weakness is the very small Tfh response, a not very clear PD-1 and CXCR5 staining to identify Tfh, and a lack of a steady-state (prior to immunisation) comparison of Tfh numbers in the different mouse strains. The latter makes it impossible to know what fraction of the response is antigen-specific.

Reviewer #1 (Public review):

Summary:

This study presents evidence that the addition of the two GTPases EngA and ObgE to reactions comprised of rRNAs and total ribosomal proteins purified from native bacterial ribosomes can bypass the requirements for non-physiological temperature shifts and Mg⁺² ion concentrations for in vitro reconstitution of functional E. coli ribosomes.

Strengths:

This advance allows ribosome reconstitution in a fully reconstituted protein synthesis system containing individually purified recombinant translation factors, with the reconstituted ribosomes substituting for native purified ribosomes to support protein synthesis. This work potentially represents an important development in the long-term effort to produce synthetic cells.

Weaknesses:

While much of the evidence is solid, the analysis is incomplete in certain respects that detract from the scientific quality and significance of the findings:

(1) The authors do not describe how the native ribosomal proteins (RPs) were purified, and it is unclear whether all subassemblies of RPs have been disrupted in the purification procedure. If not, additional chaperones might be required beyond the two GTPases described here for functional ribosome assembly from individual RPs.

(2) Reconstitution studies in the past have succeeded by using all recombinant, individually purified RPs, which would clearly address the issue in the preceding comment and also eliminate the possibility that an unknown ribosome assembly factor that co-purifies with native ribosomes has been added to the reconstitution reactions along with the RPs.

(3) They never compared the efficiency of the reconstituted ribosomes to native ribosomes added to the "PURE" in vitro protein synthesis system, making it unclear what proportion of the reconstituted ribosomes are functional, and how protein yield per mRNA molecule compares to that given by the PURE system programmed with purified native ribosomes.

(4) They also have not examined the synthesized GFP protein by SDS-PAGE to determine what proportion is full-length.

(5) The previous development of the PURE system included examinations of the synthesis of multiple proteins, one of which was an enzyme whose specific activity could be compared to that of the native enzyme. This would be a significant improvement to the current study. They could also have programmed the translation reactions containing reconstituted ribosomes with (i) total native mRNA and compared the products in SDS-PAGE to those obtained with the control PURE system containing native ribosomes; (ii) with specifc reporter mRNAs designed to examine dependence on a Shine-Dalgarno sequence and the impact of an in-frame stop codon in prematurely terminating translation to assess the fidelity of initiation and termination events; and (iii) an mRNA with a programmed frameshift site to assess elongation fidelity displayed by their reconstituted ribosomes.

Reviewer #1 (Public review):

Summary:

In this article by Xiao et al., the authors aimed to identify the precise targets by which magnesium isoglycyrrhizinate (MgIG) functions to improve liver injury in response to ethanol treatment. The authors found through a series of in vivo and molecular approaches that MgIG treatment attenuates alcohol-induced liver injury through a potential SREBP2-IdI1 axis. This manuscript adds to a previous set of literature showing MgIG improves liver function across a variety of etiologies, and also provides mechanistic insight into its mechanism of action.

Strengths:

(1) The authors use a combination of approaches from both in-vivo mouse models to in-vitro approaches with AML12 hepatocytes to support the notion that MgIG does improve liver function in response to ethanol treatment.

(2) The authors use both knockdown and overexpression approaches, in vivo and in vitro, to support most of the claims provided.

(3) Identification of HSD11B1 as the protein target of MgIG, as well as confirmation of direct protein-protein interactions between HSD11B1/SREBP2/IDI1, is novel.

Weaknesses:

Major weaknesses can be classified into 3 groups:

(1) The results do not support some claims made.

(2) Qualitative analyses of some of the lipid measures, as opposed to more quantitative analyses.

(3) There are no appropriate readouts of Srebp2 translocation and/or activity.

More specific comments:

(1) A few of the claims made are not supported by the references provided. For instance, line 76 states MgIG has hepatoprotective properties and improved liver function, but the reference provided is in the context of myocardial fibrosis.

(2) MgIG is clinically used for the treatment of liver inflammatory disease in China and Japan. In the first line of the abstract, the authors noted that MgIG is clinically approved for ALD. In which countries is MgIG approved for clinical utility in this space?

(3) Serum TGs are not an indicator of liver function. Alterations in serum TGs can occur despite changes in liver function.

(4) There are discrepancies in the results section and the figure legends. For example, line 302 states Idil is upregulated in alcohol fed mice relative to the control group. The figure legend states that the comparison for Figure 2A is that of ALD+MgIG and ALD only.

(5) Oil Red O staining provided does not appear to be consistent with the quantification in Figure 1D. ORO is nonspecific and can be highly subjective. The representative image in Figure 1C appears to have a much greater than 30% ORO (+) area.

(6) The connection between Idil expression in response to EtOH/PA treatment in AML12 cells with viability and apoptosis isn't entirely clear. MgIG treatment completely reduces Idi1 expression in response to EtOH/PA, but only moderate changes, at best, are observed in viability and apoptosis. This suggests the primary mechanism related to MgIG treatment may not be via Idi1.

(7) The nile red stained images also do not appear representative with its quantification. Several claims about more or less lipid accumulation across these studies are not supported by clear differences in nile red.

(8) The authors make a comment that Hsd11b1 expression is quite low in AML12 cells. So why did the authors choose to knockdown Hsd11b1 in this model?

(9) Line 380 - the claim that MGIG weakens the interaction between HSD11b1 and SREBP2 cannot be made solely based on one Western blot.

(10) It's not clear what the numbers represent on top of the Western blots. Are these averages over the course of three independent experiments?

(11) The claim in line 382 that knockdown of Hsd11b1 resulted in accumulation of pSREBP2 is not supported by the data provided in Figure 6D.

(12) None of the images provided in Figure 6E support the claims stated in the results. Activation of SREBP2 leads to nuclear translocation and subsequent induction of genes involved in cholesterol biosynthesis and uptake. Manipulation of Hsd11b1 via OE or KD does not show any nuclear localization with DAPI.

(13) The entire manuscript is focused on this axis of MgIG-Hsd11b1-Srebp2, but no Srebp2 transcriptional targets are ever measured.

(14) Acc1 and Scd1 are Srebp1 targets, not Srebp2.

(15) A major weakness of this manuscript is the lack of studies providing quantitative assessments of Srebp2 activation and true liver lipid measurements.

DOI: 10.1016/j.devcel.2026.01.006

Resource: None

Curator: @scibot

SciCrunch record: RRID:ZFIN_ZDB-ALT-081105-1

What is this?

Reviewer #1 (Public review):

Summary:

This manuscript addresses an important question: how do circadian clocks adjust to a complex rhythmic environment with multiple daily rhythms? The focus is on the temperature and light cycles (TC and LD) and their phase relationship. In nature, TC usually lags the LD cycle, but the phase delay can vary depending on seasonal and daily weather conditions. The authors present evidence that circadian behavior adjusts to different TC/LD phase relationships, that temperature-sensitive tim splicing patterns might underlie some of these responses, and that artificial selection for preferential evening or morning eclosion behavior impacts how flies respond to different LD/TC phase relationship

Strength:

Experiments are conducted on control strains and strains that have been selected in the laboratory for preferential morning or evening eclosion phenotypes. This study is thus quite unique as it allows us to probe whether this artificial selection impacted how animals respond to different environmental conditions, and thus gives hints on how evolution might shape circadian oscillators and their entrainment. The authors focused on circadian locomotor behavior and timeless (tim) splicing because warm and cold-specific transcripts have been described as playing an important role in determining temperature-dependent circadian behavior. Not surprisingly, the results are complex, but there are interesting observations. In particular, the "late" strain appears to be able to adjust more efficiently its evening peak in response to changes in the phase relationship between temperature and light cycles, but the morning peak seems less responsive in this strain. Differences in the circadian pattern of expression of different tim mRNA isoforms are found under specific LD/TC conditions.

