Reviewer #2 (Public Review):

Summary:

Here the authors describe a model for tracking time-varying coupling between neurons from multi-electrode spike recordings. Their approach extends a GLM with static coupling between neurons to include dynamic weights, learned by a long-short-term-memory (LSTM) model. Each connection has a corresponding LSTM embedding and is read out by a multi-layer perceptron to predict the time-varying weight.

Strengths:

This is an interesting approach to an open problem in neural data analysis. I think, in general, the method would be interesting to computational neuroscientists.

Weaknesses:

It is somewhat difficult to interpret what the model is doing. I think it would be worthwhile to add some additional results that make it more clear what types of patterns are being described and how.

Major Issues:

Simulation for dynamic connectivity. It certainly seems doable to simulate a recurrent spiking network whose weights change over time, and I think this would be a worthwhile validation for this DyNetCP model. In particular, I think it would be valuable to understand how much the model overfits, and how accurately it can track known changes in coupling strength. If the only goal is "smoothing" time-varying CCGs, there are much easier statistical methods to do this (c.f. McKenzie et al. Neuron, 2021. Ren, Wei, Ghanbari, Stevenson. J Neurosci, 2022), and simulations could be useful to illustrate what the model adds beyond smoothing.

Stimulus vs noise correlations. For studying correlations between neurons in sensory systems that are strongly driven by stimuli, it's common to use shuffling over trials to distinguish between stimulus correlations and "noise" correlations or putative synaptic connections. This would be a valuable comparison for Figure 5 to show if these are dynamic stimulus correlations or noise correlations. I would also suggest just plotting the CCGs calculated with a moving window to better illustrate how (and if) the dynamic weights differ from the data.

Reviewer #1 (Public Review):

Summary:

People with Parkinson's disease often experience a variety of nonmotor symptoms, the biological bases of which remain poorly understood. Johansson et al began to study potential roles of the dorsal raphe nucleus (DRN) degeneration in the pathophysiology of neuropsychiatric symptoms in PD.

Strengths:

Boi et al validated a transgenic reporter mouse line that can reliably label dopaminergic neurons in the DRN. This brain region shows severe neurodegeneration and has been proposed to contribute to the manifestation of neuropsychiatric symptoms in PD. Using this mouse line (and others), Boi and colleagues characterized electrophysiological and morphological phenotypes of dopaminergic and serotoninergic neurons in the raphe nucleus. This study involved very careful topographical registration of recorded neurons to brain slices for post hoc immunohistochemical validation of cell identity, making it an elegant and thorough piece of work.

In relevance to PD pathophysiology, the authors evaluated the physiological and morphological changes of DRN serotoninergic and dopaminergic neurons after a partial loss of nigrostriatal dopamine neurons, which serves as a mouse model of early parkinsonian pathology. Moreover, the authors identified a series of physiological and morphological changes of subtypes of DRN neurons that depend on nigral dopaminergic neurodegeneration, LC noradrenergic neurodegeneration, or both. Indeed this works highlights the importance of LC noradrenergic degeneration in PD pathophysiology.

Overall, this is a well-designed study with high significance to the Parkinson's research field.

Reviewer #2 (Public Review):

In this paper, Boi et al. thoroughly classified the electrophysiological and morphological characteristics of serotonergic and dopaminergic neurons in the DRN and examined the alterations of these neurons in the 6-OHDA-induced mouse PD model. Using whole-cell patch clamp recording, they found that 5-HT and dopamine (DA) neurons in the DRN are electrophysiologically well-distinguished from each other. In addition, they characterized distinct morphological features of 5-HT and DA neurons in the DRN. Notably, these specific features of 5-HT and DA neurons in the DRN exhibited different changes in the 6-OHDA-induced PD model. Then the authors utilized desipramine (DMI) to separate the effects of nigrostriatal DA depletion and noradrenalin (NA) depletion which are induced by 6-OHDA. Interestingly, protection from NA depletion by DMI pretreatment reversed the changes in 5-HT neurons, while having a minor impact on the changes in DA neurons in the DRN. These data indicate that the role of NA lesion in the altered properties of DRN 5-HT neurons by 6-OHDA is more critical than the one of DA lesion.

Overall, this study provides foundational data on the 5-HT and DA neurons in the DRN and their potential involvement in PD symptoms. Given the defects of the DRN in PD, this paper may offer insights into the cellular mechanisms that may underlie non-motor symptoms associated with PD. Despite the importance of the primary claim proposed by the authors, however, the interpretation of the authors on some DMI experiments is not explained well.

Reviewer #3 (Public Review):

Summary:

Using ex vivo electrophysiology and morphological analysis, Boi et al. investigate the electrophysiological and morphological properties of serotonergic and dopaminergic subpopulations in the dorsal raphe nucleus (DRN). They performed labor-intensive and rigorous electrophysiology with posthoc immunohistochemistry and neuronal reconstruction to delineate the two major cell classes in the DRN: DRN-DA and DRN-5HT, named according to their primary neurotransmitter machinery. They find that the dopaminergic (DRN-DA) and serotonergic (DRN-5HT) neurons are electrophysiologically and morphologically distinct, and are altered following striatal injection of the toxin 6-OHDA. However, these alterations were largely prevented in DRN-5HT neurons by pre-treatment with desipramine. These findings suggest an important interplay between catecholaminergic systems in healthy and parkinsonian conditions, as well as a relationship between neuronal structure and function.

Strengths:

Large, well-validated dataset that will be a resource for others.<br /> Complementary electrophysiological and anatomical characterizations.<br /> Conclusions are justified by the data.<br /> Relevant for basic scientists interested in DRN cell types and physiology<br /> Relevant for those interested in serotonin and/or DRN neurons in Parkinson's Disease

Weaknesses:

Given the scope of the author's questions and hypotheses, I did not identify any major weaknesses.

Reviewer #1 (Public Review):

Summary:

This is a study on the role of the retrosplenial cortex (RSC) and the hippocampus in working memory. Working memory is a critical cognitive function that allows temporary retention of information for task execution. The RSC, which is functionally and anatomically connected to both primary sensory (especially visual) and higher cognitive areas, plays a key role in integrating spatial-temporal context and in goal-directed behaviors. However, the specific contributions of the RSC and the hippocampus in working memory-guided behaviors are not fully understood due to a lack of studies that experimentally disrupt the connection between these two regions during such behaviors.

In this study, researchers employed eArch3.0 to silence hippocampal axon terminals in the RSC, aiming to explore the roles of these brain regions in working memory. Experiments were conducted where animals with silenced hippocampal axon terminals in the RSC performed a delayed non-match to place (DNMP) task. The results indicated that this manipulation impaired memory retrieval, leading to decreased performance and quicker decision-making in the animals. Notably, the authors observed that the effects of this impairment persisted beyond the light-activation period of the opsin, affecting up to three subsequent trials. They suggest that disrupting the hippocampal-RSC connection has a significant and lasting impact on working memory performance.

Strengths:

They conducted a study exploring the impact of direct hippocampal inputs into the RSC, a region involved in encoding spatial-temporal context and transferring contextual information, on spatial working memory tasks. Utilizing eArch3.0 expressed in hippocampal neurons via the viral vector AAV5-hSyn1-eArch3.0, they aimed to bilaterally silence hippocampal terminals located at the RSC in rats pre-trained in a DNMP task. They discovered that silencing hippocampal terminals in the RSC significantly decreased working memory performance in eArch+ animals, especially during task interleaving sessions (TI) that alternated between trials with and without light delivery. This effect persisted even in non-illuminated trials, indicating a lasting impact beyond the periods of direct manipulation. Additionally, they observed a decreased likelihood of correct responses following TI trials and an increased error rate in eArch+ animals, even after incorrect responses, suggesting an impairment in error-corrective behavior. This contrasted with baseline sessions where no light was delivered, and both eArch+ and control animals showed low error rates.

Weaknesses:

While I agree with the authors that the role of hippocampal inputs to the RSC in spatial working memory is understudied and merits further investigation, I find that the optogenetic experiment, a core part of this manuscript that includes viral injections, could be improved. The effects were rather subtle, rendering some of the results barely significant and possibly too weak to support major conclusions. Additionally, no mechanistic investigation was conducted beyond referencing previous reports to interpret the core behavioral phenotypes.

Reviewer #2 (Public Review):

The authors examine the impact of optogenetic inhibition of hippocampal axon terminals in the retrosplenial cortex (RSP) during the performance of a working memory T-maze task. Performance on a delayed non-match-to-place task was impaired by such inhibition. The authors also report that inhibition is associated with faster decision-making and that the effects of inhibition can be observed over several subsequent trials. The work seems reasonably well done and the role of hippocampal projections to retrosplenial cortex in memory and decision-making is very relevant to multiple fields. However, the work should be expanded in several ways before one can make firm conclusions on the role of this projection in memory and behavior.

(1) The work is very singular in its message and the experimentation. Further, the impact of the inhibition on behavior is very moderate. In this sense, the results do not support the conclusion that the hippocampal projection to retrosplenial cortex is key to working memory in a navigational setting.

(2) There are no experiments examining other types of behavior or working memory. Given that the animals used in the studies could be put through a large number of different tasks, this is surprising. There is no control navigational task. There is no working memory test that is non-spatial. Such results should be presented in order to put the main finding in context.

(3) The actual impact of the inhibition on activity in RSP is not provided. While this may not be strictly necessary, it is relevant that the hippocampal projection to RSP includes, and is perhaps dominated by inhibitory inputs. I wonder why the authors chose to manipulate hippocampal inputs to RSP when the subiculum stands as a much stronger source of afferents to RSP and has been shown to exhibit spatial and directional tuning of activity. The points here are that we cannot be sure what the manipulation is really accomplishing in terms of inhibiting RSP activity (perhaps this explains the moderate impact on behavior) and that the effect of inhibiting hippocampal inputs is not an effective means by which to study how RSP is responsive to inputs that reflect environmental locations.

(4) The impact of inhibition on trials subsequent to the trial during which optical stimulation was actually supplied seems trivial. The authors themselves point to evidence that activation of the hyperpolarizing proton pump is rather long-lasting in its action. Further, each sample-test trial pairing is independent of the prior or subsequent trials. This finding is presented as a major finding of the work, but would normally be relegated to supplemental data as an expected outcome given the dynamics of the pump when activated.

(5) In the middle of the first paragraph of the discussion, the authors make reference to work showing RSP responses to "contextual information in egocentric and allocentric reference frames". The citations here are clearly deficient. How is the Nitzan 2020 paper at all relevant here?

(6) The manuscript is deficient in referencing and discussing data from the Smith laboratory that is similar. The discussion reads mainly like a repeat of the results section.

Reviewer #1 (Public Review):

Summary:

The manuscript entitled "Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity" by Panda, S et al. reports an extensive biochemical analysis of the result from a Tn screen that identified alr1 as being required for acetic acid tolerance. In the end, they demonstrate that reduced D-Ala pools in the ∆alr1 mutant lead to a drastic reduction in D-Ala-D-Ala dipeptide. They show that this is due to the ability of organic acid anions to limit the D-Ala-D-Ala ligase enzyme Ddl. They demonstrate that:

(1) Acetate exposure in the ∆alr1 results in reduced D-Ala-D-Ala dipeptide, but not the monomers.

(2) Acetate can bind to purified Ddl in vitro.

(3) This binding results in reduced enzyme activity.

(4) Other organic acid anions such as lactate, proprionate, and itaconitate can also inhibit Ddl.

The experiments are clearly described and logically laid out. I have only a few minor comments to add.

Strengths:

The most significant strength is the exceptional experimental data that supports the authors' hypotheses.

Weaknesses:

Only minor weaknesses were identified by this reviewer.

(1) Which allele is alr1, the one upstream of MazEF or the one in the Lysine biosynthetic operon?

(2) Figure 3B. Where does the C3N2 species come from in the WT and why is it absent in the mutants? It is about 25% of the total dipeptide pool.

(3) Figure 3D could perhaps be omitted. I understand that the authors attained statistical significance in the fitness defect, but biologically this difference is very minor. One would have to look at the isotopomer distribution in the Dat overexpressing strain to make sure that increased flux actually occurred since there are other means of affecting activity (e.g. allosteric modulators).

(4) In Figure 4A, why is the complete subunit UDP-NAM-AEKAA increasing in each strain upon acetate challenge if there was such a stark reduction in D-Ala-D-Ala, particularly in the ∆alr1 mutant? For that matter, why are the levels of UDP-NAM-AEKAA in the ∆alr1 mutant identical to that of WT with/out acetate?

(5) Figure 4B. Is there no significant difference between ddl and murF transcripts between WT and ∆alr1 under acetate stress? This comparison was not labeled if the tests were done.

(6) Although tricky, it is possible to measure intracellular acetate. It might be of interest to know where in the Ddl inhibition curve the cells actually are.

Reviewer #2 (Public Review):

The authors aimed at elucidating the development of high altitude polycythemia which affects mice and men staying in a hypoxic atmosphere at high altitude (hypobaric hypoxia; HH). HH causes increased erythropoietin production which stimulates the production of red blood cells. The authors hypothesize that increased production is only partially responsible for exaggerated red blood cell production, i.e. polycythemia, but that decreased erythrophagocytosis in the spleen contributes to high red blood cells counts.

The main strength of the study is the use of a mouse model exposed to HH in a hypobaric chamber. However, not all of the reported results are convincing due to some smaller effects which one may doubt to result in the overall increase in red blood cells as claimed by the authors. Moreover, direct proof for reduced erythrophagocytosis is compromised due to a strong spontaneous loss of labelled red blood cells, although effects of labelled E. coli phagocytosis are shown.

Comments on latest version:

The authors have partly addressed my comments.

(1) The response to my question regarding unchanged MCH is a kind of "hand waiving" - maybe it would require substantially more extensive work to clarify this issue

(2) The moderate if not marginal difference in normal vs splenectomy argues against a significant role of the spleen - even if the difference was slightly larger in HH

(3) There is still overinterpretation of data. My Q was: Is the reduced phagocytic capacity in Fig 4B significant? Response: "This is indicative of a diminished phagocytic capacity, particularly when contrasted<br /> with NN conditions." I guess that is a "no"

(4) I assume my question with respect to bi- or trivalent iron chelators was misunderstood.

In general, as indicated above, it is an interesting hypothesis which is corroborated by data in several instances. Maybe the scientific community should decide whether it is all in all conclusive.

Reviewer #3 (Public Review):

The manuscript by Yang et al. investigated in mice how hypobaric hypoxia can modify the RBC clearance function of the spleen, a concept that is of interest. Via interpretation of their data, the authors proposed a model that hypoxia causes an increase in cellular iron levels, possibly in RPMs, leading to ferroptosis, and downregulates their erythrophagocytic capacity.

Comments on revised version:

The manuscript has now improved with all the new data, supporting the model proposed by the authors. However, it remains not very easy to follow for the conclusions and experimental details. Some of the most important remaining comments are listed below:

(1) Lines 401-406 - The conclusions in this new fragment sound a bit overstated - the authors do not directly measure erytrophagocytosis capacity, only the total RBC parameters in the circulation. The increase is also very mild biologically between sham and splenectomized mice in HH conditions.

(2) scRNA seq data are still presented in a way that is very difficult to understand. The readers could not see from the graphics that macrophages are depleted. The clusters are not labelled - some clusters in the bin 'macrophahes+DC' seem actually to be more represented in Fig. 3E; Fig. 3F does not correspond to Fig. 3D. It would be maybe more informative to present like in Figure D side by side NN versus HH? The authors could consider moving the data from supplements that relate to RPMs to the main figure and making it consistent for the Clusters - eg, the authors show data for Cluster 0 in the supplement, and the same Cluster is not marked as macrophages in the main figure. This is quite difficult to follow.

(3) Figure 3G has likely mislabeled axis for F4/80 and CD11b - such mistakes should be avoided in a second revised version of the manuscript, and this data is now redundant with the data shown as new Figure 5A.

(4) The data from new Figure 4 should be better mentioned in the main body of the manuscript - all panels are mentioned twice in the text, first speaking about the decline of labelled RBCs and second referring to phagocytic capacity, whereas this figure only illustrates the decline of labelled RBCs, not directly phagocytic capacity of RPMs. What is lacking, as opposed to typical RBC life span assay, is the time '0' ('starting point') - this is particularly important as we can observe a big drop in labelled RBCs for eg 7 days between NN and HH group, actually implying increased removal of labelled RBCs within the first days of hypoxia exposure. What should be better labelled in this figure is that the proportion of RBCs are labelled RBCs not all RBCs (Y axis in individual panels). Overall, the new Figure 4 brings new data to the study, but how it is presented and discussed is not at the 'state-of-the-art' level (eg, missing the time '0') and is not very straightforward to the reader.

(5) In Figure 7, the experiments with Tuftsin are not very easy to follow, especially for the major conclusions. In panels A and B, the focus is the drug itself under NN conditions, with RBC removal as a readout. Then, in the next panels, the authors introduce HH, and then look at the F4/80 and iron staining. What was exactly the major point the authors wanted to make here?

(6) The data from Figure 8 are informative but do not address the individual cell types - eg, a drop in HO1 or FT may be due to the depletion of RPMs. An increase of TFR1 could be due to the retention of RBCs, the same as maybe labile iron. The data from PBMC are only very loosely linked to these phenotypes observed in the total spleen, and the reason for the regulation of the same proteins in PBMC might be different. It goes back to the data in Figure 3A-C, where also total splenocytes are investigated for their viability.

(7) Can the authors provide the data for the purity (eg cell surface markers) of their primary splenic macrophage cultures? Only ensuring that these are macrophages or addressing the readouts from Figure 8 in RPMs could link ferroptosis to RPMs under HH conditions.

(8) All the data are not presented as individual data points which is not widely applied in papers.

(9) No gating strategies are nicely illustrated or described.

Reviewer #1 (Public Review):

A descriptive manuscript investigating the ability of a peptide, implicated in development, to induce signalling responses indicative of immunity. The work clearly documents the ability of the synthetic peptide to induce these responses, and open future work to link this back to physiology.

Comments on revised version:

Congratulations to the authors for the improvements to the manuscript.

I still have reservations, as raised by other reviewers, about whether the outputs observed can definitively be classified as immune/defence outputs without assaying an impact upon microbial growth. Indeed, this is challenging to address as many of the outputs are shared by multiple pathways. This is especially the case here as the peptide could have different effects in different tissues or cells with different expression levels of the receptors (e.g. hypothetically - no expression = no effect; weak expression - cell wall loosening and susceptibility; high expression - strong response and 'defence' response). I do however appreciate that the authors have toned down some of the conclusions regarding the defence response and also they included further reference to outputs also being from developmental pathways.

Reviewer #3 (Public Review):

Previously, it has been shown the essential role of IDA peptide and HAESA receptor families in driving various cell separation processes such as abscission of flowers as a natural developmental process, of leaves as a defense mechanism when plants are under pathogenic attack or at the lateral root emergence and root tip cell sloughing. In this work, Olsson et al. show for the first time the possible role of IDA peptide in triggering plant innate immunity after the cell separation process occurred. Such an event has been previously proposed to take place in order to seal open remaining tissue after cell separation to avoid creating an entry point for opportunistic pathogens. The elegant experiments in this work demonstrate that IDA peptide is triggering the defense-associated marker genes together with immune specific responses including release of ROS and intracellular CA2+. Thus, the work highlights an intriguing direct link between endogenous cell wall remodeling and plant immunity. Moreover, the upregulation of IDA in response to abiotic and especially biotic stimuli are providing a valuable indication for potential involvement of HAE/IDA signalling in other processes than plant development.

Comments on revised version:

We thank the authors for addressing our previous comments. Overall, we are satisfied with the improvements and appreciate the hard work that has gone into this manuscript. We wish you all the best on the further publication pathway.

Reviewer #1 (Public Review):

This study presents valuable data on effector proteins (=virulence factors) used by the bacterial pathogen Legionella pneumophila that target host vesicle trafficking GTPases during infection. The evidence supporting the claims of the authors is robust, and the data suggest a sophisticated interplay between multiple effectors with the goal of temporarily exploiting host cell Rab10 during infection.

The authors have done a nice job addressing my earlier concerns. I have no further criticism about the revised paper.

Reviewer #2 (Public Review):

This manuscript explores the interplay between Legionella Dot/Icm effectors that modulate ubiquitination of the host GTPase Rab10. Rab10 undergoes phosphoribosyl-ubiquitination (PR-Ub) by the SidE family of effectors which is required for its recruitment to the Legionella containing vacuole (LCV). Through a series of elegant experiments using effector gene knockouts, co-transfection studies and careful biochemistry, Kubori et al further demonstrate that:

(1) The SidC family member SdcB contributes to the polyubiquitination (poly-Ub) of Rab10 and its retention at the LCV membrane.

(2) The transglutaminase effector, MavC acts as an inhibitor of SdcB by crosslinking ubiquitin at Gln41 to lysine residues in SdcB.

Reviewer #1 (Public Review):

Summary:

This study brings new information about the function of serotonin-gated ion channels 5-HT3AR, by describing the conformational changes undergoing during ligands binding. These results can be potentially extrapolated to other members of the Cys-loop ligand-gated ion channels. By combining fluorescence microscopy with electrophysiological recordings, the authors investigate structural changes inside and outside the orthosteric site elicited by agonists, partial agonists, and antagonists. The results are convincing and correlate well with the observations from cryo-EM structures. The work will be of important significance and broad interest to scientists working on channel biophysics but also drug development targeting ligand-gated ion channels.

Strengths:

The authors present an elegant and well-designed study to investigate the conformational changes on 5-HT3AR where they combine electrophysiological and fluorometry recordings. They determined four positions suitable to act as sensors for the conformational changes of the receptor: two inside and two outside the agonist binding site. They make a strong point showing how antagonists produce conformational changes inside the orthosteric site similarly as agonists do but they failed to spread to the lower part of the ECD, in agreement with previous studies and Cryo-EM structures. They also show how some loss-of-function mutant receptors elicit conformational changes (changes in fluorescence) after partial agonist binding but failed to produce measurable ionic currents, pointing to intermediate states that are stabilized in these conditions. The four fluorescence sensors developed in this study may be good tools for further studies on characterizing drugs targeting the 5-HT3R. The major conclusions of the manuscript seem well justified.

Weaknesses:

Weaknesses have been very well addressed during the review process.

Reviewer #2 (Public Review):

Summary:

This study focuses on the 5-HT3 serotonin receptor, a pentameric ligand-gated ion channel important in chemical neurotransmission. There are many cryo-EM structures of this receptor with diverse ligands bound, however assignment of functional states to the structures remains incomplete. The team applies voltage-clamp fluorometry to measure, at once, both changes in ion channel activity, and changes in fluorescence. Four cysteine mutants were selected for fluorophore labeling, two near the neurotransmitter site, one in the ECD vestibule, and one at the ECD-TMD junction. Agonists, partial agonists, and antagonists were all found to yield similar changes in fluorescence, a proxy for conformational change, near the neurotransmitter site. The strength of the agonist correlated to a degree with propagation of this fluorescence change beyond the local site of neurotransmitter binding. Antagonists failed to elicit a change in fluorescence in the vestibular of the ECD-TMD junction sites. The VCF results further turned up evidence supporting intermediate (likely pre-active) states.

Strengths:

The experiments appear rigorous, the problem the team tackles is timely and important, the writing and the figures are for the most part very clear. We sorely need approaches orthogonal to structural biology to annotate conformational states and observe conformational transitions in real membranes- this approach, and this study, get right to the heart of what is missing.

Weaknesses:

The weaknesses in the study itself are overall minor, I only suggest improvements geared toward clarity. What we are still missing is application of an approach like this to annotate the conformation of the part of the receptor buried in the membrane; there is an important debate about which structure represents which state, and that is not addressed in the current study.

Reviewer #3 (Public Review):

Summary:

The authors have examined the 5-HT3 receptor using voltage clamp fluorometry, which enables them to detect structural changes at the same time as the state of receptor activation. These are ensemble measurements, but they enable an impressive scheme of the action of different agonists and antagonists to be built up. The growing array of structural snapshots of 5-HT3 receptors is used to good effect to understand the results.

Strengths:

The combination of rigorously tested fluorescence reporters with oocyte electrophysiology across a large panel of ligands is a solid development for this receptor type.

Weaknesses:

In their revision, the authors corrected all the weaknesses of the original submission.

Joint Public Review:

Summary:

This important manuscript investigates a subpopulation of glutamatergic neurons in the suprammamillary nucleus that projects to the pre-optic hypothalamus area (SuM-VGLUT2+::POA). First, they define the neural circuitry of these neurons, which contact many stress/threat-associated brain regions. Then they employ fibre photometry to measure the activity of these neurons during various threatening tasks and find the responses correlate well with threat stimuli. Finally, they stimulate these neurons and find multiple lines of evidence that mice find this aversive and will act to avoid receiving this stimulation. In sum, they provide solid evidence that this neuronal population represents a new node in stress response circuitry that allows the animal to produce flexible behaviours in response to stress, which will be of interest to neuroscientists across several sub-fields.

Strengths:

Overall this is a solid manuscript tackling an important question. Coping with stress by an animal in danger is essential for survival. This manuscript identifies a novel population of neurons in the murine supramamillary nucleus (SuM) projecting to the pre-optic hypothalamus area among other regions that is involved in this important process. The evidence to support the conclusions is solid.

Specific strengths:

• The topic is novel.

• The manuscript follows a logical structure and neatly moves through the central story. Several potential alternate interpretations are well-controlled for.

• The manuscript employs an array of different tasks to provide converging evidence for their conclusions.

• The authors provide excellent evidence of the specificity of the function of this neuronal population, both from anatomical studies and from behavioural studies (e.g. demonstrating that activity of gabaergic neurons in the same region does not correlate with behaviours in the same way).

• The study is well-powered (sample sizes are good) and the effects are convincing.

Weaknesses:

* Not all of the reviewer comments were addressed in the manuscript itself, although this was acknowledged in the author's responses to reviewers. One key example is as follows:

* The authors did not entirely address comments related to rigor but they at least acknowledged it. For example, in multiple places they argue that WT, purchased mice are probably not different in baseline behavior compared to Vgltu2-IRES-Cre because it is unlikely that adding the IRES-Cre will change behavior. However, they do not acknowledge that transgenic lines are not from the exact same genetic background and generation number, and there is ample evidence in the literature that transgenic mice on a B6J background can differ in basal phenotypes from one another and B6J. In one place they show some basal behavior, at least in heat map form though not quantified. Had the authors decided to apply this more pervasively, it would have made the story even more compelling in terms of a stress/threat-induced phenotype.

Comments on revised version from the Reviewing Editor:

The authors have done a thorough job of answering the reviewer queries, and a good job of explaining why they have not answered a particular point. Indeed, there is so much additional information in response to the reviewers that I hope readers of the manuscript will read the reviews and responses as well! I think they add a lot.

Reviewer #3 (Public Review):

Summary:

Chang et al. investigated the mechanisms governing collagen fibrillogenesis, firstly demonstrating that cells within tail tendons are able to uptake exogenous collagen and use this to synthesize new collagen-1 fibrils. Using an endocytic inhibitor, the authors next showed that endocytosis was required for collagen fibrillogenesis and that this process occurs in a circadian rhythmic manner. Using knockdown and overexpression assays, it was then demonstrated that collagen fibril formation is controlled by vacuolar protein sorting 33b (VPS33b), and this VPS33b-dependent fibrillogenesis is mediated via Integrin alpha-11 (ITGA11). Finally, the authors demonstrated increased expression of VPS33b and ITGA11 at the gene level in fibroblasts from patients with idiopathic pulmonary fibrosis (IPF), and greater expression of these proteins in both lung samples from IPF patients and in chronic skin wounds, indicating that endocytic recycling is disrupted in fibrotic diseases.

Strengths:

The authors have performed a comprehensive functional analysis of the regulators of endocytic recycling of collagen, providing compelling evidence that VPS33b and ITGA11 are crucial regulators of this process.

Weaknesses:

Throughout the study, several different cell types have been used (immortalised tail tendon fibroblasts, NIHT3T cells, and HEK293T cells). In general, it is not clear which cells have been used for a particular experiment, and the rationale for using these different cell types is not explained. In addition, some experimental details are missing from the methods.

There is also a lack of functional studies in patient-derived IPF fibroblasts which means the link between endocytic recycling of collagen and the role of VPS33b and ITGA11 cannot be fully established.

Reviewer #2 (Public Review):

Summary:

In this manuscript, the authors describe a mechanism, by which fluorescently-labelled Collagen type I is taken up by cells via endocytosis and then incorporated into newly synthesized fibers via an ITGA11 and VPS33B-dependent mechanism. The authors claim the existence of this collagen recycling mechanism and link it to fibrotic diseases such as IPF and chronic wounds.

Strengths:

The manuscript is well-written, and experimentally contains a broad variation of assays to support their conclusions. Also, the authors added data of IPF patient-derived fibroblasts, patient-derived lung samples, and patient-derived samples of chronic wounds that highlight a potential in vivo disease correlation of their findings.

The authors were also analyzing the membrane topology of VPS33B and could unravel a likely 'hairpin' like conformation in the ER membrane.

Weaknesses:

Experimental evidence is missing that supports the non-degradative endocytosis of the labeled collagen.

The authors show and mention in the text that the endocytosis inhibitor Dyngo®4a shows an effect on collagen secretion. It is not clear to me how specific this readout is if the inhibitor affects more than endocytosis. This issue was unfortunately not further discussed. The authors use commercial rat tail collagen, it is unclear to me which state the collagen is in when it's endocytosed. Is it fully assembled as collagen fiber or are those single heterotrimers or homotrimers?

The Cy-labeled collagen is clearly incorporated into new fibers, but I'm not sure whether the collagen is needed to be endocytosed to be incorporated into the fibers or if that is happening in the extracellular space mediated by the cells.

In general for the collagen blots, due to the lack of molecular weight markers, what chain/form of collagen type I are you showing here?

Besides the VPS33B siRNA transfected cells the authors also use CRISPR/Cas9-generated KO. The KO cells do not seem to be a clean system, as there is still a lot of mRNA produced. Were the clones sequenced to verify the KO on a genomic level? For the siRNA transfection, a control blot for efficiency would be great to estimate the effect size. To me it is not clear where the endocytosed collagen and VPS33B eventually meet in the cells and whether they interact. Or is ITGA11 required to mediate this process, in case VPS33B is not reaching the lumen?

The authors show an upregulation of ITGA11 and VPS33B in IPF patients-derived fibroblasts, which can be correlated to an increased level of ColI uptake, however, it is not clear whether this increased uptake in those cells is due to the elevated levels of VPS33B and/or ITGA11.

Reviewer #1 (Public Review):

Summary:

The authors describe that the endocytic pathway is crucial for ColI fibrillogenesis. ColI is endocytosed by fibroblasts, prior to exocytosis and formation of fibrils, which can include a mixture of endogenous/nascent ColI chains and exogenous ColI. ColI uptake and fibrillogenesis are regulated by circadian rhythm as described by the authors in 2020, thanks to the dependence of this pathway on circadian-clock-regulated protein VPS33B. Cells are capable of forming fibrils with recently endocytosed ColI when nascent chains are not available. Previously identified VPS33B is demonstrated not to have a role in endocytosis of ColI, but to play a role in fibril formation, which the authors demonstrate by showing the loss of fibril formation in VPS33B KO, and an excess of insoluble fibrils - along-side a decrease in soluble ColI secretion - in VPS33B overexpression conditions. A VPS33B binding protein VIPAS39 is also shown to be required for fibrillogenesis and to colocalise with ColI. The authors thus conclude that ColI is internalised into endosomal structures within the cell, and that ColI, VPS33B, and VIPA39 are co-trafficked to the site of fibrillogenesis, where along with ITGA11, which by mass spectrometric analysis is shown to be regulated by VPS33B levels, ColI fibrils are formed. Interestingly, in involved human skin sections from idiopathic pulmonary fibrosis (IPF) patients, ITGA11 and VPS33B expression is increased compared to healthy tissue, while in patient-derived fibroblasts, uptake of fluorescently-labelled ColI is also increased. This suggests that there may be a significant contribution of endocytosis-dependent fibrillogenesis in the formation of fibrotic and chronic wound-healing diseases in humans.

Strengths:

This is an interesting paper that contributes an exciting novel understanding of the formation of fibrotic disease, which despite its high occurrence, still has no robust therapeutic options. The precise mechanisms of fibrillogenesis are also not well understood, so a study devoted to this complex and key mechanism is well appreciated. The dependence of fibrillogenesis on VPS33B and VIPA39 is convincing and robust, while the distinction between soluble ColI secretion and insoluble fibrillar ColI is interesting and informative.

Weaknesses:

There are a number of limitations to this study in its current state. Inhibition of ColI uptake is performed using Dyngo4a, which although proposed as an inhibitor of Clathrin-dependent endocytosis is known to be quite un-specific. This may not be a problem however, as the endocytic mechanism for ColI also does not seem to be well defined in the literature, in fact, the principle mechanism described in the papers referred to by the authors is that of phagocytosis. It would be interesting to explore this important part of the mechanism further, especially in relation to the intracellular destination of ColI. The circadian regulation does not appear as robust as the authors' last paper, however, there could be a larger lag between endocytosis of ColI and realisation of fibrils. The authors state that the endocytic pathway is the mechanism of trafficking and that they show ColI, VPS33B, and VIPA39 are co-trafficked. However, the only link that is put forward to the endosomes is rather tenuously through VPS33B/VIPA39. There is no direct demonstration of ColI localisation to endosomes (ie. immunofluorescence), and this is overstated throughout the text. Demonstrating the intracellular trafficking and localisation of ColI, and its actual relationship to VPS33B and VIPA39, followed by ITGA11, would broaden the relevance of this paper significantly to incorporate the field of protein trafficking. Finally, the "self-formation" of ColI fibrils is discussed in relation to the literature and the concentration of fluorescently-tagged ColI, however as the key message of the paper is the fibrillogenesis from exocytosed colI, I do not feel like it is demonstrated to leave no doubt. Specific inhibition of intracellular trafficking steps, or following the progressive formation of ColI fibrils over time by immunofluorescence would demonstrate without any further doubt that ColI must be endocytosed first, to form fibrils as a secondary step, rather than externally-added ColI being incorporated directly to fibrils, independent of cellular uptake.

Reviewer #1 (Public Review):

Summary:

The authors quantitatively describe the complex binding equilibria of BRAF and its inhibitors resulting in some cases in the paradoxical activation of BRAF dimer when bound to ATP competitive inhibitors. The authors use a biophysical tour de force involving FRET binding assays, NMR, kinase activity assays, and DEER spectroscopy.

Strengths:

The strengths of the study are the beautifully conducted assays that allow for a thorough characterization of the allostery in this complex system. Additionally, the use of F-NMR and DEER spectroscopy provides important insights into the details of the process.

The resulting model for binding of inhibitors and dimerization (Figure 4) is very helpful.

Weaknesses:

This is a complex system and its communication is inherently challenging. It might be of interest to the broader readership to understand the implications of the model for drug development and therapy.

Reviewer #2 (Public Review):

Summary:

This manuscript uses FRET, 19F-NMR, and DEER/EPR solution measurements to examine the allosteric effects of a panel of BRAF inhibitors (BRAFi). These include first-generation aC-out BRAFi, and more recent Type I and Type II aC-in inhibitors. Intermolecular FRET measurements quantify Kd for BRAF dimerization and inhibitor binding to the first and second subunits. Distinct patterns are found between aC-in BRAFi, where Type I BRAFi binds equally well to the first and second subunits within dimeric BRAF. In contrast, Type II BRAFi shows stronger affinity for the first subunit and weaker affinity for the second subunit, an effect named "allosteric asymmetry". Allosteric asymmetry has the potential for Type II inhibitors to promote dimerization while favoring occupancy of only one subunit (BBD form), leading to the enrichment of an active dimer.

Measurements of in vitro BRAF kinase activity correlate amazingly well with the calculated amounts of the half-site-inhibited BBD forms with Type II inhibitors. This suggests that the allosteric asymmetry mechanism explains paradoxical activation by this class of inhibitors. DEER/EPR measurements further examine the positioning of helix aC. They show systematic outward movement of aC with Type II inhibitors, relative to the aC-in state with Type I inhibitors, and further show that helix aC adopts multiple states and is therefore dynamic in apo BRAF. This makes a strong case that negative cooperativity between sites in the BRAF dimer can account for paradoxical kinase activation by Type II inhibitors by creating a half-site-occupied homodimer, BBD. In contrast, Type I inhibitors and aC-out inhibitors do not fit this model, and are therefore proposed to be explained by previously proposed models involving negative allostery between subunits in BRAF-CRAF heterodimers, RAS priming, and transactivation.

Strengths:

This study integrates orthogonal spectroscopic and kinetic strategies to characterize BRAF dynamics and determine how it impacts inhibitor allostery. The unique combination of approaches presented in this study represents a road map for future work in the important area of protein kinase dynamics. The work represents a worthy contribution not only to the field of BRAF regulation but to protein kinases in general.

Weaknesses:

Some questions remain regarding the proposed model for Type II inhibitors and its comparison to Type I and aC-out inhibitors that would be useful to clarify. Specifically, it would be helpful to address whether the activation of BRAF by Type II inhibitors, while strongly correlated with BBD model predictions in vitro, also depends on CRAF via BRAF-CRAF in cells and therefore overlaps with the mechanisms of paradoxical activation by Type I and aC-out inhibitors.

Reviewer #1 (Public Review):

Summary:

Szathmary and colleagues explore the parabolic growth regime of replicator evolution. Parabolic growth occurs when nucleic acid strain separation is the rate limiting step of the replication process which would have been the case for non-enzymatic replication of short oligonucleotide that could precede the emergence of ribozyme polymerases and helicases. The key result is that parabolic replication is conducive to the maintenance of genetic diversity, that is, coexistence of numerous master sequences (the Gause principle does not apply). Another important finding is that there is no error threshold for parabolic replication except for the extreme case of zero fidelity.

Strengths:

I find both the analytic and the numerical results to be quite convincing and well described. The results of this work are potentially important because they reveal aspects of a realistic evolutionary scenario for the origin of replicators.

Weaknesses:

There are no obvious technical weaknesses. It can be argued that the results represent an incremental advance because many aspects of parabolic replication have been explored previously (the relevant publications are properly cited). Obviously, the work is purely theoretical, experimental study of parabolic replication is due. In the opinion of this reviewer, though, these are understandable limitations that do not actually detract from the value of this work.

Reviewer #2 (Public Review):

Summary:

A dominant hypothesis concerning the origin of life is that, before the appearance of the first enzymes, RNA replicated non-enzymatically by templating. However, this replication was probably not very efficient, due to the propensity of single strands to bind to each other, thus inhibiting template replication. This phenomenon, known as product inhibition, has been shown to lead to parabolic growth instead of exponential growth. Previous works have shown that this situation limits competition between alternative replicators and therefore promotes RNA population diversity. The present work examines this scenario in an agent-based model of RNA replication, taking into account finite population size, mutations and differences in GC content. The main results are (1) confirmation that parabolic growth promotes diversity, but that when the population size is small enough, sequences least efficient at replicating may nevertheless go extinct; (2) the observation that fitness is not only controlled by the replicability of sequences, but also by their GC content ; (3) the observation that parabolic growth attenuates the impact of mutations and, in particular, that the error threshold to which exponentially growing sequences are subject can be exceeded, enabling sequence identity to be maintained at higher mutation rates.

Strengths:

The analyses are sound and the observations intriguing. Indeed, while it has been noted previously that parabolic growth promotes coexistence, this is the first work to show that it can also mitigate the error threshold catastrophe, which is often presented as a major obstacle to our understanding of the origin of life.

Weaknesses:

A general weakness, which can however be seen as inherent in an agent-based model that aims to be more realistic than earlier, more phenomenological models, is the proliferation of parameters. The choice and values of these parameters are generally justified and, in many cases, several values are tested to assess the robustness of the results, but it can be difficult for the reader to identify the modeling choices that are truly critical from those that are less so.

Reviewer #4 (Public Review):

Summary:

Masala N et al showed interesting aberrant calcium microwaves in the hippocampus when synapsin promoter driven GCaMPs were expressed for a long period of time. These aberrant hippocampal Ca2+ micro-waves depend on the viral titre of the GECI. The microwave of Ca2+ was not observed when GECI was expressed only a sparse set of neurons.

Strengths:

These findings are important to wide neuroscience community especially when considering a great number of investigators are using similar approaches. Results look convincing and are consistent across several laboratories.

Weaknesses:

Synapsin promoter labels both excitatory pyramidal neurons and inhibitory neurons. To avoid aberrant Ca2+ microwave, a combination of Flex virus and CaMKII-Cre or Thy-1-GCaMP6s and 6f mice were tested. However, all these approaches limit the number of infected pyramidal neurons. While the comprehensive display of these results is appreciated, one additional important test would be more informative. To distinguish whether the microwave of Ca2+ is sufficiently caused via the expression of GCaMP in interneurons, or just a matter of pyramidal neuron density, testing Flex-GCaMP6 in interneuron specific mouse lines such as PV-Cre and SOM-Cre will provide further clarifications.

Reviewer #2 (Public Review):

Summary:

The authors describe and quantify a phenomenon in the CA1 and CA3 of the hippocampus that they call aberrant Ca2+ micro-waves. Micro-waves are sometimes seen during 2-photon calcium imaging of populations of neurons under certain conditions. They are spatially confined slow calcium events that start in a few cells and slowly spread to neighboring groups of cells. This phenomenon has been uttered between researchers in the field at conferences, but no one has taken the time to carefully capture and quantify micro-waves and pin down the causes. The authors show that micro-waves are dependent on the viral titre of the genetically encoded calcium indicators (GECIs), the genetic promoter (synapsin), the neuronal subtype (granule cells in the dentate gyrus do not produce micro-waves and they are not seen in the neocortex), and the density of GECI expression. The authors should be commended for their work and for raising awareness to all labs doing any form of calcium imaging in populations of neurons. The authors also come up with alternative approaches to avoid artifactual micro-waves such as reducing the transduction titre (1:2 dilution of virus) and a transduction method employing sparser and cre-dependent GECI expression in principal cells using a CaMKII promoter.

Strengths:

The micro-waves reported in the paper were robustly observed across 4 laboratories and 3 different countries with various experimenters and calcium imaging set-ups. This adds significant strength to the work.

The age of mice used covered a broad range (from 6 to 43 weeks). This is a strength because it covers most ages that are used in labs that regularly do calcium imaging.

Another strength is they used different GCaMP variants (GCaMP6m, GCaMP6s, GCaMP7f), as well as a red indicator: RCaMP. This shows the micro-waves are not an issue with any particular GECI, as the authors suggest.

The authors include many movies of micro-waves. This is extremely useful for researchers in the field to view them in real-time so they can identify them in their own data.

They provide a useful table with specific details of the virus injected, titre, dilution, and other information along with the incidence of micro-waves. A nice look-up table for researchers to see if their viral strategy is associated with a high or low incidence of micro-waves.

Weaknesses:

The effect of mico-waves on single cell function was not analyzed. It would be useful, for example, if we knew the influence of micro-waves on place fields. Can a place cell still express a place field in a hippocampus that produces micro-waves? What effect might a microwave passing over a cell have on its place field? Mice were not trained in these experiments, so the authors do not have the data. However, they do briefly discuss these ideas.

Reviewer #3 (Public Review):

Summary:

The work by Masala and colleagues highlights a striking artifact that can result from a particular viral method for expressing genetically encoded calcium indicators (GECIs) in neurons. In a cross-institutional collaboration, the authors find that viral transduction of GECIs in the hippocampus can result in aberrant slow-traveling calcium (Ca2+) micro-waves. These Ca2+ micro-waves are distinct from previously described ictal activity but nevertheless are likely a pathological consequence of overexpression of virally transduced proteins. Ca2+ micro-waves will most-likely obscure the physiology that most researchers are interested in studying with GECIs, and their presence indicates that the neural circuit is in an unintended pathological state. Interestingly this pathology was not observed using the same viral transduction methods in other brain regions. The authors recommend several approaches that may help other experimenters avoid this confound in their own data such as reducing the titer of viral injections or using recombinase-dependent expression. The intent of this manuscript is to raise awareness of the potential unintended consequences of viral overexpression, particularly for GECIs. A rigorous investigation into the exact causes of Ca2+ micro-waves or the mechanisms supporting them are beyond the authors' intended scope.

Strengths:

The authors clearly demonstrate that Ca2+ micro-waves occur in the CA1 and CA3 regions of the hippocampus following large volume, high titer injections of adeno-associated viruses (AAV1 and AAV9) encoding GECIs. The supplementary videos provide undeniable proof of their existence.

By forming an inter-institutional collaboration, the authors demonstrate that this phenomenon is robust to changes in surgical techniques or imaging conditions.

Weaknesses:

I believe that the weaknesses of the manuscript are appropriately highlighted by the authors themselves in the discussion. The manuscript does not attempt to exhaustively characterize the conditions under which calcium micro-waves occur. Rather, the authors raise awareness of this problem.

Reviewer #1 (Public Review):

This paper identifies GABA cells in the preoptic hypothalamus and others in the posterior hypothalamus which are involved in REM sleep rebound (the increase in REM sleep) after selective REM sleep deprivation. By calcium photometry, these preoptic cells are most active during REM, and show more calcium signals during REM deprivation, suggesting they respond to "REM pressure". Inhibiting these cells ontogenetically diminishes REM sleep. The optogenetic and photometry work is carried out to a high standard, the paper is well written, and the findings are interesting and enhance our understanding of REM sleep regulation. The new findings make it clear that as for the circuitry that regulates NREM sleep, REM sleep circuitry is also quite distributed in the brain. It is unclear if there is a true "REM center". The study of mechanisms of catching up on lost sleep (sleep homeostasis), has previously focused on NREM sleep, where various circuits have been identified. That there is a special mechanism that also tracks time awake and compensates with REM sleep is intriguing.

In a broader context, the existence of REM rebound suggests that REM sleep must have a function, otherwise why catch up on it. There is a lot of literature that suggests REM contributes to emotional processing, for example. The new findings deepen our appreciation of REM regulation. As REM sleep is often disturbed in stress (e.g. post-traumatic stress disorder) and in depression, understanding more about REM regulation could ultimately aid treatments for people living with these conditions.

Reviewer #2 (Public Review):

Maurer et al investigated the contribution of GAD2+ neurons in the preoptic area (POA), projecting to the tuberomammillary nucleus (TMN), to REM sleep regulation. They applied an elegant design to monitor and manipulate activity of this specific group of neurons: a GAD2-Cre mouse, injected with retrograde AAV constructs in the TMN, thereby presumably only targeting GAD2+ cells projecting to the TMN. Using this set-up in combination with technically challenging techniques including EEG with photometry and REM sleep deprivation, the authors found that this cell-type studied becomes active shortly (≈40sec) prior to entering REM sleep and remains active during REM sleep. Moreover, optogenetic inhibition of GAD2+ cells inhibits REM sleep by a third, and also impairs the rebound in REM sleep in the following hour. Thus, the data makes a convincing case for a role of GAD2+ neurons in the POA projecting to the TMN in REM sleep regulation.

Reviewer #2 (Public Review):

Summary:

Roy et al. investigated the role of non-canonical DNA structures called G-quadruplexes (G4s) in long-range chromatin interactions and gene regulation. Introducing a G4 array into chromatin significantly increased the number of long-range interactions, both within the same chromosome (cis) and between different chromosomes (trans). G4s functioned as enhancer elements, recruiting p300 and boosting gene expression even 5 megabases away. The study proposes a mechanism where G4s directly influence 3D chromatin organization, facilitating communication between regulatory elements and genes.

Strength:

The findings are valuable for understanding the role of G4-DNA in 3D genome organization and gene transcription.

Weaknesses:

The study would benefit from more robust and comprehensive data, which would add depth and clarity.

(1) Lack of G4 Structure Confirmation: The absence of direct evidence for G4 formation within cells undermines the study's foundation. Relying solely on in vitro data and successful gene insertion is insufficient.

(2) Alternative Explanations: The study does not sufficiently address alternative explanations for the observed results. The inserted sequences may not form G4s or other factors like G4-RNA hybrids may be involved.

(3) Limited Data Depth and Clarity: ChIP-qPCR offers limited scope and considerable variation in some data makes conclusions difficult.

(4) Statistical Significance and Interpretation: The study could be more careful in evaluating the statistical significance and magnitude of the effects to avoid overinterpreting the results.

Reviewer #3 (Public Review):

Summary:

This paper aims to demonstrate the role of G-quadruplex DNA structures in the establishment of chromosome loops. The authors introduced an array of G4s spanning 275 bp, naturally found within a very well-characterized promoter region of the hTERT promoter, in an ectopic region devoid of G-quadruplex and annotated gene. As a negative control, they used a mutant version of the same sequence in which G4 folding is impaired. Due to the complexity of the region, 3 G4s on the same strand and one on the opposite strand, 12 point mutations were made simultaneously (G to T and C to A). Analysis of the 3D genome organization shows that the WT array establishes more contact within the TAD and throughout the genome than the control array. Additionally, a slight enrichment of H3K4me1 and p300, both enhancer markers, was observed locally near the insertion site. The authors tested whether the expression of genes located either nearby or up to 5 Mb away was up-regulated based on this observation. They found that four genes were up-regulated from 1.5 to 3-fold. An increased interaction between the G4 array compared to the mutant was confirmed by the 3C assay. For in-depth analysis of the long-range changes, they also performed Hi-C experiments and showed a genome-wide increase in interactions of the WT array versus the mutated form.

Strengths:

The experiments were well-executed and the results indicate a statistical difference between the G4 array inserted cell line and the mutated modified cell line.

Weaknesses:

The control non-G4 sequence contains 12 point mutations, making it difficult to draw clear conclusions. These mutations not only alter the formation of G4, but also affect at least three Sp1 binding sites that have been shown to be essential for the function of the hTERT promoter, from which the sequence is derived. The strong intermingling of G4 and Sp1 binding sites makes it impossible to determine whether all the observations made are dependent on G4 or Sp1 binding. As a control, the authors used Locked Nucleic Acid probes to prevent the formation of G4. As for mutations, these probes also interfere with two Sp1 binding sites. Therefore, using this alternative method has the same drawback as point mutations. This major issue should be discussed in the paper. It is also possible that other unidentified transcription factor binding sites are affected in the presented point mutants.

Reviewer #1 (Public Review):

Summary:

In this manuscript, Chowdhury and co-workers provide interesting data to support the role of G4-structures in promoting chromatin looping and long-range DNA interactions. The authors achieve this by artificially inserting a G4-containing sequence in an isolated region of the genome using CRISPR-Cas9 and comparing it to a control sequence that does not contain G4 structures. Based on the data provided, the authors can conclude that G4-insertion promotes long-range interactions (measured by Hi-C) and affects gene expression (measured by qPCR) as well as chromatin remodelling (measured by ChIP of specific histone markers).

Whilst the data presented is promising and partially supports the authors' conclusion, this reviewer feels that some key controls are missing to fully support the narrative. Specifically, validation of actual G4-formation in chromatin by ChIP-qPCR (at least) is essential to support the association between G4-formation and looping. Moreover, this study is limited to a genomic location and an individual G4-sequence used, so the findings reported cannot yet be considered to reflect a general mechanism/effect of G4-formation in chromatin looping.

Strengths:

This is the first attempt to connect genomics datasets of G4s and HiC with gene expression. The use of Cas9 to artificially insert a G4 is also very elegant.

Weaknesses:

Lack of controls, especially to validate G4-formation after insertion with Cas9. The work is limited to a single G4-sequence and a single G4-site, which limits the generalisation of the findings.

Reviewer #3 (Public Review):

Summary:

The manuscript uses a combination of evolutionary approaches and structural/dynamics observations to provide mechanistic insights in the adaptation of the Spike protein during the evolution of SARS-COV-2 variants. The conclusion that CAP sites should be taken in particular account when considering the impact of the emergence of new strains and mutations is warranted.

Strengths:

The results presented in this work are very well outlined with well-written text, pleasant and well-described pictures, didactical and clear description of the methods, e.g. the discussion of how the MD equilibration procedure is applied and evaluated is clear and well argument.<br /> The citation of relevant similar results with different approaches strengthens the reasoning; in particular, comparing the calculated scores with previous experimentally obtained data is one of the strongest points of the manuscript.

Weaknesses:

There are no replicas of the molecular dynamics (MD) simulations, understandable since it's not a MD-focused paper. However, the comparison of multiple replicas could enhance the reliability of the findings.

Reviewer #2 (Public Review):

The authors set out to identify CAPs (Candidate Adaptive Polymorphyisms), i.e., simply put mutations that carry a potential functional advantage, and utilize computational methods based on the perturbation of C-alpha positions with an Elastic Network Model to determine if dynamics of CAP residues are different in any way.

The authors have addressed the main methodological concerns.

However, one point remains. The specific comparison of which CAPs have been previously identified by other means, particularly with other computational methods that look into dynamics is still lacking. It is unfortunate that the authors do not present such analysis, particularly with respect to single point mutational analysis of Teruel et al. in Plos Comp. Bio. If CAP positions were previously identified by other means it adds strength to the methodology used by the authors. The authors also do not discuss their results in light of the work of Lam et al. (Sci. Comm, 2020) where an evolutionary analysis of Spike/ACE2 binding across homologues is performed. I believe that such deeper discussion of the current results in light of previous work, adds strength to the analysis presented in this manuscript as the methodology is different. Even if all results were not new, with the method being different from the other means by which such results were obtained, it would be still a worthy contribution to the field. Furthermore, for the community at large trying to understand the importance of particular positions in Spike, knowing that a particular position identified here was also identified by works X, Y, Z adds a lot of to the field. I can only think that the authors may imagine that if one of their CAPs was identified by other means previously, it takes away from the merit of their work, but it is actually the opposite. I urge the authors to not brush away this. In fact, more important than any methodological aspect of the present work, this strengthening of evidence for particular positions by several independent methods is the most important evidence that the authors can contribute to the field.

Reviewer #1 (Public Review):

The manuscript by Oleh et al. uses in vitro electrophysiology and compartmental modeling (via NEURON) to investigate the expression and function of HCN channels in mouse L2/3 pyramidal neurons. The authors conclude that L2/3 neurons have developmentally regulated HCN channels, the activation of which can be observed when subjected to large hyperpolarizations. They further conclude via blockade experiments that HCN channels in L2/3 neurons influence cellular excitability and pathway-specific EPSP kinetics, which can be neuromodulated. While the authors perform a wide range of slice physiology experiments, concrete evidence that L2/3 cells express functionally relevant HCN channels is limited. There are serious experimental design caveats and confounds that make drawing strong conclusions from the data difficult. Furthermore, the significance of the findings is generally unclear, given modest effect sizes and a lack of any functional relevance, either directly via in vivo experiments or indirectly via strong HCN-mediated changes in known operations/computations/functions of L2/3 neurons.

Specific points:

(1) The interpretability and impact of this manuscript are limited due to numerous methodological issues in experimental design, data collection, and analysis. The authors have not followed best practices in the field, and as such, much of the data is ambiguous and/or weak and does not support their interpretations (detailed below). Additionally, the authors fail to appropriately explain their rationale for many of their choices, making it difficult to understand why they did what they did. Furthermore, many important references appear to be missing, both in terms of contextualizing the work and in terms of approach/method. For example, the authors do not cite Kalmbach et al 2018, which performed a directly comparable set of experiments on HCN channels in L2/3 neurons of both humans and mice. This is an unacceptable omission. Additionally, the authors fail to cite prior literature regarding the specificity or lack thereof of Cs+ in blocking HCN. In describing a result, the authors state "In line with previous reports, we found that L2/3 PCs exhibited an unremarkable amount of sag at 'typical' current commands" but they then fail to cite the previous reports.

(2) A critical experimental concern in the manuscript is the reliance on cesium, a nonspecific blocker, to evaluate HCN channel function. Cesium blocks HCN channels but also acts at potassium channels (and possibly other channels as well). The authors do not acknowledge this or attempt to justify their use of Cs+ and do not cite prior work on this subject. They do not show control experiments demonstrating that the application of Cs+ in their preparation only affects Ih. Additionally, the authors write 1 mM cesium in the text but appear to use 2 mM in the figures. In later experiments, the authors switch to ZD7288, a more commonly used and generally accepted more specific blocker of HCN channels. However, they use a very high concentration, which is also known to produce off-target effects (see Chevaleyre and Castillo, 2002). To make robust conclusions, the authors should have used both blockers (at accepted/conservative concentrations) for all (or at least most) experiments. Using one blocker for some experiments and then another for different experiments is fraught with potential confounds.

(3) A stronger case could be made that HCN is expressed in the somatic compartment of L2/3 cells if the authors had directly measured HCN-isolated currents with outside-out or nucleated patch recording (with appropriate leak subtraction and pharmacology). Whole-cell voltage-clamp in neurons with axons and/or dendrites does not work. It has been shown to produce erroneous results over and over again in the field due to well-known space clamp problems (see Rall, Spruston, Williams, etc.). The authors could have also included negative controls, such as recordings in neurons that do not express HCN or in HCN-knockout animals. Without these experiments, the authors draw a false equivalency between the effects of cesium and HCN channels, when the outcomes they describe could be driven simply by multiple other cesium-sensitive currents. Distortions are common in these preparations when attempting to study channels (see Williams and Womzy, J Neuro, 2011). In Fig 2h, cesium-sensitive currents look too large and fast to be from HCN currents alone given what the authors have shown in their earlier current clamp data. Furthermore, serious errors in leak subtraction appear to be visible in Supplementary Figure 1c. To claim that these conductances are solely from HCN may be misleading.

(4) The authors present current-clamp traces with some sag, a primary indicator of HCN conductance, in Figure 2. However, they do not show example traces with cesium or ZD7288 blockade. Additionally, the normalization of current injected by cellular capacitance and the lack of reporting of input resistance or estimated cellular size makes it difficult to determine how much current is actually needed to observe the sag, which is important for assessing the functional relevance of these channels. The sag ratio in controls also varies significantly without explanation (Figure 6 vs Figure 7). Could this variability be a result of genetically defined subgroups within L2/3? For example, in humans, HCN expression in L2/3 varies from superficial and deep neurons. The authors do not make an effort to investigate this. Regardless of inconsistencies in either current injection or cell type, the sag ratio appears to be rather modest and similar to what has already been reported previously in other papers.

(5) In the later experiments with ZD7288, the authors measured EPSP half-width at greater distances from the soma. However, they use minimal stimulation to evoke EPSPs at increasingly far distances from the soma. Without controlling for amplitude, the authors cannot easily distinguish between attenuation and spread from dendritic filtering and additional activation and spread from HCN blockade. At a minimum, the authors should share the variability of EPSP amplitude versus the change in EPSP half-width and/or stimulation amplitudes by distance. In general, this kind of experiment yields much clearer results if a more precise local activation of synapses is used, such as dendritic current injection, glutamate uncaging, sucrose puff, or glutamate iontophoresis. There are recording quality concerns here as well: the cell pictured in Figure 3a does not have visible dendritic spines, and a substantial amount of membrane is visible in the recording pipette. These concerns also apply to the similar developmental experiment in 6f-h, where EPSP amplitude is not controlled, and therefore, attenuation and spread by distance cannot be effectively measured. The outcome, that L2/3 cells have dendritic properties that violate cable theory, seems implausible and is more likely a result of variable amplitude by proximity.

(6) Minimal stimulation used for experiments in Figures 3d-i and Figures 4g-h does not resolve the half-width measurement's sensitivity to dendritic filtering, nor does cesium blockade preclude only HCN channel involvement. Example traces should be shown for all conditions in 3h; the example traces shown here do not appear to even be from the same cell. These experiments should be paired (with and without cesium/ZD). The same problem appears in Figure 4, where it is not clear that the authors performed controls and drug conditions on the same cells. 4g also lacks a scale bar, so readers cannot determine how much these measurements are affected by filtering and evoked amplitude variability. Finally, if we are to believe that minimal stimulation is used to evoke responses of single axons with 50% fail rates, NMDA receptor activation should be minimal to begin with. If the authors wish to make this claim, they need to do more precise activation of NMDA-mediated EPSPs and examine the effects of ZD7288 on these responses in the same cell. As the data is presented, it is not possible to draw the conclusion that HCN boosts NMDA-mediated responses in L2/3 neurons.

(7) The quality of recordings included in the dataset has concerning variability: for example, resting membrane potentials vary by >15-20 mV and the AP threshold varies by 20 mV in controls. This is indicative of either a very wide range of genetically distinct cell types that the authors are ignoring or the inclusion of cells that are either unhealthy or have bad seals.

(8) The authors make no mention of blocking GABAergic signaling, so it must be assumed that it is intact for all experiments. Electrical stimulation can therefore evoke a mixture of excitatory and inhibitory responses, which may well synapse at very different locations, adding to interpretability and variability concerns.

(9) The investigation of serotonergic interaction with HCN channels produces modest effect sizes and suffers the same problems as described above.

(10) The computational modeling is not well described and is not biologically plausible. Persistent and transient K channels are missing. Values for other parameters are not listed. The model does not seem to follow cable theory, which, as described above, is not only implausible but is also not supported by the experimental findings.

Taken together, there are serious methodological and analytical concerns that need to be addressed before the authors' claims can be supported. Combined with the small effect sizes and high data variability throughout the paper, this makes it hard to see how the manuscript could make a strong contribution to advancing our understanding of L2/3 cortical pyramidal neuron function.

Reviewer #2 (Public Review):

Summary:

This paper by Olah et al. uncovers a previously unknown role of HCN channels in shaping synaptic inputs to L2/3 cortical neurons. The authors demonstrate using slice electrophysiology and computational modeling that, unlike layer 5 pyramidal neurons, L2/3 neurons have an enrichment of HCN channels in the proximal dendrites. This location provides a locus of neuromodulation for inputs onto the proximal dendrites from L4 without an influence on distal inputs from L1. The authors use pharmacology to demonstrate the effect of HCN channels on NMDA-mediated synaptic inputs from L4. The authors further demonstrate the developmental time course of HCN function in L2/3 pyramidal neurons. Taken together, this a well-constructed investigation of HCN channel function and the consequences of these channels on synaptic integration in L2/3 pyramidal neurons.

Strengths:

The authors use careful, well-constrained experiments using multiple pharmacological agents to asses HCN channel contributions to synaptic integrations. The authors also use a voltage clamp to directly measure the current through HCN channels across developmental ages. The authors also provide supplemental data showing that their observation is consistent across multiple areas of the cerebral cortex.

Weaknesses:

The gradient of the HCN channel function is based almost exclusively on changes in EPSP width measured at the soma. While providing strong evidence for the presence of HCN current in L2/3 neurons, there are space clamp issues related to the use of somatic whole-cell voltage clamps that should be considered in the discussion.

Reviewer #3 (Public Review):

Summary:

The authors study the function of HCN channels in L2/3 pyramidal neurons, employing somatic whole-cell recordings in acute slices of visual cortex in adult mice and a bevy of technically challenging techniques. Their primary claim is a non-uniform HCN distribution across the dendritic arbor with a greater density closer to the soma (roughly opposite of the gradient found in L5 PT-type neurons). The second major claim is that multiple sources of long-range excitatory input (cortical and thalamic) are differentially affected by the HCN distribution. They further describe an interesting interplay of NMDAR and HCN, serotonergic modulation of HCN, and compare HCN-related properties at 1, 2 and 6 weeks of age. Several results are supported by biophysical simulations.

Strengths:

The authors collected data from both male and female mice, at an age (6-10 weeks) that permits comparison with in vivo studies, in sufficient numbers for each condition, and they collected a good number of data points for almost all figure panels. This is all the more positive, considering the demanding nature of multi-electrode recording configurations and pipette-perfusion. The main strength of the study is the question and focus.

Weaknesses:

Unfortunately, in its present form, the main claims are not adequately supported by the experimental evidence: primarily because the evidence is indirect and circumstantial, but also because multiple unusual experimental choices (along with poor presentation of results) undermine the reader's confidence. Additionally, the authors overstate the novelty of certain results and fail to cite important related publications. Some of these weaknesses can be addressed by improved analysis and statistics, resolving inconsistent data across figures, reorganizing/improving figure panels, more complete methods, improved citations, and proofreading. In particular, given the emphasis on EPSPs, the primary data (for example EPSPs, overlaid conditions) should be shown much more.

However, on the experimental side, addressing the reviewer's concerns would require a very substantial additional effort: direct measurement of HCN density at different points in the dendritic arbor and soma; the internal solution chosen here (K-gluconate) is reported to inhibit HCN; bath-applied cesium at the concentrations used blocks multiple potassium channels, i.e. is not selective for HCN (the fact that the more selective blocker ZD7288 was used in a subset of experiments makes the choice of Cs+ as the primary blocker all the more curious); pathway-specific synaptic stimulation, for example via optogenetic activation of specific long-range inputs, to complement / support / verify the layer-specific electrical stimulation.

Reviewer #1 (Public Review):

Summary:

Organization of cell surface receptors in membrane nanodomains is important for signaling, but how this is regulated is poorly understood. In this study the authors employ TIRFM single-molecule tracking combined with multiple analyses to show that ligand exposure increases diffusion of the immune receptor FLS2 in the plasma membrane and its co-localization with remorin REM1.3 in a manner dependent on the phosphosite S938. They additionally show that ligand increases dwell time of FLS2, and this is linked to FLS2 endocytosis, also in a manner dependent on S938 phosphorylation. The study uncovers a regulatory mechanism of FLS2 localization in the nanodomain crucial for signaling.

Strengths:

TIRFM single-molecule tracking, FRAP, FRET and endocytosis experiments were nicely done. A role of S938 phosphorylation is convincing.

Weaknesses:

In the previous submission, reviewers pointed out multiple issues, which the reviewers believed the authors can address in the revision. The revised version does improve to some extent but still contains many issues in terms of data analysis and writing.

Reviewer #2 (Public Review):

Summary:

The research conducted by Yaning Cui and colleagues delves into understanding FLS2-mediated immunity. This is achieved by comparing the spatiotemporal dynamics of a FLS2-S938A mutant and FLS2-WT, especially in relation to their association with the remorin protein. To delineate the differences between the FLS2-S938A mutant and FLS2-WT, they utilized a plethora of advanced fluorescent imaging techniques. By analyzing surface dynamics and interactions involving the receptor signal co-receptor BAK1 and remorin proteins, the authors propose a model of how FLS2 and BAK1 are assembled and positioned within a remorin-specific nano-enviroment during FLS2 ligand-induced immune responses.

Strengths:

These techniques offer direct visualizations of molecular dynamics and interactions, helping us understand their spatial relationships and interactions during innate immune responses.

Advanced cell biology imaging techniques are crucial for obtaining high-resolution insights into the intracellular dynamics of biomolecules. The demonstrated imaging systems are excellent examples to be used in studying plant immunity by integrating other functional assays.

Weaknesses:

It's essential to acknowledge that every fluorescence-based method, just like biochemical assays, comes with its unique limitations. These often pertain to spatial and temporal resolutions, as well as the sensitivity of the cameras employed in each setup. Meticulous interpretation is pivotal to guarantee an accurate depiction and to steer clear of potential misunderstandings when employing specific imaging systems to analyze molecular attributes. Moreover, a discerning interpretation and accurate image analysis can offer invaluable guidance for future studies on plant signaling molecules using these nice cell imaging techniques.

For instance, although single-particle analysis couldn't conclusively link FLS2 and remorin, FLIM-FRET effectively highlighted their ligand-triggered association and the disengagement brought on by mutations. While these methodologies seemed to present differing outcomes, they were described in the manuscript as harmonious. In reality, these differences could highlight distinct protein populations active in immune responses, each accentuated differently by the respective imaging techniques due to their individual spatial and temporal limitations. Addressing these variations is imperative, especially when designing future imaging explorations of immune complexes.

Reviewer #1 (Public Review):

Summary:

In this paper, Misic et al showed that white matter properties can be used to classify subacute back pain patients that will develop persisting pain.

Strengths:

Compared to most previous papers studying associations between white matter properties and chronic pain, the strength of the method is to perform a prediction in unseen data. Another strength of the paper is the use of three different cohorts. This is an interesting paper that provides a valuable contribution to the field.

Weaknesses:

The authors imply that their biomarker could outperform traditional questionnaires to predict pain: "While these models are of great value showing that few of these variables (e.g. work factors) might have significant prognostic power on the long-term outcome of back pain and provide easy-to-use brief questionnaires-based tools, (21, 25) parameters often explain no more than 30% of the variance (28-30) and their prognostic accuracy is limited.(31)". I don't think this is correct; questionnaire-based tools can actually achieve far greater prediction than their model in about half a million individuals from the UK Biobank (Tanguay-Sabourin et al., A prognostic risk score for the development and spread of chronic pain, Nature Medicine 2023).

Moreover, the main weakness of this study is the sample size. It remains small despite having 3 cohorts. This is problematic because results are often overfitted in such a small sample size brain imaging study, especially when all the data are available to the authors at the time of training the model (Poldrack et al., Scanning the horizon: towards transparent and reproducible neuroimaging research, Nature Reviews in Neuroscience 2017). Thus, having access to all the data, the authors have a high degree of flexibility in data analysis, as they can retrain their model any number of times until it generalizes across all three cohorts. In this case, the testing set could easily become part of the training making it difficult to assess the real performance, especially for small sample size studies.

Even if the performance was properly assessed, their models show AUCs between 0.65-0.70, which is usually considered as poor, and most likely without potential clinical use. Despite this, their conclusion was: "This biomarker is easy to obtain (~10 min 18 of scanning time) and opens the door for translation into clinical practice." One may ask who is really willing to use an MRI signature with a relatively poor performance that can be outperformed by self-report questionnaires?

Overall, these criticisms are more about the wording sometimes used and the inference they made. I think the strength of the evidence is incomplete to support the main claims of the paper.

Despite these limitations, I still think this is a very relevant contribution to the field. Showing predictive performance through cross-validation and testing in multiple cohorts is not an easy task and this is a strong effort by the team. I strongly believe this approach is the right one and I believe the authors did a good job.

Minor points:

Methods:

I get the voxel-wise analysis, but I don't understand the methods for the structural connectivity analysis between the 88 ROIs. Have the authors run tractography or have they used a predetermined streamlined form of 'population-based connectome'? They report that models of AUC above 0.75 were considered and tested in the Chicago dataset, but we have no information about what the model actually learned (although this can be tricky for decision tree algorithms).

Minor:<br /> What results are shown in Figure 7? It looks more descriptive than the actual results.

Reviewer #2 (Public Review):

The present study aims to investigate brain white matter predictors of back pain chronicity. To this end, a discovery cohort of 28 patients with subacute back pain (SBP) was studied using white matter diffusion imaging. The cohort was investigated at baseline and one-year follow-up when 16 patients had recovered (SBPr) and 12 had persistent back pain (SBPp). A comparison of baseline scans revealed that SBPr patients had higher fractional anisotropy values in the right superior longitudinal fasciculus SLF) than SBPp patients and that FA values predicted changes in pain severity. Moreover, the FA values of SBPr patients were larger than those of healthy participants, suggesting a role of FA of the SLF in resilience to chronic pain. These findings were replicated in two other independent datasets. The authors conclude that the right SLF might be a robust predictive biomarker of CBP development with the potential for clinical translation.

Developing predictive biomarkers for pain chronicity is an interesting, timely, and potentially clinically relevant topic. The paradigm and the analysis are sound, the results are convincing, and the interpretation is adequate. A particular strength of the study is the discovery-replication approach with replications of the findings in two independent datasets.

The following revisions might help to improve the manuscript further.

- Definition of recovery. In the New Haven and Chicago datasets, SBPr and SBPp patients are distinguished by reductions of >30% in pain intensity. In contrast, in the Mannheim dataset, both groups are distinguished by reductions of >20%. This should be harmonized. Moreover, as there is no established definition of recovery (reference 79 does not provide a clear criterion), it would be interesting to know whether the results hold for different definitions of recovery. Control analyses for different thresholds could strengthen the robustness of the findings.

- Analysis of the Chicago dataset. The manuscript includes results on FA values and their association with pain severity for the New Haven and Mannheim datasets but not for the Chicago dataset. It would be straightforward to show figures like Figures 1 - 4 for the Chicago dataset, as well.

- Data sharing. The discovery-replication approach of the present study distinguishes the present from previous approaches. This approach enhances the belief in the robustness of the findings. This belief would be further enhanced by making the data openly available. It would be extremely valuable for the community if other researchers could reproduce and replicate the findings without restrictions. It is not clear why the fact that the studies are ongoing prevents the unrestricted sharing of the data used in the present study.

Reviewer #3 (Public Review):

Summary:

Authors suggest a new biomarker of chronic back pain with the option to predict the result of treatment. The authors found a significant difference in a fractional anisotropy measure in superior longitudinal fasciculus for recovered patients with chronic back pain.

Strengths:<br /> The results were reproduced in three different groups at different studies/sites.

Weaknesses:<br /> - The number of participants is still low.<br /> - An explanation of microstructure changes was not given.<br /> - Some technical drawbacks are presented.

Reviewer #1 (Public Review):

Galanti et al. present an innovative new method to determine the susceptibility of large collections of plant accessions towards infestations by herbivores and pathogens. This work resulted from an unplanned infestation of plants in a greenhouse that was later harvested for sequencing. When these plants were extracted for DNA, associated pest DNA was extracted and sequenced as well. In a standard analysis, all sequencing reads would be mapped to the plant reference genome and unmapped reads, most likely originating from 'exogenous' pest DNA, would be discarded. Here, the authors argue that these unmapped reads contain valuable information and can be used to quantify plant infestation loads.

For the present manuscript, the authors re-analysed a published dataset of 207 sequenced accessions of Thlaspi arvense. In this data, 0.5% of all reads had been classified as exogenous reads, while 99.5% mapped to the T. arvense reference genome. In a first step, however, the authors repeated read mapping against other reference genomes of potential pest species and found that a substantial fraction of 'ambiguous' reads mapped to at least one such species. Removing these reads improved the results of downstream GWAs, and is in itself an interesting tool that should be adopted more widely.

The exogenous reads were primarily mapped to the genomes of the aphid Myzus persicae and the powdery mildew Erysiphe cruciferarum, from which the authors concluded that these were the likely pests present in their greenhouse. The authors then used these mapped pest read counts as an approximate measure of infestation load and performed GWA studies to identify plant gene regions across the T. arvense accessions that were associated with higher or lower pest read counts. In principle, this is an exciting approach that extracts useful information from 'junk' reads that are usually discarded. The results seem to support the authors' arguments, with relatively high heritabilities of pest read counts among T. arvense accessions, and GWA peaks close to known defence genes. Nonetheless, I do feel that more validation would be needed to support these conclusions, and given the radical novelty of this approach, additional experiments should be performed.

A weakness of this study is that no actual aphid or mildew infestations of plants were recorded by the authors. They only mention that they anecdotally observed differences in infestations among accessions. As systematic quantification is no longer possible in retrospect, a smaller experiment could be performed in which a few accessions are infested with different quantities of aphids and/or mildew, followed by sequencing and pest read mapping. Such an approach would have the added benefit of allowing causally linking pest read count and pest load, thereby going beyond correlational associations.

On a technical note, it seems feasible that mildew-infested leaves would have been selected for extraction, but it is harder to explain how aphid DNA would have been extracted alongside plant DNA. Presumably, all leaves would have been cleaned of live aphids before they were placed in extraction tubes. What then is the origin of aphid DNA in these samples? Are these trace amounts from aphid saliva and faeces/honeydew that were left on the leaves? If this is the case, I would expect there to be substantially more mildew DNA than aphid DNA, yet the absolute read counts for aphids are actually higher. Presumably read counts should only be used as a relative metric within a pest organism, but this unexpected result nonetheless raises questions about what these read counts reflect. Again, having experimental data from different aphid densities would make these results more convincing.

Reviewer #2 (Public Review):

Summary:

Galanti et al investigate genetic variation in plant pest resistance using non-target reads from whole-genome sequencing of 207 field lines spontaneously colonized by aphids and mildew. They calculate significant differences in pest DNA load between populations and lines, with heritability and correlation with climate and glucosinolate content. By genome-wide association analyses they identify known defence genes and novel regions potentially associated with pest load variation. Additionally, they suggest that differential methylation at transposons and some genes are involved in responses to pathogen pressure. The authors present in this study the potential of leveraging non-target sequencing reads to estimate plant biotic interactions, in general for GWAS, and provide insights into the defence mechanisms of Thlaspi arvense.

Strengths:

The authors ask an interesting and important question. Overall, I found the manuscript very well-written, with a very concrete and clear question, a well-structured experimental design, and clear differences from previous work. Their important results could potentially have implications and utility for many systems in phenotype-genotype prediction. In particular, I think the use of unmapped reads for GWAS is intriguing.

Weaknesses:

I found that several of the conclusions are incomplete, not well supposed by the data and/or some methods/results require additional details to be able to be judged. I believe these analyses and/or additional clarifications should be considered.

Reviewer #1 (Public Review):

Summary:

The authors establish a recombinant insect cell expression and purification scheme for the antiviral Dicer complex of C. elegans. In addition to Dicer-1, the complex harbors two additional proteins, the RIG-I-like helicase DRH-1 and the dsRNA-binding protein RDE-4. The authors show that the complex prefers blunt-end dsRNA over dsRNAs that contain overhangs. Furthermore, whereas ATP-dependent dsRNA cleavage only exacerbates regular dsRNA cleavage activity, the presence of RDE-4 is essential to ATP-dependent and ATP-independent dsRNA cleavage. Single-particle cryo-EM studies of the ternary C. elegans Dicer complex reveal that the N-terminal domain of DRH-1 interacts with the helicase domain of DCR-1, thereby relieving its autoinhibitory state. Last, the authors show that the ternary complex is able to processively cleave long dsRNA, an activity primarily relying on the helicase activity of DRH-1.

Strengths:

• First thorough biochemical characterization of the antiviral activity of C. elegans Dicer in complex with the RIG-I like helicase DRH-1 and the dsRNA-binding protein RDE-4<br /> • Discovery that RDE-4 is essential to dsRNA processing, whereas ATP hydrolysis is not<br /> • Discovery of an autoinhibitory role of DRH-1's N-terminal domain (in analogy to the CARD domains of RIG-I)<br /> • First structural insights into the ternary complex DCR-1:DRH-1:RDE-4 by cryo-EM to medium resolution<br /> • Trap experiments reveal that the ternary DCR-1 complex cleaves blunt-ended dsRNA processively. Likely, the helicase domain of DRH-1 is responsible for this processive cleavage.