Weaknesses:

These observations are interesting, but in the absence of specific genetic manipulations, it is difficult to establish a causative link between tim molecular phenotypes and behavior. The study is thus quite descriptive. It would be worth testing available tim splicing mutants, or mutants for regulators of tim splicing, to understand in more detail and more directly how tim splicing determines behavioral adaptation to different phase relationships between temperature and light cycles. Also, I wonder whether polymorphisms in or around tim splicing sites, or in tim splicing regulators, were selected in the early or late strains.

I also have a major methodological concern. The authors studied how the evening and morning phases are adjusted under different conditions and different strains. They divided the daily cycle into 12h morning and 12h evening periods, and calculated the phase of morning and evening activity using circular statistics. However, the non-circadian "startle" responses to light or temperature transitions should have a very important impact on phase calculation, and thus at least partially obscure actual circadian morning and evening peak phase changes. Moreover, the timing of the temperature-up startle drifts with the temperature cycles, and will even shift from the morning to the evening portion of the divided daily cycle. Its amplitude also varies as a function of the LD/TC phase relationship. Note that the startle responses and their changes under different conditions will also affect SSD quantifications.

For the circadian phase, these issues seem, for example, quite obvious for the morning peak in Figure 1. According to the phase quantification on panel D, there is essentially no change in the morning phase when the temperature cycle is shifted by 6 hours compared to the LD cycle, but the behavior trace on panel B clearly shows a phase advance of morning anticipation. Comparison between the graphs on panels C and D also indicates that there are methodological caveats, as they do not correlate well.

Because of the various masking effects, phase quantification under entrainment is a thorny problem in Drosophila. I would suggest testing other measurements of anticipatory behavior to complement or perhaps supersede the current behavior analysis. For example, the authors could employ the anticipatory index used in many previous studies, measure the onset of morning or evening activity, or, if more reliable, the time at which 50% of anticipatory activity is reached. Termination of activity could also be considered. Interestingly, it seems there are clear effects on evening activity termination in Figure 3. All these methods will be impacted by startle responses under specific LD/TC phase relationships, but their combination might prove informative.

Reviewer #1 (Public review):

Summary:

The manuscript by Hao Jiang et al described a systematic approach to identify proline hydroxylation proteins. The authors implemented a proteomic strategy with HILIC-chromatographic separation and reported an identification with high confidence of 4993 sites from HEK293 cells (4 replicates) and 3247 sites from RCC4 cells with 1412 sites overlapping between the two cell lines. A small fraction of about 200 sites from each cell line were identified with HyPro immonium ion. The authors investigated the conditions and challenges of using HyPro immonium ions as a diagnostic tool. The study focused the validation analysis of Repo-man (CDCA2) proline hydroxylation comparing MS/MS spectra, retention time and diagnostic ions of purified proteins with corresponding synthetic peptides. Using SILAC analysis and recombinant enzyme assay, the study evaluated Repo-man HyPro604 as a target of PHD1 enzyme.

Strengths:

The study involved extensive LCMS runs for in-depth characterization of proline hydroxylation proteins including four replicated analysis of 293 cells and three replicated analysis of RCC4 cells with 32 HILIC fractions in each analysis. The identification of over 4000 confident proline hydroxylation sites from the two cell lines would be a valuable resource for the community. The characterization of Repo-man proline hydroxylation is a novel finding.

Weaknesses:

As a study mainly focused on methodology, there are some potential technical weaknesses discussed below.

(1) The study applied HILIC-based chromatographic separation with a goal to enrich and separate hydroxyproline containing peptides. The separation effects for peptides from 293 cells and RCC4 cells seems somewhat different (Figure 2A and Figure S1A), which may indicate that the application efficiency of the strategy may be cell line dependent.

(2) The study evaluated the HyPro immonium ion as a diagnostic ion for HyPro identification showcasing multiple influential factors and potential challenges. It is important to note that with only around 5% of the identifications had HyPro immonium ion, it would be very challenging to implement this strategy in a global LCMS analysis to either validate or invalidate HyPro identifications. In comparison, acetyllysine immonium ion was previously reported to be a useful marker for acetyllysine peptides (PMID: 18338905) and the strategy offered a sensitivity of 70% with a specificity of 98%.

(3) The authors aimed to identify potential PHD targets by comparing the HyPro proteins identified with or without PHD inhibitor FG-4592 treatment. The workflow followed a classification strategy, rather than a typical quantitative proteomics approach for comprehensive analysis.

(4) The authors performed inhibitor treatment and in vitro PHD1 enzyme assay to validate that Repo-man can be hydroxylated by PHD1. It remains unknown if PHD1 expression in cells is sufficient to stimulate Repo-man hydroxylation.

Reviewer #1 (Public review):

Summary:

This study aimed to determine whether bacterial translation inhibitors affect mitochondria through the same mechanisms. Using mitoribosome profiling, the authors found that most antibiotics, except telithromycin, act similarly in both systems. These insights could help in the development of antibiotics with reduced mitochondrial toxicity.

They also identified potential novel mitochondrial translation events, proposing new initiation sites for MT-ND1 and MT-ND5. These insights not only challenge existing annotations but also open new avenues for research on mitochondrial function.

Strengths:

Ribosome profiling is a state-of-the-art method for monitoring the translatome at very high resolution. Using mitoribosome profiling, the authors convincingly demonstrate that most of the analyzed antibiotics act in the same way on both bacterial and mitochondrial ribosomes, except for telithromycin. Additionally, the authors report possible alternative translation events, raising new questions about the mechanisms behind mitochondrial initiation and start codon recognition in mammals.

Weaknesses:

All the weaknesses I previously highlighted were adequately addressed.

Reviewer #1 (Public review):

Summary:

In this manuscript, Yamazaki et al. conducted multiple microscopy-based GFP localization screens, from which they identified proteins that are associated with PM/cell wall damage stress response. Specifically, the authors identified that bud-localized TMD-containing proteins and endocytotic proteins are associated with PM damage stress. The authors further demonstrated that polarized exocytosis and CME are temporally coupled in response to PM damage, and CME is required for polarized exocytosis and the targeting of TMD-containing proteins to the damage site. From these results, the authors proposed a model that CME delivers TMD-containing repair proteins between the bud tip and the damage site.

Strengths:

Overall, this is a well-written manuscript, and the experiments are overall well-conducted. The authors identified many repair proteins and revealed the temporal coordination of different categories of repair proteins. Furthermore, the authors demonstrated that CME is required for targeting of repair proteins to the damage site, as well as cellular survival in response to stress related to PM/cell wall damage. Although the roles of CME and bud-localized proteins in damage repair are not completely new to the field, this work does have conceptual advances by identifying novel repair proteins and proposing the intriguing model that the repairing cargoes are shuttled between the bud tip and the damaged site through coupled exocytosis and endocytosis.