Weaknesses:

• Cryo-EM Structure of the ternary Dicer-1:DRH-1:RED-4 complex to only medium resolution<br /> • High-resolution structure of the C-terminal domain of DRH-1 bound to dsRNA does not reveal the mechanism of how blunt-end dsRNA and overhang-containing one are being discriminated<br /> • The cryo-EM structure of DCR1:DRH-1:RDE-4 in the presence of ATP only reveals the helicase and CTD domains of DRH-1 bound to dsRNA. No information on dsRNA termini recognition is presented. The paragraph seems detached from the general flow of the manuscript.

Reviewer #2 (Public Review):

Summary:

To investigate the evolutionary relationship between the RNAi pathway and innate immunity, this study uses biochemistry and structural biology to investigate the trimeric complex of Dicer-1, DRH-1 (a RIGI homologue) and RDE-4 , which exists in C. elegans. The three subunits were co-expressed to promote stable purification of the complex. This complex promoted ATP-dependent cleavage of blunt-ended dsRNAs. A detailed kinetic analysis was also carried out to determine the role of each subunit of the trimeric complex in both the specificity and efficiency of cleavage. These studies indicate that RDE-4 is critical for cleavage while DRC-1 is primarily involved in the specificity of the reaction, and DRH-1 promotes ATP hydrolysis. Finally, a moderate density (6-7 angstrom) cryo-EM structure of the trimeric complex is provided.

Strengths:

(1) Newly described methods for studying the C. elegans DICER complex<br /> (2) New structure, albeit only moderate resolution<br /> (3) Kinetic study of the complex in the presence and absence of individual subunits and mutations, provide detailed insight into the contribution of each subunit

Weaknesses:

(1) Limited insight due to limited structural resolution.

Reviewer #1 (Public Review):

Summary:

In this work, Odenwald and colleagues show that mutant biotin ligases used to perform proximity-dependent biotin identification (TurboID) can be used to amplify signal in fluorescence microscopy and to label phase-separated compartments that are refractory to many immunofluorescence approaches. Using the parasite Trypanosoma brucei, they show that fluorescent methods such as expansion microscopy and CLEM, which require bright signals for optimal detection, benefit from the elevated signal provided by TurboID fusion proteins when coupled with labeled streptavidin. Moreover, they show that phase-separated compartments, where many antibody epitopes are occluded due to limited diffusion and potential sequestration, are labeled reliably with biotin deposited by a TurboID fusion protein that localizes within the compartment. They show successful labeling of the nucleolus, likely phase-separated portions of the nuclear pore, and stress granules. Lastly, they use a panel of nuclear pore-TurboID fusion proteins to map the regions of the T. brucei nuclear pore that appear to be phase-separated by comparing antibody labeling of the protein, which is susceptible to blocking, to the degree of biotin deposition detected by streptavidin, which is not.

Strengths:

Overall, this study shows that TurboID labelling and fluorescent streptavidin can be used to boost signal compared to conventional immunofluorescence in a manner similar to tyramide amplification, but without having to use antibodies. TurboID could prove to be a viable general strategy for labeling phase-separated structures in cells, and perhaps as a means of identifying these structures, which could also be useful.

Weaknesses:

However, I think that this work would benefit from additional controls to address if the improved detection that is being observed is due to the increased affinity and smaller size of streptavidin/biotin compared to IgGs, or if it has to do with the increased amount of binding epitope (biotin) being deposited compared to the number of available antibody epitopes. I also think that using the biotinylation signal produced by the TurboID fusion to track the location of the fusion protein and/or binding partners in cells comes with significant caveats that are not well addressed here, mostly due to the inability to discern which proteins are contributing to the observed biotin signal.

To dissect the contributions of the TurboID fusion to elevating signal, anti-biotin antibodies could be used to determine if the abundance of the biotin being deposited by the TurboID is what is increasing detection, or if streptavidin is essential for this. Alternatively, HaloTag or CLIP tagging could be used to see if diffusion of a small molecule tag other than biotin can overcome the labeling issue in phase-separated compartments. There are Halo-biotin substrates available that would allow the conjugation of 1 biotin per fusion protein, which would allow the authors to dissect the relative contributions of the high affinity of streptavidin from the increased amount of biotin that the TurboID introduces.

The idea of using the biotin signal from the TurboID fusion as a means to track the changing localization of the fusion protein or the location of interacting partners is an attractive idea, but the lack of certainty about what proteins are carrying the biotin signal makes it very difficult to make clear statements. For example, in the case of TurboID-PABP2, the appearance of a biotin signal at the cell posterior is proposed to be ALPH1, part of the mRNA decapping complex. However, because we are tracking biotin localization and biotin is being deposited on a variety of proteins, it is not formally possible to say that the posterior signal is ALPH1 or any other part of the decapping complex. For example, the posterior labeling could represent a localization of PABP2 that is not seen without the additional signal intensity provided by the TurboID fusion. There are also many cytoskeletal components present at the cell posterior that could be being biotinylated, not just the decapping complex. Similar arguments can be made for the localization data pertaining to MLP2 and NUP65/75. I would argue that the TurboID labeling allows you to enhance signal on structures, such as the NUPs, and effectively label compartments, but you lack the capacity to know precisely which proteins are being labeled.

Reviewer #2 (Public Review):

Summary:

The authors noticed that there was an enhanced ability to detect nuclear pore proteins in trypanosomes using a streptavidin-biotin-based detection approach in comparison to conventional antibody-based detection, and this seemed particularly acute for phase-separated proteins. They explored this in detail for both standard imaging but also expansion microscopy and CLEM, testing resolution, signal strength, and sensitivity. An additional innovative approach exploits the proximity element of biotin labelling to identify where interacting proteins have been as well as where they are.

Strengths:

The data is high quality and convincing and will have obvious application, not just in the trypanosome field but also more broadly where proteins are tricky to detect or inaccessible due to phase separation (or some other steric limitations). It will be of wide utility and value in many cell biological studies and is timely due to the focus of interest on phase separation, CLEM, and expansion microscopy.

Reviewer #3 (Public Review):

Summary:

The authors aimed to investigate the effectiveness of streptavidin imaging as an alternative to traditional antibody labeling for visualizing proteins within cellular contexts. They sought to address challenges associated with antibody accessibility and inconsistent localization by comparing the performance of streptavidin imaging with a TurboID-HA tandem tag across various protein localization scenarios, including phase-separated regions. They aimed to assess the reliability, signal enhancement, and potential advantages of streptavidin imaging over antibody labeling techniques.

Overall, the study provides a convincing argument for the utility of streptavidin imaging in cellular protein visualization. By demonstrating the effectiveness of streptavidin imaging as an alternative to antibody labeling, the study offers a promising solution to issues of accessibility and localization variability. Furthermore, while streptavidin imaging shows significant advantages in signal enhancement and preservation of protein interactions, the authors must consider potential limitations and variations in its application. Factors such as the fact that tagging may sometimes impact protein function, background noise, non-specific binding, and the potential for off-target effects may impact the reliability and interpretation of results. Thus, careful validation and optimization of streptavidin imaging protocols are crucial to ensure reproducibility and accuracy across different experimental setups.

Strengths:

- Streptavidin imaging utilizes multiple biotinylation sites on both the target protein and adjacent proteins, resulting in a substantial signal boost. This enhancement is particularly beneficial for several applications with diluted antigens, such as expansion microscopy or correlative light and electron microscopy.

- This biotinylation process enables the identification and characterization of interacting proteins, allowing for a comprehensive understanding of protein-protein interactions within cellular contexts.

Weaknesses:

- One of the key advantages of antibodies is that they label native, endogenous proteins, i.e. without introducing any genetic modifications or exogenously expressed proteins. This is a major difference from the approach in this manuscript, and it is surprising that this limitation is not really mentioned, let alone expanded upon, anywhere in the manuscript. Tagging proteins often impacts their function (if not their localization), and this is also not discussed.

- Given that BioID proximity labeling encompasses not only the protein of interest but also its entire interacting partner history, ensuring accurate localization of the protein of interest poses a challenge.

- The title of the publication suggests that this imaging technique is widely applicable. However, the authors did not show the ability to track the localization of several distinct proteins on the same sample, which could be an additional factor demonstrating the outperformance of streptavidin imaging compared with antibody labeling. Similarly, the work focuses only on small 2D samples. It would have been interesting to be able to compare this with 3D samples (e.g. cells encapsulated in an extracellular matrix) or to tissues.

Reviewer #1 (Public Review):

The manuscript by Wang et al. investigates the role of Rnf220 in hindbrain development and Hox expression. The authors suggest that Rnf220 controls Hox expression in the hindbrain by regulating WDR5 levels. The authors combine in vivo experiments with experiments in P19 cells to demonstrate this mechanism. However, the in vivo data does not provide strong support for the claims the authors make and the role of Rnf in Hox maintenance and pons development is unclear.

Specific concerns with in vivo data:

A major issue throughout the paper is that Hox expression analysis is done exclusively through quantitative PCR, with values ranging from 2-fold to several thousand-fold upregulation, with no antibody validation for any Hox protein (presumably they are all upregulated).

In Figure 1, massive upregulation of most Hox genes in the brainstem is shown after e16.5 but the paper quickly focuses on analysis of PN nuclei. What are the other consequences of this broad upregulation of Hox genes in the brainstem? There is no discussion of the overall phenotype of the mice, the structure of the brainstem, the migration of neurons, etc. The very narrow focus on motor cortex projections to PN nuclei seems bizarre without broad characterization of the mice, and the brainstem in particular. There is only a mention of "severe motor deficits" from previous studies, but given the broad expression of Rnf220, the fact that is a global knockout, and the effects on spinal cord populations shown previously the justification for focusing on PN nuclei does not seem strong.

It is stated that cluster 7 in scRNA-seq corresponds to the PN nuclei. The modest effect shown on Hox3-5 expression in that data in Figure 1 is inconsistent with the larger effect shown in Figure 2.

Presumably, Hox genes are not the only targets of Rnf220 as shown in the microarray/RNA-sequencing data. There is no definitive evidence that any phenotypes observed (which are also not clear) are specifically due to Hox upregulation. The only assay the authors use to look at a Hox-dependent phenotype in the brainstem is the targeting of PN nuclei by motor cortex axons. This is only done in 2 animals and there are no details as to how the data was analyzed and quantified. The only 2 images shown are not convincing of a strong phenotype, they could be taken at slightly different levels or angles. At the very least, serial sections should be shown and the experiment repeated in more animals. There is also no discussion of how these phenotypes, if real, would relate to previous work by the Rijli group which showed very precise mechanisms of synaptic specificity in this system.

The temporal aspect of this regulation in vivo is not clear. The authors show some expression changes begin at e16.5 but are also present at 2 months. Is the presumed effect on neural circuits a result of developmental upregulation at late embryonic stages or does the continuous overexpression in adult mice have additional influence? Are any of the Hox genes upregulated normally expressed in the brainstem, or PN specifically, at 2 months? Why perform single-cell sequencing experiments at 2 months if this is thought to be mostly a developmental effect? Similarly, the significance of the upregulated WRD5 in the pons and pontine nuclei at 2 months in Figure 3 is not clear.

In Figure 3C the levels of RNF220 in wt and het don't seem to be that different.

Based on the single-cell experiments, and the PN nuclei focus, the rescue experiments are confusing. If the Rnf220 deletion has a sustained effect for up to 2 months, why do the injections in utero? If the focus is the PN nuclei why look at Hox9 expression and not Hox3-5 which are the only Hox genes upregulated in PN based on sc-sequencing? No rescue of behavior or any phenotype other than Hox expression by qPCR is shown and it is unclear whether upregulation of Hox9 paralogs leads to any defects in the first place. The switch to the Nes-cre driver is not explained. Also, it seems that wdr5 mRNA levels are not so relevant and protein levels should be shown instead (same for rescue experiments in P19 cells).

Other:<br /> What is the relationship between Retinoic acid and WRD5? In Figure 3E there is no change in WRD5 levels without RA treatment in Rnf KO but an increase in expression with RA treatment and Rnf KO. However, the levels of WRD5 do not seem to change with RA treatment alone. Does Rnf220 only mediate WDR5 degradation in the presence of RA? This does not seem to be the case in experiments in 293 cells in Figure 4.

Why are the levels of Hox upregulation after RA treatment so different in Figure 5 and Figure Supplement 5?

In Figures 4B+C which lanes are input and which are IP? There is no quantitation of Figure 4D, from the blot it does look that there is a reduction in the last 2 columns as well. The band in the WT flag lane seems to have a bubble. Need to quantitate band intensities. Same for E, the effect does not seem to be completely reversed with MG132.

Reviewer #2 (Public Review):

Wang, Liu, et al. identified Rnf220 and Wdr5 as novel regulators of Hox gene expression during pons development. Phenotypic characterization of Rnf220 deficient mice with single-cell transcriptomics, qRT-PCR, and axonal tracing methods show that Rnf220 knockdown causes de-repression of Hox gene expression at multiple stages of pons development to regulate the final formation of the pontine nuclei neural circuit. Additionally, they also perform exhaustive expression analysis of multiple genes in the Hox family cluster to identify specific gene groups that are targeted by Rnf220. Furthermore, they also demonstrate that Rnf220 modulates Hox gene expression by directly binding to Wdr5, thus targeting it for ubiquitination and subsequent degradation. To elucidate the molecular mechanism of this interaction, they perform detailed immunoprecipitation assays and identify the precise Wdr5 amino acid residues that are targeted by Rnf220. Intriguingly, they show that inhibition of Wdr5 in Rnf220 deficient mice reverses the de-repression of Hox gene expression suggesting the direct involvement of Rnf220-Wdr5 interaction in modulating Hox gene expression during pons development. These data highlight the role of a new form of Hox gene regulation via the ubiquitination of epigenetic modulator Wdr5.

The conclusions of this paper are mostly supported by the data provided, but the downstream molecular and tissue-level effects of Wdr5 knockdown/inhibition need to be further characterized to establish its definitive role in pons development.

(1) Figure 1E shows that Rnf220 knockdown alone could not induce an increase in Hox expression without RA, which indicates that Rnf220 might endogenously upregulate Retinoic acid signaling. The authors should test if RA signaling is downstream of Rnf220 by looking at differences in the expression of Retinaldehyde dehydrogenase genes (as a proxy for RA synthesis) upon Rnf220 knockdown.

(2) In Figure 2C-D further explanation is required to describe what criteria were used to segment the tissue into Rostral, middle, and caudal regions. Additionally, it is unclear whether the observed change in axonal projection pattern is caused due to physical deformation and rearrangement of the entire Pons tissue or due to disruption of Hox3-5 expression levels. Labeling of the tissue with DAPI or brightfield image to show the structural differences and similarities between the brain regions of WT and Rnf220 +/- will be helpful.

(3) Line 192-195. These roles of PcG and trxG complexes are inconsistent with their initial descriptions in the text - lines 73-74.

(4) In Figure 4D, the band in the gel seems unclear and erased. Please provide a different one. These data show that neither Rnf220 nor wdr5 directly regulates Hox gene expressions. The effect of double knockdown in the presence of RA suggests that they work together to suppress Hox gene expression via a different downstream target. This point should be addressed in the text and discussion section of the paper. example for the same data which shows a full band with lower intensity.

(5) In Figure 4G the authors could provide some form of quantitation for changes in ubiquitination levels to make it easier for the reader. They should also describe the experimental procedures and conditions used for each of the pull-down and ubiquitination assays in greater detail in the methods section.

(6) Figure 5 shows that neither Rnf220 nor wdr5 directly regulate Hox gene expressions. The effect of double knockdown in the presence of RA suggests that they work together to suppress Hox gene expression via a different downstream target. This point should be addressed in the text and discussion section of the paper.

(7) In Figure 6, while the reversal of changes in Hox gene expression upon concurrent Rnf220; Wdr5 inhibition highlights the importance of Wdr5 in this regulatory process, the mechanistic role of wdr5 and its functional consequences are unclear. To answer these questions, the authors need to: (i) Assay for activated and repressive epigenetic modifications upon double knockdown of Rnf220 and Wdr5 similar to that shown in Figure 4- supplement 1. This will reveal if wdr5 functions according to its intended role as part of the TrxG complex. (ii) The authors need to assay for changes in axon projection patterns in the double knockdown condition to see if Wdr5 inhibition rescues the neural circuit defects in Rnf220 +/- mice.

Reviewer #1 (Public Review):

Summary:

The authors were trying to achieve that Tgif1 expression is regulated by EAK1/2 and PTH in a time-dependent manner, and its roles in suppressing Pak3 for facilitating osteoblast adhesion. The authors further tried to achieve that the Tgif1-Pak3 signaling plays a significant role in osteoblast migration to the site of bone repair and bone remodeling.

Strengths:

- In a previous study, they demonstrated that Tgif1 is a target gene of PTH, and the absence of Tgif1 failed to increase bone mass by PTH treatment (Saito et al., Nat Commun., 2019). In this study, they found that Tgif1-Pak3 signaling prompts osteoblast migration through osteoblast adhesion to prompt bone regeneration. This novel finding provides a better understanding of how Tgif1 expression in osteoblasts regulates adherence, spreading, and migration during bone healing and bone remodeling.<br /> - The authors demonstrated that ERK1/2 and PTH regulate Tgif1 expression in a time-dependent manner and its role in suppressing Pak3 through various experimental approaches such as luciferase assay, ChIP assay, and gene silencing. These results contribute to the overall strength of the article.

Weaknesses:

None after substantial revisions especially in vivo parts.

Reviewer #2 (Public Review):

Summary:

Bolamperti S. et al. 2023 investigates whether expression of TG-interacting factor (Tgif1) is essential for osteoblastic cellular activity regarding morphology, adherence, migration/recruitment, and repair. Towards this end, germ-line Tgif1 deletion (Tgif1-/-) mice or male mice lacking expression of Tgif1 in mature osteoblastic and osteocytic cells (Dmp1-Cre+; Tgif1fl/fl) and corresponding controls were studied in physiological, bone anabolic, and bone fracture-repair conditions. Both Tgif1-/- and Dmp1-Cre+; Tgif1fl/fl exhibited decreased osteoblasts on cancellous bone surfaces and adherent to collagen I-coated plates. Tgif1-/- mice exhibit impaired healing in the tibial midshaft fracture model, as indicated by decreased bone volume (BV/Cal.V), osteoid (OS/BS), and low osteoblasts (number and surface). Likewise, both Tgif1-/- and Dmp1-Cre+; Tgif1fl/fl show impaired PTH 1-34, (100 µg/kg, 5x/wk for 3 wks) osteoblast activation in vivo, as detected by increases in quiescent bone surfaces. Mechanistic in vitro studies then utilized primary osteoblasts isolated from Tgif1-/- mice and siRNA Tgif1 knockdown OCY454 cells to further investigate and identify the downstream Tgif1 target driving these osteoblastic impairments. In vitro, Tgif1-/- osteoblastic and Tgif1 knockdown OCY454 cells exhibit decreased migration, abnormal morphology, and decreased focal adhesions/cell. Unexpectantly though, localization assays revealed Tgif1 to primarily concentrate in the nucleus and not to co-localize with focal adhesions (paxillin, talin). Also, expression of major focal adhesion components (paxillin, talin, FAK, Src etc.) or the Cdc42 family was not altered by loss of Tgif1 expression. In contrast, PAK3 expression is markedly upregulated by loss of Tgif1. In silico analysis followed by mechanistic molecular assays involving ChIP, siRNA (Tgif1, PAK3), and transfection (rat PAK3 promoter) techniques show that Tgif1 physically binds to a specific site in the PAK3 promoter region. Further, the knockdown of PAK3 rescues the Tgif1-deficient abnormal morphology in OCY454 cells. This is the first study to identify the novel transcriptional repression of PAK3 by Tgif1 as well as the specific Tgif1 binding site within the PAK3 promoter.

Strengths:

This work has a plethora of strengths. The co-authors achieved their aim in eliciting the role of Tgif1 expression to osteoblastic cellular functions (morphology, spreading/attachment, migration). Further, this work is the first to depict the novel mechanism of Tgif1 transcriptional repression of PAK3 by a through usage of mechanistic molecular assays (In silico analysis, ChIP, siRNA, transfection etc.). The conclusions are well supported and justified by these findings, as the appropriate controls, sample sizes (statistical power), statistics, and assays were fully utilized.

Claims and conclusions justified by data? Yes. absolutely

Weaknesses:

None. All reviewer comments were fully addressed.

Reviewer #2 (Public Review):

Summary:

in this paper authors show that the degree of pigmentation for RPE cells is not correlated with a level of maturation and function. They suggest that this status could be different in vitro than in vivo but do not provide proper experiments to validate this hypothesis. However, it is the first time that the absence of correlation between pigmentation and function is studied.

Strengths:

The methods are good and experiments very rigorous

Comments on current version:

The authors have modified their title and focus on QC for in vitro process

Reviewer #3 (Public Review):

Summary:

Nakai-Futatsugi et al. present a novel method to analyze the correlation between the degree of pigmentation and the gene expression profile of human-induced pluripotent stem cell-derived RPE (iPSC-RPE) cells at the single cell level. This was achieved with the use of ALPS (Automated Live imaging and cell Picking system), an invention developed by the same authors. Briefly, it allows one to choose and photograph a specific cell from a culture dish and proceed to single cell digital RNA-seq. The authors identify clusters of cells that present differential gene expression, but this showed no association with the degree of pigmentation of the cells. Further data analysis allowed the authors to correlate the degree of pigmentation to some degree with the expression of complement and lysosome-related genes.

Strengths:

An important amount of data related to gene expression and heterogeneity of the iPSC-RPE population has been generated in this work.

Weaknesses:

However, the justification of the analysis, and the physiological relevance of the hypothesis and the findings could be strengthened.

Importantly, I fail to grasp from the introduction what is the previous evidence that leads to the hypothesis. Why would color intensity be related to the quality of cell transplantation? In fact, cell transplantation is not evaluated at all in this work. The authors mention "quality metrics for clinical use", but this concept is not further explained. Neither is the concept of "sufficient degree of pigmentation" explained.<br /> On the other hand, the positive correlation of cluster formation with complement and lysosome-related genes is not discussed.

As a consequence it is very difficult to evaluate the impact of these findings on the field.

Reviewer #1 (Public Review):

Summary:

A novel serine protease and a inhibitor pair regulate cell migration in the neural crest.

Strengths:

The reproduction of classical cranial neural crest extirpations and their phenocopy by SerpinE2 morpholino are remarkable. Very scholarly written and data of the highest quality.

Weaknesses:

All were improved upon revision.

Reviewer #2 (Public Review):

Summary:

The authors conducted research on the role of SerpinE2 and HtrA1 in neural crest migration using Xenopus embryos. The data presented in this study was of high quality and supported the authors' conclusions. The discovery of the potential molecular connection between SerpinE2 and HtrA1 in neural crest cell migration in vivo is significant, as understanding this pathway could potentially lead to treatments for aggressive cancers and pregnancy-related disorders.

Strengths:

Previous research has shown that SerpinE2 and HtrA1 can have both positive and negative effects on cell migration, but their molecular interplay and role in neural crest migration are not well-established. This study is the first to reveal a potential connection between these two proteins in neural crest cell migration in vivo. The authors found that SerpinE2 promotes neural crest migration by inhibiting HtrA1. Additionally, overexpression of Sdc4 partly alleviates neural crest migration issues caused by SerpinE2 knockdown or HtrA1 overexpression. These findings suggest that the SeprinE2-HtrA1-Sdc4 pathway is crucial for neural crest migration.

Weaknesses:

To further increase the study's credibility, it may be helpful to use techniques like western blotting, qRT-PCR, or in situ hybridization to verify the efficiency of SerpinE2 and HtrA1 knockdown and/or overexpression.

Reviewer #1 (Public Review):

Summary:

Building upon their famous tool for the deconvolution of human transcriptomics data (EPIC), Gabriel et al. implemented a new methodology for the quantification of the cellular composition of samples profiled with Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq). To build a signature for ATAC-seq deconvolution, they first created a compendium of ATAC-seq data and derived chromatin accessibility marker peaks and reference profiles for 21 cell types, encompassing immune cells, endothelial cells, and fibroblasts. They then coupled this novel signature with the EPIC deconvolution framework based on constrained least-square regression to derive a dedicated tool called EPIC-ATAC. The method was then assessed using real and pseudo-bulk RNA-seq data from human peripheral blood mononuclear cells (PBMC) and, finally, applied to ATAC-seq data from breast cancer tumors to show it accurately quantifies their immune contexture.

Strengths:

Overall, the work is of very high quality. The proposed tool is timely; its implementation, characterization, and validation are based on rigorous methodologies and resulted in robust results. The newly-generated, validation data and the code are publicly available and well-documented. Therefore, I believe this work and the associated resources will greatly benefit the scientific community.

Weaknesses:

A few aspects can be improved to clarify the value and applicability of the EPIC-ATAC and the transparency of the benchmarking analysis.

Most of the validation results in the main text assess the methods on all cell types together, by showing the correlation, RMSE, and scatterplots of the estimated vs. true cell fractions. This approach is valuable for showing the overall method performance and for detecting systematic biases and noisy estimates. However, it provides very limited insights regarding the capability of the methods to estimate the individual cell types, which is the ultimate aim of deconvolution analysis. This limitation is exacerbated for rare cell types, which could even have a negative correlation with the ground truth fractions, but not weigh much on the overall RMSE and correlation. I would suggest integrating into the main text and figures an in-depth assessment of the individual cell types. In particular, it should be shown and discussed which cell types can be accurately quantified and which ones are less reliable.

In the benchmarking analysis, EPIC-ATAC is compared to several deconvolution methods, most of which were originally developed for transcriptomics data. This comparison is not completely fair unless their peculiarities and the limitations of tweaking them to work with ATAC-seq data are discussed. For instance, some methods (including the original EPIC) correct for cell-type-specific mRNA bias, which is not present in ATAC-seq data and might, thus, result in systematic errors.

On a similar note, it could be made more explicit which adaptations were introduced in EPIC, besides the ad-hoc ATAC-seq signature, to make it applicable to this type of data.

Given that the final applicability of EPIC-ATAC is on real bulk RNA-seq data, whose characteristics might not be completely recapitulated by pseudo-bulk samples, it would be interesting to see EPIC and EPIC-ATAC compared on a dataset with matched, real bulk RNA-seq and ATAC-seq, respectively. It would nicely complement the analysis of Figure 7 and could be used to dissect the commonalities and peculiarities of these two approaches.

Reviewer #2 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

Currently, the tool has a narrow applicability in that it estimates the percentage of immune cells in a bulk ATAC-seq experiment.

Comments:

(1) Has any benchmarking been done on the runtime of the tool? Although EPIC-ATAC seems to "win" in benchmarking metrics, sometimes the differences are quite small. If EPIC-ATAC takes forever to run, compared to another tool that is a lot quicker, might some people prefer to sacrifice 0.01 in correlation for a quicker running tool?

(2) In Figure 3B the data points look a bit squashed in the bottom-left corner. Could the plot be replotted with the data point spread out? There also seems to be some inter-patient variability. Could the authors comment on that?

(3) Could the authors comment on the possibility of expanding EPIC-ATAC into more than a percentage prediction tool? Perhaps EPIC-ATAC could remove the immune cell signal from the bulk ATAC-seq data to "purify" the uncharacterised cells in silico, or generate pseudo-ATAC-seq tracks of the identified cell types.

Reviewer #1 (Public Review):

Cellulose is the major component of the plant cell wall and as such is a major component of all plant biomass on the planet. It is made at the cell surface by a large membrane-bound complex known as the cellular synthase complex. It is the structure of the cellulose synthase complex that determines the structure of the cellulose microfibril, the unit of cellulose found in nature. Consequently, while understanding the molecular structure of individual catalytic subunits that synthesise individual beta 1-4 glucose chains is important, to really understand cellulose synthesis it is necessary to understand the structure of the entire complex.

In higher plants, cellulose is synthesised by a large membrane-bound complex composed of three different CESA proteins. During cellulose synthesis in the primary cell wall, this is composed of members of groups CESA1, CESA3, and CESA6. While the authors have previously presented structural data on CESA8, required for cellulose synthesis in the secondary cell wall, here they provide structural and enzymatic analysis of CESA1, CESA3, and CESA6 from soya beans.

The authors have utilised their established protocol to purify trimers for all three classes of CESA proteins and obtain structural information using electron microscopy. The structures reveal some subtle, but interesting differences between the structures obtained in this study and that previously obtained for CESA8. In particular, they identify a change in the position of transmembrane helices 7 that in previous structures formed part of the transmembrane channel. In the structure of CESA1 TM7 is shifted laterally to a position more towards the periphery of the protomer, where it is stabilised by inter-protomer interactions. This creates a large lipid-exposed channel opening that is likely encountered by the growing cellulose chain. In the discussion, the authors speculate this channel might facilitate lateral movement of cellulose chains in the membrane which would allow them to associate to form the microfibril. There is, however, no explanation for why this might be different for CESA proteins involved in primary and secondary cell wall CESA proteins.

Interactions within the trimer as stabilised by the plant conserved regions (PCR), while in common with previous studies that class-specific regions (CSR) are not resolved, are likely highly disordered as has been suggested in previous studies. As the name suggests these regions are likely to be important for determining how different CESA proteins interact, but it remains to be seen how they achieve this. Similarly, the N-terminal domain (NTD) remains rather intriguing. In the CESA3 structure, the NTD forms a stalk that protrudes into the cytoplasm that was previously observed for CESA8, while it remains unresolved in CESA1 and CESA6. The authors suggest the inability to resolve this region is likely the result of the NTD being able to form multiple conformations. Loss of the NTD does not prevent the formation of trimers and CESA1 and CESA3 are still able to interact. Previous bioinformatic studies suggest that the CSR part of the NTD is also highly class-specific (Carrol et al. 2011 Frontiers in Plant Science 2, 5-5) suggesting it is also likely to participate in interactions between different CESA proteins. This analysis provides little new information on the structure of the NTD or how it functions as part of the cellulose synthase complex.

The other important point regarding cellulose synthesis is how the different CESA trimers function during cellulose synthesis and complex assembly. The authors provide biochemical evidence that mixed complexes of two different CESA proteins are able to synergistically increase the rate of cellulose synthesis. This increase is not dramatic, around 2-fold as it is unclear what brings about this increase and whether it results from the ability to form larger complexes favouring greater rates of cellulose synthesis.

It is clear however from electron microscopy that mixing of CESA proteins can lead to the formation of large aggregates not seen with single CESA proteins. The aggregates observed do not form rosette-type shapes but appear to be much more random aggregates of different CESA trimers. The authors suggest that this is likely a result of the fact that the complexes are not constrained in two dimensions by the membrane, however, if these are biologically relevant interactions that form aggregates it is somewhat surprising that they do not form hexameric structures, particularly since they are essentially forming as a single layer.

Overall the study provides some important data and raises a number of important questions.

Reviewer #2 (Public Review):

Summary:

In their manuscript entitled "In vitro function, assembly and interaction of primary cell wall cellulose synthase homotrimers" Purushotham et al. purify and functionally and structurally characterize the primary cell wall cellulose synthase isoforms from soybeans. Overall, the manuscript is well-written and contributes several important observations.

Strengths:

The structural and functional characterization of all three primary cell wall CesA isoforms contributes significantly to important problems in plant biochemistry.

The demonstration that the isolated CesA monomers and homotrimers are catalytically active in vitro, interact with each other, and show catalytic cooperativity between the homotrimers.

Weaknesses:

The paper could be further strengthened by addressing the following:

Are the interactions between the homotrimers observed via the pull-down assays stable enough to co-elute on the sizing column or are they transient interactions?

The authors show that the monomeric CesA isoforms can interact with each other using pull-down assays (Figure Supplement 4e). Are these interactions stable or transient? Have the authors tried running the mixed monomers over a sizing column? If you mix all three isoform monomers can you form heterotrimers?

The authors demonstrate via truncation that the N-terminus of the CesA is not involved in the interactions between the isoforms and propose that the CSR hook-like extensions are the primary mediator of trimer-trimer interactions. This argument would be strengthened by equivalent truncation experiments in which the CSR region is removed.

The statement on page 6 that "All CesA isoforms show greatest catalytic activity at neutral pH" seems to contradict the data in Figure 1e and the subsequent statements.

Reviewer #3 (Public Review):

Summary:

Cellulose is a major component of the primary cell wall of growing cells and it is made by cellulose synthases (CESAs) organized into multi-subunit complexes in the plasma membrane. Previous results have resolved the structure of secondary cell wall CESAs, which are only active in a subset of cells. Here, the authors evaluate the structure of CESAs from soybeans (Glycine max, Gm) via cryo-EM and compare these structures to secondary cell wall CESAs. First, they expressed GmCESA1, GmCESA3, or GmCESA6 in insect cells, purified these proteins as both monomers and homotrimers and demonstrated their capacity to incorporate 3H-labelled glucose into the cellulase-sensitive product in a pH and divalent cation (e.g., Mg2+) -dependant fashion (Figure 1). Although CESA1, CESA3, and a CESA6-like isoform are essential for cellulose synthesis in Arabidopsis, in this study, monomers and homotrimers both showed catalytic activity, and there was more variation between individual isoforms than between their oligomerization states (i.e., CESA3 monomers and trimers showed similar activities, which were substantially different from CESA1 monomers or trimers).

They next use cryo-EM to solve the structure of each homotrimer to ~3.0 to 3.3 A (Figure 2). They compare this with PttCESA8 and find important similarities, such as the unidentified density at a positively-charged region near Arg449, Lys452, and Arg453, and differences, such as the position and relatively low resolution (suggesting higher flexibility) of TM7, which presumably creates a large lateral lipid-exposed channel opening, rather than the transmembrane pore in PttCESA8. Like PttCESA8, an oligosaccharide in the translocation channel was co-resolved with the protein structure. Neither the N-terminal domains nor the CSRs (a plant-specific insert into the cytosolic loop between TM2 and TM3) are resolved well.

Several previous models have proposed that the cellulose synthase complexes may be composed of multiple heterotrimers, but since the authors were able to isolate beta-glucan-synthesizing homotrimers, their results challenge this model. Using the purified trimers, the authors investigated how the CESA homotrimers might assemble into higher-order complexes. They detected interactions between each pair of CESA homotrimers via pull-down assays (Figure 3), although these same interactions were also detected among monomers (Supplemental Figure 4). Neither catalytic activity nor these inter-homotrimer interactions required the N-terminal domain (Figure 4). When populations of homotrimers were mixed, they formed larger aggregations in vitro (Figure 4) and displayed increased activity, compared to the predicted additive activity of each enzyme alone (Figure 5). Intriguingly, this synergistic behavior is observed even when one trimer is chemically inactivated before mixing (Supplemental Figure 6), suggesting that the synergistic effects are due to structural interactions.

Strengths:

The main strength of this manuscript is its detailed characterization of the structure of multiple CESAs, which complements previous studies of secondary cell wall CESAs. They provide a comprehensive comparison of these new structures with previously resolved CESA structures and discuss several intriguing similarities and differences. The synergistic activity observed when different homotrimers are mixed is a particularly interesting result. These results provide fundamental in vitro support for a cellulose synthase complex comprised of a hexamer of CESA homotrimers.

Weaknesses:

There are several weaknesses in the manuscript. The authors do not present any data to indicate that GmCESA1, GmCESA3, and GmCESA6 are primary cell wall CESAs (e.g. expression patterns, phylogenetic evidence). Furthermore, their evidence that these proteins make cellulose in vitro is limited to the beta-glucanase-sensitive digestion of the product. Previous reports characterizing CESA structures have used multiple independent methods: sensitivity and resistance of the product to various enzymes, linkage analysis, and importantly, TEM of the product to ensure that it makes genuine cellulose microfibrils, rather than amorphous beta-glucan. Without demonstrating that GmCESA1, GmCESA3, and GmCESA6 are genuinely synthesizing cellulose microfibrils (via TEM) and that they are primary cell wall CESAs (via expression patterns & phylogenetic evidence), it is difficult to place the results into context. Finally, the authors indicate that they were unable to isolate heterotrimers in vitro, but they do not present any evidence of these experiments, which is essential to evaluate their conclusion that these CESAs operate as homotrimers in vitro.

Reviewer #1 (Public Review):

Summary:

This manuscript successfully established a new short-term model of diabetic retinopathy by treating zebrafish embryos with high concentrations of monosaccharides, resembling the hyperangiogenic characteristics observed in proliferative diabetic retinopathy in patients. They found that excessive angiogenesis induced by glucose and noncaloric monosaccharides was achieved by activating the quiescent endothelial cells into proliferating tip cells. Importantly, the authors further confirmed the effects of monosaccharides on inducing excessive angiogenesis were mediated by the foxo1a-marcksl1a pathway.

Strengths:

These results showed the potentially detrimental effects of the noncaloric monosaccharides on blood vessel function and provided novel insights into the underlying mechanisms.

Weaknesses:

The mechanism of noncaloric monosaccharides inducing excessive sprouting angiogenesis is not solid enough.

Reviewer #2 (Public Review):

In the manuscript entitled "Noncaloric monosaccharides induce excessive sprouting angiogenesis in zebrafish via foxo1a-marcksl1a signal". Liu et al. observed that glucose and noncaloric monosaccharides can prompt an excessive formation of blood vessels, particularly intersegmental vessels (ISVs). They propose that these branched vessels arise from the ectopic activation of quiescent endothelial cells (ECs) into tip cells. Moreover, through single-cell transcriptome sequencing analysis of embryonic endothelial cells exposed to glucose, they noted an increased proportion of arterial and capillary endothelial cells, proliferative endothelial cells, along with a series of upregulated genes in categories of blood vessel morphogenesis, development, and pro-angiogenesis. The authors provide evidence suggesting that caloric and noncaloric monosaccharides (NMS) induce excessive angiogenesis via the foxo1a-Marcksl1a pathway.

The authors address an important problem about the effects of artificially sweetened beverages such as noncaloric monosaccharides on blood vessels. However, the study lacks adequate experimental data and comprehensive analyses to support the mechanistic conclusions, which require extensive revisions.

Reviewer #3 (Public Review):

The authors have investigated the effect of noncaloric monosaccharides on angiogenesis in the zebrafish embryo. These compounds are used as substitutes of sugars to sweeten beverages and they are commonly used by diabetic patients. The authors show that noncaloric monosaccharides and glucose similarly induce excessive blood vessel formation due to the increased formation of tip cells by endothelial cells. The authors show that this excessive angiogenesis involved the foxo1a-marcksl1a pathway.

A limitation of the study is that the mechanism of angiogenesis in the retinal circulation and in peripheral vasculature is certainly different.

This result suggests that these noncaloric monosaccharides share common side effects with glucose. Consequently, more caution should be taken with regard to the use of these artificial sweeteners. This work is of interest for better management of diabetes.

Reviewer #1 (Public Review):

Summary:

This impressive study by Bandet and Winship uses 2-photon imaging in awake behaving mice to examine long-term changes in neural activity and functional connectivity after focal ischemic stroke. The authors discover that there are long-lasting perturbations in neural activity and functional connectivity, specifically within peri-infarct cortex but not more distant cortical regions. Overall I thought the study provided important new findings that were supported by compelling data.

Strengths:

This is a technically challenging study and the experiments appear to be well done. The manuscript was written in a concise manner, and the figures were clearly presented. The analytic tools were rigorous and appropriate, leading to novel insights regarding neural activity patterns during movement or rest. The discovery of long-lasting impairments in neural activity/functional connectivity is important (and often overlooked) given that future stroke studies need to recognize what problems exist in order to properly rectify them. The authors also question the spatial extent to which functional changes occur after stroke, at least at the single cell level. Overall, I think this was a well-executed study whose primary conclusions were justified by the data presented.

Weaknesses:

I found very little in the way of weaknesses. The authors addressed my comments about the methodology, statistical analysis, normalization of data and discussion points about cortical plasticity during stroke recovery.

Reviewer #2 (Public Review):

This study investigates the excitability of neurons in the peri-infarct cortex during recovery from ischemic stroke. The excitability of neurons in the peri-infarct cortex during stroke recovery has produced contradictory findings: some studies suggest hyper-excitability to direct-brain stimulation, while others indicate diminished responsiveness to physical stimuli. However, most studies have used anesthetized animals, which can disrupt cortical activity and functional connectivity. The present study used two-photon Ca2+ imaging after focal photothrombotic stroke to examine neural activity patterns in awake mice. The authors found reduced neuronal spiking in the peri-infarct cortex that was strongly correlated with motor performance deficits. Additionally, the authors found disruptions in neural activation, functional connectivity, and assembly architecture in the immediate peri-infarct region but not in the distal cortex regions.

The findings of this study are very important as they show that there is no measurable change in terms of neuronal activation and reorganization in distal regions of remapped cortical response areas after stroke.

Reviewer #1 (Public Review):

Summary:

This is an interesting study by Xu et al showing the effects of infection with the Treponema pallidum virus (which causes syphilis disease) on neuronal development using iPSC-derived human brain organoids as a model and single-cell RNA sequencing. This work provides an important insight into the impact of the virus on human development, bridging the gap between the phenomena observed in studies using animal models as well as non-invasive human studies showing developmental abnormalities in fetuses infected with the virus in utero through maternal vertical transmission.

Using single-cell RNAseq in combination with qPCR and immunofluorescence techniques, the authors show that T. pallidum infected organoids are smaller in size, in particular during later growth stages, contain a larger number of undifferentiated neuronal lineage cells, and exhibit decreased numbers of specific neuronal subcluster, which the authors have identified as undifferentiated hindbrain neurons.

The study is an important first step in understanding how T. pallidum affects human neuronal development and provides important insight into the potential mechanisms that underlie the neurodevelopmental abnormalities observed in infected human fetuses. Several important weaknesses have also been noted, which need to be addressed to strengthen the study's conclusions.

Strengths:

(1) The study is well written, and the data quality is good for the most part.

(2) The study provides an important first step in utilizing human brain organoids to study the impact of T. pallidum infection on neuronal development.

(3) The study's conclusions may provide important insight to other researchers focused on studying how viral infections impact neuronal development.

Weaknesses:

(1) It is unclear how T. pallidum infection was validated in the organoids. If not all cells are infected, this could have important implications for the study's conclusions, in particular the single-cell RNAseq experiments. Were only cells showing the presence of the virus selected for sequencing? A detailed description of how infection was validated and the process of selection of cells for RNAseq would strongly support the study's conclusions.

(2) The authors show that T. pallidum infection results in impaired development of hindbrain neurons. How does this finding compare to what has already been shown in animal studies? Is a similar deficit in this brain region observed with this specific virus? It would be useful to strengthen the study's conclusions if the authors added a discussion about the observed deficits in hindbrain neuronal development, and prior literature on similar studies conducted in animal models or human patients. Does T. pallidum preferentially target these neurons, or is this a limitation of the current organoid model system?

(3) The authors show that T. pallidum-infected organoids are smaller in size by measuring organoid diameter during later stages of organoid growth, with no change during early stages. Does that represent insufficient infection at the early stages? Is this due to increased cell death or lack of cell division in the infected organoids? Experiments using IHC to quantify levels of cleaved caspase and/or protein markers for cell proliferation would be able to address these questions.

4) In Figure 1D authors show differences in rosette-like structure in the infected organoids. The representative images do not appear to be different in any of the discussed components (e.g., the sox2 signal looks fairly similar between the two conditions). No quantification of these structures was presented. Authors should provide quantification or a more representative image to support their statement.

5) The IHC images shown in Figures 3E, G, and Figure 4E look very similar between the two conditions despite the discussed decrease in the text. A more suitable representative image should be presented, or the analysis should be amended to reflect the observed results.

Reviewer #2 (Public Review):

Summary:

This study provides an important overview of infectious etiology for neurodevelopment delay.

Strengths:

Strong RNA evaluation.

Weaknesses:

The study lacks an overview of other infectious agents. The study should address the epigenetic contributors (PMID: 36507115) and the role of supplements in improving outcomes (PMID: 27705610).<br /> Addressing the above - with references included - is recommended.

Reviewer #3 (Public Review):

This article is the first report to study the effects of T. pallidum on the neural development of an iSPC-derived brain organoid model. The study indicates that T. pallidum inhibits the differentiation of subNPC1B neurons into hindbrain neurons, hence affecting brain organoid neurodevelopment. Additionally, the TCF3 and notch signaling pathways may be involved in the inhibition of the subNPC1B-hindbrain neuron differentiation axis. While the majority of the data in this study support the conclusions, there are still some questions that need to be addressed and data quality needs to be improved. The study provides valuable insights for future investigations into the mechanisms underlying congenital neurodevelopment disability.

Reviewer #1 (Public Review):

Summary:

This manuscript aimed to investigate the emergence of emotional sensitivity and its relationship with gestational age. Using an oddball paradigm and event-related potentials, the authors conducted an experiment in 120 healthy neonates with a gestational age range of 35 to 40 weeks. A significant developmental milestone was identified at 37 weeks gestational age, marking a crucial juncture in neonatal emotional responsiveness.

Strengths:

This study has several strengths, by providing profound insights into the early development of social-emotional functioning and unveiling the role of gestational age in shaping neonatal perceptual abilities. The methodology of this study demonstrates rigor and well-controlled experimental design, particularly involving matched control sounds, which enhances the reliability of the research. Their findings not only contribute to the field of neurodevelopment, but also showcase potential clinical applications, especially in the context of autism screening and early intervention for neurodevelopmental disorders.

Weaknesses:

More details should be provided in terms of inclusion and exclusion criteria for the participants, as well as missing data due to the non-cooperation of newborns during the experimental process. Potential differences between preterm and full-term infants are worth exploring. Several aspects of EEG data analyses and data interpretation should be better clarified.

Reviewer #2 (Public Review):

Summary:

This is an important and very interesting report on a change in newborns' neural abilities to distinguish auditory signals as a function of the gestational age (GA) of the infant at birth (from 35 weeks GA to 40 weeks GA). The authors tested neural discrimination of sounds that were labeled 'happy' vs 'neutral' by listeners that represent two categories of sound, either human voices or auditory signals that mimic only certain properties of the human vocal signals. The finding is that a change occurs in neural discrimination of the happy and neutral auditory signals for infants born at or after 37 weeks of gestation, and not prior (at 35 or 36 weeks of gestation), and only for discrimination of the human vocal signals; no change occurs in discrimination of the nonhuman signals over the 35- to 40-week gestational ages tested. The neural evidence of discrimination of the vocal happy-neutral distinction and the absence of the discrimination of the control signals is convincing. The authors interpret this as a 'landmark' in infants' ability to detect changes in emotional vocal signals, and remark on the potential value of the test as a marker of the infants' interest in emotional signals, underscoring the fact that children at risk for autism spectrum disorder may not show the discrimination. Although the finding is novel and interesting, additional discussion is essential so that readers understand two potential caveats affecting this interpretation.

Strengths:

The event-related potential (ERP) method and results are clear, well-described, and convincing.

Weaknesses/ Information needed:

First, readers need to see spectrograms that show the 0-4000 Hz in more detail, rather than what is now shown (0-10,000 Hz). The vocal signals in clearer spectrograms will show I believe the initial consonant burst and formant frequencies that are unique to human speech and give rise to the perception of the consonant sounds in the vocal signals like 'dada' and 'tutu' that were tested. The control signals will presumably not show these abrupt acoustic changes at their onset, even though they appear (from the oscillograms) to approximate the amplitude envelope. The primary cue distinguishing the happy and neutral signals in both the vocal and control signals is the pitch of the signals (high vs low), but the burst of energy representing the consonants is only contained in the vocal signals; it has no comparable match in the control signals. It is possible that the presence of a sharp acoustic onset (a unique characteristic of consonants in human speech) is especially alerting to the infants, and that this acoustic cue, in the context of the pitch change, enhances discrimination in the vocal case. One way to test this would be to use only vowel sounds to represent the vocal signals, without consonants. Another critical detail that the authors need to include about the signals is an explanation of how the control signals were generated. The text states that the Fo and amplitude envelope of the vocal signals were mimicked in the control signals, but what was the signal used for the controls? Was a pure tone complex modulated, or was pink noise used to generate the control signals? Or were the original vocal signals simply filtered in some way to create the controls, which would preserve the Fo and amplitude envelope? If merely filtered, the control signals still may be perceived as 'vocal' signals, rather than as nonspeech (the Supplement contains the sounds, and some of the control sounds can be perceived, to my ear, as 'vocal' signals).

Second, there is no information in the manuscript or supplement about the auditory environment of the participants, nor discussion of the fetus' ability to hear in the womb. In the womb, infants are listening to the mothers' bone-conducted speech (which is full of consonant sounds), and we know from published studies that infants can discern differences not only in the prosody of the speech they hear in the womb, but the phonetic characteristics of the mother's speech. The ability at 37 weeks GA or beyond to discriminate the pitch changes in the vocal, but not control signals, could thus be due to additional experience in utero to speech. Another experiential explanation is that the infants born at 37 weeks GA and beyond may be exposed to greater amounts of speech after birth, when compared to those born at 35 and 36 weeks GA, from the attending nurses and from their caregivers, and this speech is also full of consonant sounds. What these infants hear is likely to be 'infant-directed speech,' which is significantly higher in pitch, mirroring the signals tested here. At 37 weeks GA, infants are likely more robust, may sleep less, and are likely more alert. If infants' exposure to speech, either after birth, or their auditory ability to discern differences in speech in utero, is enhanced at 37 weeks GA and beyond, then an 'experience-related' explanation is a viable alternative to a maturational explanation, and should be discussed. Perhaps both are playing a role. As the authors state, many more signals need to be tested to discern how the effect should be interpreted, and other viable interpretations of the current results discussed.

Reviewer #1 (Public Review):

Summary:

In this manuscript, the authors describe a new pipeline to measure changes in vasculature diameter upon opt-genetic stimulation of neurons.

The work is interesting and the topic is quite relevant to better understand the hemodynamic response on the graph/network level.

Strengths:

The manuscript provides a pipeline that allows for the detection of changes in the vessel diameter as well as simultaneously allowing for the location of the neurons driven by stimulation.

The resulting data could provide interesting insights into the graph-level mechanisms of regulating activity-dependent blood flow.

The interesting findings include that vessel radius changes depend on depth from the cortical surface and that dilations on average happen closer to the activated neurons.

Weaknesses:

The utility of a pipeline depends on the generalization properties.

While the proposed pipeline seems to work for the data the authors acquired, it is unclear if this pipeline will actually generalize to novel data sets possibly recorded by a different microscope (e.g. different brand), or different imagining conditions (e.g. illumination or different imagining artifacts) or even to different brain regions or animal species, etc.

The authors provide a 'black-box' approach that might work well for their particular data sets and image acquisition settings but it is left unclear how this pipeline is actually widely applicable to other conditions as such data is not provided.

In my experience, without well-defined image pre-processing steps and without training on a wide range of image conditions pipelines typically require significant retraining, which in turn requires generating sufficient amounts of training data, partly defying the purpose of the pipeline.

It is unclear from the manuscript, how well this pipeline will perform on novel data possibly recorded by a different lab or with a different microscope.

Analysis

Some of the chosen analysis results seem to not fully match the shown data, or the visualization of the data is hard to interpret in the current form. Additionally, some measures seem not fully adapted to the current situation (e.g. the efficiency measure does not consider possible sources or sinks). Thus, some additional analysis work might be required to account for this.

Reviewer #2 (Public Review):

Summary:

The authors develop a highly detailed pipeline to analyze hemodynamic signals from in vivo two-photon fluorescence microscopy. This includes motion correction, segmentation of the vascular network, diameter measurements across time, mapping neuronal position relative to the vascular network, and analyzing vascular network properties (interactions between different vascular segments). For the segmentation, the authors use a Convolution Neural Network to identify vessel (or neural) and background pixels and train it using ground truth images based on semi-automated mapping followed by human correction/annotation. Considerable processing was done on the segmented images to improve accuracy, extract vessel center lines, and compute frame-by-frame diameters. The model was tested with artificial diameter increases and Gaussian noise and proved robust to these manipulations.

Network-level properties include Assortativity - a measure of how similar a vessel's response is to nearby vessels - and Efficiency - the ease of flow through the network (essentially, the combined resistance of a path based on diameter and vessel length between two points).

Strengths:

This is a very powerful tool for cerebral vascular biologists as many of these tasks are labor intensive, prone to subjectivity, and often not performed due to the complexity of collecting and managing volumes of vascular signals. Modelling is not my specialty so I cannot speak too specifically, but the model appears to be well-designed and robust to perturbations. It has many clever features for processing the data.

The authors rightly point out that there is a real lack in the field of knowledge of vascular network activity at single-vessel resolution. Network anatomy has been studied, but hemodynamics are typically studied either with coarse resolution or in only one or a few vessels at a time. This pipeline has the potential to change that.

Weaknesses:

The authors apply their method to in vivo data. However, there are some weaknesses in the design that make it hard to accept many of the conclusions and even to see that the method could yield much useful data with this type of application. Primarily, the acquisition of a large volume of tissue is very slow. In order to obtain a network of vascular activity, large volumes are imaged with high resolution. However, the volumes are scanned once every 42 seconds following stimulation. Most vascular responses to neuronal activation have come and gone in 42 seconds so each vessel segment is only being sampled at a single time point in the vascular response. So all of the data on diameter changes are impossible to compare since some vessels are sampled during the initial phase of the vascular response, some during the decay, and many probably after it has already returned to baseline. The authors attempt to overcome this by alternating the direction of the scan (from surface to deep and vice versa). But this only provides two sample points along the vascular response curve and so the problem still remains.

A second problem is the use of optogenetic stimulation to activate the tissue. First, it has been shown that blue light itself can increase blood flow (Rungta et al 2017). The authors note the concern about temperature increases but that is not the same issue. The discussion mentions that non-transgenic mice were used to control for this with "data not shown". This is very important data given these earlier reports that have found such effects and so should be included. Secondly, there doesn't seem to be any monitoring of neural activity following the photo-stimulation. The authors repeatedly mention "activated" neurons and claim that vessel properties change based on distance from "activated" neurons. But I can't find anything to suggest that they know which neurons were active versus just labeled. Third, the stimulation laser is focused at a single depth plane. Since it is single-photon excitation, there is likely a large volume of activated neurons. But there is no way of knowing the spatial arrangement of neural activity and so again, including this as a factor in the analysis of vascular responses seems unjustified.

The study could also benefit from more clear illustration of the quality of the model's output. It is hard to tell from static images of 3-D volumes how accurate the vessel segmentation is. Perhaps some videos going through the volume with the masks overlaid would provide some clarity. Also, a comparison to commercial vessel segmentation programs would be useful in addition to benchmarking to the ground truth manual data.

Another useful metric for the model's success would be the reproducibility of the vessel responses. Seeing such a large number of vessels showing constrictions raises some flags and so showing that the model pulled out the same response from the same vessels across multiple repetitions would make such data easier to accept.

A number of findings are questionable, at least in part due to these design properties.

There are unrealistically large dilations and constrictions indicated. These are likely due to artifacts of the automated platform. Inspection of these results by eye would help understand what is going on.

In Figure 6, there doesn't seem to be much correlation between vessels with large baseline level changes and vessels with large stimulus-evoked changes. It would be expected that large arteries would have a lot of variability in both conditions and veins much less. There is also not much within-vessel consistency. For instance, the third row shows what looks like a surface vessel constricting to stimulation but a branch coming off of it dilating - this seems biologically unrealistic.

As mentioned, the large proportion of constricting capillaries is not something found in the literature. Do these happen at a certain time point following the stimulation? Did the same vessel segments show dilation at times and constriction at other times? In fact, the overall proportion of dilators and constrictors is not given. Are they spatially clustered? The assortativity result implies that there is some clustering, and the theory of blood stealing by active tissue from inactive tissue is cited. However, this theory would imply a region where virtually all vessels are dilating and another region away from the active tissue with constrictions. Was anything that dramatic seen?

As mentioned, the claims about distance to active neurons are not meaningful if there is no measure of which neurons were active and which weren't. But even still, the claim is overly strong as the average distance to the nearest neuron for dilators was ~17 microns and for constrictors it was ~22 microns - about a half a neuronal soma difference.

The distance to the nearest neuron likely will depend on depth as well - neurons are quite sparse superficially and very dense in layer 4. The capillary network varies much less (see Blinder et al 2016 Nature Neuroscience). So the distance of a neuron to the nearest capillary may not vary much with depth, but the distance from the capillary to the nearest neuron might vary quite a lot.<br /> Why were nearly all vessels > 5um diameter not responding >2SD above baseline? Did they have highly variable baselines or small responses? Usually, bigger vessels respond strongly to local neural activity.

Reviewer #1 (Public Review):

The work by Ginatt et al. uses genome-scale metabolic modeling to identify and characterize trophic interactions between rhizosphere-associated bacteria. Beyond identifying microbial species associated with specific host and soil traits (e.g., disease tolerance), a detailed understanding of the interactions underlying these associations is necessary for developing targeted microbiome-centered interventions for plant health. It has nonetheless remained challenging to define the roles of specific organisms and metabolic species in natural rhizobiomes. Here, the authors combine microbial compositional data obtained through metagenomic sequencing with a new collection of genome-scale models to predict interactions in the native rhizosphere communities of apple rootstocks. To do this, they have established processes to integrate these sources of data and model specific trophic exchanges, which they use to obtain testable hypotheses for targeted modulation of microbiota members in situ.

The authors carry out a careful model curation process based on metagenomic sequencing data and existing model generation tools, which, together with basing the in silico medium composition on known root exudates, strengthens their predictions of interaction network features. Moreover, its reliance on genome-scale models provides a broader basis for linking sequence-based information to predictions of function on a multispecies level beyond rhizosphere microbiomes.

Having generated a set of predicted trophic interactions, the authors carried out a detailed analysis linking features of these interactions to organism taxonomy and broader ecosystem properties. Intriguingly, the organisms predicted to grow in the first iteration of their framework (i.e., on only root exudates) broadly correspond to taxonomic groups experimentally shown to benefit from these compounds. Additionally, the simulations predicted some patterns of vitamin and amino acid secretion that are known to form the basis for interactions in the rhizosphere. Together, these outcomes underscore the applicability of this method to help disentangle trophic interaction networks in complex microbiomes.

The methodology described in this paper represents a useful and promising framework to better understand the complexity of microbial interaction networks in situ. However, the degree to which the predictions can vary according to environmental composition remains difficult to quantify, and the work does not address the sensitivity of the modeling predictions beyond a simulated medium containing 33 root exudates. I find this especially important given that relatively few (84 of 243) species were predicted to grow even after cross-feeding, suggesting that a richer medium could lead to different interaction network structures. While the authors do state the importance of environmental composition and have carefully designed an in silico medium, I believe that simulating a broader set of resource pools would add necessary insight into both the predictive power of the models themselves and trophic interactions in the rhizosphere more generally.

Reviewer #2 (Public Review):

Summary:

The authors present a framework for exploiting shotgun metagenomics and metabolomics data along with constraint-based analysis (CBA) to study, in their case, the dynamics and interactions between the apple rootstock and rhizosphere's microbial community. This study should be considered as a follow-up of Berihu et al. (2022) where the shotgun data were first introduced. A set of 395 Metagenome-Assembled Genomes (MAGs) was derived from those reads and from the latter, using an automatic Genome-scale Metabolic Model (GSMM) reconstruction tool (CarveMe), 243 GSMMs. Metabolomics data from a set of studies were gathered to describe/represent root exudates. Flux Variability Analysis (FVA), a type of constraint-based analysis, was conducted iteratively. Three distinct in silico media were used (optimal, poor, and realistic, with the latter informed by metabolomics data) to examine the potential impact of root exudates on bacterial growth. Additionally, the study investigated the extent to which compounds secreted by bacteria could support the growth of other community members. Further, an exchange network representing all potential metabolic exchanges within the rhizosphere community was built and motifs on it were classified with healthy and/or symptomized soil.

Strengths:

The study provides a great starting point for how one can bring together shotgun metagenomics and other omics technologies such as metabolomics with metabolic modelling approaches. MAGs and the automatic reconstruction of corresponding GSMMs become more and more a common practice and frameworks for their analysis and interpretation are more than needed. The usage of FVA instead of the Flux Balance Analysis allows the authors to get all the range of potentially produced metabolites. The iterative approach can highlight what species are supported by the plant and which need the first to join the community while correlating microbial metabolic interactions with soil performance through differential abundance can bring up valid hypotheses to examine further. On top of that, avoiding modelling approaches that require community objective functions and optimization of that makes the simulation more realistic.

Weaknesses:

There are two main drawback approaches like the one described here, both related only partially to the authors' work yet with great impact in the presented framework. First, the usage of automatic GSMM reconstruction requires great caution. It is indicative of how the semi-curated AGORA models are still considered reconstructions and expect the user to parameterize those in a model. In this study, CarveMe was used. CarveMe is a well-known tool with several pros [1]. Yet, several challenges need to be considered when using it [2]. For example, the biomass function used might lead to an overestimation of auxotrophies. Also, as its authors admit in their reply paper, CarveMe does gap fill in a way [3]; models are constructed to ensure no gaps and also secure a minimum growth. However, curation of such a high number of GSMMs is probably not an option. Further, even if FVA is way more useful than FBA for the authors' aim, it does not yet ensure that when a species secretes one compound (let's say metabolite A), the same flux vector, i.e. the same metabolic functioning profile, secretes another compound (metabolite B) at the same time, even if the FVA solution suggests that metabolite B could be secreted in general.

Besides those challenges, the suggested framework is promising and such approaches can work as the starting point for the next step in microbial ecology studies in general; from soil to marine and host ecosystems. The authors highlight perfectly this angle stating that this framework is currently conceptual and that it can be only used to formulate new hypotheses. Unbiased constraint-based approaches that focus on metabolite exchanges would benefit such approaches.

[1] Mendoza, Sebastián N., et al. "A systematic assessment of current genome-scale metabolic reconstruction tools." Genome biology 20.1 (2019): 1-20.<br /> [2] Price, Morgan. "Erroneous predictions of auxotrophies by CarveMe." Nature Ecology & Evolution 7.2 (2023): 194-195.<br /> [3] Machado, Daniel, and Kiran R. Patil. "Reply to: Erroneous predictions of auxotrophies by CarveMe." Nature Ecology & Evolution 7.2 (2023): 196-197.<br /> [4] Ylva Katarina Wedmark, Jon Olav Vik, Ove Øyås bioRxiv 2023.09.05.556413; doi: https://doi.org/10.1101/2023.09.05.556413

Reviewer #3 (Public Review):

Summary:

This study presents a solid framework for the metabolic modeling of microbial species and resources in the rhizosphere environment. It is an ambitious effort to tackle the huge complexity of the rhizosphere and reveal the plant-microbiota interactions therein. Considering previously published data by Berihu et al., going through a series of steps, the framework then finds associations between an apple tree disease state and both microbes and metabolites. The framework is well explained and motivated. I think that further work should be done to validate the method, both using synthetic data, with a known ground truth and following up on key findings experimentally.

Strengths:

- The manuscript is well written with a good balance between detail and readability. The framework steps are well-motivated and explained.

- The authors faithfully acknowledge the limitations of their approach and do not try to "over-sell" their conclusions.

- The presented framework has the potential for significant discovery if the hypotheses generated are followed up with experimental validation.

Weaknesses:

- When presenting a computational framework, best practices include running it on artificial (synthetic) data where the ground truth is known and therefore the precision and accuracy of the method may be assessed. This is not an optional step, the same way that positive/negative controls in lab experiments are not optional. Without this validation step, the manuscript is severely limited. The authors should ask themselves: what have we done to convince the reader that the framework actually works, at least on our minimal synthetic data?

Justification of claims and conclusions:

The claims and conclusions are sufficiently well justified since the limitations of this approach are acknowledged by the authors.

Reviewer #1 (Public Review):

Summary:

Gain-of-function mutations and amplifications of PPM1D are fond across several human cancers and are associated with advanced tumor stage, worse prognosis, and increased lymph node metastasis. This manuscript presents important findings that SOD1 inhibition is a potential strategy to achieve therapeutic synergism for PPM1D-mutant leukemia; and demonstrates the redox landscape of PPM1D-mutant cells.

Strengths:

In this manuscript, Zhang and colleagues investigate the synthetic-lethal dependencies of PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) in leukemia cells using CRISPR/Cas9 screening. They identified that SOD1 (superoxide dismutase-1) as the top hit, whose loss reduces cellular growth in PPM1D-mutant cells, but not wildtype (WT) cells. Consistently, the authors demonstrate that PPM1D-mutant cells are more sensitive to SOD1 inhibitor treatment. By performing different in vitro studies, they show that PPM1D-mutant leukemia cells have elevated level of reactive oxygen species (ROS), decreased basal respiration, increased genomic instability, and impaired non-homologous end-joining repair. These data highlight the potential of SOD1 inhibition as a strategy to achieve therapeutic synergism for PPM1D-mutant leukemia; and demonstrates the redox landscape of PPM1D-mutant cells.

Weaknesses:

While the current study has identified synthetic lethality of PPM1D-mutant leukemia cells upon SOD1 inhibition, the underlying mechanism remains elusive. Although ROS levels have been assessed between wild-type (WT) and PPM1D-mutant leukemia cells, the specific redox alterations induced by SOD1 inhibition in PPM1D mutant versus WT cells have not been elucidated. To address this gap, direct comparisons of ROS levels using various probes should be conducted between PPM1D mutant and WT cells under conditions of SOD1 inhibition.

Reviewer #3 (Public Review):

Summary:

Authors performed a genome-wide CRISPR-based screen for synthetic lethal interactions in leukemic cells expressing a mutant form of PPM1D and identified SOD1. Loss of SOD1 or its inhibition with small molecule compounds reduced survival of the cells containing truncated PPM1D. Further analysis revealed that mitochondria are functionally deficient in PPM1D mutant cells resulting in increased levels of ROS. Surprisingly, expression profiling and reverse phase protein arrays revealed that PPM1D mutant cells did not respond appropriately to the increased levels of ROS. The precise molecular mechanism underlying this phenotype remains currently unclear, nevertheless the study convincingly shows that PPM1D mutant cells are vulnerable to oxidative stress.

Strengths:

Experimental procedures used in the study are appropriate and overall the presented data are very convincing. The study identified an important vulnerability of leukemic cells that carry PPM1D mutation and provides a fundamental background for testing SOD1 inhibitors in preclinical research. In the revised version of the manuscript, authors provide several new experiments that support their former conclusions. In particular, they showed that deletion of SOD1 in AML cells improved survival of the transplanted mice and this effect was more prominent when using cells carrying the mutant PPM1D. Further, they included an important control experiment that showed decreased SOD1 activity after treatment with ATN-224 inhibitor.

Weaknesses:

In the opinion of reviewer, there are no obvious weaknesses in this study. In broader view, the findings presented here using in vitro cultures will need to be validated in vivo by future research. Cell lines used in the study were generated by CRSIPR approaches in AML cells that have already been transformed. In addition, genome editing is inheritably connected with a risk of off target effects. It would therefore be great to identify AML samples carrying the PPM1D mutation that has been naturally selected during the transformation process.

Reviewer #1 (Public Review):

Warming and precipitation regime change significantly influences both above-ground and below-ground processes across Earth's ecosystems. Soil microbial communities, which underpin the biogeochemical processes that often shape ecosystem function, are no exception to this, and although research shows they can adapt to this warming, population dynamics and ecophysiological responses to these disturbances are not currently known. The Qinghai-Tibet Plateau, the Third Pole of the Earth, is considered among the most sensitive ecosystems to climate change. The manuscript described an integrated, trait-based understanding of these dynamics with the qSIP data. The experimental design and methods appear to be of sufficient quality. The data and analyses are of great value to the larger microbial ecological community and may help advance our understanding of how microbial systems will respond to global change. There are very few studies in which the growth rates of bacterial populations from multifactorial manipulation experiments on the Qinghai-Tibet Plateau have been investigated via qSIP, and the large quantity of data that comprises the study described in this manuscript, will substantially advance our knowledge of bacterial responses to warming and precipitation manipulations.

Reviewer #1 (Public Review):

Osteoarthritis (OA) is associated with painful, chronic inflammation that often leads to severe joint pain and joint stiffness for people over the age of 55. There is no effective therapeutic drug in the treatment of osteoarthritis. The authors found that mice without Cbfβ in their chondrocytes develop spontaneous OA. Authors uncovered that the deficiency of Cbfβ caused increased canonical Wnt signaling and inflammatory response, and decreased Hippo/YAP signaling and TGF-β signaling in articular cartilage. Authors showed that ACLT surgery-induced OA decreased Cbfβ and Yap expression and increased active β-catenin expression in articular cartilage, while local AAV-mediated Cbfβ overexpression promoted Yap expression, diminished active β-catenin expression in OA lesions. The authors demonstrated that AAV-mediated Cbfβ overexpression in knee joints of mice with OA showed the significant protective effect of Cbfβ on articular cartilage in the ACLT OA mouse model. The results from the study demonstrated Cbfβ maintains articular cartilage homeostasis through inhibiting Wnt/β-catenin signaling and increasing Hippo/Yap, and TGFβ signaling. Importantly, the authors proved that local Cbfβ overexpression could be an effective strategy for treatment of OA. The data shown in the study demonstrated that the findings are novel and very significant, and the authors' claims and conclusions are justified by their data. The paper is generally excellent with an interesting scientific premise and strong scientific rigor. The findings in this manuscript are novel, the manuscript is clearly written, and the findings will make a significant impact in the field.

Reviewer #2 (Public Review):

In this manuscript, Chen et al. reported that the core binding factor beta (Cbfβ), a heterodimeric subunit of the RUNX family transcription factors (TFs), is crucial in maintaining cartilage homeostasis and counteracting traumatic OA pathology. Using mouse models in which Cbfβ is conditionally inactivated in the Col2a1+ and Acan+ cells, the authors claimed that Cbfβ ablation led to articular cartilage (AC) degeneration, which is associated with aberrant cartilage gene expression and chondrocyte signaling, particularly the elevated Wnt/Catenin and the decreased Hippo/YAP and TGFβ signaling. The authors further showed that Cbfβ transcripts are decreased in human OA cartilage, and sustaining Cbfβ expression in mouse knee joints mitigated the severity of surgery-evoked OA.

On the whole, the work reported is interesting and exciting. Genetic and biochemical data support key statements. Both in vivo and in vitro experiments were well designed with proper controls; semiquantitative data were digitalized and processed for statistical significance. Furthermore, new findings were adequately discussed in contrast to the current available knowledge. However, the conceptual novelty of this study is slightly compromised by recent publications showing that Cbfβ reduction is associated with OA (Che et al. 2023; Li et al. 2021). Also, the authors claimed that multiple signaling pathways were affected by Cbfβ ablation in cartilage cells; many of them, however, are indirect effects given the nature of Cbfβ as a TF. The authors also showed that pSMAD2/3 and active βCatenin decreased and increased upon Cbfβ depletion in the mouse AC cartilage. However, how the deficiency of Cbfβ, a widely expressed TF, affected the posttranslational modification of SMAD2/3 and βCatenin is unclear and needs further discussion. Overall, Cbfβ's role in cartilage and OA pathology is an emerging area of study; the authors provided a set of genetic evidences showing that Cbfβ is indispensable for cartilage homeostasis.

Reviewer #3 (Public Review):

The authors comprehensively demonstrated the Cbfβ gene, which is involved in articular cartilage homeostasis, can promote articular cartilage regeneration and repair in osteoarthritis (OA) through regulating Hippo/YAP signaling TGF-β signaling, and canonical Wnt signaling. First, the authors demonstrated the deletion of Cbfβ can induce the OA phenotypes including decreased articular cartilage and osteoblasts, and increased osteoclasts and subchondral bone hyperplasia, and induce the early onset of OA. Additionally, the authors showed that the deficiency of Cbfβ in cartilage can increase canonical Wnt signaling and decrease TGF-β and Hippo signaling. Finally, the authors demonstrated that the overexpression of Cbfβ can inhibit Wnt signaling and enhance Hippo/YAP signaling in knee joints articular cartilage of ACLT-induced OA mice and protect against ACLT-induced OA. The manuscript is overall well-constructed, and the authors provided evidence to support their findings.

In Fig. 7I, it could be better to show the statistical analysis between normal and AAV-mediated Cbfβ ACLT mice groups.

In Fig. 9H-K, in the quantification analysis, the OARSI score in the DMM+AAV-YFP group is higher than in the sham group significantly. However, the SO staining results appear to show no significant difference between the DMM+AAV-luc-YFP group (Fig. 9I) and the sham group (Fig. 9H).

Reviewer #1 (Public Review):

In this paper, Nikolaou et al. demonstrated that CYRI-B expression is upregulated in a mouse model of pancreatic ductal adenocarcinoma (PDAC). Interestingly, they found that, while CYRI-B KO promotes the early stages of tumour progression, it prevents the formation of metastasis at later stages. Focusing on the latter, the authors highlight a role for CYRI-B in controlling the membrane availability of the LPA receptor LPAR1, which is required to support PDAC cell chemotaxis towards serum or LPA.

Strengths: the in vivo and imaging data are very solid, and convincingly support the authors' conclusions. The KPC model is well-established in PDAC research and is a very powerful tool to investigate disease onset and progression. The imaging approaches used are of a very high standard. Good data presentation with the use of super-plots.

Weaknesses: the authors focused on chemotaxis, but did not present any evidence with regard to the role of CYRI-B in 3D cell invasion, which is a key process associated with cell invasion. The data presented clearly show a specific effect towards liver metastasis, while diaphragm and bowel metastasis were not affected by CYRI-B deletion. It would be beneficial to include a discussion about this, providing some potential explanation behind this observation.

This work is of interest to cell biologists not only working in pancreatic cancer but also more broadly to researchers interested in vesicular trafficking, plasma membrane receptor dynamics and cell migration.

Reviewer #2 (Public Review):

The manuscript expands on the previous work from the lab where novel interactors of Rac1 GTPase (CYRI-A and B) provide localized inhibition by sequestration of activated Rac1. These novel regulators are fascinating as they complement the functions of the classical negative modulators of GTPases, GAPs and GDIs. The current manuscript focuses on the in vivo role of CYRI-B in pancreatic cancer progression, and distinct CYRI-B functions are shown for early and later stages. The in vivo data following CYRI-B depletion (no change in proliferation, reduced metastatic potential) is substantiated with in vitro analyses of receptor uptake, temporal recruitment of CYRI-B on macropinosomes and reduced chemotaxis.

The authors describe in detail the role of CYRI-B in pancreatic adenocarcinoma, building from their prior studies mapping CYRI-B function in the regulation of polarity, motility and chemotaxis. The experiments are well-designed and performed, and the text was clearly written. However, the results partially support some of their conclusions. The interpretation of the data and the discussion in the context of human pancreatic tumours would help the understanding and impact of the work.

The hypothesis is that depletion of CYRI-B would promote localized Rac1 activation at the membrane. However, the authors show that CYRI-B is found overexpressed in PDAC, consistent with other papers where its high expression correlates with poor outcome of many cancers. The prediction is that Rac1 functions modulated by CYRI-B would be inhibited in those tumours where CYRI-B is overexpressed. Is this the case and has it been formally demonstrated?

Most experiments use the depletion of CYRI-B to probe its function. It would be useful to readers and important to elaborate on how the specific CYRI-B functions shown upon depletion would fit with the in vivo observation of CYRI-B overexpressed in tumours. For example, loss of CYRI-B reduces chemotaxis potential. How this result can be conciliated with the predicted increase in Rac1activation in the absence of CYRI-B? Conversely, a prediction of CYRI-B overexpression in human tumours would imply the inactivation of Rac1 whereas chemotaxis is promoted. The discussion could be improved with the addition of the authors' views and further explanations in this context.

Similarly, it is confusing to extrapolate a proposed increase in LPAR1 internalization by macropinocytosis with CYRI-B overexpression in PDAC. It is predicted that Rac1 would be locally inhibited in this scenario, and thus micropinocytosis would be compromised. It will be good to spell out what the authors envisage happens. For example, uptake could be switched to another receptor uptake process that would not involve CYRI-B sequestration of Rac1. Discussion of the potential alternatives will strengthen the manuscript.

"..LPAR1 is a cargo of CYRI-B dependent macropinocytosis" (page 21). This statement reads as an overinterpretation of the specificity of the process. It may suggest that there is a cargo selectivity by CYRI-B, which has not been formally demonstrated or is well accepted. Macropinocytosis is thought to occur as a bulk engulfment of the membrane and thus any receptor at the cell surface would be internalised non-specifically. The demonstrated reduction in LPAR1 uptake could be proportional to the interference with micropinocytosis rate by CYRI-B depletion for example

Furthermore, the readers would benefit from more clear explanations of the differences and similarities between CYRI-A and CYRI-B. It will be important to clarify the specificity of the proposed functions of each protein. Both localize at the macropinosomes, modulate engulfment and regulate integrin a5b1 trafficking. It will be informative to specify if CYRI-A is also upregulated in human tumours, has a similar outcome as CYRI-B in vivo and also regulates LPAR1 uptake.

Upon depletion of CYRI-B in pancreatic tumour cells in vivo, the presence of similar levels of jaundice is confusing. Less metastasis is detected in the mesentery. Are liver metastasis affected in the absence of CYRI-B?

Reviewer #3 (Public Review):

The authors first characterize their mouse model of pancreatic cancer and show that CYRI-B mRNA is detectable in pancreatic lesions and that its amount increases over time. They also show that genetic deletion of CYRI-B accelerates pancreatic ductal adenocarcinoma (PDAC), leading to lower survival of mice. This is accompanied by higher levels of phospho-(i.e. activated)-JNK and -ERK, which are likely two of the factors driving cancer cell proliferation. Using in vivo transplantation, the authors further demonstrate that cancer cells depleted for CYRI-B exhibit decreased numbers of metastases in the mesentery, despite showing similar proliferation as control cells.<br /> Cancer cell migration can be driven by LPA, which binds LPAR1 at the surface of PDAC cells. Investigation of chemotactic migration of cancer cells towards fetal bovine serum as a source of LPA further shows that cancer cells depleted for CYRI-B and expressing GFP as control exhibit strongly reduced chemotactic migration, while cells re-expressing CYRI-B-GFP show normal chemotactic migration. Furthermore, this restored migration is blocked by using the LPAR1/3 inhibitor K116425, showing that CYRI-B is required for the chemotactic migration of PDAC cells in a gradient of serum LPA.