Weaknesses:

While the results presented in this manuscript are convincing, they might not be sufficient to support some of the authors' claims. Especially in the last two result sessions, the authors claimed CME delivers TMD-containing repair proteins from the bud tip to the damage site. The model is no doubt highly possible based on the date, but caveats still exist. For example, the repair proteins might not be transported from one localization to another localization, but are degraded and re-synthesized. Although the Gal-induced expression system can further support the model to some extent, I think more direct verification (such as FLIP or photo-convertible fluorescence tags to distinguish between pre-existing and newly synthesized proteins) would significantly improve the strength of evidence.

Review on revised version:

The authors addressed most of concerns that were originally raised, primarily by revising the text and figures and expanding the discussion, which improves the clarity of the manuscript. Although the authors did not address my major concern on the shuttling/trafficking model experimentally, I do understand the limitation of resources and time. The authors noted that they planned to do these experiments for their future work, and such studies would be more definitive evaluations for the proposed model. Overall I think this is a very interesting and well-conducted study and I enjoyed reading this manuscript. I look forward to their following research of this study.

Reviewer #1 (Public review):

Summary:

This manuscript by Feng et al. uses mouse models to study the embryonic origins of HSPCs. Using multiple types of genetic lineage tracing, the authors aimed to identify whether BM-resident endothelial cells retain hematopoietic capacity in adult organisms. Through an important mix of various labeling methodologies (and various controls), they reach the conclusion that BM endothelial cells contribute up to 3% of hematopoietic cells in young mice.

Strengths:

The major strength of the paper lies in the combination of various labeling strategies, including multiple Cdh5-CreER transgenic lines, different CreER lines (col1a2), and different reporters (ZsGreen, mTmG), including a barcoding-type reporter (PolyLox). This makes it highly unlikely that the results are driven by a rare artifact due to one random Cre line or one leaky reporter. The transplantation control (where the authors show no labeling of transplanted LSKs from the Cdh5 model) is also very supportive of their conclusions.

Weaknesses:

We believe that the work of ruling out alternative hypotheses, though initiated, was left incomplete. We specifically think that the authors need to properly consider whether there is specific, sparse labeling of HSPCs (in their native, non-transplant, model, in young animals). Polylox experiments, though an exciting addition, are also incomplete without additional controls. Some additional killer experiments are suggested.

Reviewer #1 (Public review):

Summary:

Morgan et al. studied how paternal dietary alteration influenced testicular phenotype, placental and fetal growth using a mouse model of paternal low protein diet (LPD) or Western Diet (WD) feeding, with or without supplementation of methyl-donors and carriers (MD). They found diet- and sex-specific effects of paternal diet alteration. All experimental diets decreased paternal body weight and the number of spermatogonial stem cells, while fertility was unaffected. WD males (irrespective of MD) showed signs of adiposity and metabolic dysfunction, abnormal seminiferous tubules, and dysregulation of testicular genes related to chromatin homeostasis. Conversely, LPD induced abnormalities in the early placental cone, fetal growth restriction, and placental insufficiency, which were partly ameliorated by MD. The paternal diets changed the placental transcriptome in a sex-specific manner and led to a loss of sexual dimorphism in the placental transcriptome. These data provide a novel insight into how paternal health can affect the outcome of pregnancies, which is often overlooked in prenatal care.

Strengths:

The authors have performed a well-designed study using commonly used mouse models of paternal underfeeding (low protein) and overfeeding (Western diet). They performed comprehensive phenotyping at multiple timepoints, including the fathers, the early placenta, and the late gestation feto-placental unit. The inclusion of both testicular and placental morphological and transcriptomic analysis is a powerful, non-biased tool for such exploratory observational studies. The authors describe changes in testicular gene expression revolving around histone (methylation) pathways that are linked to altered offspring development (H3.3 and H3K4), which is in line with hypothesised paternal contributions to offspring health. The authors report sex differences in control placentas that mimic those in humans, providing potential for translatability of the findings. The exploration of sexual dimorphism (often overlooked) and its absence in response to dietary modification is novel and contributes to the evidence-base for the inclusion of both sexes in developmental studies.

Weaknesses:

The data are overall consistent with the conclusions of the authors. The paternal and pregnancy data are discussed separately, instead of linking the paternal phenotype to offspring outcomes. Some clarifications regarding the methods and the model would improve the interpretation of the findings.

(1) The authors insufficiently discuss their rationale for studying methyl-donors and carriers as micronutrient supplementation in their mouse model. The impact of the findings would be better disseminated if their role were explained in more detail.

(2) It is unclear from the methods exactly how long the male mice were kept on their respective diets at the time of mating and culling. Male mice were kept on the diet between 8 and 24 weeks before mating, which is a large window in which the males undergo a considerable change in body weight (Figure 1A). If males were mated at 8 weeks but phenotyped at 24 weeks, or if there were differences between groups, this complicates the interpretation of the findings and the extrapolation of the paternal phenotype to changes seen in the fetoplacental unit. The same applies to paternal age, which is an important known factor affecting male fertility and offspring outcomes.

(3) The male mice exhibited lower body weights when fed experimental diets compared to the control diet, even when placed on the hypercaloric Western Diet. As paternal body weight is an important contributor to offspring health, this is an important confounder that needs to be addressed. This may also have translational implications; in humans, consumption of a Western-style diet is often associated with weight gain. The cause of the weight discrepancy is also unaddressed. It is mentioned that the isocaloric LPD was fed ad libitum, while it is unclear whether the WD was also fed ad libitum, or whether males under- or over-ate on each experimental diet.

(4) The description and presentation of certain statistical analyses could be improved.

(i) It is unclear what statistical analysis has been performed on the time-course data in Figure 1A (if any). If one-way ANOVA was performed at each timepoint (as the methods and legend suggest), this is an inaccurate method to analyse time-course data.

(ii) It is unclear what methods were used to test the relative abundance of microbiome species at the family level (Figure 2L), whether correction was applied for multiple testing, and what the stars represent in the figure. 3) Mentioning whether siblings were used in any analyses would improve transparency, and if so, whether statistical correction needed to be applied to control for confounding by the father.

Reviewer #1 (Public review):

Meiotic recombination at chromosome ends can be deleterious, and its initiation-the programmed formation of DSBs-has long been known to be suppressed. However, the underlying mechanisms of this suppression remained unclear. A bottleneck has been the repetitive sequences embedded within chromosome ends, which make them challenging to analyze using genomic approaches. The authors addressed this issue by developing a new computational pipeline that reliably maps ChIP-seq reads and other genomic data, enabling exploration of previously inaccessible yet biologically important regions of the genome.

In budding yeast, chromosome ends (~20 kb) show depletion of axis proteins (Red1 and Hop1) important for recruiting DSB-forming proteins. Using their newly developed pipeline, the authors reanalyzed previously published datasets and data generated in this study, revealing heretofore unseen details at chromosome ends. While axis proteins are depleted at chromosome ends, the meiotic cohesin component Rec8 is not. Y' elements play a crucial role in this suppression. The suppression does not depend on the physical chromosome ends but on cis-acting elements. Dot1 suppresses Red1 recruitment at chromosome ends but promotes it in interior regions. Sir complex renders subtelomeric chromatin inaccessible to the DSB-forming machinery.

The high-quality data and extensive analyses provide important insights into the mechanisms that suppress meiotic DSB formation at chromosome ends. To fully realise this value, several aspects of data presentation and interpretation should be clarified to ensure that the conclusions are stated with appropriate precision and that remaining future issues are clearly articulated.

(1) To assess the chromosome fusion effects on overall subtelomeric suppression, authors should guide how to look at the data presented in Figure 2b-c. Based on the authors' definition of the terminal 20 kb as the suppressed region, SK1 chrIV-R and S288c chrI-L would be affected by the chromosome fusion, if any. In addition, I find it somewhat challenging to draw clear conclusions from inspecting profiles to compare subtelomeric and internal regions. Perhaps, applying a quantitative approach - such as a bootstrap-based analysis similar to those presented earlier-would be easier to interpret.

(2) The relationship between coding density and Red1 signal needs clarification. An important conclusion from Figure 3 is that the subtelomeric depletion of Red1 primarily reflects suppression of the Rec8-dependent recruitment pathway, whereas Rec8-independent recruitment appears similar between ends and internal regions. Based on the authors' previous papers (referencess 13, 16), I thought coding (or nucleosome) density primarily influences the Rec8-independent pathway. However, the correlations presented in Figure 2d-e (also implied in Figure 3a) appear opposite to my expectation. Specifically, differences in axis protein binding between chromosome ends and internal regions (or within chromosome ends), where the Rec8-dependent pathway dominates, correlate with coding density. In contrast, no such correlation is evident in rec8Δ cells, where only the Rec8-independent pathway is active and end-specific depletion is absent. One possibility is that masking coding regions within Y' elements influences the correlation analysis. Additional analysis and a clearer explanation would be highly appreciated.

(3) The Dot1-Sir3 section staring from L266 should be clarified. I found this section particularly difficult to follow. It begins by stating that dot1∆ leads to Sir complex spreading, but then moves directly to an analysis of Red1 ChIP in sir3∆ without clearly articulating the underlying hypothesis. I wonder if this analysis is intended to explain the differences observed between dot1∆ and H3K79R mutants in the previous section. I also did not get the concluding statement - Dot1 counteracts Sir3 activity. As sir3Δ alone does not affect subtelomeric suppression, it is unclear what Dot1 counteracts. Perhaps, explicitly stating the authors' working model at the outset of this section would greatly clarify the rationale, results, and conclusions.

Reviewer #1 (Public review):

Summary:

In this study, Nagao and Mochizuki examine the fate of germline chromosome ends during somatic genome differentiation in the ciliate Tetrahymena thermophila. During sexual reproduction, a new somatic genome is created from a zygotic, germline-derived genome by extensive programmed DNA elimination events. It has been known for some time that the termini of the germline chromosomes are eliminated, but the exact process and kinetics of the elimination events have not been thoroughly investigated. The authors first use germline-specific telomere probes to show that the loss of these chromosome ends occurs with similar timing as other DNA elimination events. By comparative analysis of the assembled germline and somatic genomes, the authors find that the ends of each of the germline chromosomes are composed of a few hundred kilobases of micronuclear limited sequences (MLS) that are removed starting around 14 hours after the start of conjugation, which initiates sexual development. They then develop an in situ hybridization assay to track the fate of one end of chromosome 4 while simultaneously following the adjacent macronuclear destined sequence (MDS) retained in the new somatic genome. This allows the authors to more clearly show that these adjacent chromosomal segments are initially amplified in the developing genome before the terminal MLS is eliminated. Finally, they mutate the chromosome breakage sequence (CBS) that normally separates the MLS terminus from the adjacent MDS region, to show that strains that develop with only one mutant chromosome can produce viable sexual progeny, but it appears that both the MLS and the MDS from the mutant chromosome are lost. If both chromosome copies have the CBS mutation, the cells arrest during development and do not eliminate many germline-limited sequences and fail to produce viable progeny. Overall, this study provides many new insights into the fate of germline chromosome ends during somatic genome remodeling and suggests extensive coordination of different DNA elimination events in Tetrahymena.

Strengths:

Overall, the experiments were well executed with appropriate controls. The findings are generally robust. Importantly, the study provides several novel findings. First, the authors provide a fairly comprehensive characterization of the size of the MLS at the end of each germline chromosome. I'm not sure whether this has been published elsewhere. Second, the authors develop a novel method to study the fate of chromosome termini during development and use it to conclusively track the elimination of these termini. Third, the authors show that the elimination of these termini appears to occur concurrently with most other DNA elimination events during somatic genome differentiation. And fourth, the authors show that failure to separate these eliminated sequences from the normally retained chromosome alters the fate of these adjacent MDS and the loss of the cells' ability to produce viable progeny.

Weaknesses:

It appears the authors did extensive analysis of the MLS chromosome ends, but did not provide too much information related to their composition. If this has not been published elsewhere, it would be useful to describe the proportion of unique and repetitive sequences and provide more information about the general composition of the chromosome ends. Such information would help the reader understand the nature of these MLS and how they may or may not differ from other eliminated sequences. Although the development of the novel FISH probes for large chromosome ends allowed for these novel discoveries, the signal in several images was visible, but often quite faint. I'm not sure there is anything the authors could do to improve the signal-to-noise ratio, but one needs to stare at the images carefully to understand the findings. One main weakness in the opinion of this reviewer is that the authors did very little to understand why, when a terminal MLS and the adjacent MDS fail to get separated because of failure in chromosome breakage, both segments are eliminated. The authors propose that possibly essential genes in the MDS get silenced, and the resulting lack of gene expression is the issue, but this and other possibilities were not tested. The study would provide more mechanistic insight if they had tried to assess whether the MDS on the CBS mutant chromosome becomes enriched in silencing modifications (e.g., H3K9me3). Alternatively, the authors could have examined changes in gene expression for some of the loci on the neighbouring MDS. The other main weakness is that since the authors only mutated the end of one germline chromosome, it is not clear whether the elimination of the MDS adjacent to the terminal MLS on chromosome 4 when the CBS is mutated is a general phenomenon, i.e., would happen at all chromosome ends, or is unique to the situation at Chromosome 4R. Knowing whether it is a general phenomenon or not would provide important insight into the authors' findings.

Reviewer #1 (Public review):

Summary:

A hallmark of cortical development is the temporal progression of lineage programs in radial glia progenitors (RGs) that orderly generate a large set of glutamatergic projection neuron types, which are deployed to the cortex in a largely inside-out sequence. This process is thought to contribute to the formation of proper cortical circuitry, but the underlying cellular and molecular mechanisms remain poorly understood. To a large extent, this is due to technical limitations that can fate map RGs and their progeny with cell type resolution, and manipulate gene expression with proper cell and temporal resolution. Building on the TEMPO technique that Tsumin Lee group developed, here Azur et al show that the RNA binding protein Imp1 functions as a dosage- and stage-dependent post-transcriptional mechanism that orchestrates developmental stage transitions in radial glial progenitors, and controls neuronal fate decisions and spatial organization of neuronal and glial cell progeny. Their results suggest that while transcriptional regulators define available cellular states and gate major transitions, post-transcriptional mechanisms like Imp1 provide an additional layer of control by modulating stage-specific transcript stability. Imp1 thus acts as a temporal coordinator whose dosage and timing determine whether developmental transitions are temporarily delayed or blocked. These findings establish a new framework for understanding how post-transcriptional mechanisms integrate with transcriptional and epigenetic regulatory layers to control cortical temporal patterning.