Using live cell imaging, the authors show that CYRI-B-GFP and LPAR1-mCherry localize to macropinocytic cups and to macropinosomes, indicating that LPAR1 can be internalized by PDAC cells through macropinocytosis. This notion is supported by immunofluorescence analyses showing that PDAC cells depleted for CYRI-B have reduced LPAR1-mCherry internalization upon stimulation with LPA, compared to cells rescued by CYRI-B-GFP expression. Collectively, the authors suggest that CYRI-B regulates macropinocytic uptake of LPAR1, thus regulating the chemotactic migration of PDAC cells towards LPA, which supports the metastasis of pancreatic cancer.

This is an interesting manuscript that makes a convincing case for the involvement of CYRI-B as a driver of PDAC. A particular strength is the expert use of different mouse models and derived cancer cell lines. The major conclusions are supported by the data presented. The results could be further strengthened by detecting CYRI-B protein (in addition to mRNA) in cancer lesions and also by staining endogenous CYRI-B and LPAR1 in the macropinocytosis experiments.

Reviewer #1 (Public Review):

Hoving and colleagues investigated the mechanisms of contact inhibition of locomotion (CIL) in Schwann cells using cell migration assays, in combination with siRNA as well as an ex-vivo model for collective cell migration of the peripheral nervous system. They found that N-cadherin is needed for proper cell repulsion during CIL. Schwann Cells depleted of N-cadherin failed CIL when encountering other Schwann cells depleted of N-cadherin, however they maintained CIL when encountering Schwann cells expressing N-cadherin. Depletion of alpha-catenin and to some degree p120 did not have the same effect as N-cadherin depletion. Further, they determined that the extracellular domain is needed for CIL as well as an interaction with Glypican-4. Glypicans often act as co-receptors for other signaling molecules, and so the authors further narrowed CIL's dependence to Slit signaling. N-cadherin was needed for proper Slit surface expression, again, dependent on the extracellular domain, and depletion of both Slit2 and 3 lead to a cell clumping and rounding phenotype. Finally, using an ex-vivo model of Schawnn cell migration they showed that rSlit lead to a similar cell rounding and clumping phenotype, ultimately leading to an inhibition of cell migration.

Strengths

This was a very methodical examination of what is needed for CIL in cultured Schwann cells. The data presented largely supports the findings and the linking of N-cad to glypican-4 to Slit signaling further illuminates this process helping to define the molecular players. The mechanistic insight goes further in that they demonstrate the Slit does not get to the cell surface without the expression of the extracellular domain of N-cad.

Weaknesses

The conclusions that can be drawn from this study remain a little narrow since only Schwann cells were used. This is not so much a weakness in that authors were indeed investigating the periphery nervous system regeneration but it does limit their findings. The experiments carried out in the ex-vivo system only touch on one aspect of their cell culture work, the mechanism of Slit. No other aspects of their cell culture system was tested ex-vivo which

Reviewer #2 (Public Review):

Schwann cells actively repair and regenerate peripheral nerves following tissue injury. Central to this process is the collective cell migration of 'cords' of Schwann cells, which guide the regenerating axons across an injury site. Previously published research from the Lloyd lab shows that at the injury site, Schwann cell cords are maintained via N-cadherin-based cell-cell adhesions; however, when cultured under low density conditions, Schwann cells display cell repulsion and contact inhibition of locomotion (CIL) phenotypes, suggesting Schwann cell behaviour is plastic. In this study, Hoving, Lloyd and colleagues build upon their previous work to show that Slit2/3/Robo signalling triggers cell repulsion between Schwann cells in an N-cadherin-dependent manner. This in turn induces contact inhibition of locomotion to propel Schwann cells to migrate collectively and with direction. The authors show that N-cadherin has a dual function in Schwann cell migration: to keep migrating Schwann cells together as a group, and concomitantly present Slit2/3 repulsive cues to cells to trigger cell repulsion locally. Their data also show that extracellular N-cadherin is required for cell repulsion, independent of cell-cell adhesion functions. The authors use a combination of in vitro Schwann cell cultures and live cell imaging, with an ex vivo precision cut tissue slice system to show that Slit2/3-dependent CIL underpins proper Schwann cell migration in an injury model.

This is a very well executed and important study, which provides new insights into mechanisms of CIL and places CIL in the context of tissue repair and regeneration in adult tissues. The experiments are well designed, and the main findings and conclusions are based on robust and convincing data.

Reviewer #3 (Public Review):

The submitted paper by Hoving et al addresses the role of N-cadherin in Schwann cell collective cell migration and its previously unknown relationship with the slit/robo signaling pathway. The main conclusion is that N-cadherin has two distinct functions. One that is dependent on its classical role as a cell-cell junction protein promoting cell clustering and one that promotes cell repulsion and polarity independently of the formation of cell adhesion complexes. The second function is mediated by the Slit/Robo pathway. It is proposed that N-cadherin and Glypican-4 act together to present Slit2/3 at the surface of Schwann cells in order to trigger Robo signaling on neighboring cells.

The data about N-cadherin loss of function and the associated rescue experiments with the various truncated forms of N-cadherin are well substantiated by proper controls for efficiency and specificity. They show that the extracellular domain of Ncadherin is the one required for the repulsive effect. The experiments performed to distinguish the roles in adhesion and repulsion seem clear and conclusive. In addition, the fact the slit signal needs to be provided in a polarized manner for directional migration to occur is also clearly demonstrated in vitro and on slice assays. Overall the model that Ncadherin plays two different roles, a repulsive one via presentation of slit at the cell surface and a cell adhesion one via formation of adherens junctions, is well supported by the data and will be of interest beyond the subfield of the authors.

However, other parts of the manuscript seem weaker. If N-cadherin presentation of the Slit signal is so critical why are repulsion rates still very high in cells without N-cadherin? Same is observed with Glypican4 knockdowns. In both loss of function 50% of cell collisions lead to repulsion (compared to 70% amongst control cells). While significant such drop remains modest. The authors propose a cooperative role of Glypican-4 and N-cadherin at the cell surface as co-binding factors for Slit2/3 but they have not checked whether double knockdown of N-cad and Glypican4 might have a stronger effect. Could Glypican and N-cadherin present Slit at the cell surface independently in a somewhat redundant manner? Can Glypican and Slit interact physically in absence of N-cadherin? They also have not further analyzed the putative colocalization fo Ncad and Glypican at the cell surface.

The data supporting a role for N-cadherin in Slit's trafficking to the cell surface seem also circumstantial. While western blot data seem to indicate no change in Slit protein level after N-cad knockdown, immunostaining for Slit in such condition show a dramatic loss of Slit signal. These two independent data sets are difficult to reconcile and are not designed to address whether Slit reaches the cell surface in control or N-cadherin knockdown conditions.

If Slit signaling is so critical for repulsion why in double sit2/3 knockdown 40% of collisions still lead to repulsion. Also, no analysis of cell collision are provided upon Robo1/2 knockdown for comparison with Slit knockdowns. Altogether, these relatively mild effects of n-cad, slit or glypican knockdown on repulsion seem to indicate that other signals might contribute to contact-inhibition and polarization/repulsion of cells upon physical contact but this is unfortunately not discussed. All statements related to cell polarity stem from the overall cell morphology without being substantiated by actual polarity analysis (using markers such as detection of Rac-GTP or using a proxy such as the golgi-nucleus axis). The authors present the cell cluster generated after Sox2 expression and Sox2 + exposure to recombinant Slit2 as lacking polarity, however in one case cells do not present any flat membrane at their free edge whereas in the other case they do. This suggests a minimal cell polarity with a protrusive-like organization away from the contact. Finally, Robo1/2 siRNA knockdown are used but contrary to the other loss of functions it seems that controls for knockdown efficiency/specificity were not provided.

Therefore, while the study is overall well documented and based on solid data, some weaknesses exist.

The overall topic is clearly of broad interest as N-cadherin is protein essential in various biological settings from development to disease but the range of its biological functions remains to be fully explored. This study clearly adds to the current knowledge and how N-cadherin might act in vivo and in particular how it could mediate crosstalks between various signaling pathways.

Reviewer #1(Public Review):

In this manuscript the authors report an experiment to assess how training on a perceptual task may not only increase performance on that task but impact on the appearance of the trained stimuli. They compare discrimination performance, coherence thresholds, and estimation biases for random dot motion direction relative to horizontal rightward in three groups of observers before and after 3 days in which they either trained on a discrimination task, an estimation task, or did not train. The authors report significant increases in discrimination performance post training compared to not training. They also report increases in estimation biases when assessed as the average estimate (over a bimodal distribution that crosses 0) but not when assessed as the mode of the bimodal distribution. They conclude that training resulted in "increases in already-large estimation biases away from horizontal".

The methods and results are strengthened by the combination of classical psychophysical techniques and sophisticated computational modelling. One weakness is the possibility is misleading summary statistics when dealing with bimodal distributions. Convincing evidence that observers perceived stimulus directions as further from horizontal (in the absolute sense) following training is not presented in the current manuscript. Irrespective, this work is likely to impact the field.

Reviewer #2 (Public Review):

It is well-known that repeated exposure to perceptual stimuli improves discrimination performance, but less is known about the effects on perceptual appearance. In the present work, the authors tackle this question and focus on one particular effect on perceptual appearance termed boundary avoidance, i.e. the tendency to perceive (or report) a stimulus as biased away from a discrimination boundary.

In the study, participants performed either a motion discrimination task (clockwise or counterclockwise with respect to a reference axis) or an estimation task (reproducing the orientation of the motion stimulus). Participants were divided in three groups which either i) trained on the discrimination task, ii) trained on the estimation task or iii) received no training (control group). Performance in both tasks was assessed prior and after training. The main behavioral finding is that training (which did not involve feedback) improved discrimination performance and increased estimation precision, but at the same time appeared to increase the boundary avoidance effect. Thus, the authors conclude that perceptual learning improved performance at the cost of appearance.

To explain these effects, the authors created a computational model in which performance improvements were implemented as a gain increase of neurons sensitive to the trained motion directions. Repulsive biases away from the reference orientation were implemented by a combination of two modeling choices: i) Even during estimation, participants perform an implicit categorization such that they assume that their percept was created by a stimulus in line with their categorization (clockwise or counterclockwise). This effectively biases their response away from the boundary. ii) There is an abundance of neurons tuned to the horizontal reference axis (the "boundary") which likewise leads to a repulsive bias. Overall, the authors conclude that the model was able to explain the major behavioral effects, including the a priori presence of repulsive biases, the increase in performance, the increase in estimation precision and the increase of the repulsive bias.

It is well-known that repeated exposure to perceptual stimuli improves discrimination performance, but less is known about the effects on perceptual appearance. In the present work, the authors tackle this question and focus on one particular effect on perceptual appearance termed boundary avoidance, i.e. the tendency to perceive (or report) a stimulus as biased away from a discrimination boundary. On first glance, it was a pleasure reading this paper due to a number of aspects the authors got quite right in my opinion:<br /> - A clear and well-explained research question.<br /> - The results are generally well-presented. Much effort and expertise was put into the Figures and many helpful auxiliary Figures are included as a Supplement.<br /> - The writing was concise and clear.

However, as outlined below, I'm afraid that the main conclusion of the study and the main motivation for computational modeling are not backed up by the data.

(1) No evidence for a change in overestimation<br /> Overestimation is (rightly) defined by the authors as a bias of the perceived orientations towards more extreme values (visualized also in Fig. 2F). However, as acknowledged by the authors, there is nearly no evidence for such an effect. The modal estimation response (correct trials) doesn't change significantly between the sessions. The mean, which is the primary measure used by the authors, is not an appropriate measure for an overestimation, as it is severely biased by accuracy. It was unclear to me why it was chosen as the primary measure for nearly all figures and analyses, given that the authors were aware of (and reported) a more suited measure.

In my opinion, the mode of the correct responses would be the best way to quantify the overestimation bias. An alternative would be looking at the average absolute (unsigned) distance from the boundary, possibly including both correct and incorrect responses. However, such a "mean of absolute differences" approach would be affected by lucky guessing trials, which could manifest in a probability mass close to the boundary (and the proportion of which changes with overall accuracy). Therefore I see the mode as the strongest and least confounded measure.

(2) Nature of the biases<br /> Although, as outlined in 1), there might actually be no evidence for a *change* in overestimation bias, there clearly was a baseline overestimation bias. However, the reported biases appear extremely large. For instance, for the 2{degree sign} orientation the modal estimation is close to 20{degree sign}. To me this raises the question whether we're really dealing with a pure perceptual effect (18{degree sign} misperception seems quite suboptimal) or whether there are some other psychological effects at work that could be rather classified as a response bias.

In particular, I wondered whether the baseline bias is partly explained by participants "wanting to make sure" they indicate the correct category in estimation and therefore bias their estimation response away from the ambiguous proximity of the cardinal axes? Does it require more effort to set estimation orientation close to a cardinal axis while still making sure that it has the correct categorical orientation. I guess there was no horizontal reference line on the screen which would help with this?

The overall discrimination-focused task design might have contributed to this bias. First, because the participants trained on estimation also performed a discrimination task (pre/post) which very likely could have affected their response style. Second, the presented orientations during estimation were likewise 50:50 around the horizontal reference which could shift the focus towards "getting the sign right" rather than "getting the precise orientation right".

(3) The mechanism of the model<br /> As a disclaimer a priori, I am not very familiar with this particular modeling literature (but this may be the case for other readers as well). For this reason I could have used a bit more guidance about how the model works. My understanding is that there a three key mechanisms: 1) Gain modulation which explains the improvement in discrimination; 2) Warping which partly explains boundary avoidance; 3) Implicit categorization which likewise partly explains boundary avoidance. In addition, there are two levels of analysis: 1) the pre-training state (a priori presence of a repulsive bias) and 2) learning effects (bias and performance increase through training). If the models were to be kept as part of a revised manuscript, my suggestion would be to structure the corresponding section in the Results ("Observer Model") a bit more along these anchors. I suggest also providing a bit more explanation already at this point. For instance, I consider the fact that implicit categorization effectively works through Bayes rule by assuming a uniform(?) prior over either the negative or positive orientation axis, as very relevant. I assume that other priors would have been conceivable for conditioning on the response, e.g. taking into account the actual (objective or subjective) distribution of orientations for the particular choice category, so this is a non-trivial modeling choice.<br /> Intuitively, I would have also thought that if more resources are devoted to the cardinal directions (and the decoder is unaware of this), this would lead to a bias *towards* the cardinal directions. If more neurons fire particularly strong to near-cardinal orientations (such as the +-4{degree sign} in training), why would the decoder be repulsed *away* from the cardinal orientation? I trust the authors that the presentation is correct, but to me, this was not obvious and I would have wished for some guidance.

Reviewer #1 (Public Review):

Identifying individual BCR/Ab chain sequences that are members of the same clone is a long-standing problem in the analysis of BCR/Ab repertoire sequencing data. The authors propose a new method designed to be scalable for application to huge repertoire data sets without sacrificing accuracy. Their approach utilizes Hamming Distance between CDR3 sequences followed by clustering for a fast, high-precision approach to classifying pairs of sequences as related or not, and then refines the classification using mutation information from germline-encoded regions. They compare their method with other state-of-the-art methods using synthetic data.

The authors address an important problem in an interesting, innovative, and rigorous way, using probabilistic representations of CDR3 differences, frequencies of shared and not-shared mutations, and the relationships between the two under hypotheses of related pairs and unrelated pairs, and from these develop an approach for determining thresholds for classification and lineage assignment. Benchmarking shows that the proposed method, the complete method including both steps, outperforms other methods.

Strengths of the method include its theoretical underpinnings which are consistent with an immunologist's intuition about how related and unrelated sequences would compare with each other in terms of the metrics to use and how those metrics are related to each other.

I have two high-level concerns:<br /> (1) It isn't clear how the real and synthetic data are being used to estimate parameters for the classifier and evaluate the classifier to avoid circularity. It seems like the approach is used to assign lineages in the data from [1], and then properties of this set of lineages are used to estimate parameters that are then used to refine the approach and generate synthetic data that is used to evaluate the approach. This may not be a problem with the approach but rather with its presentation, but it isn't entirely clear what data is being used and where for what purpose. An understanding of this is necessary in order to truly evaluate the method and results.<br /> (2) Regarding the data used for benchmarking - given the intertwined fashion by which the classification approach and synthetic data generation approach appear to have been developed, it is not surprising that the proposed approach outperforms the other methods when evaluated on the synthetic data presented here. It would be better to include in the benchmark the data used by the other methods to benchmark themselves or also generate synthetic data using their data generation procedures.

An improved method for BCR/Ab sequence lineage assignment would be a methodologic advancement that would enable more rigorous analyses of BCR/Ab repertoires across many fields, including infectious disease, cancer, autoimmune disease, etc., and in turn, enable advancement in our understanding of humoral immune responses. The methods would have utility to a broad community of researchers.

Reviewer #2 (Public Review):

This manuscript describes a new algorithm for clonal family inference based on V and J gene identity, sequence divergence in the CDR3 region, and shared mutations outside the CDR3. Specifically, the algorithm starts by grouping sequences that have the same V and J genes and the same CDR3 length. It then performs single-linkage clustering on these groups based on CDR3 Hamming distance, then further refines these groups based on shared mutations.

Although there are a number of algorithms that use a similar overall strategy, a couple of aspects make this work unique. First, a persistent challenge for algorithms such as this one is how to set a cutoff for single-linkage clustering: if it is too low, then one separates clusters that should be together, and if too high one joins together clusters that should be separate. Here the authors leverage a rich collection of probabilistic tools to make an optimal choice. Specifically, they model the probability distributions of within- and between-cluster CDR3 Hamming distances, with parameters depending on CDR3 length and the "prevalence" of clonal sequence pairs (i.e. family size distribution). This allows the algorithm to make optimal choices for separating clusters, given the particular chosen distance metric, and assuming the sample in question has been accurately modeled. Second, the algorithm uses a highly efficient means of doing single-linkage clustering on nucleotide sequences.

This leads to a fast and highly performant algorithm on data meant to replicate the original sample used in algorithm design. The ideas are new and beautifully developed. The application to real data is interesting, especially the point about dN/dS.

However, the paper leaves open the question of how this inference algorithm works on samples other than the one used for simulation and as a template for validation. If I understand the simulation procedure correctly - that one takes a collection of inferred trees from the real data, then re-draws the root sequence and the identity of the mutations on the branches - then the simulated data should be very close to the data used to develop the methods in the paper. This consideration seems especially important given that key methods in this paper use mutation counts and overall mutation counts are preserved.

Repertoires come in all shapes and sizes: infants to adults, healthy to cancerous, and naive to memory to plasma-cell-just-after-vaccination. If this is being proposed as a general-purpose clonal inference algorithm rather than one just for this sample, then a more diverse set of validations are needed.

It is unclear how to run the code. The software repo has a nice readme explaining the file layout, dependencies, and input file format, but the repo seems to be lacking an `inference.ipynb` mentioned there which runs an analysis. Perhaps this is a typo and refers to `inference.py`, which in addition to the documented cdr3 clustering, seems to have functions to run both clustering methods. However, it does not seem to have any documentation or help messages about how to run these functions.

The results are not currently reproducible, because the simulated data is not available. The data availability statement says that no data have been generated for this manuscript, however simulated data has been generated, and that is a key aspect of the analysis in the paper.

More detail is needed to understand the timing comparisons. The new software is clearly written to use many threads. Were the other software packages run using multiple threads? What type of machine was used for the benchmarks?

Reviewer #3 (Public Review):

B cell receptors are produced through a combination of random V(D)J recombination and somatic hypermutation. Identifying clonal lineages - cells that descend from a common V(D)J rearrangement - is an important part of B cell repertoire analysis. Here, the authors developed a new method to identify clonal lineages from BCR data. This method builds off of prior advances in the field and uses both an adaptive clonal distance threshold and shared somatic hypermutation information to group B cells into clonal lineages.

The major strength of this paper is its thorough quantitative treatment of the subject and integration of multiple improvements into the clonal clustering process. By their simulation results, the method is both highly efficient and accurate.

The only notable weakness we identified is that much of the impact of the method will depend on its superiority to existing approaches, and this is not convincingly demonstrated by Fig. 4. In particular, little detail is given on how the other clonal clustering programs were run, and this can significantly impact their performance. More specifically:

(1) Scoper supports multiple methods for clonal clustering, including both adaptive CDR3 distance thresholds (Nouri and Kleinstein, 2018) and shared V-gene mutations (Nouri and Kleinstein, 2020). It is not clear which method was used for benchmarking. The specific functions and settings used should have been detailed and justified. Spectral clustering with shared V gene mutations would be the most comparable to the authors' method. Similar detail is needed for partis.<br /> (2) It is not clear how the adaptive thresholds and shared mutation analysis in the authors' method differ from prior approaches such as scoper and partis.<br /> (3) The scripts for performing benchmarking analyses, as well as the version numbers of programs tested, are not available.<br /> (4) Similar to above, P. 10 describes single linkage hierarchical clustering with a fixed threshold as a "crude method" that "suffers from inaccuracy as it loses precision in the case of highly-mutated sequences and junctions of short length." As far as we could tell, this statement is not backed up by either citations or analyses in the paper. It should not be difficult for the authors to test this though using their simulations, as this method is also implemented in scoper.

References<br /> Nouri N, Kleinstein SH. 2020. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLOS Comput Biol 16:e1007977. doi:10.1371/journal.pcbi.1007977<br /> Nouri N, Kleinstein SH. 2018. A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data. Bioinformatics 34:i341-i349. doi:10.1093/bioinformatics/bty235

Reviewer #1 (Public Review):

Summary:

Doxorubincin has long been known to cause bone loss by increasing osteoclast and suppressing osteoblast activities. The study by Wang et al. reports a comprehensive investigation into the off-target effects of doxorubicin on bone tissues and potential mechanisms.. They used a tumor-free model with wild type mice and found that even a single dose of doxorubicin has a major influence by increasing leukopenia and DAMPs and inflammasomes in macrophages and neutrophils, and inflammation-related cell death (pyroptosis and NETosis). The gene knockout study shows that AIM2 and NLRP3 are the major contributors to bone loss. Overall, the study confirmed previous findings regarding the impact of doxorubicin on tissue inflammation and expands the research further into bone tissue. The presented data presented are consistent; however, a major question remains regarding whether doxorubicin drives inflammation and its related events. Most in vitro study showed that the effect of doxorubincin cannot be demonstrated without LPS priming. This observation raises the question of whether doxorubincin itself could activate the inflammasome and the related events. In vivo study, on the other hand, suggested that it doesn't require LPS. The inconsistency here was not explained further. Moreover, a tumor-free mouse model was used for the study; however, immune responses in tumor bearing models would likely be distinct from tumor-free ones. The justification for using tumor-free models is not well-established.

Strengths:

The paper includes a comprehensive study that shows the effects of doxorubincin on cytokine levels in serum, release of DAMPs and NETosis, and leukopenia using both in vivo and in vitro models. Bone marrow cells, macrophages and neutrophils were isolated from the bone marrow, and the levels of cytokines in serum were also determined.

They employed multiple knockout models with deficiency in Aim 2, Nlirp3, and double deficiencies to dissect the functional involvement of these two inflammasomes.

The experiments in general are well designed. The paper is also logically written, and figures were clearly labeled.

Weaknesses:

Most of the data presented are correlative, and there is not much effort to dissect the underlying molecular mechanism.

It is not entirely clear why a tumor free model is chosen to study immune responses, as immune responses can differ significantly with or without tumor-bearing.

Immune responses in isolated macrophages, neutrophils and bone marrow cells require priming with LPS, while such responses are not observed in vivo. There is no explanation for these differences.

The band intensities on Western blots in Fig. 4 and Fig. 5 are not quantified, and the numbers of repeats are also not provided.

Many abbreviations are used throughout the text, and some of the full names are not provided.

Fig. 5B needs a label on X axis.

Reviewer #2 (Public Review):

Summary:

Wang and collaborators have evaluated the impact of inflammation on bone loss induced by Doxorubicin, which is commonly used in chemotherapy to treat various cancers. In mice, they show that a single injection of Doxorubicin induces systemic inflammation, leukopenia, and a significant bone loss associated with increased bone-resorbing osteoclast numbers. In vitro, the authors show that Doxorubicin activates the AIM2 and NLRP3 inflammasomes in macrophages and neutrophils. Importantly, they show that the full knockouts (germline deletions) of AIM2 (Aim2-/-) and NLRP3 (Nlrp3-/-) and Caspase 1 (Casp1-/-) limit (but do not completely abolish) bone loss induced 4 weeks after a single injection of Doxorubicin in mice. From these results, they conclude that Doxorubicin activates inflammasomes to cause inflammation-associated bone loss.

Strength:

This manuscript provides functional experiments demonstrating that NRLP3 and/or AIM2 loss-of-functions (and thus the systemic impairment of the inflammatory response) prevent bone-loss induced by Doxorubicin in mice.

Weaknesses:

Numerous studies have reported that Doxorubicin induces systemic inflammation and activates the inflammasome in myeloid cells and various other cell types. It is also known that systemic inflammation and Doxorubicin treatment lead to bone loss. Hence, the key conclusions drawn from this work have been known already or were very much expected. Therefore, the novelty appears somewhat limited. One important limitation is the lack of experiments that could determine which cell lineages are involved in bone loss induced by Doxorubicin in vivo, while the tools to do so exist. The characterization of the bone phenotype is incomplete, and unfortunately does not tell us whether the inflammasome is activated in some of the cell lineages present in bones in vivo. Another limitation is that the relative importance of the inflammasomes compared to cell senescence and autophagy, which are also induced by Doxorubicin, has not been evaluated. Hence the main molecular mechanisms responsible for bone loss induced by Doxorubicin in vivo remains unknown. Lastly, it would have been interesting, on a more clinical point of view, to compare the few relevant treatments that could limit the deleterious effect of Doxorubicin on bone loss while preserving the toxicity on tumor cells.

Reviewer #1 (Public Review):

In this manuscript by Buchanan and colleagues, the authors set out to determine if mutations associated with resistance to the Plasmodium apicoplast inhibitor azithromycin (AZ) had a measurable impact on the fitness of Plasmodium berghei and P. falciparum parasites as they traverse both the mosquito host and vertebrate liver.

The Plasmodium endosymbiotic organelles - the mitochondrion and apicoplast - are attractive drug targets as they (1) possess essential functions across the multi-host multi-compartment life cycle of these parasites, and (2) are of bacterial origin and thus are vulnerable to inhibition both to extant antibiotics, and novel drugs with high parasite specificity.

Historically however the high resistance propensity of drug targets encoded in the organellar genomes (most notably atovaquone and doxycycline) has precluded the use of these drugs in an endemic setting, limiting these potent compounds to use in prophylaxis for travelers from non-endemic countries. Several studies in the last decade now fairly definitively show that mutations conferring resistance to atovaquone in the mitochondrial gene cytochrome b are, in a mutation-dependent manner, totally or near-totally compromised in their ability to infect, grow, and escape the mosquito host, leading to a reexamination of the potential utility of this extraordinarily potent drug in endemic settings. Symmetries exist between the Plasmodium mitochondrion and apicoplast, which both appear to have highly fexpanded roles in the mosquito and liver relative to the blood stages. Thus, the authors set out to explore whether mutations in essential apicoplast genes were, in a similar manner to mutations in cytochrome B, associated with fitness effects in the mosquito and/or liver.

Towards this, the authors selected for several AZ-resistant parasite populations, all of which acquired mutations in the apicoplast genome-encoded ribosomal protein Rpl4. Interestingly, the authors observed contrasting fitness effects caused by these mutations, both between mutants within Plasmodium species, and between species. In P. berghei, AZ mutants were compromised in their ability to form oocysts and sporozoites, and a large proportion of sporozoites lacked an intact apicoplast and displayed aberrant gliding behaviour. Similarly, in the liver, Rpl4 mutant P. berghei liver schizonts were smaller, had fewer nuclei, and appeared extremely limited in their ability to cause a patent infection - crucially in particular via mosquito bites. Surprisingly, a P. falciparum Rpl4 mutant (notably in a different position of the protein) had no impact on sporogony but appeared to have a strong impact on liver schizont development in a liver-humanized mouse model, suggesting that establishment of blood stage infection in a subsequent human host would be less likely for mutant parasites.

This is a well-executed study, that presents novel and noteworthy findings. The impact of drug-resistance-conferring mutations in Plasmodium outside of the blood stage is woefully understudied, primarily due to significant challenges associated with studying Plasmodium, especially P. falciparum, in both the mosquito and liver which the authors navigate commendably. The results presented in this manuscript leverage state-of-the-art techniques and clearly support the authors' conclusion that AZ-conferring resistance mutations have a strong negative effect on the ability of Plasmodium parasites to both reinfect and cause symptomatic infection in a subsequent vertebrate host. This could indicate that apicoplast-targeted inhibitors are more attractive as co-drugs for malaria treatment than previously thought, due to the reduced probability of the spread of resistance, which has been a perennial issue in malaria therapeutic care.

Reviewer #2 (Public Review):

Summary:

This manuscript answers an important question about the transmission of Plasmodium parasites resistant to apicoplast inhibitors, specifically azithromycin. This study builds on previous work showing the inability to transmit parasites resistant to mitochondrial inhibitor, atovaquone, based on fitness defects in transmission stages in the mosquito. The transmissibility of drug-resistant parasites is grounded in the basic biology of the Plasmodium lifecycle and has implications for the selection of drug regimens for clinical treatment, so these questions are highly significant. The authors clearly demonstrate severe defects in mosquito stages of azithromycin-resistant (AZR) P. berghei (rodent species) inhibiting transmission of AZR parasites. However, surprisingly AZR P. falciparum (human species) is unaffected in mosquito stages, rather defects are observed in liver-stage development suggesting AZR P. falciparum can transmit but may not mount a productive blood infection. The differences in the observed defects in the 2 species are important and well demonstrated in the results but are obscured in the title/summary of the manuscript. The results demonstrate that AZR parasites are unlikely to spread.

Strengths:

The authors performed experiments with both P. berghei (rodent species) and P. falciparum (human species). P. falciparum is the more relevant species from a clinical standpoint, however, there are limitations to studying the full lifecycle of P. falciparum which only infects humans and some primates, for example requiring humanized mice without intact immune systems. Pberghei is commonly used in lifecycle analyses as a proxy for experimental tractability, however, there are cases where the biology of P. berghei does not reflect that in P. falciparum. So the use of both species is complementary and most informative. Specific modification of the apicoplast genome, where AZR mutations are located, is not currently possible so matched genotypes could not be produced but multiple AZR mutants were analyzed for each species. Acknowledging these limitations in the experimental systems available, the authors perform a thorough set of experiments to pinpoint the specific defects in AZR Pb vs Pf during mosquito and liver developmental stages. The results show phenotypic differences between AZR Pb and Pf in mosquito stages which was not expected but in line with differences in apicoplast biology of Pb vs Pf that are important to document and be aware of when using P. berghei as a model for P. falciparum development.

Weaknesses:

The claim that human AZR malaria parasites (P. falciparum) is not readily transmitted to mosquitoes is incorrect, as stated in the title and abstract. Strictly speaking, transmission refers to the infection of a human host by another via mosquitos. The evidence that AZR Pf is unaffected in mosquito development indicates that transmission is not reduced compared to WT Pf. Rather transmitted AZR Pf has disrupted liver stage development and may not mount a productive blood infection. This distinction between the phenotypes of AZR Pb vs Pf is surprising, significant (suggesting differences between Pb and Pf and/or specific mutations in Rpl4), and should be more accurately represented in the title/abstract. To their credit, the authors performed thorough experiments to pinpoint the specific defects in AZR Pb vs Pf, but the current claim about AZR Pf is misleading.

Additional context:

Clinical trials (MORDOR studies) in several African countries have shown that biannual administration of azithromycin reduces childhood mortality (PMID: 31167050). The mechanism of this survival benefit is unknown and may be multifactorial. The findings in this manuscript can also be considered in the context that azithromycin is a commonly used antibiotic and may be administered for purposes other than malaria treatment. In theory, AZR-resistant parasites could be selected in asymptomatic patients not receiving malaria treatment but receiving azithromycin. This study indicates that mass distribution of azithromycin for other clinical applications would not result in adverse effects on malaria transmissions in the same population.

Reviewer #3 (Public Review):

Summary:

Drug resistance is a perennial problem for malaria control and strategies to prevent the acquisition and spread of drug resistance mutations are desperately needed. One strategy is to identify drug resistance mutations that arise in blood-stage parasites, but cannot be readily spread to a new human host. Since malaria parasites must survive and replicate in mosquitoes in order to be transmitted, mutations with elevated mosquito-stage fitness defects will not spread efficiently. Buchanan and coworkers focus on the drug azithromycin and its known role of inhibiting the ribosomes found in parasite apicoplast organelles. Apicoplast organelles are known to have elevated metabolic activity in mosquito stage parasites and azithromycin resistance mutations could interfere with mosquito stage parasite development and parasite transmission.

To address this hypothesis, azithromycin-resistant P. berghei and P. falciparum parasites were generated and analyzed for transmission defects. All lines had mutations in the apicoplast ribosomal protein Rpl4 consistent with the known role of azithromycin inhibiting the 50S ribosomal subunit. Overall, the three lines (3 berghei and one falciparum) had phenotypes that should limit parasite transmission, however, detailed characterization showed that there were surprising differences between the two parasite species and even between the P. berghei lines. The P. berghei lines produced fewer oocysts and sporozoites with aberrant apicoplast morphology compared to wild-type controls. Sporozoites from azithromycin-resistant lines appeared to have motility defects and typically were not able to infect mice (one strain produced infections when 10,000 sporozoites were injected, but not when 1,000 were).

By contrast, the azithromycin-resistant P. falciparum strain did not display any mosquito-stage phenotypes and produced motile sporozoites with intact apicoplast organelles. These sporozoites, however, developed abnormally in a humanized mouse model with reduced liver-stage nuclear division and abnormal apicoplast morphology. These defects combined with a five-fold lower prevalence suggest that azithromycin-resistant P. falciparum parasites experience significant fitness costs during liver stage development (at least those harboring the G76V mutation).

Strengths:

This work was carefully conducted and transparently presented. It provides a comprehensive view of how parasite development is impacted by azithromycin resistance mutations during the mosquito and liver stages in P. berghei and P. falciparum. It adds a new dimension to the growing literature on the transmissibility of drug-resistant parasites, by showing that mutations in the apicoplast genome can impact transmission.

Weaknesses:

Whether these liver-stage defects in P. falciparum are severe enough to completely block subsequent blood-stage infection remains to be seen and would require experiments with humanized mice continuously grafted with human red blood cells - a difficult and expensive model system.

Reviewer #1 (Public Review):

Mohseni and Elhaik's article offers a critical evaluation of Geometric Morphometrics (GM), a common tool in physical anthropology for studying morphological differences and making phylogenetic inferences. I read their article with great interest, although I am not a geneticist or an expert on PCA theory since the problem of morphology-based classification is at the core of paleoanthropology.

The authors developed a Python package for processing superimposed landmark data with classifier and outlier detection methods, to evaluate the adequacy of the standard approach to shape analysis via modern GM. They call into question the accuracy, robustness, and reproducibility of GM, and demonstrate how PCA introduces statistical artefacts specific to the data, thus challenging its scientific rigor. The authors demonstrate the superiority of machine learning methods in classification and outlier detection tasks. The paper is well-written and provides strong evidence in support of the authors' argument. Thus, in my opinion, it constitutes a major contribution to the field of physical anthropology, as it provides a critical and necessary evaluation of what has become a basic tool for studying morphology, and of the assumptions allowing its application for phylogenetic inferences. Again, I am not an expert in these statistical methods, nor a geneticist, but the authors' contribution is of substantial relevance to our field (physical anthropology). The examples of NR fossils and HLD 6 are cases in point, in line with other notable examples of critical assessment of phylogenetic inferences made on the basis of PCA results of GM analysis. For example, see Lordkipanidze et al.'s (2014) GM analyses of the Dmanisi fossils, suggesting that the five crania represent a single regional variant of Homo erectus; and see Schwartz et al.'s (2014) comment on their findings, claiming that the dental, mandibular, and cranial morphology of these fossils suggest taxic diversity. Schwartz et al. (2014) ask, "Why did the GMA of 78 landmarks not capture the visually obvious differences between the Dmanisi crania and specimens commonly subsumed H. erectus? ... one wonders how phylogenetically reliable a method can be that does not reflect even easily visible gross morphological differences" (p. 360).

As an alternative to the PCA step in GM, the authors tested eight leading supervised learning classifiers and outlier detection methods on three-dimensional datasets. The authors demonstrated inconsistency of PCA clustering with the taxonomy of the species investigated for the reconstruction of their phylogeny, by analyzing a database comprising landmarks of 6 known species that belong to the Old World monkeys tribe Papionini, using PCA for classification. The authors also demonstrated that high explained variance should not be used as an estimate of high accuracy (reliability). Then, the authors altered the dataset in several ways to simulate the characteristic nature of paleontological data.

The authors excluded taxa from the database to study how PCA and alternative classifiers are affected by partial sampling, and the results presented in Figures 4 and 5, among others, are quite remarkable in showing the deviations from the benchmark data. These results expose the perils of applying PCA and GM for interpreting morphological data. Furthermore, they provide evidence showing that the alternative classifiers are superior to PCA, and that they are less susceptible to experimenter intervention. Similar results, i.e., inconsistencies in the PC plots, were obtained in examinations of the effect of removing specimens from the dataset and in the interesting test of removing landmarks to simulate partial morphological data, as is often the case with fossils. To test the combined effect of these data alterations, the authors combined removal of taxa, specific samples, and landmarks from the dataset. In this case, as well, the PCA results indicate deviation from the benchmark data. However, the ML classifiers could not remedy the situation. The authors discuss how these inconsistencies may lead to different interpretations of the data, and in turn, different phylogenetic conclusions. Lastly, the authors simulated the situation of a specimen of unknown taxonomy using outlier detection methods, demonstrating LOF's ability to identify a novelty in the morphospace.

References<br /> Bookstein FL. 1991. Morphometric tools for landmark data: geometry and biology [Orange book]. Cambridge New York: Cambridge University Press.<br /> Cooke SB, and Terhune CE. 2015. Form, function, and geometric morphometrics. The Anatomical Records 298:5-28.<br /> Lordkipanidze D, et al. 2013. A complete skull from Dmanisi, Georgia, and the evolutionary biology of early Homo. Science 342: 326-331.<br /> Schwartz JH, Tattersall I, and Chi Z. 2014. Comment on "A complete skull from Dmanisi, Georgia, and the evolutionary biology of Early Homo". Science 344(6182): 360-a.

Reviewer #2 (Public Review):

I completely agree with the basic thrust of this study. Yes, of course, machine learning is FAR better than any variant of PCA for the paleosciences. I agree with the authors' critique early on that this point is not new per se - it is familiar to most of the founders of the field of GMM, including this reviewer. A crucial aspect is the dependence of ALL of GMM, PCA or otherwise, on the completely unexamined, unformalized praxis by which a landmark configuration is designed in the first place. I must admit that I am stunned by the authors' estimate of over 32K papers that have used PCA with GMM.

But beating a dead horse is not a good way of designing a motor vehicle. I think the manuscript needs to begin with a higher-level view of the pathology of its target disciplines, paleontology and paleoanthropology, along the lines that David Hull demonstrated for numerical taxonomy some decades ago. That many thousands of bad methodologies require some sort of explanation all of their own in terms of (a) the fears of<br /> biologists about advanced mathematics, (b) the need for publications and tenure, (c) the desirability of covers of Nature and Science, and (d) the even greater glory of getting to name a new "species." This cumulative pathology of science results in paleoanthro turning into a branch of the humanities, where no single conclusion is treated as stable beyond the next dig, the next year or so of applied genomics, and the next chemical trace analysis. In short, the field is not cumulative.