Strengths:

The authors apply a novel genetic fate mapping and gene manipulation technology (TEMPO) with cellular resolution. This reveals a dosage- and stage-dependent post-transcriptional mechanism that orchestrates developmental stage transitions in radial glial progenitors, and controls neuronal fate decisions and spatial organization of neuronal and glial cell/astrocyte progeny.

Weaknesses:

The endogenous developmental expression pattern of Imp1 and TEMPO-mediated overexpression are not well described or characterized with cellular resolution (whether only in radial glial cells or also in post-mitotic neurons). Thus, the interpretations of the overexpression phenotypes are not always clear.

Reviewer #1 (Public review):

Summary:

This manuscript examines the passage of an intrathecal CSF tracer into skull bone marrow, cortex, and venous compartments using serial MRI at multiple time points. The study builds on recent anatomical and imaging work suggesting direct communication between CSF spaces and bone marrow in the skull. It extends these observations to a larger, clinically heterogeneous human cohort. The imaging methodology is carefully executed, and the dataset is rich. The findings are potentially important for understanding CSF drainage pathways and their associations with inflammation, sleep quality, and cognition. However, key aspects of the interpretation - particularly regarding tracer kinetics and the definition of "clearance" - require clarification and, in my view, reconsideration.

Strengths:

(1) The study employs a well-established intrathecal contrast-enhanced MRI approach with multiple post-injection time points, enabling the assessment of regional tracer dynamics.

(2) The analysis of skull bone marrow in distinct anatomical regions (near the superior sagittal sinus, lateral fissure, and cisterna magna) is novel and informative.

(3) The cohort size is relatively large for an intrathecal tracer study in humans, and the authors make commendable efforts to relate imaging findings to clinical variables such as inflammation, sleep quality, and cognitive performance.

(4) The manuscript is clearly written, the figures are informative, and the discussion is well grounded in recent anatomical and experimental literature on skull-meningeal connections.

Weaknesses:

The central interpretation that a higher percentage increase in skull bone marrow tracer signal at 4.5 hours reflects reduced clearance is not convincingly justified. Based on the existing CSF tracer literature, the 4-6 hour time window is generally considered an enrichment or inflow phase rather than a clearance phase. Later time points (15 and 39 hours) are more likely to reflect clearance or washout. An alternative interpretation - that a higher signal at 4.5 hours reflects more pronounced tracer entry - should be considered and discussed.

Relatedly, the manuscript lacks a clear conceptual separation between tracer enrichment and clearance phases across time points. If 4.5 hours is intended to represent clearance, this assumption requires more vigorous justification and alignment with prior work.

CSF passage via the nasal/olfactory pathway is insufficiently discussed. Previous human imaging studies have questioned the importance of peri-olfactory CSF clearance, yet the present findings suggest delayed enrichment in the nasal turbinates. This discrepancy should be explicitly addressed, including a discussion of potential methodological limitations (e.g., timing of acquisitions, ROI definition, or sensitivity to slow drainage pathways).

More generally, given the descriptive nature of the study and the limited temporal sampling, some conclusions regarding directionality and efficiency of "drainage" may be overstated and would benefit from more cautious framing.

Reviewer #1 (Public review):

Summary:

In the work from Qiu et al., a workflow aimed at obtaining the stabilization of a simple small protein against mechanical and chemical stressors is presented.

Strengths:

The workflow makes use of state-of-the-art AI-driven structure generation and couples it with more classical computational and experimental characterizations in order to measure its efficacy. The work is well presented, and the results are thorough and convincing.

Weaknesses:

I will comment mostly on the MD results due to my expertise.

The Methods description is quite precise, but is missing some important details:

(1) Version of GROMACS used.

(2) The barostat used.

(3) pH at which the system is simulated.

(4) The pulling is quite fast (but maybe it is not a problem)

(5) What was the value for the harmonic restraint potential? 1000 is mentioned for the pulling potential, but it is not clear if the same value is used for the restraint, too, during pulling.

(6) The box dimensions.

From this last point, a possible criticism arises: Do the unfolded proteins really still stay far enough away from themselves to not influence the result? This might not be the major influence, but for correctness, I would indicate the dimensions of the box in all directions and plot the minimum distance of the protein from copies of itself across the boundary conditions over time.

Additionally, no time series are shown for the equilibration phases (e.g., RMSD evolution over time), which would empower the reader to judge the equilibration of the system before either steered MD or annealing MD is performed.

Joint Public Review:

Pippadpally et al. investigate how the conserved E3 ubiquitin ligase Highwire (Hiw/Phr1), a well-established negative regulator of synaptic growth, is functionally and spatially regulated. Using a GFP-tagged Hiw transgene in Drosophila, the authors report that disruption of endocytosis via loss of AP-2, synaptojanin, or Rab11-mediated recycling endosome function leads to accumulation of Hiw in neuronal cell bodies as enlarged foci, altogether accompanied by synaptic overgrowth. Provided that the Hiw foci are sensitive to aliphatic alcohol treatment, the authors propose that impaired endocytosis promotes liquid-liquid phase separation of the E3 ubiquitin ligase, reducing its ability to degrade the MAPKKK Wallenda and thereby activating JNK signalling. Crosstalk with BMP signalling and roles for autophagy are also explored within this framework.

Strengths

The work provides a novel tool, the GFP-tagged Hiw transgene, to study the spatio-temporal regulation of the E3 ubiquitin ligase Highwire (Hiw/Phr1) in Drosophila, and its impact on synaptic growth. The results presented point to a potentially thought-provoking connection between endocytic defects, Hiw condensation, Hiw down-regulation and synaptic overgrowth. The specific effects of the endocytic mutants on the redistribution of the Hiw to the neuronal cell body and the genetic interactions between the endocytosis and JNK pathway mutants are convincing.

Weaknesses

Several conclusions are insufficiently supported at this point. For example, evidence that the Hiw foci represent bona fide liquid-liquid phase (LLP) separated condensates is limited. Sensitivity to 1,6-hexanediol is not definitive proof of their liquid condensate nature, and their recovery kinetics after 1,6-hexanediol wash-out and their morphology are inconsistent with a pure liquid behaviour. Furthermore, the claim that the Hiw foci are non-vesicular is not strongly supported, as it is only based on the lack of colocalization with a handful of endosomal proteins.

Importantly, the appearance of the putative condensates is correlative rather than causative for synaptic overgrowth, and in the absence of a mechanistic link between endocytosis and Hiw condensation, the causality is difficult to address. Of note is that the putative condensates are already present (albeit to a lesser extent) in the absence of endocytic defects and that the conclusions rely heavily on overexpressed GFP-Hiw, which may perturb normal protein behaviour and artificially induce condensation or aggregation.

The use of hypomorphic mutants in genetic experiments also introduces some ambiguity in their interpretation, as the results may reflect dosage effects from multiple pathways rather than pathway order. Finally, the manuscript would benefit from a more comprehensive reference to relevant literature on JNKKKs and BMP signalling, as well as on the recycling endosome function in synaptic growth and the regulation of the aforementioned pathways.

Overall, while the work presents thought-provoking observations and a potentially interesting regulatory model, additional experimental rigor and broader contextualization are needed to substantiate the proposed mechanism and its biological relevance.