It is not obvious that the authors' suggestion of supervised machine learning will remedy this situation, since (a) that field itself is undergoing massive changes month by month with the advent of applications AI, and even more relevant (b) the best ML algorithms, those based on deep neural nets, are (literally) unpublishable - we cannot see how their decisions have actually been computed. Instead, to stabilize, the field will need to figure out how to base its inferences on some syntheses of actual empirical theories.

It's not that this reviewer is cynical, but it is fair to suggest a revision conveying a concern for the truly striking lack of organized skepticism in the literature that is being critiqued here. A revision along those lines would serve as a flagship example of exactly the deeper argument that reference (17) was trying to seed, that the applied literature obviously needs a hundred times more of. Such a review would do the most good if it appeared in one of the same journals - AJBA, Evolution, Journal of Human Evolution, Paleobiology - where the bulk of the most highly cited misuses of PCA themselves have appeared.

Reviewer #3 (Public Review):

Mohseni and Elhaik challenge the widespread use of PCA as an analytical and interpretive tool in the study of geometric morphometrics. The standard approach in geometric morphometrics analysis involves Generalised Procrustes Analysis (GPA) followed by Principal Component Analysis (PCA). Recent research challenges PCA outcomes' accuracy, robustness, and reproducibility in morphometrics analysis. In this paper, the authors demonstrate that PCA is unreliable for such studies. Additionally, they test and compare several Machine-Learning methods and present MORPHIX, a Python package of their making that incorporates the tools necessary to perform morphometrics analysis using ML methods.

Mohseni and Elhaik conducted a set of thorough investigations to test PCA's accuracy, robustness, and reproducibility following renewed recent criticism and publications where this method was abused. Using a set of 2 and 3D morphometric benchmark data, the authors performed a traditional analysis using GPA and PCA, followed by a reanalysis of the data using alternative classifiers and rigorous testing of the different outcomes.

In the current paper, the authors evaluated eight ML methods and compared their classification accuracy to traditional PCA. Additionally, common occurrences in the attempted morphological classification of specimens, such as non-representative partial sampling, missing specimens, and missing landmarks, were simulated, and the performance of PCA vs ML methods was evaluated.

The main problem with this manuscript is that it is three papers rolled into one, and the link doesn't work. The title promises a new Python package, but the actual text of the manuscript spends relatively little time on the Python package itself and barely gives any information about the package and what it includes or its usefulness. It is definitely not the focus of the manuscript. The main thrust of the manuscript, which takes up most of the text, is the analysis of the papionin dataset, which shows very convincingly that PCA underperforms in virtually all conditions tested. In addition, the manuscript includes a rather vicious attack against two specific cases of misuse of PCA in paleoanthropological studies, which does not connect with the rest of the manuscript at all.

If the manuscript is a criticism of PCA techniques, this should be reflected in the title. If it is a report of a new Python package, it should focus on the package. Otherwise, there should be two separate manuscripts here.

The criticism of PCA is valid and important. However, pointing out that it is problematic in specific cases and is sometimes misused does not justify labeling tens of thousands of papers as questionable and does not justify vilifying an entire discipline. The authors do not make a convincing enough case that their criticism of the use of PCA in analyzing primate or hominin skulls is relevant to all its myriad uses in morphometrics. The criticism is largely based on statistical power, but it is framed as though it is a criticism of geometric morphometrics in general.

Joint Public Review:

Roget et al. build on their previous work developing a simple theoretical model to examine whether ageing can be under natural selection, challenging the mainstream view that ageing is merely a byproduct of other biological and evolutionary processes. The authors propose an agent-based model to evaluate the adaptive dynamics of a haploid asexual population with two independent traits: fertility timespan and mortality onset. Through computational simulations, their model demonstrates that ageing can give populations an evolutionary advantage. Notably, this observation arises from the model without invoking any explicit energy tradeoffs, commonly used to explain this relationship.

Additionally, the theoretical model developed here indicates that mortality onset is generally selected to start before the loss of fertility, irrespective of the initial values in the population. The selected relationship between the fertility timespan and mortality onset depends on the strength of fertility and mortality effects, with larger effects resulting in the loss of fertility and mortality onset being closer together. By allowing for a trans-generational effect on ageing in the model, the authors show that this can be advantageous as well, lowering the risk of collapse in the population despite an apparent fitness disadvantage in individuals. Upon closer examination, the authors reveal that this unexpected outcome is a consequence of the trans-generational effect on ageing increasing the evolvability of the population (i.e., allowing a more effective exploration of the parameter landscape), reaching the optimum state faster.

The simplicity of the proposed theoretical model represents both the major strength and weakness of this work. On one hand, with an original and rigorous methodology, the logic of their conclusions can be easily grasped and generalised, yielding surprising results. Using just a handful of parameters and relying on direct competition simulations, the model qualitatively recapitulates the negative correlation between lifespan and fertility without requiring energy tradeoffs. This alone makes this work an important milestone for the rapidly growing field of adaptive dynamics, opening many new avenues of research, both theoretically and empirically.

On the other hand, the simplicity of the model also makes its relationship with living organisms difficult to gauge, leaving open questions about how much the model represents the reality of actual evolution in a natural context. In particular, a more explicit discussion on how the specifics of the model can impact the results and their interpretation is needed. For example, the lack of mechanistic details on the trans-generational effect on ageing makes the results difficult to interpret. Even if analytical results are obtained, most of the observations appear derived from simulations as they are currently presented. Also, the choice of parameters for the simulations shown in the paper and how it relates to our biological knowledge is not fully addressed by the authors. Finally, the conclusions of evolvability are insufficiently supported, as the authors do not show if the wider genotypic variability in populations with the ageing trans-generational effect is, in fact, selected.

Reviewer #1 (Public Review):

Summary:

In this study, Faniyan and colleagues build on their recent finding that renal Glut2 knockout mice display normal fasting blood glucose levels despite massive glucosuria. Renal Glut2 knockout mice were found to exhibit increased endogenous glucose production along with decreased hepatic metabolites associated with glucose metabolism. Crh mRNA levels were higher in the hypothalamus while circulating ACTH and corticosterone was elevated in this model. While these mice were able to maintain normal fasting glucose levels, ablating afferent renal signals to the brain resulted in substantially lower blood glucose levels compared to wildtype mice. In addition, the higher CRH and higher corticosterone levels of the knockout mice were lost following this denervation. Finally, acute phase proteins were altered, plasma Gpx3 was lower, and major urinary protein MUP18 and its gene expression were higher in renal Glut2 knockout mice. Overall, the main conclusion that afferent signaling from the kidney is required for renal glut2 dependent increases in endogenous glucose production is well supported by these findings.

Strengths:

An important strength of the paper is the novelty of the identification of kidney to brain communication as being important for glucose homeostasis. Previous studies had focused on other functions of the kidney modulated by or modulating brain function. This work is likely to promote interest in CNS pathways that respond to afferent renal signals and the response of the HPA axis to glucosuria. Additional strengths of this paper stem from the use of incisive techniques. Specifically, the authors use isotope enabled measurement of endogenous glucose production by GC-MS/MS, capsaicin ablation of afferent renal nerves, and multifiber recording from the renal nerve. The authors also paid excellent attention to rigor in the design and performance of these studies. For example, they used appropriate surgical controls, confirmed denervation through renal pelvic CGRP measurement, and avoided the confounding effects of nerve regrowth over time. These factors strengthen confidence in their results. Finally, humans with glucose transporter mutations and those being treated with SGLT2 inhibitors show a compensatory increase in endogenous glucose production. Therefore, this study strengthens the case for using renal Glut2 knockout mice as a model for understanding the physiology of these patients.

Weaknesses:

A few weaknesses exist. Most concerns relate to the interpretation of this study's findings. The authors state that loss of glucose in urine is sensed as a biological threat based on the HPA axis activation seen in this mouse model. This interpretation is understandable but speculative. Importantly, whether stress hormones mediate the increase in endogenous glucose production in this model and in humans with altered glucose transporter function remains to be demonstrated conclusively. For example, the paper found several other circulating and local factors that could be causal. This model is also unable to shed light on how elevated stress hormones might interact with insulin resistance, which is known to increase endogenous glucose production. That issue is of substantial clinical relevance for patients with T2D and metabolic disease. Finally, while findings from the Glut2 knockout mice are of scientific interest, it should be noted that the Glut2 receptor is critical to the function of pancreatic islets and as such is not a good candidate for pharmacological targeting

Reviewer #2 (Public Review):

Summary:

The authors previously generated renal Glut2 knockout mice, which have high levels of glycosuria but normal fasting glucose. They use this as an opportunity to investigate how compensatory mechanisms are engaged in response to glycosuria. They show that renal and hepatic glucose production, but not metabolism, is elevated in renal Glut2 male mice. They show that renal Glut2 male mice have elevated Crh mRNA in the hypothalamus, and elevated plasma levels of ACTH and corticosterone. They also show that temporary denervation of renal nerves leads to a decrease in fasting and fed blood glucose levels in female renal Glut2 mice, but not control mice. Finally, they perform plasma proteomics in male mice to identify plasma proteins with a greater than 25% (up or down) between the knockouts and controls.

Strengths:

The question that is trying to be addressed is clinically important: enhancing glycosuria is a current treatment for diabetes, but is limited in efficacy because of compensatory increases in glucose production.

Weaknesses:

(1) Although I appreciate that the initial characterization of the mice in another publication showed that both males and females have glycosuria, this does not mean that both sexes have the same mechanisms giving rise to glycosuria. There are many examples of sex differences in HPA activation in response to threat, for example. There is an unfounded assumption here that males and females have the same underlying mechanisms of glycosuria that undermines the significance of the findings.

(2) The authors state that they induced the Glut2 knockout with taxomifen as in their previous publication. The methods of that publication indicate that all experiments were completed within 14 days of inducing the Glut2 knockout. This means that the last dose of tamoxifen was delivered 14 days prior to the experimental endpoint of each experiment. This seems like an important experimental constraint that should be discussed in this manuscript. Is the glycosuria that follows Glut2 knockout only a temporary change? If so, then the long-term change in glycosuria that follows SGLT2 inhibition in humans might not be best modelled by this knockout. Please specify when the surgeries to implant a jugular catheter or ablate the renal nerves performed relative to the Glut2 knockout in the Methods.

(3) I am still unclear what group was used for controls. Are these wild-type mice who receive tamoxifen? Are they KspCadCreERT2;Glut2loxP/loxP mice who do not receive tamoxifen? This is important and needs to be specified.

(4) The authors should report some additional control measures for the renal denervation that could also impact blood glucose and perhaps some of their other measures. The control measures, which one would like to see unimpacted by renal denervation, include body weights, food consumption and water intake, and glycosuria itself.

(5) The graphical abstract shows a causal link between the hypothalamus and the liver that is unsupported by any of the current findings. That arrow should be removed or a question mark should be added next to the arrow.

(6) Though the authors have toned down their language implying a causal link between the HPA measures and compensatory elevation of blood glucose in the face of glycosuria, the title still implies this causal link. It is still the case that their data do not support causation. There are many potential ways to establish a causal link but those experiments are not performed here. The renal afferents are correlated with Crh content of the PVN, but nothing has been done to show that the Crh content is important for elevating blood glucose. In light of this, the title should be toned down. Perhaps something like "Renal nerves maintain blood glucose production and elevated HPA activity in response to glycosuria". The link between HPA and glucose is not shown in this paper.

Reviewer #1 (Public Review):

Summary:

The study investigated how root cap cell corpse removal affects the ability of microbes to colonize Arabidopsis thaliana plants. The findings demonstrate how programmed cell death and its control in root cap cells affect the establishment of symbiotic relationships between plants and fungi. Key details on molecular mechanisms and transcription factors involved are also given. The study suggests reevaluating microbiome assembly from the root tip, thus challenging traditional ideas about this process. While the work presents a key foundation, more research along the root axis is recommended to gain a better understanding of the spatial and temporal aspects of microbiome recruitment.

Reviewer #2 (Public Review):

Summary:

The authors identify the root cap as an important key region for establishing microbial symbioses with roots. By highlighting for the first time the crucial importance of tight regulation of a specific form of programmed cell death of root cap cells and the clearance of their cell corpses, they start unraveling the molecular mechanisms and its regulation at the root cap (e.g. by identifying an important transcription factor) for the establishment of symbioses with fungi (and potentially also bacterial microbiomes).

Strengths:

It is often believed that the recruitment of plant microbiomes occurs from bulk soil to rhizosphere to endosphere. These authors demonstrate that we have to re-think microbiome assembly as a process starting and regulated at the root tip and proceeding along the root axis.

Weaknesses:

The study is a first crucial starting point to investigate the spatial recruitment of beneficial microorganisms along the root axis of plants. It identifies e.g. an important transcription factor for programmed cell death, but more detailed investigations along the root axis are now needed to better understand - spatially and temporally - the orchestration of microbiome recruitment.

Reviewer #1 (Public Review):

Summary:

In this paper, the authors performed molecular dynamics (MD) simulations to investigate the molecular basis of the association of alpha-synuclein chains under molecular crowding and salt conditions. Aggregation of alpha-synuclein is linked to the pathogenesis of Parkinson's disease, and the liquid-liquid phase separation (LLPS) is considered to play an important role in the nucleation step of the alpha-synuclein aggregation. This paper re-tuned the Martini3 coarse-grained force field parameters, which allows long-timescale MD simulations of intrinsically disordered proteins with explicit solvent under diverse environmental perturbation. Their MD simulations showed that alpha-synuclein does not have a high LLPS-forming propensity, but the molecular crowding and salt addition tend to enhance the tendency of droplet formation and therefore modulate the alpha-synuclein aggregation. The MD simulation results also revealed important intra and inter-molecule conformational features of the alpha-synuclein chains in the formed droplets and the key interactions responsible for the stability of the droplets. These MD simulation data add biophysical insights into the molecular mechanism underlying the association of alpha-synuclein chains, which is important for understanding the pathogenesis of Parkinson's disease.

Strengths:

(1) The re-parameterized Martini 3 coarse-grained force field enables the large-scale MD simulations of the intrinsically disordered proteins with explicit solvent, which will be useful for a more realistic description of the molecular basis of LLPS.

(2) This paper showed that molecular crowding and salt contribute to the modulation of the LLPS through different means. The molecular crowding minimally affects surface tension, but adding salt increases surface tension. It is also interesting to show that the aggregation pathway involves the disruption of the intra-chain interactions arising from C-terminal regions, which potentially facilitates the formation of inter-chain interactions.

Weaknesses:

(1) Although the authors emphasized the advantage of the Martini3 force field for its explicit description of solvent, the whole paper did not discuss the water's role in the aggregation and LLPS.

(2) This paper discussed the effects of crowders and salt on the surface tension of the droplets. The calculation of the surface tension relies on the droplet shape. However, for the formed clusters in the MD simulations, the typical size is <10, which may be too small to rigorously define the droplet shape. As shown in previous work cited by this paper [Benayad et al., J. Chem. Theory Comput. 2021, 17, 525−537], the calculated surface tension becomes stable when the chain number is larger than 100.

(3) In this work, the Martini 3 force field was modified by rescaling the LJ parameters \epsilon and \sigma with a common factor \lambda. It has not been very clearly described in the manuscript why these two different parameters can be rescaled by a common factor and why it is necessary to separately tune these two parameters, instead of just tuning the coefficient \epsilon as did in a previous work [Larsen et al., PLoS Comput Biol 16: e1007870].

(4) Both the sizes and volume fractions of the crowders can affect the protein association. It will be interesting to perform MD simulations by adding crowders with various sizes and volume fractions. In addition, in this work, the crowders were modelled by fullerenes, which contribute to protein aggregation mainly by entropic means as discussed in the manuscript. It is not very clear how the crowder effect is sensitive to the chemical nature of the crowders (e.g., inert crowders with excluded volume effect or crowders with non-specific attractive interactions with proteins, etc) and therefore the force field parameters.

Reviewer #2 (Public Review):

In the manuscript "Modulation of α-Synuclein Aggregation Amid Diverse Environmental Perturbation", Wasim et al describe coarse-grained molecular dynamics (cgMD) simulations of α-Synuclein (aSyn) at several concentrations and in the presence of molecular crowding agents or high salt. They begin by bench-marking their cgMD against all-atom simulations by Shaw. They then carry 2.4-4.3 µs cgMD simulations under the above-noted conditions and analyze the data in terms of protein structure, interaction network analysis, and extrapolated fluid mechanics properties. This is an interesting study because a molecular scale understanding of protein droplets is currently lacking, but I have a number of concerns about how it is currently executed and presented.

(1) It is not clear whether the simulations have reached a steady state. If they have not, it invalidates many of their analysis methods and conclusions.

(2) The benchmarking used to validate their cgMD methods is very minimal and fails to utilize a large amount of available all-atom simulation and experimental data.

(3) They also miss opportunities to compare their simulations to experimental data on aSyn protein droplets.

(4) Aspects such as network analysis are not contextualized by comparison to other protein condensed phases.

(5) Data are not made available, which is an emerging standard in the field.

Reviewer #1 (Public Review):

Summary:

The authors' research group had previously demonstrated the release of large multivesicular body-like structures by human colorectal cancer cells. This manuscript expands on their findings, revealing that this phenomenon is not exclusive to colorectal cancer cells but is also observed in various other cell types, including different cultured cell lines, as well as cells in the mouse kidney and liver. Furthermore, the authors argue that these large multivesicular body-like structures originate from intracellular amphisomes, which they term "amphiectosomes." These amphiectosomes release their intraluminal vesicles (ILVs) through a "torn-bag mechanism." Finally, the authors demonstrate that the ILVs of amphiectosomes are either LC3B positive or CD63 positive. This distinction implies that the ILVs either originate from amphisomes or multivesicular bodies, respectively.

Strengths:

The manuscript reports a potential origin of extracellular vesicle (EV) biogenesis. The reported observations are intriguing.

Weaknesses:

It is essential to note that the manuscript has issues with experimental designs and lacks consistency in the presented data. Here is a list of the major concerns:

(1) The authors culture the cells in the presence of fetal bovine serum (FBS) in the culture medium. Given that FBS contains a substantial amount of EVs, this raises a significant issue, as it becomes challenging to differentiate between EVs derived from FBS and those released by the cells. This concern extends to all transmission electron microscopy (TEM) images (Figure 1, 2P-S, S5, Figure 4 P-U) and the quantification of EV numbers in Figure 3. The authors need to use an FBS-free cell culture medium.

(2) The data presented in Figure 2 is not convincingly supportive of the authors' conclusion. The authors argue that "...CD81 was present in the plasma membrane-derived limiting membrane (Figures 2B, D, F), while CD63 was only found inside the MV-lEVs (Fig. 2A, C, E)." However, in Figure 2G, there is an observable CD63 signal in the limiting membrane (overlapping with the green signals), and in Figure 2J, CD81 also exhibits overlap with MV-IEVs.

(3) Following up on the previous concern, the authors argue that CD81 and CD63 are exclusively located on the limiting membrane and MV-IEVs, respectively (Figure 2-A-M). However, in lines 104-106, the authors conclude that "The simultaneous presence of CD63, CD81, TSG101, ALIX, and the autophagosome marker LC3B within the MV-lEVs..." This statement indicates that CD63 and CD81 co-localize to the MV-IEVs. The authors need to address this apparent discrepancy and provide an explanation.

(4) The specificity of the antibodies used in Figure 2 should be validated through knockout or knockdown experiments. Several of the antibodies used in this figure detect multiple bands on western blots, raising doubts about their specificity. Verification through additional experimental approaches is essential to ensure the reliability and accuracy of all the immunostaining data in this manuscript.

(5) In Figures 2P-R, the morphology of the MV-IEVs does not resemble those shown in Figures 1-A, H, and D, indicating a notable inconsistency in the data.

(6) There are no loading controls provided for any of the western blot data. Additionally, for Figures 2-S4B, the authors should run the samples from lanes i-iii in a single gel.

(7) In Figure 2-S4, is there co-localization observed between LC3RFP (LC3A?) with other MV-IFV markers? How about LC3B? Does LC3B co-localize with other MV-IFV markers?

(8) The TEM images presented in Figure 2-S5, specifically F, G, H, and I, do not closely resemble the images in Figure 2-S5 K, L, M, N, and O. Despite this dissimilarity, the authors argue that these images depict the same structures. The authors should provide an explanation for this observed discrepancy to ensure clarity and consistency in the interpretation of the presented data.

(9) For Figures 3C and 3-S1, the authors should include the images used for EV quantification. Considering the concern regarding potential contamination introduced by FBS (concern 1), it is advisable for the authors to employ an independent method to identify EVs, thereby confirming the reliability of the data presented in these figures.

(10) Do the amphiectosomes released from other cell types as well as cells in mouse kidneys or liver contain LC3B positive and CD63 positive ILVs?

Reviewer #2 (Public Review):

Summary:

The authors had previously identified that a colorectal cancer cell line generates small extracellular vesicles (sEVs) via a mechanism where a larger intracellular compartment containing these sEVs is secreted from the surface of the cell and then tears to release its contents. Previous studies have suggested that intraluminal vesicles (ILVs) inside endosomal multivesicular bodies and amphisomes can be secreted by the fusion of the compartment with the plasma membrane. The 'torn bag mechanism' considered in this manuscript is distinctly different because it involves initial budding off of a plasma membrane-enclosed compartment (called the amphiectosome in this manuscript, or MV-lEV). The authors successfully set out to investigate whether this mechanism is common to many cell types and to determine some of the subcellular processes involved.

The strengths of the study are:

(1) The high-quality imaging approaches used, seem to show good examples of the proposed mechanism.

(2) They screen several cell lines for these structures, also search for similar structures in vivo, and show the tearing process by real-time imaging.

(3) Regarding the intracellular mechanisms of ILV production, the authors also try to demonstrate the different stages of amphiectosome production and differently labelled ILVs using immuno-EM.<br /> Several of these techniques are technically challenging to do well, and so these are critical strengths of the manuscript.

The weaknesses are:

(1) Most of the analysis is undertaken with cell lines. In fact, all of the analysis involving the assessment of specific proteins associated with amphiectosomes and ILVs are performed in vitro, so it is unclear whether these processes are really mirrored in vivo. The images shown in vivo only demonstrate putative amphiectosomes in the circulation, which is perhaps surprising if they normally have a short half-life and would need to pass through an endothelium to reach the vessel lumen unless they were secreted by the endothelial cells themselves.

(2) The analysis of the intracellular formation of compartments involved in the secretion process (Figure 2_S5) relies on immuno-EM, which is generally less convincing than high-/super-resolution fluorescence microscopy because the immuno-labelling is inevitably very sporadic and patchy. High-quality EM is challenging for many labs (and seems to be done very well here), but high-/super-resolution fluorescence microscopy techniques are more commonly employed, and the study already shows that these techniques should be applicable to studying the intracellular trafficking processes.

(3) One aspect of the mechanism, which needs some consideration, is what happens to the amphisome membrane, once it has budded off inside the amphiectosome. In the fluorescence images, it seems to be disrupted, but presumably, this must happen after separation from the cell to avoid the release of ILVs inside the cell. There is an additional part of Figure 1 (Figure 1Y onwards), which does not seem to be discussed in the text (and should be), that alludes to amphiectosomes often having a double membrane.

(4) The real-time analysis of the amphiectosome tearing mechanism seemed relatively slow to me (over three minutes), and if this has been observed multiple times, it would be helpful to know if this is typical or whether there is considerable variation.

Overall, I think the authors have been successful in identifying amphiectosomes secreted from multiple cell lines and demonstrating that the ILVs inside them have at least two origins (autophagosome membrane and late endosomal multivesicular body) based on the markers that they carry. The analysis of intracellular compartments producing these structures is rather less convincing and it remains unclear what cells release these structures in vivo.

I think there could be a significant impact on the EV field and consequently on our understanding of cell-cell signalling based on these findings. It will flag the importance of investigating the release of amphiectosomes in other studies, and although the authors do not discuss it, the molecular mechanisms involved in this type of 'ectosomal-style' release will be different from multivesicular compartment fusion to the plasma membrane and should be possible to be manipulated independently. Any experiments that demonstrate this would greatly strengthen the manuscript.

In general, the EV field has struggled to link up analysis of the subcellular biology of sEV secretion and the biochemical/physical analysis of the sEVs themselves, so from that perspective, the manuscript provides a novel angle on this problem.

Reviewer #3 (Public Review):

Summary:

In this manuscript, the authors describe a novel mode of release of small extracellular vesicles. These small EVs are released via the rupture of the membrane of so-called amphiectosomes that resemble "morphologically" Multivesicular Bodies.

These structures have been initially described by the authors as released by colorectal cancer cells (https://doi.org/10.1080/20013078.2019.1596668). In this manuscript, they provide experiments that allow us to generalize this process to other cells. In brief, amphiectosomes are likely released by ectocytosis of amphisomes that are formed by the fusion of multivesicular endosomes with autophagosomes. The authors propose that their model puts forward the hypothesis that LC3 positive vesicles are formed by "curling" of the autophagosomal membrane which then gives rise to an organelle where both CD63 and LC3 positive small EVs co-exist and would be released then by a budding mechanism at the cell surface that appears similar to the budding of microvesicles /ectosomes. Very correctly the authors make the distinction from migrasomes because these structures appear very similar in morphology.

Strengths:

The findings are interesting despite that it is unclear what would be the functional relevance of such a process and even how it could be induced. It points to a novel mode of release of extracellular vesicles.

Weaknesses:

This reviewer has comments and concerns concerning the interpretation of the data and the proposed model. In addition, in my opinion, some of the results in particular micrographs and immunoblots (even shown as supplementary data) are not of quality to support the conclusions.

Reviewer #1 (Public Review):

Summary:

This study aims to understand how cell fusion contributes to wound healing using a laser-induced injury in the notum epithelium of a developing fruit fly. The authors meticulously characterize the epithelial fusion events using a live imaging approach and report that syncytia arise by 'border breakdown' and 'cell shrinking'. The syncytial epithelial cells also appear to outcompete mononucleated cells and preferentially dissolve their tangential borders, which correlates with the accumulation of actin at the leading edge.

Strengths:

The strength of this study is the authors' live imaging approach to capture these dynamic fusion events that are a fundamental, yet poorly understood biological process.

Weaknesses:

A major weakness is that all the authors' conclusions are based on descriptive studies, in which the role of cell fusion is not directly tested. This is particularly important because other models of wound-induced polyploidization have demonstrated that another cytoskeletal protein, myosin, was upregulated and dependent on endoreplication, and not cell fusion. Therefore it remains unclear to what extent cell fusion, endoreplication, or both are required to outcompete mononucleated cells as well as pool actin as described in this study.

Reviewer #2 (Public Review):

Summary:

Overall, this study provides a thorough description of the formation of syncytia following wounding of the proliferation-competent diploid epithelium of the pupal notum. While this phenomenon has already been described briefly for this particular tissue by the Galko lab in Wang et al 2015, the authors provide a much more detailed description and characterisation of the process providing some novel insights (radial versus tangential border breakdown, cell shrinkage, timings, syncytia outcompeting mononucleated cells, etc.).

Strengths:

This paper provides an elegant, thorough, descriptive characterisation of syncytia-driven wound closure using state-of-the-art confocal live imaging of the pupal notum. The authors show that laser-induced wounding of this diploid, proliferation-competent epithelium results in the formation of syncytia of various sizes in the first few cell rows around the wound edge, which progressively become bigger as healing proceeds. This results in ~50% of cells becoming part of these syncytia. The cell fusion events were convincingly demonstrated by showing the disappearance of p120ctnRFP and E-Cadherin-GFP from cell-cell borders as well as cytoplasmic GFP mixing of GFP-positive cells with a GFP-negative cell.

Apart from cell-cell fusion by border breakdown that mostly happens in the first 2h following wounding, the authors also found that at later stages of wound healing cell shrinkage following cytoplasmic mixing contributed to sycytia formation.

Next, the authors provided some convincing evidence that syncytia outcompete mononuclear cells for being positioned in the first cell row around the wound.

The authors then show that radial border breakdown occurs much less frequently than tangential border breakdown. They suggest that radial border breakdown reduces the requirement for cell-cell intercalations. They also hypothesise that tangential border breakdown might allow fused cells to share resources and provide more resources to be used near the wound edge, e.g. for actomyosin cable formation. To test this, the authors generate single-cell clones that overexpress Actin-GFP. They then show convincingly how a single Actin-GFP-positive cell in the second cell row fuses with one GFP-negative cell in the first cell row. The Actin-GFP signal then spreads in the fused cell and labels some previously unlabelled actin-rich structure near the wound edge which most likely is the actomyosin cable. This provides some evidence for resource sharing by cytoplasmic mixing following fusion.

Weaknesses:

The authors provide some convincing evidence that syncytia outcompete mononuclear cells for being positioned in the first cell row around the wound. The authors suggest that the syncytial cells might be better able to close the wound. However, some genetic studies would need to be done to establish this more convincingly. E.g. Could the authors genetically block syncytia formation and then show that these wounds now heal slower?

The authors suggest that radial border breakdown reduces the requirement for cell intercalation. While this might be true it also raises the question of how the various syncytia facing the wound border change shape to allow the shrinkage of the first cell row over time to allow wound closure. None of the four movies included in the study shows the whole wound healing process until the later stages, making it hard to assess this. It would be good to include one such movie showing the syncytia in the whole wound and comment on this point.

The authors hypothesise that tangential border breakdown might allow fused cells to share resources and provide more resources to be used near the wound edge, e.g. for actomyosin cable formation. They show convincingly through the fusion of a single Actin-GFP-positive cell in the second cell row with a GFP-negative cell in the first cell row that Actin-GFP spreads in the fused cell and labels the previously unlabelled actomyosin cable. While the hypothesis of resource sharing to improve healing is intriguing and makes sense, this experiment doesn't necessarily prove the benefit of resource sharing. It does show cytoplasmic mixing following fusion, now allowing the GFP-labelled actin to diffuse and be incorporated into the actomyosin cable. In a wild-type condition, fusion would not increase the total concentration of resources, although it would increase the total amount of resources within this bigger fused cell. The question is whether resource sharing without increasing the protein concentration is beneficial and increases the efficiency of certain wound healing mechanisms. There might be a benefit of cell fusion, if for example certain resources were only present in limited amounts or if protein transport could increase the concentration locally. To provide better evidence for the hypothesis that resource sharing improves wound healing, maybe the authors could look at the actomyosin cable in a wounded epithelium (such as in Figure 4E, F), in which all cells express MyoII-GFP. The authors could compare the average intensity of the actomyosin cable at the wound edge in mononucleated cells versus in syncytia. If resource sharing is indeed beneficial, it might be that the actomyosin cable is stronger/brighter in syncytia or it forms quicker.

The biggest limitation of this study is that the authors don't address how the formation of these syncytia is regulated. While the manuscript in its current form provides some valuable new insights into syncytial-driven wound closure, it would be much more informative if it also provided some mechanistic details. The authors could test if some of the mechanisms shown to regulate syncytial formation in other types of syncytia-driven wound healing are also involved here. E.g. Yorkie was shown to negatively regulate cell fusion in adult syncytial-driven wound closure (Losick et al 2013). The authors could test for the effect of Yorkie-RNAi in the epithelium on wound closure and syncytia formation. Expression of the dominant negative RacN17 also blocked cell fusion in adult syncytial-driven wound closure (Losick et al 2013).

Moreover, JNK activation was shown to be needed in larval syncytial-driven wound closure (Galko and Krasnow 2004). The authors could test JNK pathway reporters to assess pathway activation or test if the JNK pathway is needed for syncytial-driven wound closure by expressing a dominant-negative form of Basket JNK in the epithelium.

Or could syncytia formation be regulated by changes in Integrin-mediated adhesion as shown by the Galko lab in Wang et al 2015? They show that wounding provoked a striking relocalization of PINCH and ILK, indicating the disassembly of functional FA complexes concomitant with syncytium formation. Maybe the authors could investigate some of these.

Another general question that the authors raise but don't address enough is whether syncytia-driven wound closure in proliferation-competent epithelia is any different from the one in post-mitotic, polyploid epithelia. Since the mechanism regulating the former is not known, this remains unclear.

Finally, it is not clear, whether syncytia in these proliferation-competent epithelia get resolved after wound healing. Do they get removed and replaced by mononucleated proliferation-competent cells or do the syncytia stay in the epithelium like a scar? The authors should provide some images of wound areas a few hours after wound closure is complete and comment on this.

Minor points:

Figure 3: It would be better to have the microcopy images alongside the quantifications.

Figure 4A: The syncytium at the wound edge here doesn't look straight but wavy. Does it not form an actomyosin cable that straightens the front? Or are there lamellipodia/filopodia?

248: The authors suggest an interesting hypothesis that mitochondria or ER could be pooled in fused cells. It would be nice to see some evidence: e.g. by labeling mitochondria and assessing where they are in syncytia versus mononucleated cells and whether they are concentrated around the wound edge.

141-145 (Figure 4B and C) This example is not completely convincing. First, it is hard to see where the wound edge is. Second, it would be good to include an even later time point when the cell is clearly no longer at the wound edge.

Reviewer #3 (Public Review):

Summary:

White et al. described laser-induced wound healing of the Drosophila pupal notum. They found that the epithelial monolayer is dynamically induced to form syncytia by cell-cell fusion as an important part of repair. They reveal two processes: cell shrinking and border breakage that occur as part of syncytia formation. Expression of GFP in the cytoplasms of some epithelial cells reveals that cytoplasmic contents mix following injury and the GFP rapidly diffuses between cells. Using live imaging they observe that syncytia expand towards the wound, maintain their positions close to the leading edge, and apparently displace smaller cells. They propose that syncytia redistribute cellular components towards the wound facilitating repair and show that labelled actin becomes concentrated at the leading edge.

Strengths:

The manuscript is interesting and on an important and emerging topic of wound healing in a genetically tractable organism. The manuscript is very well written.

Weaknesses:

There are three major issues that the authors must address:

(1) Is cell-cell fusion sufficient to enhance/facilitate wound healing?

(2) Characterization of "border breakdown"; Is this phenomenon disassembly of apical junctions following membrane fusion?

(3) Are cells really shrinking or is it only the apical domains that "shrink" as the cells join the syncytium?

Reviewer #1 (Public Review):

Summary:

This is an original manuscript submission by Tatekoshi et al entitled, "Human induced pluripotent stem cell-derived cardiomyocytes to study inflammation-induced diastolic dysfunction." Based on the premise that treated HIV individuals commonly have heart failure with preserved ejection fraction, yet robust animal models have not been established, the team developed iPS-CM models to study HFpEF with this angle in mind. The group established iPS-CMs using standard methods and studied TNFa and IFNy effects on calcium transients. They observed that both cytokines increased calcium transient decay and downstroke times, which could be reversed by mitoTempo treatment in the case of TNFa. To determine how mitochondrial dysfunction may impact the cytokine-induced calcium transient changes, the team measured OCR treatment changes. They observed that NAC and TNFa co-treated cells demonstrated reduced OCR. The team went on to test the effects of antiretroviral therapies including tenofovir, relategravir, elvitegravir, and darunavir at 3-10 uM levels in iPS-CMs. The team noted that ART treatments reversed the diastolic dysfunction associated with TNFa treatment suggesting that ART therapies may improve diastolic dysfunction that is associated with TNFa signaling directly in cardiomyocytes. Following up on this treatment effect, the team screened several other candidates across drug classes and identified that dapagliflozin (SGLT2i) reversed diastolic dysfunction induced by TNFa. Finally, the team collected human serum from patients with HIV+ patients from two hospitals - Northwestern with diastolic dysfunction by cMRI, and UCSF with normal diastolic function by echo. Both cohort serum samples did not change calcium transients in iPS-CMs. However, due to numerous and significant major methodological concerns, and the potential low impact of the study results, this manuscript is expected to be of very low impact to the field in its current form.

Strengths:

1) From a significance standpoint, understanding the mechanisms of HFpEF, particularly in conditions such as HIV would be very impactful.

2) Collecting HIV patient serum and identifying a plasma factor that impacts cardiac function could be very significant if successful.

Weaknesses:

(1) I am not convinced how this study relates to HIV individual HFpEF, and the study design does not seem to be well thought out.

(2) The connectivity of the study experiments is loose, and data analysis and conclusions are broadly overstated and misinterpreted.

(3) For example the study lacks any measure of diastolic contractile function, and even if performed, the relevance of TNFa treatments to cells in vitro in these immature cell contexts would remain unclear. There is surprisingly no reported molecular analyses of potential mechanisms of the calcium transient changes. The study falls short in molecular detail and instead relies on drug treatments and responses that are hard to interpret with dosages that are not well justified and treatments that are numerous. Unclear what changes in calcium transients mean functionally without a comprehensive assessment of CM biomechanical contraction and relaxation measurements, and this would also require parallel molecular investigations of potential targets of any phenotypes observed.

(4) Calcium transient data need to be better illustrated such as with representative peak tracings. The data overall is with too few samples, particularly given the inherent heterogeneity of iPS-CM studies. The iPS-CM system as a model for diastolic dysfunction remains unestablished.

(5) There are unclear dose choices for the various ART drugs tested, as well as the other drugs tested such as SGLT2i. Besides the observation that SLC5A2 (SGLT2 target) is not established to be expressed in adult mammalian cardiomyocytes.

(6) HIV plasma samples were not tested for cytokine levels, but this could be done to assess the validity of the final experiments. It is unclear what is being tested with these experiments.

(7) The choice of serum controls from a second institution (UCSF) opens up concerns over batch effects unrelated to differences in diastolic dysfunction. However, there were no differences with the Northwestern samples. It is unclear why this data is included as it does not add to the impact of the study.

(8) There are concerns about the quality of the iPS-CMs since there is no cell imaging or molecular analyses. Figure 5 Supplement 1 images are of low quality and low resolution to assess cell quality. Overall the iPS-CM QC data is extremely sparse

Reviewer #2 (Public Review):

The authors investigated the role of inflammatory molecules in diastolic dysfunction and screened antiviral and cardioprotective pharmacological agents for their potential to reverse inflammation-mediated diastolic dysfunction. This study focuses on heart failure with preserved ejection fraction (HFpEF) in people living with HIV (PLWH), a condition often challenging to study due to the lack of suitable animal models. Using human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), researchers simulated HFpEF in vitro. They observed that inflammatory cytokines impaired cardiomyocyte relaxation, mimicking HFpEF, while SGLT2 inhibitors and mitochondrial antioxidants reversed this effect. Exposure to serum from HIV patients did not induce dysfunction in hiPSC-CMs. These findings suggest hiPSC-CMs as a promising model for understanding HFpEF mechanisms and testing potential treatments.

Comments to improve the study:

The manuscript is well-written, and the results are well-illustrated. However, there are some topics that are not well-connected, and the rationale and hypothesis are not clearly defined beforehand, such as mitochondrial membrane potential, mitochondrial ROS, and angiogenic potential.

As the hiPSC cardiomyocytes are treated with various reagents to measure diastolic dysfunction, it is important to confirm whether the treatment time and dose used were sufficient to exert a functional effect. Dose and time-dependent experiments are essential, or at least sufficient citations should be provided for selecting the dose for IFN and TNF.

After IFN and TNF treatment, determining the expression levels of molecular markers of DD/HFpEF is crucial. Again, if sufficient evidence is available, it can be cited.

The Methods section describes TMRE colocalization and immunofluorescence, but no images are provided.

The concentration of TNF and IFN in patients is critical, which was acknowledged and discussed as a limitation of the study by the authors. Authors should consider this aspect, and if not feasible, clinical reports should be cited to provide a rough estimation of their concentration.

Reviewer #3 (Public Review):

Summary:

In this manuscript, Weng et al. detect a neuron-specific transcriptome that regulates aging. The authors first profile neuron-specific responses during aging at a time point where a loss in memory function is present. They discover signatures unique to neurons which validate their pipeline and reveal the loss of neuron identity with age. For example, old neurons reduce the expression of genes related to synaptic function and neuropeptide signaling and increase the expression of chromatin regulators, insulin peptides, and glycoproteins. The authors discover the detrimental effect of selected upregulated genes (utx-1, ins-19, and nmgp-1) by knocking them down in the whole body and detecting improvement of short memory functions. They then use their pipeline to test neuronal profiles of long-lived insulin/IGF mutants. They discover that genes related to stress response pathways are upregulated upon longevity (e.g. dod-24, F08H9.4) and that they are required for improved neuron function in long-lived individuals.

Strengths:

Overall, the manuscript is well-written, and the experiments are well-described. The authors take great care to explain their reasoning for performing experiments in a specific way and guide the reader through the interpretation of the results, which makes this manuscript an enjoyable and interesting read. Using neuron-specific transcriptomic analysis in aged animals the authors discover novel regulators of learning and memory, which underlines the importance of cell-specific deep sequencing. The time points of the transcriptomic profiling are elegantly chosen, as they coincide with the loss of memory and can be used to specifically reveal gene expression profiles related to neuron function. The authors showcase on the dod-24 example how powerful this approach is. In long-lived insulin/IGF-1 receptor mutants body-wide dod-24 expression differs from neuron-specific profiles. Importantly, the depletion of dod-24 has an opposing effect on lifespan and learning memory. The dataset will provide a useful resource for the C. elegans and aging community.

Weaknesses:

While this study nicely describes the neuron-specific profiles, the authors do not test the relevance in a tissue-specific way. It remains unclear if modifying the responses only in neurons has implications for either memory or potentially for lifespan. The authors point to this in the text and refer to tissue-specific datasets. However, it is possible that the tissue-specific profile changes with age. The authors should consider mining publicly available cell-specific aging datasets and performing neuron-specific RNAi to test the functional relevance of the neuron-specific response. This would strengthen the importance of cell-specific profiling.

Reviewer #1 (Public Review):

The authors perform RNA-seq on FACS-isolated neurons from adult worms at days 1 and 8 of adulthood to profile the gene expression changes that occur with cognitive decline. Supporting data are included indicating that by day 7 of adulthood, learning and memory are reduced, indicating that this time point or after represents cognitively aged worms. Neuronal identity genes are reduced in expression within cognitively aged worms, whereas genes involved in proteostasis, transcription/chromatin, and stress response are elevated. A number of specific examples are provided, representing markers of specific neuronal subtypes, and correlating expression changes to the erosion of particular functions (e.g. motor neurons, chemosensory neurons, aversive learning neurons, etc).

To investigate whether the upregulation of genes in neurons with age is compensatory or deleterious, the authors reduced the expression of a set of three significantly upregulated genes and performed behavioral assays in young adults. In each case, reduction of expression improved memory, consistent with a model in which age-associated increases impair neuronal function. This claim would be bolstered by an experiment elevating the expression of these genes in young neurons, which should reduce the learning index if the hypothesis is correct.

The authors then characterize learning and memory in wild-type, daf-2, and daf-2/daf-16 worms with age and find that daf-2 worms have an extended ability to learn for approximately 10 days longer than wild types. This was daf-16 dependent. Memory was extended in daf-2 as well, and strikingly, daf-2;daf-16 had no short-term memory even at day 1. Transcriptomic analysis of FACS-sorted neurons was performed on the three groups at day 8. The authors focus their analysis on daf-2 vs. daf-2;daf-16 and present evidence that daf-2 neurons express a stress-resistance gene program. One question that remains unanswered is how well the N2 and daf-2;daf-16 correlate overall, and are there differences? This may be informative as wild type and daf-2;daf-16 mutants are not phenotypically identical when it comes to memory, and there may be differences that can be detected despite the overlap in the PCA. This analysis could reveal the daf-16 targets involved in memory.

The authors tested eight candidate genes that were more highly expressed in daf-2 neurons vs. daf-2;daf-16 and showed that reduction of 2 and 5 of these genes impaired learning and memory, respectively, in daf-2 worms. This finding implicates specific neuronal transcriptional targets of IIS in maintaining cognitive ability in daf-2 with age, which, importantly, are distinct from those in young wild type worms.

Reviewer #2 (Public Review):

Weng et al. perform a comprehensive study of gene expression changes in young and old animals, in wild-type and daf-2 insulin receptor mutants, in the whole animal, and specifically in the nervous system. Using this data, they identify gene families that are correlated with neuronal ageing, as well as a distinct set of genes that are upregulated in neurons of aged daf-2 mutants. This is particularly interesting as daf-2 mutants show both extended lifespans and healthier neurons in aged animals, reflected by better learning/memory in older animals compared with wild-type controls. Indeed, the knockdown of several of these upregulated genes resulted in poorer learning and memory. In addition, the authors showed that several genes upregulated during ageing in wild-type neurons also contribute to learning and memory; specifically knockdown of these genes in young animals resulted in improved memory. This indicates that (at least in this small number of cases), genes that show increased transcript levels with age in the nervous system somehow suppress memory, potentially by having damaging effects on neuronal health.

Finally, from a resource perspective, the neuronal transcriptome provided here will be very useful for C. elegans researchers as it adds to other existing datasets by providing the transcriptome of older animals (animals at day 8 of adulthood) and demonstrating the benefits of performing tissue-specific RNAseq instead of whole-animal sequencing.

The work presented here is of high quality and the authors present convincing evidence supporting their conclusions. I only have a few comments/suggestions:

(1) Do the genes identified to decrease learning/memory capacity in daf-2 animals (Figure 4d/e) also impact neuronal health? daf-2 mutant worms show delayed onset of age-related changes to neuron structure (Tank et al., 2011, J Neurosci). Does knockdown of the genes shown to affect learning also affect neuron structure during ageing, potentially one mechanism through which they modulate learning/memory?

(2) The learning and memory assay data presented in this study uses the butanone olfactory learning paradigm, which is well established by the same group. Have the authors tried other learning assays when testing for learning/memory changes after the knockdown of candidate genes? Depending on the expression pattern of these genes, they may have more or less of an effect on olfactory learning versus for example gustatory or mechanosensory-based learning.

(3) I have a comment on the 'compensatory vs dysregulatory' model as stated by the authors on page 7. I understand that this model presents the two main options, but perhaps this is slightly too simplistic: the gene expression that rises during ageing may be detrimental for memory (= dysregulatory), but at the same time may also be beneficial for other physiological roles in other tissues (=compensatory).

Reviewer #1 (Public Review):

Summary:

The manuscript by Relovska and colleagues aims to decipher the importance of sterol homeostasis on male reproduction and, in particular, the impact of altered sterol homeostasis in sperm cells. To this end, they are generating a global line of Dhcr24 transgenic mice by mating Dhcr24fl/fl mice (overexpressing the construct in the Rosa269c gene locus) with EIla 100 CRE mice (expressing Cre recombinase in the early mouse embryo).

The data provided are robust, using a range of approaches from sperm analysis (structure, function) to lipid analysis. Results show that overexpression of DHCR24 (TG) leads to altered sterol homeostasis in spermatozoa. Sperm from TG mice have abnormal mitochondria and sperm tails. TG spermatozoa have reduced efficiency in undergoing the acrosomal reaction. Furthermore, the data suggest that TG spermatozoa have an altered metabolism with increased oxygen consumption. These data highlight that desmosterol depletion and/or altered sterol homeostasis impact sperm morphology, number, motility, and metabolism, resulting in reduced male fertility.

Strengths:

The manuscript is clear and well-written, and the results are presented in high-quality figures.

Weaknesses:

The main concern is the clear analysis of the rodent model. Indeed, the use of this particular Cre leads to whole-body overexpression, the remaining question is whether the observed effects are directly mediated by the testicular impacts of Dhcr24 overexpression. Even if it is a testicular effect, we can't conclude where it comes from. Is it at the level of spermatogenesis, as the authors speculate? Furthermore, the authors mention that normally, Dhcr24c is mainly expressed in spermatogonia, so it's not clear why they focus only on spermatozoa, which in WT males do not normally express dhcr24 according to the authors. It is worth clarifying the testicular phenotype in more detail.

The lower level of TG in aged mice could suggest an extinction of the transgene at least in sperm during aging, which could be difficult to reconcile with the observed phenotype. With this in mind, it would be interesting to define the penetrance of the phenotype during aging, to define variability between mice, and to clearly define potential correlations between sterol levels and fertility disorders, or altered sperm parameters.

Reviewer #2 (Public Review):

Summary:

Sterols, including desmosterol and cholesterol, play critical roles in male fertility including membrane rearrangements associated with sperm capacitation, steroidogenesis, and germ cell development. Relovska, Sona, et al. investigated the effects of global overexpression of classic cholesterol biosynthesis enzyme DHCR24 in a mouse model, focusing on the impacts on sperm function and male fertility. While mice were viable and did not exhibit altered plasma cholesterol levels or obesity, the authors demonstrated that concentrations of relevant sterols in sperm from transgenic mice were altered compared to WT mouse sperm, including the expected depletion of desmosterol. The transgenic males exhibited several indicators of reduced sperm function and fertility. Mitochondrial dysfunction was indicated by a noted depletion of localization in the distal middle-piece of up to approximately 20-25% of transgenic sperm flagella, and alterations in mitochondrial membrane potential and oxygen consumption rates in transgenic sperm were noted.

Strengths:

The authors demonstrate that DHCR24 overexpression was achieved and that sperm sterol levels are altered. The conclusions that global DHCR24 overexpression impacts mitochondrial localization and male fertility parameters are supported by the number of different supporting assessments utilized to reach these conclusions and this is a strength. Overall, the authors achieve their aim of demonstrating DHCR24 overexpression impacts on indicators of sperm function and fertility including reduced sperm counts and sperm motility, reduced fertility in mating trials with aged males, and reduced IVF success when sperm were capacitated in conditions of higher sperm concentrations in vitro. The authors further investigate sperm mitochondrial localization and function. While a mitochondrial sheath can form in sperm from transgenic mice, 25% of the sperm exhibit a shortened mitochondrial sheath where a distal portion of the middle piece of the sperm flagella lacks mitochondria and instead exhibits exposed outer dense fibers.

Weaknesses:

In the current study, the authors conclude that desmosterol may not act as an LXR activator in testicular cells based on assessment of relevant mRNA levels in whole testis that indicated the relevant transcripts were not altered in transgenic testes. However, caution should be taken in utilizing whole testis transcriptomics to rule out a role in specific cell populations within the testis with minor relative representation, such as macrophages or undifferentiated spermatogonia. This is an important distinction for a few reasons. The authors reveal through single-cell assessments of DHCR24 expression in WT testis that it is most highly expressed in undifferentiated spermatogonia. Further, the authors previously reported that DHCR24 over-expression in myeloid/macrophage populations did impact LXR activation impacting atherosclerosis. Taken together with emerging evidence that testis macrophages may impact spermatogonial fate decisions, the potential for DHCR24 to impact these minor testicular cell populations should not yet be ruled out. The significance of individual observations needs to be clarified through improved reporting of methodologies, specific biological and technical replicates, and statistical significance for each individual assessment. The lack of these details obfuscates the ability of the reader to interpret or replicate several reported observations which is a weakness.

(1) The fertility trials indicate a reduced number of pups/litter in aged but not younger transgenic males. However, the data for the aged males includes three data points of 0 pups, which brings to question if the data points each represent the average pups/litter for individual males or individual litters with multiple litters separately included for fertile males. Clarification could help in interpreting whether litter sizes were reduced, or if litter frequency and/or fertility of individual males was reduced. In the latter case, behavioral infertility would not be excluded from consideration.

(2) The statistical significance is not clear for altered acrosome reaction data, hyperactivated motility data, waveform analysis, mitochondrial membrane potential, and some of the sperm morphology assessments. In many assessments, the biological and technical replicates assessed need to be clarified.

(3) Methods utilized for image assessment of waveform analysis and mitochondrial membrane potential are lacking detail sufficient for replication of the assessments or for reader interpretation of how conclusions were reached.

Summary of impact:

Overall, the novel observations in this study are consistent with a role for controlled sterol concentrations being important for male fertility and indicate that this model will be useful to further investigate sterol biosynthesis contributions to testis function including steroidogenesis, spermatogenesis, and sperm function including capacitation.

Reviewer #3 (Public Review):

Summary:

The authors have created DHCR24 knockin mice and noted changes in the sperm sterol composition. Concurrently, alterations in the quantity, motility, and function of the sperm in DHCR24 knockin mice were identified.

Strengths:

The manuscript offers an intriguing perspective on how disruptions in sperm sterol composition can lead to sperm abnormalities.

Weaknesses:

From the current data, several issues remain to be clarified, including the fertility test results, which merit a more detailed presentation to ascertain whether differences stem from individual variability or overall changes. The authors suggest an increase in ROS in the sperm of DHCR24 knockin mice, leading to sperm damage, which also requires further confirmation. Moreover, the quality of some data requires verification or improvement, such as the morphological analysis of testicular sections and the OCR experiments.

Reviewer #3 (Public Review):

The author presents a novel theory and computational model suggesting that grid cells do not encode space, but rather encode non-spatial attributes. Place cells in turn encode memories of where those specific attributes occurred. The theory accounts for many experimental results and generates useful predictions for future studies. The model's simplicity and potential explanatory power will interest others in the field, though there are a number of concerns that should first be addressed.

A crucial assumption of the model is that the content of experience must be constant in space. It's difficult to imagine a real-world example that satisfies this assumption. Odors and sounds are used as examples. While they are often more spatially diffuse than an objects on the ground, odors and sounds have sources that are readily detectable. Animals can easily navigate to a food source or to a vocalizing conspecific. This assumption is especially problematic because it predicts that all grid cells should become silent when their preferred non-spatial attribute (e.g. a specific odor) is missing. I'm not aware of any experimental data showing that grid cells become silent. On the contrary, grid cells are known to remain active across all contexts that have been tested, including across sleep/wake states. Unlike place cells, grid cells do not seem to turn off. Since grid cells are active in all contexts, their preferred attribute must also be present in all contexts, and therefore they would not convey any information about the specific content of an experience.

The proposed novelty of this theory is that other models all assume that grid cells encode space. This isn't quite true of models based on continuous attractor networks, the discussion of which is notably absent. More specifically, these models focus on the importance of intrinsic dynamics within the entorhinal cortex in generating the grid pattern. While this firing pattern is aligned to space during navigation and therefore can be used as a representation of that space, the neural dynamics are preserved even during sleep. Similarly, it is because the grid pattern does not strictly encode physical space that grid-like signals are also observed in relation to other two-dimensional continuous variables.

The use of border cells or boundary vector cells as the main (or only) source of spatial information in the hippocampus is not well supported by experimental data. Border cells in the entorhinal cortex are not active in the center of an environment. Boundary-vector cells can fire farther away from the walls but are not found in the entorhinal cortex. They are located in the subiculum, a major output of the hippocampus. While the entorhinal-hippocampal circuit is a loop, the route from boundary-vector cells to place cells is much less clear than from grid cells. Moreover, both border cells and boundary-vector cells (which are conflated in this paper) comprise a small population of neurons compared to grid cells.

Reviewer #1 (Public Review):

Huber proposes a theory where the role of the medial temporal lobe (MTL) is memory, where properties of spatial cells in the MTL can be explained through memory function rather than spatial processing or navigation. Instantiating the theory through a computational model, the author shows that many empirical phenomena of spatial cells can be captured, and may be better accounted through a memory theory. It is an impressive computational account of MTL cells with a lot of theoretical reasoning and aims to tightly relate to various spatial cell data.

In general, the paper is well written, but likely due to the complexity, there are various aspects of the paper that are difficult to understand. One point is that it is not entirely clear to me that it is a convincing demonstration of purely memory rather than navigation, but rather an account of the findings through the lens of memory. Below, I raise several big-picture theoretical questions. I also have some clarification questions about the model (where I also have some theoretical question marks - due to not achieving a full understanding).

(1) Although the theory is based on memory, it also is based on spatially-selective cells. Not all cells in the hippocampus fulfill the criteria of place/HD/border/grid cells, and place a role in memory. E.g., Tonegawa, Buszaki labs' work does not focus on only those cells, and there are certainly a lot of non-pure spatial cells in monkeys (Martinez-Trujillo) and humans (iEEG). Does the author mainly focus on saying that "spatial cells" are memory, but do not account for non-spatial memory cells? This seems to be an incomplete account of memory - which is fine, but the way the model is set up suggests that *all* memory is, place (what/where), and non-spatial attributes ("grid") - but cells that don't fulfil these criteria in MTL (Diehl et al., 2017, Neuron; non-grid cells; Schaeffer et al., 2022, ICML; Luo et al., 2024, bioRxiv) certainly contribute to memory, and even navigation. This is also related to the question of whether these cell definitions matter at all (Luo et al., 2024).

The authors note "However, this memory conjunction view of the MTL must be reconciled with the rodent electrophysiology finding that most cells in MTL appear to have receptive fields related to some aspect of spatial navigation (Boccara et al., 2010; Grieves & Jeffery, 2017). The paucity of non-spatial cells in MTL could be explained if grid cells have been mischaracterized as spatial." Is the author mainly talking about rodent work?

(2) Related to the last point, how about non-grid multi-field mEC cells? In theory, these also should be the same; but the author only presents perfect-look grid cells. In empirical work, clearly, this is not the case, and many mEC cells are multi-field non-grid cells (Diehl et al., 2017). Does the model find these cells? Do they play a different role?

As noted by the author "Because the non-spatial attributes are constant throughout the two-dimensional surface, this results in an array of discrete memory locations that are approximately hexagonal (as explained in the Model Methods, an "online" memory consolidation process employing pattern separation rapidly turns an approximately hexagonal array into one that is precisely hexagonal). "

If they are indeed all precisely hexagonal, does that mean the model doesn't have non-grid spatial cells?

(3) Theoretical reasons for why the model is put together this way, and why grid cells must be coding a non-spatial attribute: Is this account more data-driven (fits the data so formulated this way), or is it theoretical - there is a reason why place, border, grid cells are formulated to be like this. For example, is it an efficient way to code these variables? It can be both, like how the BVC model makes theoretical sense that you can use boundaries to determine a specific location (and so place cell), but also works (creates realistic place cells).

But in this case, the purpose of grid cell coding a non-spatial attribute, and having some kind of system where it doesn't fire at all locations seems a little arbitrary. If it's not encoding a spatial attribute, it doesn't have to have a spatial field. For example, it could fire in the whole arena - which some cells do (and don't pass the criteria of spatial cells as they are not spatially "selective" to another location, related to above).

(4) Why are grid cells given such a large role for encoding non-spatial attributes? If anything, shouldn't it be lateral EC or perirhinal cortex? Of course, they both could, but there is less reason to think this, at least for rodent mEC.

(5) Clarification: why do place cells and grid cells differ in terms of stability in the model? Place cells are not stable initially but grid cells come out immediately. They seem directly connected so a bit unclear why; especially if place cell feedback leads to grid cell fields. There is an explanation in the text - based on grid cells coding the on-average memories, but these should be based on place cell inputs as well. So how is it that place fields are unstable then grid fields do not move at all? I wonder if a set of images or videos (gifs) showing the differences in spatial learning would be nice and clarify this point.

(6) Other predictions. Clearly, the model makes many interesting (and quite specific!) predictions. But does it make some known simple predictions?<br /> • More place cells at rewarded (or more visited) locations. Some empirical researchers seem to think this is not as obvious as it seems (e.g., Duvellle et al., 2019; JoN; Nyberg et al., 2021, Neuron Review).<br /> • Grid cell field moves toward reward (Butler et al., 2019; Boccera et al., 2019).<br /> • Grid cells deform in trapezoid (Krupic et al., 2015) and change in environments like mazes (Derikman et al., 2014).

Reviewer #2 (Public Review):

The manuscript describes a new framework for thinking about the place and grid cell system in the hippocampus and entorhinal cortex in which these cells are fundamentally involved in supporting non-spatial information coding. If this framework were shown to be correct, it could have high impact because it would suggest a completely new way of thinking about the mammalian memory system in which this system is non-spatial. Although this idea is intriguing and thought-provoking, a very significant caveat is that the paper does not provide evidence that specifically supports its framework and rules out the alternate interpretations. Thus, although the work provides interesting new ideas, it leaves the reader with more questions than answers because it does not rule out any earlier ideas.

Basically, the strongest claim in the paper, that grid cells are inherently non-spatial, cannot be specifically evaluated versus existing frameworks on the basis of the evidence that is shown here. If, for example, the author had provided behavioral experiments showing that human memory encoding/retrieval performance shifts in relation to the predictions of the model following changes in the environment, it would have been potentially exciting because it could potentially support the author's reconceptualization of this system. But in its current form, the paper merely shows that a new type of model is capable of explaining the existing findings. There is not adequate data or results to show that the new model is a significantly better fit to the data compared to earlier models, which limits the impact of the work. In fact, there are some key data points in which the earlier models seem to better fit the data.

Overall, I would be more convinced that the findings from the paper are impactful if the author showed specific animal memory behavioral results that were only supported by their memory model but not by a purely spatial model. Perhaps the author could run new experiments to show that there are specific patterns of human or animal behavior that are only explained by their memory model and not by earlier models. But in its current form, I cannot rule out the existing frameworks and I believe some of the claims in this regard are overstated.

In addition to the broader concerns noted above regarding the absence of any specific behavioral data that are explained by their model and not by existing spatial models, I am additionally concerned that this manuscript does not explain a number of important key empirical results in the rodent grid cell literature.

* The paper does not fully take into account all the findings regarding grid cells, some of which very clearly show spatial processing in this system. For example, findings on grid-by-direction cells (e.g., Sargolini et al. 2006) would seem to suggest that the entorhinal grid system is very specifically spatial and related to path integration. Why would grid-by-direction cells be present and intertwined with grid cells in the author's memory-related reconceptualization? It seems to me that the existence of grid-by-direction cells is strong evidence that at least part of this network is specifically spatial.

* I am also concerned that the paper does not do enough to address findings regarding how the elliptical shape of grid fields shifts when boundaries of an environment compress in one direction or change shape/angles (Lever et al., & Krupic et al). Those studies show compression in grid fields based on boundary position, and I don't see how the authors' model would explain these findings.

* Are findings regarding speed modulation of grid cells problematic for the paper's memory results?

* A further issue is that the paper does not seem to adequately address developmental findings related to the timecourses of the emergence of different cell types. In their simulation, researchers demonstrate the immediate emergence of grid fields in a novel environment, while noting that the stabilization of place cell positions takes time. However, these simulation findings contradict previous empirical developmental studies (Langston et al., 2010). Those studies showed that head direction cells show the earliest development of spatial response, followed by the appearance of place cells at a similar developmental stage. In contrast, grid cells emerge later in this developmental sequence. The gradual improvement in spatial stability in firing patterns likely plays a crucial role in the developmental trajectory of grid cells. Contrary to the model simulation, grid cells emerge later than place cells and head direction cells, yet they also hold significance in spatial mapping.

* The model simulations suggest that certain grid patterns are acquired more gradually than others. For instance, egocentric grid cells require the stabilization of place cell memories amidst ongoing consolidation, while allocentric grid cells tend to reflect average place field positions. However, these findings seemingly conflict with empirical studies, particularly those on the conjunctive representation of distance and direction in the earliest grid cells. Previous studies show no significant differences were found in grid cells and grid cells with directional correlates across these age groups, relative to adults (Wills et al., 2012). This indicates that the combined representation of distance and direction in single mEC cells is present from the earliest ages at which grid cells emerge.

Reviewer #1 (Public Review):

Summary:

The goal of this study was to use in vitro cell populations to determine mechanisms that may be important for the propagation of epimutations induced by EDCs in vivo. To do this, authors exposed induced pluripotent stem cells (iPS), somatic cells (Sertoli, granulosa), and primordial germ cell like cells (PGCLCs) to BPS, and conducted epigenomic and transcriptomic analyses on outcomes. The importance of estrogen receptors, and the relationship of epigenomic results to genomic sites expressing EREs, were also determined in the different cell types. Results revealed differential effects of BPS in each cell population on each of these endpoints, and that epimutations were prevalent in enhancer regions with EREs with the exception of PGCLCs (which do not express ERs). The authors speculate that because epimutations also occurred in regions without EREs, especially in PGCLCs, other mechanisms may be in place. Finally, epimutations induced in iPSCs exposed to BPS that were subsequently differentiated into PGCLCs demonstrated that most epimutations were corrected.

Strengths:

A strength of this work is the use of different cell types representing somatic cells that would be the major recipient of EDC exposure; pluripotent cells representing preimplantation embryos; and PGCLCs that model the early germline in which epigenetic reprogramming takes place. Work differentiating the iPSCs from PGCLCs with or without BPS exposure at the iPSC level is also very informative as it suggests that most epimutations are corrected, at least in vitro. The paper is well-written and studies were technically well-executed and validated. Results are novel and likely to be of interest to those interested in transgenerational inheritance of environmentally-induced traits, as well as others more broadly interested in epigenetic mechanisms.

Critique/Weaknesses:

(1) A problem with in vitro work is that homogeneous cell lines/cultures are, by nature, absent from the rest of the microenvironment. The authors need to discuss this.

(2) What are n's/replicates for each study? Were the same or different samples used to generate the data for RNA sequencing, methylation beadchip analysis, and EM-seq? This clarification is important because if the same cultures were used, this would allow comparisons and correlations within samples.

(3) In Figure 1, it is interesting that the 50 uM BPS dose mainly resulted in hypermethylation whereas 100 uM appears to be mainly hypomethylation. (This is based on the subjective appearance of graphs). The authors should discuss and/or present these data more quantitatively. For example, what percentage of changes were hypo/hypermethylation for each treatment? How many DMRs did each dose induce? For the RNA-seq results, again, what were the number of up/down-regulated genes for each dose?

(4) Also in Figure 1, were there DMRs or genes in common across the doses? How did DMRs relate to gene expression results? This would be informative in verifying or refuting expectations that greater methylation is often associated with decreased gene expression.

(5) In Figure 2, was there an overlap in the hypo- and/or hyper-methylated DMCs? Please also add more description of the data in 2b to the legend including what the dot sizes/colors mean, etc. Some readers (including me) may not be familiar with this type of data presentation. Some of this comes up in Figure 4, so perhaps allude to this earlier on, or show these data earlier.

(6) iPSCs were derived from male mice MEFs, and subsequently used to differentiate into PGCLCs. The only cell type from an XX female is the granulosa cells. This might be important, and should be mentioned and its potential significance discussed (briefly).

(7) EREs are only one type of hormone response element. The authors make the point that other mechanisms of BPS action are independent of canonical endocrine signaling. Would authors please briefly speculate on the possibility that other endocrine pathways including those utilizing AREs or other HREs may play a role? In other words, it may not be endocrine signaling independent. The statement that the differences between PGCLCs and other cells are largely due to the absence of ERs is overly simplistic.

(8) Interpretation of data from the GO analysis is similarly overly simplistic. The pathways identified and discussed (e.g. PI3K/AKT and ubiquitin-like protease pathways are involved in numerous functions, both endocrine and non-endocrine. Also, are the data shown in Figure 6a from all 4 cell types? I am confused by the heatmap in 6c, which genes were significantly affected by treatment in which cell types?

(9) In Figure 7, what were the 138 genes? Any commonalities among them?

(10) The Introduction is very long. The last paragraph, beginning line 105, is a long summary of results and interpretations that better fit in a Discussion section.

(11) Provide some details on husbandry: e.g. were they bred on-site? What food was given, and how was water treated? These questions are to get at efforts to minimize exposure to other chemicals.

Reviewer #2 (Public Review):

Summary:

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

Strengths:

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

Weaknesses:

The weaknesses include the lack of reporting of replicates, superficial bioinformatic analysis, and the fact that exposures are more complicated in a whole organism than in an isolated cell line.

Reviewer #1 (Public Review):

Wang et al investigated the evolution, expression, and function of the X-linked miR-506 miRNA family. They showed that the miR-506 family underwent rapid evolution. They provided evidence that miR-506 appeared to have originated from the MER91C DNA transposons. Human MER91C transposon produced mature miRNAs when expressed in cultured cells. A series of mouse mutants lacking individual clusters, a combination of clusters, and the entire X-linked cluster (all 22 miRNAs) were generated and characterized. The mutant mice lacking four or more miRNA clusters showed reduced reproductive fitness (litter size reduction). They further showed that the sperm from these mutants were less competitive in polyandrous mating tests. RNA-seq revealed the impact of deletion of miR-506 on the testicular transcriptome. Bioinformatic analysis analyzed the relationship among miR-506 binding, transcriptomic changes, and target sequence conservation. The miR-506-deficient mice did not have apparent effect on sperm production, motility, and morphology. Lack of severe phenotypes is typical for miRNA mutants in other species as well. However, the miR-506-deficient males did exhibit reduced litter size, such an effect would have been quite significant in an evolutionary time scale. The number of mouse mutants and sequencing analysis represent a tour de force.

Strengths:

This study is a comprehensive investigation of the X-linked miR-506 miRNA family. It provides important insights into the evolution and function of the miR-506 family.

Reviewer #3 (Public Review):

Summary:

In this manuscript, the authors conducted a comprehensive study of the X-linked miR-506 family miRNAs in mice on its origin, evolution, expression, and function. They demonstrate that the X-linked miR-506 family, predominantly expressed in the testis, may be derived from MER91C DNA transposons and further expanded by retrotransposition. By genetic deletion of different combinations of 5 major clusters of this miRNA family in mice, they found these miRNAs are not required for spermatogenesis. However, by further examination, the mutant mice show mild fertility problem and inferior sperm competitiveness. The authors conclude that the X-linked miR-506 miRNAs finetune spermatogenesis to enhance sperm competition.

Strengths:

This is a comprehensive study with extensive computational and genetic dissection of the X-linked miR-506 family providing a holistic view of its evolution and function in mice. The finding that this family miRNAs could enhance sperm competition is interesting and could explain their roles in finetuning germ cell gene expression to regulate reproductive fitness.

Comments on revised version:

The authors have addressed the concerns raised.

Reviewer #1 (Public Review):

The present study conducted by Berger et al. delves into the extent to which memory formation relies on available energy reserves. While aversive memory formation has been extensively studied in this context, the investigation into appetitive memory formation has been comparatively sparse. It has long been recognized that flies can only form appetitive memory under conditions of starvation. However, the authors of this study go beyond this understanding by revealing that not only the duration of starvation matters, but it also dictates the type of memory formed, whether short- or long-term memory. The authors illustrate that internal glycogen stores play a crucial role in this process, facilitated by insulin-like signaling in octopaminergic reward neurons, which integrates internal energy reserves into memory formation. Consequently, the authors propose that octopamine serves as a negative regulator of various forms of memory, shedding light on the enduring question of the octopaminergic neuronal system's involvement in appetitive memory formation, which has been overshadowed by the focus on the dopaminergic system in recent years. Additionally, the findings contribute to the ongoing debate concerning the role of insulin receptors, whether they function within neurons themselves or in glial cells. Moreover, the authors not only convincingly demonstrate that octopamine negatively regulates appetitive memory formation, but they also propose a mechanism whereby the insulin receptor in octopaminergic neurons senses the internal energy status and subsequently modulates the activity of these neurons. The experiments are meticulously designed, employing a variety of behavioral assays, genetic tools for manipulating neuronal activity, and state-of-the-art imaging techniques. The conclusions are well supported by the data and carefully performed controlled experiments, yielding high-quality data.

Reviewer #2 (Public Review):

How organism physiological state modulates establishment and perdurance of memories is a timely question that the authors aimed at addressing by studying the interplay between energy homeostasis and food-related conditioning in Drosophila. Specifically, they studied how starvation modulates the establishment of short-term vs long-term memories and clarified the role of the monoamine Octopamine in food-related conditioning, showing that it is not per se involved in formation of appetitive short-term memories but rather gates memory formation by suppressing LTM when energy levels are high. This work clarifies previously described phenotypes and provides insight about interconnections between energy levels, feeding and formation of short-term and long-term food-related memories.

Strengths<br /> - Previous studies have documented the impact of Octopamine on different aspects of food-related behaviors (regulation of energy homeostasis, feeding, sugar sensing, appetitive memory...), but we currently lack a clear understanding of how these different functions are interconnected. The authors have used a variety of experimental approaches to systematically test the impact of internal energy levels in establishment of different forms of appetitive memory and the role of Octopamine in this process.

- The authors have used a range of approaches, performed carefully controlled experiments and produced high quality data.

Reviewer #3 (Public Review):

In this manuscript, Berger et al. study how internal energy storage influence learning and memory. Since in Drosophila melanogaster, octopamine (OA) is involved in the regulation of energy homeostasis they focus on the roles of OA. To do so they use the tyramine-β-hydroxylase (Tbh) mutant that is lacking the neurotransmitter OA and study short term memory (STM), long-term memory (LTM) and anesthesia-resistant memory (ARM). They show that the duration of starvation affects the magnitude of both short- and long-term memory. In addition, they show that OA has a suppressive effect on learning and memory. In terms of energy storage, they show that internal glycogen storage influences how long sucrose is remembered, and high glycogen suppresses memory. Finally, they show that insulin-like signaling in octopaminergic neurons, which is also related to internal energy storage, suppresses learning and memory.

The revised version of the manuscript is greatly improved, and I thank the authors for taking the comment seriously. This is an important study that extends our knowledge on OA activity in learning and memory and the effects the metabolic state has on learning and memory. The authors nicely use the genetic tools available in flies to try and unravel the complex circuitry of metabolic state level, OA activity and learning and memory. The overall take-home message of the manuscript is clear and supported by the data presented.

Reviewer #2 (Public Review):

Summary:

This paper acknowledges that most development occurs in social contexts, with other social partners. The authors put forth two main frameworks of how development occurs within a social interaction with a caregiver. The first, is that although social interaction with mature partners is somewhat bi-directional, mature social partners exogenously influence infant behaviors and attention through "attentional scaffolding", and that in this case infant attention is reactive to caregiver behavior. The second framework posits that caregivers support and guide infant attention by contingently responding to reorientations in infant behavior, thus caregiver behaviors are reactive to infant behavior. The aim of this paper is to use moment-to-moment analysis techniques to understand the directionality of dyadic interaction.

Strengths:

The question driving this study is interesting and a genuine gap in the literature. Almost all development occurs in the presence of a mature social partner. While it is known that these interactions are critical for development, the directionality of how these interactions unfold in real-time is less known.

The analyses are appropriate for the question at hand, capturing small moment-to-moment dynamics in both infant and child behavior, and their relationships with themselves and each other. Autocorrelations and cross-correlations are powerful tools that can uncover small but meaningful patterns in data that may not be uncovered with other more discretized analyses (i.e. regression).

Weaknesses:

While the authors improved their explanation of why they are using cross-correlations and the resting EEG patterns and what they mean, they did not address this specific piece of feedback: to explain their rationale for only focussing on fronto-temporal channels, rather than averaging channels across the whole brain.

Reviewer #2 (Public Review):

Summary:

Through a set of experiments and model simulations, the authors tested whether the commonly assumed world model of gravity was a faithful replica of the physical world. They found that participants did not model gravity as single, fixed vector for gravity but instead as a distribution of possible vectors. Surprisingly, the width of this distribution was quite large (~20 degrees). While previous accounts had suggested that this uncertainty was due to perceptual noise or an inferred external perturbation, the authors suggest that this uncertainty simply arises from a noisy distribution of the representation of gravity's direction. A reinforcement learning model with an initial uniform distribution for gravity's direction ultimately converged to a precision on the same order as the human participants, which lends support to the authors' conclusion and suggests that this distribution is learned through experience. What's more, further simulations suggest that representing gravity with such a wide distribution may balance speed and accuracy, providing a potentially normative explanation for the world model with gravity as a distribution.

Strengths:

The authors present surprising findings in a relatively straight-forward in a now classic experimental task. They provide a normative explanation based on a resource-rational framework for why people may have a stochastic world model instead of a deterministic world model. While the stochastic world model could be the result of people mentally simulating an external perturbation, the authors include several control experiments to test this possibility.

Weaknesses:

The possibility of inferred external perturbations, as opposed to a stochastic world model, is difficult to rule out. This could stem from how people interpret task instructions and it will likely take many, clever studies, to fully reconcile these two alternative accounts.

Reviewer #1 (Public Review):

Summary:

The study examines the role of release site clearance in synaptic transmission during repetitive activity under physiological conditions in two types of central synapses, calyx of Held and hippocampal CA1 synapses. After acute block of endocytosis by pharmacology, deeper synaptic depression or less facilitation was observed in two types of synapses. Acute block of CDC42 and actin polymerization, which possibly inhibits the activity of Intersectin, affected synaptic depression at the calyx synapse, but not at CA1 synapses. The data suggest an unexpected, fast role of the site clearance in counteracting synaptic depression.

Strengths:

The study uses acute block of the molecular targets with pharmacology together with precise electrophysiology. The experimental results are clear cut and convincing. The study also examines the physiological roles of the site clearance using action potential-evoked transmission at physiological Ca and physiological temperature at mature animals. This condition has not been examined.

Weaknesses:

Pharmacology may have some off-target effects, though acute manipulation should be appreciated and the authors have tried several reagents to verify the overall conclusions.

Reviewer #2 (Public Review):

Summary:

In this manuscript, Mahapatra and Takahashi report on the physiological consequences of pharmacologically blocking either clathrin and dynamin function during compensatory endocytosis or of the cortical actin scaffold both in the calyx of Held synapse and hippocampal boutons in acute slice preparations

Strengths:

Although many aspects of these pharmacological interventions have been studied in detail during the past decades, this is a nice comprehensive and comparative study, which reveals some interesting differences between a fast synapse (Calyx of Held) tuned to reliably transmit at several 100 Hz and a more slow hippocampal CA1 synapse. In particular the authors find that acute disturbance of the synaptic actin network leads to a marked frequency-dependent enhancement of synaptic depression in the Calyx, but not in the hippocampal synapse This striking difference between both preparations is the most interesting and novel finding.

Weaknesses:

Unfortunately, however, these findings concerning the different consequences of actin depolymerization are not sufficiently discussed in comparison to the literature. My only criticism concerns the interpretation of the ML 141 and Lat B data. With respect to the Calyx data, I am missing a detailed discussion of the effects observed here in light of the different RRP subpools SRP and FRP. This is very important since Lee at al. (2012, PNAS 109 (13) E765-E774) showed earlier that disruption of actin inhibits the rapid transition of SRP SVs to the FRP at the AZ. The whole literature on this important concept is missing. Likewise, the role of actin for the replacement pool at a cerebellar synapse (Miki et al., 2016) is only mentioned in half a sentence. There is quite some evidence that actin is important both at the AZ (SRP to FRP transition, activation of replacement pool) and at the peri-active zone for compensatory endocytosis and release site clearance. Both possible underlying mechanisms (SRP to FRP transition or release site clearance) should be better dissected.