Reviewer #1 (Public review):

In this paper, Stanojcic and colleagues attempt to map sites of DNA replication initiation in the genome of the African trypanosome, Trypanosoma brucei. Their approach to this mapping is to isolate 'short-nascent strands' (SNSs), a strategy adopted previously in other eukaryotes (including in the related parasite Leishmania major), which involves isolation of DNA molecules whose termini contain replication-priming RNA. By mapping the isolated and sequenced SNSs to the genome (SNS-seq), the authors suggest that they have identified origins, which they localise to intergenic (strictly, inter-CDS) regions within polycistronic transcription units and suggest display very extensive overlap with previously mapped R-loops in the same loci. Finally, having defined locations of SNS-seq mapping, they suggest they have identified G4 and nucleosome features of origins, again using previously generated data. Though there is merit in applying a new approach to understand DNA replication initiation in T. brucei, where previous work has used MFA-seq and ChIP of a subunit of the Origin Replication Complex (ORC), there are two significant deficiencies in the study that must be addressed to ensure rigour and accuracy.

(1) The suggestion that the SNS-seq data is mapping DNA replication origins that are present in inter-CDS regions of the polycistronic transcription units of T. brucei is novel and does not agree with existing data on the localisation of ORC1/CDC6, and it is very unclear if it agrees with previous mapping of DNA replication by MFA-seq due to the way the authors have presented this correlation. For these reasons, the findings essentially rely on a single experimental approach, which must be further tested to ensure SNS-seq is truly detecting origins. Indeed, in this regard, the very extensive overlap of SNS-seq signal with RNA-DNA hybrids should be tested further to rule out the possibility that the approach is mapping these structures and not origins.

(2) The authors' presentation of their SNS-seq data is too limited and therefore potentially provides a misleading view of DNA replication in the genome of T. brucei. The work is presented through a narrow focus on SNS-seq signal in the inter-CDS regions within polycistronic transcription units, which constitute only part of the genome, ignoring both the transcription start and stop sites at the ends of the units and the large subtelomeres, which are mainly transcriptionally silent. The authors must present a fuller and more balanced view of SNS-seq mapping across the whole genome to ensure full understanding and clarity.

Reviewer #1 (Public review):

Summary:

The study examines human biases in a regime-change task, in which participants have to report the probability of a regime change in the face of noisy data. The behavioral results indicate that humans display systematic biases, in particular, overreaction in stable but noisy environments and underreaction in volatile settings with more certain signals. fMRI results suggest that a frontoparietal brain network is selectively involved in representing subjective sensitivity to noise, while the vmPFC selectively represents sensitivity to the rate of change.

Strengths:

The study relies on a task that measures regime-change detection primarily based on descriptive information about the noisiness and rate of change. This distinguishes the study from prior work using reversal-learning or change-point tasks in which participants are required to learn these parameters from experiences. The authors discuss these differences comprehensively.

The study uses a simple Bayes-optimal model combined with model fitting, which seems to describe the data well. The model is comprehensively validated.

The authors apply model-based fMRI analyses that provide a close link to behavioral results, offering an elegant way to examine individual biases.

Weaknesses:

The authors have adequately addressed my prior concerns.

Reviewer #1 (Public review):

Summary:

The authors proposed a new method to infer connectivity from spike trains whose main novelty relies on their approach to mitigate the problem of model mismatch. The latter arises when the inference algorithm is trained or based on a model that does not accurately describe the data. They propose combining domain adaptation with a deep neural architecture and in an architecture called DeepDAM. They apply DeepDAM to an in vivo ground-truth dataset previously recorded in mouse CA1, show that it performs better than methods without domain adaptation, and evaluate its robustness. Finally, they show that their approach can also be applied to a different problem i.e., inferring biophysical properties of individual neurons.

Strengths:

(1) The problem of inferring connectivity from extracellular recording is a very timely one: as the yield of silicon probes steadily increases, the number of simultaneously recorded pairs does so quadratically, drastically increasing the possibility of detecting connected pairs.

(2) Using domain adaptation to address model mismatch is a clever idea, and the way the authors introduced it into the larger architecture seems sensible.

(3) The authors clearly put a great effort into trying to communicate the intuitions to the reader.

Weaknesses:

(1) The validation of the approach is incomplete: due to its very limited size, the single ground-truth dataset considered does not provide a sufficient basis to draw a strong conclusion. While the authors correctly note that this is the only dataset of its kind, the value of this validation is limited compared to what could be done by carefully designing in silico experiments.

(2) Surprisingly, the authors fail to compare their method to the approach originally proposed for the data they validate on (English et al., 2017).

(3) The authors make a commendable effort to study the method's robustness by pushing the limits of the dataset. However, the logic of the robustness analysis is often unclear, and once again, the limited size of the dataset poses major limitations to the authors.

(4) The lack of details concerning both the approach and the validation makes it challenging for the reader to establish the technical soundness of the study.

Although in the current form this study does not provide enough basis to judge the impact of DeepDAM in the broader neuroscience community, it nevertheless puts forward a valuable and novel idea: using domain adaptation to mitigate the problem of model mismatch. This approach might be leveraged in future studies and methods to infer connectivity.

Reviewer #1 (Public review):

Summary:

The study of Drosophila mating behaviors has offered a powerful entry point for understanding how complex innate behaviors are instantiated in the brain. The effectiveness of this behavioral model stems from how readily quantifiable many components of the courtship ritual are, facilitating the fine-scale correlations between the behaviors and the circuits that underpin their implementation. Detailed quantification, however, can be both time-consuming and error-prone, particularly when scored manually. Song et al. have sought to address this challenge by developing DrosoMating, software that facilitates the automated and high-throughput quantification of 6 common metrics of courtship and mating behaviors. Compared to a human observer, DrosoMating matches courtship scoring with high fidelity. Further, the authors demonstrate that the software effectively detects previously described variations in courtship resulting from genetic background or social conditioning. Finally, they validate its utility in assaying the consequences of neural manipulations by silencing Kenyon cells involved in memory formation in the context of courtship conditioning.

Strengths:

(1) The authors demonstrate that for three key courtship/mating metrics, DrosoMating performs virtually indistinguishably from a human observer, with differences consistently within 10 seconds and no statistically significant differences detected. This demonstrates the software's usefulness as a tool for reducing bias and scoring time for analyses involving these metrics.

(2) The authors validate the tool across multiple genetic backgrounds and experimental manipulations to confirm its ability to detect known influences on male mating behavior.

(3) The authors present a simple, modular chamber design that is integrated with DrosoMating and allows for high-throughput experimentation, capable of simultaneously analyzing up to 144 fly pairs across all chambers.

Weaknesses:

(1) DrosoMating appears to be an effective tool for the high-throughput quantification of key courtship and mating metrics, but a number of similar tools for automated analysis already exist. FlyTracker (CalTech), for instance, is a widely used software that offers a similar machine vision approach to quantifying a variety of courtship metrics. It would be valuable to understand how DrosoMating compares to such approaches and what specific advantages it might offer in terms of accuracy, ease of use, and sensitivity to experimental conditions.

(2) The courtship behaviors of Drosophila males represent a series of complex behaviors that unfold dynamically in response to female signals (Coen et al., 2014; Ning et al., 2022; Roemschied et al., 2023). While metrics like courtship latency, courtship index, and copulation duration are useful summary statistics, they compress the complexity of actions that occur throughout the mating ritual. The manuscript would be strengthened by a discussion of the potential for DrosoMating to capture more of the moment-to-moment behaviors that constitute courtship. Even without modifying the software, it would be useful to see how the data can be used in combination with machine learning classifiers like JAABA to better segment the behavioral composition of courtship and mating across genotypes and experimental manipulations. Such integration could substantially expand the utility of this tool for the broader Drosophila neuroscience community.

(3) While testing the software's capacity to function across strains is useful, it does not address the "universality" of this method. Cross-species studies of mating behavior diversity are becoming increasingly common, and it would be beneficial to know if this tool can maintain its accuracy in Drosophila species with a greater range of morphological and behavioral variation. Demonstrating the software's performance across species would strengthen claims about its broader applicability.

Reviewer #1 (Public review):

Summary:

This fundamental study identifies a new mechanism that involves a mycobacterial nucleomodulin manipulation of the host histone methyltransferase COMPASS complex to promote infection. Although other intracellular pathogens are known to manipulate histone methylation, this is the first report demonstrating specific targeting the COMPASS complex by a pathogen. The rigorous experimental design using of state-of-the art bioinformatic analysis, protein modeling, molecular and cellular interaction and functional approaches, culminating with in vivo infection modeling provide convincing, unequivocal evidence that supports the authors claims. This work will be of particular interest to cellular microbiologist working on microbial virulence mechanisms and effectors, specifically nucleomodulins, and cell/cancer biologists that examine COMPASS dysfunction in cancer biology.

Strengths:

(1) The strengths of this study include the rigorous and comprehensive experimental design that involved numerous state-of-the-art approaches to identify potential nucleomodulins, define molecular nucleomodulin-host interactions, cellular nucleomodulin localization, intracellular survival, and inflammatory gene transcriptional responses, and confirmation of the inflammatory and infection phenotype in a small animal model.

(2) The use of bioinformatic, cellular and in vivo modeling that are consistent and support the overall conclusions is a strengthen of the study. In addition, the rigorous experimental design and data analysis including the supplemental data provided, further strengthens the evidence supporting the conclusions.

Weaknesses:

(1) This work could be stronger if the MgdE-COMPASS subunit interactions that negatively impact COMPASS complex function were more well defined. Since the COMPASS complex consists of many enzymes, examining functional impact on each of the components would be interesting.

(2) Examining the impact of WDR5 inhibitors on histone methylation, gene transcription and mycobacterial infection could provide additional rigor and provide useful information related to mechanisms and specific role of WDR5 inhibition on mycobacteria infection.

(3) The interaction between MgdE and COMPASS complex subunit ASH2L is relatively undefined and studies to understand the relationship between WDR5 and ASH2L in COMPASS complex function during infection could provide interesting molecular details that are undefined in this study.

(4) The AlphaFold prediction results for all the nuclear proteins examined could be useful. Since the interaction predictions with COMPASS subunits range from 0.77 for WDR5 and 0.47 for ASH2L, it is not clear how the focus on COMPASS complex over other nuclear proteins was determined.

Comments on revisions:

The authors have addressed the weaknesses that were identified by this reviewer by providing rational explanation and specific references that support the findings and conclusions.

Reviewer #1 (Public review):

Summary:

The authors develop a Python-based analysis framework for cellular organelle segmentation, feature extraction, and analysis for live-cell imaging videos. They demonstrate that their pipeline works for two organelles (mitochondria and lysosomes) and provide a step-by-step overview of the AutoMorphoTrack package.

Strengths:

The authors provide evidence that the package is functional and can provide publication-quality data analysis for mitochondrial and lysosomal segmentation and analysis.

Weaknesses:

(1) I was enthusiastic about the manuscript as a good end-to-end cell/organelle segmentation and quantification pipeline that is open-source, and is indeed useful to the field. However, I'm not certain AutoMorphoTrack fully fulfills this need. It appears to stitch together basic FIJI commands in a Python script that an experienced user can put together within a day. The paper reads as a documentation page, and the figures seem to be individual analysis outputs of a handful of images. Indeed, a recent question on the image.sc forum prompted similar types of analysis and outputs as a simple service to the community, and with seemingly better results and integrated organelle identity tracking (which is necessary in my opinion for live imaging). I believe this is a better fit in the methods section of a broader work. https://forum.image.sc/t/how-to-analysis-organelle-contact-in-fiji-with-time-series-data/116359/5.

(2) The authors do not discuss or compare to any other pipelines that can accomplish similar analyses, such as Imaris, CellProfiler, or integrate options for segmentation, etc., such as CellPose, StarDist.

(3) Although LLM-based chatbot integration seems to have been added for novelty, the authors do not demonstrate in the manuscript, nor provide instructions for making this easy-to-implement, given that it is directed towards users who do not code, presumably.

DOI: 10.1007/978-1-0716-4901-5_16

Resource: None

Curator: @Apiekniewska

SciCrunch record: RRID:ZFIN_ZDB-ALT-140218-1

What is this?

Reviewer #1 (Public review):

Summary:

In this study, the authors mapped afferent inputs to distinct cell populations in the ventral tegmental area (VTA) using dimensionality reduction techniques, revealing markedly different connectivity patterns under normal versus drug-treated conditions. They further showed that drug-induced changes in inputs were negatively correlated with the expression of ion channels and proteins involved in synaptic transmission. Functional validation demonstrated that knockdown of a specific voltage-gated calcium channel led to reduced afferent inputs, highlighting a causal link between gene expression and connectivity.

The authors have clearly addressed the reviewers' previous comments. The study's earlier weaknesses were thoroughly discussed, and additional data were provided to strengthen the findings. Overall, the revised version incorporates more extensive datasets and analyses, resulting in a more robust and compelling study.

Reviewer #1 (Public review):

Summary:

The authors show that corticotropin-releasing factor (CRF) neurons in the central amygdala (CeA) and bed nucleus of the stria terminalis (BNST) monosynaptically target cholinergic interneurons (CINs) in the dorsal striatum of rodents. Functionally, activation of CRFR1 receptors increases CIN firing rate, and this modulation was reduced by pre-exposure to ethanol. This is an interesting finding, with potential significance for alcohol use disorders.

Strengths:

Well-conceived circuit mapping experiments identify a novel pathway by which the CeA and BNST can modulate dorsal striatal function by controlling cholinergic tone. Important insight into how CRF, a neuropeptide that is important in mediating aspects of stress, affective/motivational processes and drug-seeking, modulates dorsal striatal function.

Weaknesses:

(1) Tracing and expression experiments were performed both in mice and rats (often in non-overlapping ways). While these species are similar in many ways, differences do exist. The authors address this important point in their final text.

(2) As the authors point out, CRF likely modulates CIN activity in both direct and indirect ways. As justified, exploration of the network-level modulation of CINs by CRF (and how these processes may interact with direct modulation via CRFR1 on CINs) is left for future studies.

Reviewer #1 (Public review):

Summary:

This study presents an interesting behavioral paradigm and reveals interactive effects of social hierarchy and threat type on defensive behaviors. However, addressing the aforementioned points regarding methodological detail, rigor in behavioral classification, depth of result interpretation, and focus of the discussion is essential to strengthen the reliability and impact of the conclusions in a revised manuscript.

Strengths:

The paper is logically sound, featuring detailed classification and analysis of behaviors, with a focus on behavioral categories and transitions, thereby establishing a relatively robust research framework.

Weaknesses:

Several points require clarification or further revision.

(1) Methods and Terminology Regarding Social Hierarchy:

The study uses the tube test to determine subordinate status, but the methodological description is quite brief. Please provide a more detailed account of the experimental procedure and the criteria used for determination.

The dominance hierarchy is established based on pairs of mice. However, the use of terms like "group cohesion" - typically applied to larger groups - to describe dyadic interactions seems overstated. Please revise the terminology to more accurately reflect the pairwise experimental setup.

(2) Criteria and Validity of Behavioral Classification:

The criteria for classifying mouse behaviors (e.g., passive defense, active defense) are not sufficiently clear. Please explicitly state the operational definitions and distinguishing features for each behavioral category.

How was the meaningfulness and distinctness of these behavioral categories ensured to avoid overlap? For instance, based on Figure 3E, is "active defense" synonymous with "investigative defense," involving movement to the near region followed by return to the far region? This requires clearer delineation.

The current analysis focuses on a few core behaviors, while other recorded behaviors appear less relevant. Please clarify the principles for selecting or categorizing all recorded behaviors.

(3) Interpretation of Key Findings and Mechanistic Insights:

Looming exposure increased the proportion of proactive bouts in the dominant zone but decreased it in the subordinate zone (Figure 4G), with a similar trend during rat exposure. Please provide a potential explanation for this consistent pattern. Does this consistency arise from shared neural mechanisms, or do different behavioral strategies converge to produce similar outputs under both threats?

(4) Support for Claims and Study Limitations:

The manuscript states that this work addresses a gap by showing defensive responses are jointly shaped by threat type and social rank, emphasizing survival-critical behaviors over fear or stress alone. However, it is possible that the behavioral differences stem from varying degrees of danger perception rather than purely strategic choices. This warrants a clear description and a deeper discussion to address this possibility.

The Discussion section proposes numerous brain regions potentially involved in fear and social regulation. As this is a behavioral study, the extensive speculation on specific neural circuitry involvement, without supporting neuroscience data, appears insufficiently grounded and somewhat vague. It is recommended to focus the discussion more on the implications of the behavioral findings themselves or to explicitly frame these neural hypotheses as directions for future research.

Reviewer #1 (Public review):

Summary:

This paper investigates the control signals that drive event model updating during continuous experience. The authors apply predictions from previously published computational models to fMRI data acquired while participants watched naturalistic video stimuli. They first examine the time course of BOLD pattern changes around human-annotated event boundaries, revealing pattern changes preceding the boundary in anterior temporal and then parietal regions, followed by pattern stabilization across many regions. The authors then analyze time courses around boundaries generated by a model that updates event models based on prediction error and another that uses prediction uncertainty. These analyses reveal overlapping but partially distinct dynamics for each boundary type, suggesting that both signals may contribute to event segmentation processes in the brain.

Strengths:

The question addressed by this paper is of high interest to researchers working on event cognition, perception, and memory. There has been considerable debate about what kinds of signals drive event boundaries, and this paper directly engages with that debate by comparing prediction error and prediction uncertainty as candidate control signals.

The authors use computational models that explain significant variance in human boundary judgments, and they report the variance explained clearly in the paper.

The authors' method of using computational models to generate predictions about when event model updating should occur is a valuable mechanistic alternative to methods like HMM or GSBS, which are data-driven.

The paper utilizes an analysis framework that characterizes how multivariate BOLD pattern dissimilarity evolves before and after boundaries. This approach offers an advance over previous work focused on just the boundary or post-boundary points.

Weaknesses:

Boundaries derived from prediction error and uncertainty are correlated for the naturalistic stimuli. This raises some concerns about how well their distinct contributions to brain activity can be separated. While the authors attempt to look at the unique variance, there is a limit to how effectively this can be done without experimentally dissociating prediction error and uncertainty.

The authors reports an average event length of ~20 seconds, and they also look +20 and -20 seconds around each event boundary. Thus, it's unclear how often pre- and post-boundary timepoints are part of adjacent events. This complicates the interpretations of the reported timecourses.

Reviewer #1 (Public review):

Summary:

This manuscript offers a careful and technically impressive dissection of how subpopulations within the subthalamic nucleus support reward‑biased decision‑making. The authors recorded from STN neurons in monkeys performing an asymmetric‑reward version of a visual motion discrimination task and combined single‑unit analyses, regression modeling, and drift‑diffusion framework fitting to reveal functionally distinct clusters of neurons. Each subpopulation demonstrated unique relationships to decision variables - such as the evidence‑accumulation rate, decision bound, and non‑decision processes - as well as to post‑decision evaluative signals like choice accuracy and reward expectation. Together, these findings expand our understanding of the computational diversity of STN activity during complex, multi‑attribute choices.

Strengths:

(1) The use of an asymmetric‑reward paradigm enables a clean separation between perceptual and reward influences, making it possible to identify how STN neurons blend these different sources of information.

(2) The dataset is extensive and well‑controlled, with careful alignment between behavioral and neural analyses.

(3) Relating neuronal cluster activity to drift‑diffusion model parameters provides an interpretable computational link between neural population signals and observed behavior.

(4) The clustering analyses, validated across multiple parameters and distance metrics, reveal robust functional subgroups within STN. The differentiation of clusters with respect to both evidence and reward coding is an important advance over treating the STN as a unitary structure.

(5) By linking neural activity to predicted choice accuracy and reward expectation, the study extends the discussion of the STN beyond decision formation to include outcome monitoring and post‑decision evaluation.

Weaknesses:

(1) The inferred relationships between neural clusters and specific drift‑diffusion parameters (e.g., bound height, scaling factor, non‑decision time) are intriguing but inherently correlational. The authors should clarify that these associations do not necessarily establish distinct computational mechanisms.

(2) While the k‑means approach is well described, it remains somewhat heuristic. Including additional cross‑validation (e.g., cluster reproducibility across monkeys or sessions) would strengthen confidence in the four‑cluster interpretation.

(3) The functional dissociations across clusters are clearly described, but how these subgroups interact within the STN or through downstream basal‑ganglia circuits remains speculative.

(4) A natural next step would be to construct a generative multi‑cluster model of STN activity, in which each cluster is treated as a computational node (e.g., evidence integrator, bound controller, urgency or evaluative signal).

(5) Such a low‑dimensional, coupled model could reproduce the observed diversity of firing patterns and predict how interactions among clusters shape decision variables and behavior.

(6) Population‑level modeling of this kind would move the interpretation beyond correlational mapping and serve as an intermediate framework between single‑unit analysis and in‑vivo perturbation.

(7) Causal inference gap - Without perturbation data, it is difficult to determine whether the identified neural modulations are necessary or sufficient for the observed behavioral effects. A brief discussion of this limitation - and how future causal manipulations could test these cluster functions - would be valuable.

Reviewer #1 (Public review):

In this study, the authors took advantage of a powerful method (iEEG) in a large participant cohort (N=42) to demonstrate specific functional connectivity signatures associated with speech. The results highlight the complementary utility of functional connectivity analysis to the more traditional iEEG approaches of characterizing local neural activity.

Strengths:

This is an interesting study on the important topic of cortical mechanisms of speech perception and production in humans. The authors provide strong evidence for specific functional connectivity signatures of speech-related cortical activity.

Weaknesses:

A potential issue of the work is the interpretation of the five studied experimental conditions as representing distinct cognitive states, where "task conditions" or "behavioral states" would have been more appropriate.

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