Reviewer #3 (Public Review):

The manuscript by Mahapatra and Takahashi addresses the role of presynaptic release site clearance during sustained synaptic activity. The authors characterize the effects of pharmacologically interfering with SV endocytosis (pre-incubation with Dynasore or Pitstop-2) on synaptic short-term plasticity (STP) at two different CNS synapses (calyx of Held synapses and hippocampal SC to CA1 synapses) using patch-clamp recordings in acute slices under experimental conditions designed to closely mimic a physiological situation (37{degree sign}C and 1.3 mM external [Ca2+]). Endocytosis blocker-induced changes in STP and in the recovery from short-term depression (STD) are compared to those seen after pharmacologically inhibiting actin filament assembly (pre-incubation with Latrunculin-B or the selective Cdc42 GTPase inhibitor ML-141). Presynaptic capacitance (Cm) recordings in calyx terminals were used to establish the effects of the pharmacological maneuvers on SV endocytosis.<br /> Latrunculin-B and ML-141 neither affect SV endocytosis (assayed by Cm recordings) nor EPSC recovery following conditioning trains, but strongly enhances STD at calyx synapses. No changes in STP were observed at Latrunculin-B- or ML-141-treated SC to CA1 synapses.

Dynasore and Pitstop-2 slow down endocytosis, limit the total amount of exocytosis in response to long stimuli, enhance STD in response to 100 Hz stimulation, but profoundly accelerate EPSC recovery following conditioning 100 Hz trains at calyx synapses. At SC to CA1 synapses, Dynasore and Pitstop-2 reduce the extend of facilitation and lower relative steady-state EPSCs suggesting a change in the facilitation-depression balance in favor of the latter.

The authors use state-of-the art techniques and their data, which is clearly presented, leads to authors to conclude that endocytosis is universally important for clearance of release sites while the importance of scaffold protein-mediated site clearance is limited to 'fast synapses'.

Unfortunately, and perhaps not completely unexpected in view of the pharmacological tools chosen, there are several observations which remain difficult to understand:

(1) Blocking site clearance affects release sites that have previously been used, i.e. sites at which SV fusion has occurred and which therefore need to be cleared. Calyces use at most 20% of all release sites during a single AP, likely fewer at 1.3 mM external [Ca2+]. Even if all those 20% of release sites become completely unavailable due to a block of release site clearance, the 2nd EPSC in a train should not be reduced by >20% because ~80% of the sites cannot be affected. However, ~50% EPSC reduction was observed (Fig. 2B1, lower right panel) raising the possibility that Dynasore does more than specifically interfering with SVs endocytosis (and possibly Pitstop as well). Non-specific effects are also suggested by the observed two-fold increase in initial EPSC size in SC to CA1 synapses after Dynasore pre-incubation.

(2) More severe depression was observed at calyx synapses after blocking endocytosis which the authors attribute to a presynaptic mechanism affecting pool replenishment. When probing EPSC recovery after conditioning 100 Hz trains, a speed up was observed mediated by an "unknown mechanism" which is "masked in 2 mM [Ca2+]". These two observations, deeper synaptic depression during 100 Hz but faster recovery from depression following 100 Hz, are difficult to align and no attempt was made to find an explanation.

(3) To reconcile previous data reporting a block of Ca2+-dependent recovery (CDR) by Dynasore or Latrunculin (measured at 2 mM external [Ca2+]) with the data presented here (using 1.3 mM external [Ca2+]) reporting no effect or a speed up of recovery from depression, the authors postulate that "CDR may operate only when excessive Ca2+ enters during massive presynaptic activation" (page 10 line 244). While that is possible, such explanation ignores plenty of calyx studies demonstrating fiber stimulation-induced CDR and elucidating molecular pathways mediating fiber stimulation-induced CDR, and it also completely dismisses the strong change in recovery time course after 10 Hz conditioning (single exponential) as compared to 100 Hz conditioning (double exponential with a pronounced fast component).

Strong presynaptic stimuli such as those illustrated in Figs. 1B,C induce massive exocytosis. The illustrated Cm increase of 2 to 2.5 pF represents fusion of 25,000 to 30,000 SVs (assuming a single SV capacitance of 80 aF) corresponding to a 12 to 15% increase in whole terminal membrane surface (assuming a mean terminal capacitance of ~16 pF). Capacitance measurements can only be considered reliable in the absence of marked changes in series and membrane conductance. Documentation of the corresponding conductance traces is therefore advisable for such massive Cm jumps and merely mentioning that the first 450 ms after stimulation were skipped during analysis or referring to previous publications showing conductance traces is insufficient.<br /> All bar graphs in Figures 1 through 6 and Figures S3 through S6 compare three or even four (Fig. 5C) conditions, i.e. one control and at least two treatment data sets. It appears as if repeated t-tests were used to run multiple two-group comparisons (i.e. using the same control data twice for two different comparisons). Either a proper multiple comparison test should be used or a Bonferroni correction or similar multiple-comparison correction needs to be applied.

Finally, the terminology of contrasting "fast-signaling" (calyx synapses) and "slow-plastic" (SC synapses) synapses seems to imply that calyx synapses lack plasticity, as does the wording "conventional bouton-type synapses involved in synaptic plasticity" (page 11, line 251). I assume, the authors primarily refer to the maximum frequencies these two synapse types typically transmit (fast-signaling vs slow-signaling)?

Reviewer #2 (Public Review):

Gillespie et al. introduced a novel neurofeedback (NF) procedure to train rats in enhancing their sharp-wave ripple (SWR) rate within a short duration, a key neural mechanism associated with memory consolidation. The training, embedded within a spatial memory task, spanned 20-30 days and utilized food rewards as positive reinforcement upon SWR detection. Rats were categorized into NF and control groups, with the NF group further divided into NF and delay trials for within-subject control. While single trial differences were elusive due to the variability of SWR occurrence, the study revealed that statistically rats in NF trials exhibited a notably higher SWR rate before receiving rewards compared to delay trials. This difference was even more pronounced when juxtaposed with rats not exposed to NF training (control group). The unique design of blending the NF phase with the memory dependent spatial task enabled the authors to analyze whether the NF training influence the task performance and replay content during SWRs across three different conditions (NF trials, delay trials and control group). Interestingly, despite the NF training, there was no significant improvement or decline in the performance of the spatial memory task, and the replay content remained consistent across all three conditions. Hence, the operant conditioning only amplified the SWR rate before reward in NF trials without altering the task performance and the replay content during SWR. Moreover, considering the post-reward period, the total SWR count was consistent across all conditions as well, meaning the NF training also do not affect the total SWR count. The study concludes with the hypothesis of a potential homeostatic mechanism governing the total SWR production in rats. This research significantly extends previous work by Ishikawa et al. (2014), offering insights into the NF training with external reward on the SWR rate/counts, replay content and task performance.

Strengths:

- Integration of NF task and spatial memory task in a single trial<br /> The integration of NF training within a spatial memory task poses significant challenges. Gillespie and colleagues overcame this by seamlessly blending the NF task and the spatial memory task into a single trial. Each trial involved a rat undergoing three steps: First, initiating a trial. Second, moving to either the NF port or the delay trial port, as indicated by an LED, and then maintaining a nosepoke at one of the center ports. During this step, the rat had to keep its nose (in the NF port) until a sharp-wave ripple (SWR) exceeding a set threshold was detected, which then triggered a reward, or until a variable time elapsed (in the delay port). Third, the rat would choose one of eight arms to explore before starting the next trial. This integration of the two tasks (step two as the NF task and step three as the spatial memory task) facilitated a direct analysis of the impact of NF training on behaviorally relevant replay content during SWRs and the performance in the spatial memory task.

- Clear Group Separation<br /> A robust study design necessitates clear distinctions between experimental conditions to ensure that observed differences can be attributed to the variable under investigation. This study meticulously categorized rats into three distinct conditions: NF trials, delay trials (for within-subject control), and a control group (for across-subject control). Furthermore, for each trial, the times of interest (TOI) were separated into pre-reward and post-reward periods. This clear separation ensures that any observed differences in SWR rates and other outcomes can be confidently attributed to the effects of neurofeedback training during specific time periods, minimizing potential confounding factors.

- Evidence of SWR rate modulation<br /> The study's results offer compelling evidence that rats can be trained to modulate their SWR rates during the pre-reward period. This is evident from the observation that rats in the NF trials consistently displayed a higher SWR rate before receiving rewards compared to those in delay trials or the control group (Fig. 2). Such findings not only validate the efficacy of the NF paradigm but also underscore the potential of operant conditioning in influencing neural mechanisms. The observation that rats were able to produce larger SWR events by modulating their occurrence rate, rather than merely waiting for these events, suggests a learned strategy to generate them more efficiently.

- Evidence of SWR count homeostasis<br /> A notable finding from the study was the observation of a consistent total SWR count during both pre-reward and post-reward periods across all conditions, despite the evident increase in SWR rates during the pre-reward period in NF trials. This points to a potential homeostatic mechanism governing SWR production in rats. This balance suggests that while NF training can modulate the timing and rate of SWRs over a short duration, it doesn't influence the overall count of SWRs over a longer period. Such a mechanism might be essential in ensuring that the brain neither overcompensates nor depletes its capacity for SWRs, maintaining the overall neural balance and functionality. This discovery deepens our understanding of neural mechanisms and highlights potential avenues for future research into the regulatory processes governing neural activity.

In this revision, the paper explores a neurofeedback technique in rats that modulates hippocampal sharp-wave ripple (SWR) rates, crucial for memory replay, without altering the content of those replays. The study demonstrates that neurofeedback can specifically increase SWR rates during a task's pre-reward phase. Revisions address concerns about movement's impact on SWR rates, clarify the statistical approach used, and modify the title for accuracy, now emphasizing the modulation of memory replay rates rather than suggesting alterations to memory content itself. I think all the concerns in the previous version have been addressed.

Reviewer #3 (Public Review):

Summary:

This study implements an innovative neurofeedback procedure in rats, providing food reward upon detection of a sharp wave-ripple event (SWR) in the hippocampus. The elegant experimental design enables a within-animal comparison of the effects of this neurofeedback procedure as compared to a control condition in which equivalent reward is provided in a non-contingent manner. The neurofeedback procedure was found to increase SWR rate, followed by a compensatory reduction in SWR rate. These changes in SWR rate were not accompanied by any changes in memory performance on the memory-guided task.

Strengths:

The scientific premise for the study is outstanding. It addresses an issue of high importance, of developing ways to not merely describe correlations between SWRs (and their content) and memory performance, but to manipulate them. The authors argue clearly and convincingly that even studies that have performed causal manipulations of SWRs have important confounds and limitations, and most importantly for translational purposes, they are all invasive. So, the idea of developing a potentially non-invasive neurofeedback procedure for modulating SWRs is compelling both as an innovative new experimental manipulation in studies of SWRs, and as a potentially impactful therapeutic avenue.

In addition to addressing an important issue with an innovative approach, the study has many other strengths. The data unambiguously show that the method is effective at increasing SWR rate in each individual subject. The experimental design allows within-subject comparison of neurofeedback and control trials, where the subjects wait an equivalent amount of time. The careful analyses of SWR properties and their content establish that neurofeedback SWRs are comparable to control SWRs. The data add further evidence to the notion that SWR rate is subject to homeostatic control. The paper is also exceptionally well written, and was a pleasure to read. So, there is a clear technical advance, in that there is now a method for increasing SWR rate non-invasively, which is rigorously established and characterized.

Weaknesses:

The one overall limitation I find with this study is that it is unclear to what extent the same (or better) results could have been obtained using behavior-feedback instead of neuro-feedback. Because SWR rates are generally higher during states of quiescence compared to active movement or task engagement, it is possible that reinforcing behaviorally detected quiescent states (e.g. low movement) would indirectly increase SWR rates. The authors include an important control analysis showing higher SWR rates in the neurofeedback condition even when movement speed is controlled for by subsetting the data, demonstrating that changes in movement speed cannot be the only explanation of the results. At the same time, the observation that all 4 subjects had lower movement speeds during neurofeedback compared to control trials suggests that neurofeedback is likely reinforcing both overt (behavior) and covert (SWR) processes. Understanding the relative contributions of each to the observed SWR increase would help clarify whether the neurofeedback approach is worth the additional effort and expense compared to behavioral feedback.

Reviewer #1 (Public Review):

The study investigates parafoveal processing during natural reading, combining eye-tracking and MEG techniques, building upon the RIFT paradigm previously introduced by Pan et al. (2021). Overall, the manuscript is well-written with a clear structure, and the data analysis and experimental results are presented in a lucid manner.

The authors have addressed the issues I raised in the previous round of review to my satisfaction. However, I still have two concerns that require the authors' consideration.

Firstly, the similarity between the RIFT analysis process in this study and traditional ERP analysis could lead readers to equate RIFT with components like N400, potentially influencing their interpretation of the results. Although the author's response has somewhat clarified my queries, I seek confirmation: does RIFT itself signify "visual attention" or the "allocation of attentional resources to the flickering target words" (line 208) in this study? While this may not be pivotal, as it primarily serves as an indicator to evaluate whether contextual congruity can indeed modulate the RIFT response rather than indicating early parafoveal semantic integration, I recommend that the authors explicitly address this point in the manuscript, maybe in the discussion section, to enhance reader comprehension of the article's rationale.

Secondly, regarding the study's conclusions, there appears to be an overemphasis in stating that "semantic information ... can also be integrated with the sentence context ..." (line 21-22). As raised by Reviewer 2 (Major Point 1) and acknowledged by the authors in the limitations of the revised manuscript (lines 403-412), the RIFT effect observed likely stems from local congruency. Therefore, adjusting the conclusion to "integrated with previous context" may offer a more precise reflection of the findings.

Reviewer #2 (Public Review):

This MEG study used co-registered eye-tracking and Rapid Invisible Frequency Tagging (RIFT) to track the effects of semantic parafoveal preview during natural sentence reading. Unpredictable target words could either be congruent or incongruent with sentence context. This modulated the RIFT response already while participants were fixating the preceding word. This indicates that the semantic congruency of the upcoming word modulates visual attention demands already in parfoveal preview.<br /> The quest for semantic parafoveal preview in natural reading has attracted a lot of attention in recent years, especially with the development of co-registered eye-tracking and EEG/MEG. Evidence from dynamic neuroimaging methods using innovative paradigms as in this study is important for this debate.

Major points:

(1) The authors frame their study in terms of "congruency with sentence context". However, it is the congruency between adjective-noun pairs that determines congruency (e.g. "blue brother" vs "blue jacket", and examples p. 16 and appendix). This is confirmed by Suppl Figure 1, which shows a significantly larger likelihood of refixations to the pre-target word for incongruent sentences, probably because the pre-target word is most diagnostic for the congruency of the target word. The authors discuss some possibilities why there is variability in parafoveal preview effects in the literature. It is more likely to see effects for this simple and local congruency, rather than congruency that requires and integration and comprehension of the full sentence. Future studies should investigate whether the observed effects depend on sentence context or local congruency.

(2) The authors used MEG and provided a source estimate for the tagging response (Figure 2), which unsurprisingly is in visual cortex. The most important results are presented at the sensor level. This does not add information about the brain sources of the congruency affect, as the RIFT response probably reflects top-down effects on visual attention etc. The RIFT response can test for preview effects on visual brain responses but does not allow the localisation of context processing effects that cause them.

(3) The earliest semantic preview effects occurred around 100ms after fixating the pre-target word (discussed around l. 323). This means that at this stage the brain must have processed the pre-target and the target word and integrated their meanings (at some level). Even in the single-word literature, semantic effects at 100 ms are provocatively early. Future studies should aim at reconciling these different findings.

(4) As in previous EEG/MEG studies, the authors found a neural but no behavioural preview effect. As before, this raises the question whether the observed effect is really "critical" for sentence comprehension. If interpreted in terms of "information" and "attention", then one would expect a positive effect on behaviour, either reading speed or accuracy. The authors provide a correlation analysis with reading speed, but this does not allow causal conclusions: Some people may simply read slowly and therefore pay more attention and get a larger preview response. Some readers may hurry and therefore not pay attention and not get a preview response. In order to address this, one would have to control for reading speed and show an effect of RIFT response on comprehension performance (or vice versa, with a task that is not close to ceiling performance).

Reviewer #1 (Public Review):

Zhu, et al present a genome-wide histone modification analysis comparing patients with schizophrenia (on or off antipsychotics) to non-psychiatric controls. The authors performed analyses across the dorsolateral prefrontal cortex and tested for enrichment of nearby genes and pathways. The authors performed analysis measuring the effect of age on the epigenomic landscape as well. This paper provides a unique resource around SCZ and its epigenetic correlates, and some potentially intriguing findings in the antipsychotic response dataset.

Comments on revised version:

The authors have adequately responded to my review comments.

Reviewer #2 (Public Review):

Sasaki et al. investigated methods to entrain vasomotion in awake wild-type mice across multiple regions of the brain using a horizontally oscillating visual pattern which induces an optokinetic response (HOKR) eye movement. They found that spontaneous vasomotion could be detected in individual vessels of their wild-type mice through either a thinned cranial window or intact skull preparation using a widefield macro-zoom microscope. They showed that low-resolution autofluorescence signals coming from the brain parenchyma could be used to capture vasomotion activity using a macro-zoom microscope or optical fibre, as this signal correlates well with the intensity profile of fluorescently-labelled single vessels. They show that vasomotion can also be entrained across the cortical surface using an oscillating visual stimulus with a range of parameters (with varying temporal frequencies, amplitudes, or spatial cycles), and that the amplitude spectrum of the detected vasomotion frequency increases with repeated training sessions. The authors include some control experiments to rule out fluorescence fluctuations being due to artifacts of eye movement or screen luminance and attempt to demonstrate some functional benefit of vasomotion entraining as HOKR performance improves after repeat training. These data add in an interesting way to the current knowledge base on vasomotion, as the authors demonstrate the ability to entrain vasomotion across multiple brain areas and show some functional significance to vasomotion with regards to information processing as HOKR task performance correlates well with vascular oscillation amplitudes.

Reviewer #3 (Public Review):

Summary:

Here the authors show global synchronization of cerebral blood flow (CBF) induced by oscillating visual stimuli in the mouse brain. The study validates the use of endogenous autofluorescence to quantify the vessel "shadow" to assess the magnitude of frequency-locked cerebral blood flow changes. This approach enables straightforward estimation of artery diameter fluctuations in wild-type mice, employing either low magnification wide-field microscopy or deep-brain fibre photometry. For the visual stimuli, awake mice were exposed to vertically oscillating stripes at a low temporal frequency (0.25 Hz), resulting in oscillatory changes in artery diameter synchronized to the visual stimulation frequency. This phenomenon occurred not only in the primary visual cortex but also across a broad cortical and cerebellar surface. The induced CBF changes adapted to various stimulation parameters, and interestingly, repeated trials led to plastic entrainment. The authors control for different artefacts that may have confounded the measurements such as light contamination and eye movements but found no influence of these variables. The study also tested horizontally oscillating visual stimuli, which induce the horizontal optokinetic response (HOKR). The amplitude of eye movement, known to increase with repeated training sessions, showed a strong correlation with CBF entrainment magnitude in the cerebellar flocculus. The authors suggest that parallel plasticity in CBF and neuronal circuits is occurring. Overall, the study proposes that entrained "vasomotion" contributes to meeting the increased energy demand associated with coordinated neuronal activity and subsequent neuronal circuit reorganization.

Strengths:

-The paper describes a simple and useful method for tracking vasomotion in awake mice through an intact skull.<br /> -The work controls for artefacts in their primary measurements.<br /> -There are some interesting observations, including the nearly brain-wide synchronization of cerebral blood flow oscillations to visual stimuli and that this process only occurs after mice are trained in a visual task.<br /> -This topic is interesting to many in the CBF, functional imaging, and dementia fields.

Reviewer #1 (Public Review):

Summary:

Most studies in sensory neuroscience investigate how individual sensory stimuli are represented in the brain (e.g., the motion or color of a single object). This study starts tackling the more difficult question of how the brain represents multiple stimuli simultaneously and how these representations help to segregate objects from cluttered scenes with overlapping objects.

Strengths

The authors first document the ability of humans to segregate two motion patterns based on differences in speed. Then they show that a monkey's performance is largely similar; thus establishing the monkey as a good model to study the underlying neural representations.

Careful quantification of the neural responses in the middle temporal area during the simultaneous presentation of fast and slow speeds leads to the surprising finding that, at low average speeds, many neurons respond as if the slowest speed is not present, while they show averaged responses at high speeds. This unexpected complexity of the integration of multiple stimuli is key to the model developed in this paper.

One experiment in which attention is drawn away from the receptive field supports the claim that this is not due to the involuntary capture of attention by fast speeds.

A classifier using the neuronal response and trained to distinguish single-speed from bi-speed stimuli shows a similar overall performance and dependence on the mean speed as the monkey. This supports the claim that these neurons may indeed underlie the animal's decision process.

The authors expand the well-established divisive normalization model to capture the responses to bi-speed stimuli. The incremental modeling (eq 9 and 10) clarifies which aspects of the tuning curves are captured by the parameters.

Weaknesses

While the comparison of the overall pattern of behavioral performance between monkeys and humans is important, some of the detailed comparisons are not well supported by the data. For instance, whether the monkey used the apparent coherence simply wasn't tested and a difference between 4 human subjects and a single monkey subject cannot be tested statistically in a meaningful manner. I recommend removing these observations from the manuscript and leaving it at "The difference between the monkey and human results may be due to species differences or individual variability" (and potentially add that there are differences in the task as well; the monkey received feedback on the correctness of their choice, while the humans did not.)

A control experiment aims to show that the "fastest speed takes all" behavior is general by presenting two stimuli that move at fast/slow speeds in orthogonal directions. The claim that these responses also show the "fastest speed takes all" is not well supported by the data. In fact, for directions in which the slow speed leads to the largest response on its own, the population response to the bi-speed stimulus is the average of the response to the components. Only for the directions where the fast speed stimulus is the preferred direction is there a bias towards the faster speed (Figure 7A). The quantification of this effect in Figure 7B seems to suggest otherwise, but I suspect that this is driven by the larger amplitude of Rf in Figure 8, and the constraint that ws and wf are constant across directions. The interpretation of this experiment needs to be reconsidered.

Reviewer #2 (Public Review):

Summary:

This is a paper about the segmentation of visual stimuli based on speed cues. The experimental stimuli are random dot fields in which each dot moves at one of two velocities. By varying the difference between the two speeds, as well as the mean of the two speeds, the authors estimate the capacity of observers (human and non-human primates) to segment overlapping motion stimuli. Consistent with previous work, perceptual segmentation ability depends on the mean of the two speeds. Recordings from area MT in monkeys show that the neuronal population to compound stimuli often shows a bias towards the faster-speed stimuli. This bias can be accounted for with a computational model that modulates single-neuron firing rates by the speed preferences of the population. The authors also test the capacity of a linear classifier to produce the psychophysical results from the MT data.

Strengths:

Overall, this is a thorough treatment of the question of visual segmentation with speed cues. Previous work has mostly focused on other kinds of cues (direction, disparity, color), so the neurophysiological results are novel. The connection between MT activity and perceptual segmentation is potentially interesting, particularly as it relates to existing hypotheses about population coding.

Weaknesses:

Page 10: The relationship between (R-Rs) and (Rf-Rs) is described as "remarkably linear". I don't actually find this surprising, as the same term (Rs) appears on both the x- and y-axes. The R^2 values are a bit misleading for this reason.

Figure 9: I'm confused about the linear classifier section of the paper. The idea makes sense - the goal is to relate the neuronal recordings to the psychophysical data. However the results generally provide a poor quantitative match to the psychophysical data. There is mention of a "different paper" (page 26) involving a separate decoding study, as well as a preprint by Huang et al. (2023) that has better decoding results. But the Huang et al. preprint appears to be identical to the current manuscript, in that neither has a Figure 12, 13, or 14. The text also says (page 26) that the current paper is not really a decoding study, but the linear classifier (Figure 9F) is a decoder, as noted on page 10. It sounds like something got mixed up in the production of two or more papers from the same dataset. In any case, I think that some kind of decoding analysis would really strengthen the current paper by linking the physiology to the psychophysics, but given the limitations of the linear classifier, a more sophisticated approach might be necessary -- see for example Zemel, Dayan, and Pouget, 1998. The authors might also want to check out closely related work by Treue et al. (Nature Neuroscience 2000) and Watamaniuk and Duchon (1992).

What do we learn from the normalization model? Its formulation is mostly a restatement of the results - that the faster and slower speeds differentially affect the combined response. This hypothesis is stated quantitatively in equation 8, which seems to provide a perfectly adequate account of the data. The normalization model in equation 10 is effectively the same hypothesis, with the mean population response interposed - it's not clear how much the actual tuning curve in Figure 10A even matters, since the main effect of the model is to flatten it out by averaging the functions in Figure 10B. Although the fit to the data is reasonable, the model uses 4 parameters to fit 5 data points and is likely underconstrained; the parameters other than alpha should at least be reported, as it would seem that sigma is actually the most important one. And I think it would help to examine how robust the statistical results are to different assumptions about the normalization pool.

Reviewer #3 (Public Review):

Summary:

This study concerns how macaque visual cortical area MT represents stimuli composed of more than one speed of motion.

Strengths:

The study is valuable because little is known about how the visual pathway segments and preserves information about multiple stimuli. The study presents compelling evidence that (on average) MT neurons represent the average of the two speeds, with a bias that accentuates the faster of the two speeds. An additional strength of the study is the inclusion of perceptual reports from both humans and one monkey participant performing a task in which they judged whether the stimuli involved one vs two different speeds. Ultimately, this study raises intriguing questions about how exactly the response patterns in visual cortical area MT might preserve information about each speed, since such information could potentially be lost in an average response as described here, depending on assumptions about how MT activity is evaluated by other visual areas.

Weaknesses:

My main concern is that the authors are missing an opportunity to make clear that the divisive normalization, while commonly used to describe neural response patterns in visual areas (and which fits the data here), fails on the theoretical front as an explanation for how information about multiple stimuli can be preserved. Thus, there is a bit of a disconnect between the goal of the paper - how does MT represent multiple stimuli? - and the results: mostly averaging responses which, while consistent with divisive normalization, would seem to correspond to the perception of a single intermediate speed. This is in contrast to the psychophysical results which show that subjects can at least distinguish one from two speeds. The paper would be strengthened by grappling with this conundrum in a head-on manner.

Reviewer #1 (Public Review):

Summary:

This study compares experimental data recorded from the PFC of monkeys to the activity of recurrent neural networks trained to perform the same `task' as the monkeys, namely, to predict the delivery of reward following the presentation of visual stimuli. The visual information varied along 3 dimensions, color, shape, and width. Shape was always relevant for reward prediction, width was always irrelevant, and color was irrelevant at the beginning of the trial but became relevant later on, once it could be assessed together with shape. The neural data showed systematic changes in the representations of these features and of the expected reward as the learning progressed, and the objective of this study was to try to understand what principles could underlie these changes. The simulations and theoretical calculations indicated that the changes in PFC activity (throughout learning and throughout a trial) can be understood as an attempt by the circuitry to use an efficient representational strategy, i.e., one that uses as few spikes as possible, given that the resulting representation should be accurate enough for task performance.

Strengths:

- The paper is concise and clearly written.

- The paper shows that, in a neural circuit, the information that is decodable and the information that is task-relevant may relate in very different ways. Decodable information may be very relevant or very irrelevant. This fact is critical for interpreting the results of pure decoding studies, which often assume an equivalence. This take-home message is not emphasized by the authors, but I think is quite important.

- The results provide insight as to how neural representations may be transformed as a task is learned, which often results in subtle changes in selectivity and overall activity levels whose impact or reason is not entirely clear just by looking at the data.

Weaknesses:

The match between the real PFC and the model networks is highly qualitative, and as noted by the authors, comparisons only make sense in terms of *changes* between early and late learning. The time scales, activity levels, and decoding accuracies involved are all different between the model and recording data. This is not to disregard what the authors have done, but simply to point out an important limitation.

Reviewer #2 (Public Review):

Summary:

The study investigates the representation of irrelevant stimuli in neural circuits using neural recordings from the primate prefrontal cortex during a passive object association task. They find a significant decrease in the linear decodability of irrelevant stimuli over the course of learning (in the time window in which the stimuli are irrelevant). They then compare these trends to RNNs trained with varying levels of noise and firing rate regularization and find agreement when these levels are at an intermediate value. In a complementary analysis, they found (in both RNNs and PFC) that the magnitude of relevant and irrelevant stimuli increased and decreased, respectively, during learning. These findings were interpreted in terms of a minimization of metabolic cost in the cortex.

To understand how stimuli can be dynamically suppressed at times when they are irrelevant, the authors constructed and analyzed a reduced two-neuron model of the task. They found a mechanism in which firing rate regularization increased the probability of negative weights in the input, pushing the neural activities below the threshold. A similar mechanism was observed in RNNs.

Strengths:

The article is well-written and the figures are easily understood. The analyses are well explained and motivated. The article provides a valuable analysis of the effect of two parameters on representations of irrelevant stimuli in trained RNNs.

Weaknesses:

(1) The mechanism for suppressing dynamically relevant stimuli appears to be incomplete and does not explain clearly enough how representations of 'color' which are suppressed through negative input weights become un-suppressed in the presence of the second variable 'shape'.

(2) Interpretation of results in terms of the effect of metabolic cost on cortical dynamics is not backed up by the presented data/analyses. The change in dynamics of 'color' representations in the prefrontal cortex only qualitatively matches RNN dynamics and may arise from other causes.

Reviewer #3 (Public Review):

Summary:

In order to study the factors and neural dynamics that lead to the suppression of irrelevant information in the brain, the authors trained artificial neural networks in the execution of a task that involved the discrimination of complex stimuli with three main features: color, shape, and width. Specific combinations of color and shape led to a reward, but the temporal structure made color dynamically irrelevant at the beginning of the trial, and then it became relevant once the shape was presented. On the other hand, the width of the stimulus was always irrelevant. Importantly, non-human primates were also trained to execute this task (in a previous study by the authors) and the activity from neural populations from the dorsolateral Prefrontal Cortex (dlPFC) was recorded, allowing to compare the coding of information by the artificial neural network model with what happens in biological neural populations.

The authors changed systematically the amount of noise present in the neural network model, as well as limiting the firing rate of the artificial neurons to simulate the limitations imposed by high metabolic costs in biological neurons. They found that models with medium and low noise, as well as medium and low metabolic cost, developed information encoding patterns that resembled the patterns observed throughout learning in the dlPFC, as follows: early in the learning process, color information was strongly represented during the whole trial, as well as shape and width, whereas the color/shape combination significance (XOR operation) was weakly encoded. Late in learning, color information was initially suppressed (while it was deemed irrelevant) and became more prominent during the shape presentation. Width information coding decreased, and the XOR operation result became more strongly encoded.

Subthreshold activity dynamics were studied by training artificial networks consisting of 2 neurons, with the aim of understanding how dynamically irrelevant information is suppressed and then encoded more strongly at a different time during the trial. Under medium noise and medium metabolic cost, color information is suppressed by the divergence of the activity away from the level that triggers spikes. The authors claim that this subthreshold dynamic explains the suppression of irrelevant information in biological neural networks.

Strengths:

The study leverages the power of computational models to simulate biological networks and do manipulations that are difficult (if not impossible) to perform in vivo. The analyses of the activity of the network model are neat and thorough and provide a clear demonstration of how noise and metabolic costs may affect the information coding in the brain. The mathematical analyses are rigorous and nicely documented.

Weaknesses:

The study does not leverage the fact that they have access to the activity of individual neurons both on a neural network model and in neural recordings. The model/brain comparison results are limited to the decodability of different pieces of information during the execution of the task at different stages of learning. It would have been useful if the authors had shown response profiles of individual neurons, both biological and artificial, to strengthen the claim that the activity patterns are similar. Perhaps showing that the firing rates vary in a similar way in the large models (like they do for the 2-neuron model) would have been informative. For instance, it is possible that suppression is not occurring in the dlPFC, but that the PFC receives input with this information already suppressed. If suppression indeed happens in the PFC, response profiles associated with this process may be observed.

There is no way to say that the 2-neuron models are in any way informative of what happens in brain neurons, or even larger artificial networks since the sources of sensory input, noise, and inhibition will differ between biological and artificial networks. And because the firing patterns are not shown for large networks, it is not clear if some non-coding artificial neurons will become broadly inhibitory but maintain a relatively high firing rate (to mention only one possibility).

Reviewer #1 (Public Review):

Summary:

The authors bring together implanted radiofrequency coils, high-field MRI imaging, awake animal imaging, and sensory stimulation methods in a technological demonstration. The results are very detailed descriptions of the sensory systems under investigation.

Strengths:

- The maps are qualitatively excellent for rodent whole-brain imaging.<br /> - The design of the holder and the coil is pretty clever.

Weaknesses:

- Some unexpected regions appear on the whole brain maps, and the discussion of these regions is succinct.<br /> - The authors do not make the work and effort to train the animals and average the data from several hundred trials apparent enough. This is important for any reader who would like to consider implementing this technology.<br /> - The data is not available. This does not let the readers make their own assessment of the results.

Reviewer #2 (Public Review):

Summary:

The manuscript by Hike et al. entitled 'High-resolution awake mouse fMRI at 14 Tesla' describes the implementation of awake mouse BOLD-fMRI at high field. This work is timely as the field of mouse fMRI is working toward collecting high-quality data from awake animals. Imaging awake subjects offers opportunities to study brain function that are otherwise not possible under the more common anesthetized conditions. Not to mention the confounding effects that anesthesia has on neurovascular coupling. What has made progress in this area slow (relative to other imaging approaches like optical imaging) is the environment within the MRI scanner (high acoustic noise) - as well as the intolerance of head and body motion. This work adds to a relatively small, but quickly growing literature on awake mouse fMRI. The findings in the study include testing of an implanted head-coil (for MRI data reception). Two designs are described and the SNR of these units at 9.4T and 14T are reported. Further, responses to visual as well as whisker stimulation recorded in acclimated awake mice are shown. The most interesting finding, and most novel, is the observation that mice seem to learn to anticipate the presentation of the stimulus - as demonstrated by activations evident ~6 seconds prior to the presentation of the stimulus when stimuli are delivered at regular intervals (but not when stimuli are presented at random intervals). These kinds of studies are very challenging to do. The surgical preparation and length of time invested into training animals are grueling. I also see this work as a step in the right direction and evidence of the foundations for lots of interesting future work. However, I also found a few shortcomings listed below.

Weaknesses:

(1) The surface coil, although offering a great SNR boost at the surface, ultimately comes at a cost of lower SNR in deeper more removed brain regions in comparison to commercially available Bruker coils (at room temperature). This should be quantified. A rough comparison in SNR is drawn between the implanted coils and the Bruker Cryoprobe - this should be a quantitative comparison (if possible) - including any differences in SNR in deeper brain structures. There are drawbacks to the Cryoprobe, which can be discussed, but a more thorough comparison between the implanted coils, and other existing options should be provided (the Cryoprobe has been used previously in awake mouse experiments). Further, the details of how to build the implanted coils should be provided (shared) - this should include a parts list as well as detailed instructions on how to build the units. Also, how expensive are they? And can they be reused?

(2) In the introduction, the authors state that "Awake mouse fMRI has been well investigated". I disagree with this statement and others in the manuscript that give the reader the impression that awake experiments are not a challenging and unresolved approach to fMRI experiments in mice (or rodents). Although there are multiple labs (maybe 15 worldwide) that have conducted awake mouse experiments (with varying degrees of success/thoroughness), we are far from a standardized approach. This is a strength of the current work and should be highlighted as such. I encourage the authors to read the recent systematic review that was published on this topic in Cerebral Cortex by Mandino et al. There are several elements in there that should influence the tone of this piece including awake mouse implementations with the Bruker Cryoprobe, prevalence of surgical preparations, and evaluations of stress.

(3) The authors also comment on implanted coils reducing animal stress - I don't know where this comment is coming from, as this has not been reported in the literature (to my knowledge) and the authors don't appear to have evaluated stress in their mice.

(4) Following on the above point, measures of motion, stress, and more details on the acclimation procedure that was implemented in this study should be included.

(5) It wasn't clear to me at what times the loop versus "Figure 8" coil was being used, nor how many mice (or how much data) were included in each experiment/plot. There is also no mention of biological sex.

(6) Building on the points above, the manuscript overall lacks experimental detail (especially since the format has the results prior to the methods).

(7) An observation is made in the manuscript that there is an appreciable amount of negative BOLD signal. The authors speculate that this may come from astrocyte-mediated BOLD during brain state changes (and cite anesthetized rat and non-human primate experiments). This is very strange to me. First, the negative BOLD signal is not plotted (please do this), further, there are studies in awake mice that measure astrocyte activation eliciting positive BOLD responses (see Takata et al. in Glia, 2017).

Reviewer #1 (Public Review):

Summary:

This paper presents two experiments, both of which use a target detection paradigm to investigate the speed of statistical learning. The first experiment is a replication of Batterink, 2017, in which participants are presented with streams of uniform-length, trisyllabic nonsense words and asked to detect a target syllable. The results replicate previous findings, showing that learning (in the form of response time facilitation to later-occurring syllables within a nonsense word) occurs after a single exposure to a word. In the second experiment, participants are presented with streams of variable-length nonsense words (two trisyllabic words and two disyllabic words) and perform the same task. A similar facilitation effect was observed as in Experiment 1. The authors interpret these findings as evidence that target detection requires mechanisms different from segmentation. They present results of a computational model to simulate results from the target detection task and find that an "anticipation mechanism" can produce facilitation effects, without performing segmentation. The authors conclude that the mechanisms involved in the target detection task are different from those involved in the word segmentation task.

Strengths:

The paper presents multiple experiments that provide internal replication of a key experimental finding, in which response times are facilitated after a single exposure to an embedded pseudoword. Both experimental data and results from a computational model are presented, providing converging approaches for understanding and interpreting the main results. The data are analyzed very thoroughly using mixed effects models with multiple explanatory factors.

Weaknesses:

In my view, the main weaknesses of this study relate to the theoretical interpretation of the results.

(1) The key conclusion from these findings is that the facilitation effect observed in the target detection paradigm is driven by a different mechanism (or mechanisms) than those involved in word segmentation. The argument here I think is somewhat unclear and weak, for several reasons:

First, there appears to be some blurring in what exactly is meant by the term "segmentation" with some confusion between segmentation as a concept and segmentation as a paradigm.<br /> Conceptually, segmentation refers to the segmenting of continuous speech into words. However, this conceptual understanding of segmentation (as a theoretical mechanism) is not necessarily what is directly measured by "traditional" studies of statistical learning, which typically (at least in adults) involve exposure to a continuous speech stream followed by a forced-choice recognition task of words versus recombined foil items (part-words or nonwords). To take the example provided by the authors, a participant presented with the sequence GHIABCDEFABCGHI may endorse ABC as being more familiar than BCG, because ABC is presented more frequently together and the learned association between A and B is stronger than between C and G. However, endorsement of ABC over BCG does not necessarily mean that the participant has "segmented" ABC from the speech stream, just as faster reaction times in responding to syllable C versus A do not necessarily indicate successful segmentation. As the authors argue on page 7, "an encounter to a sequence in which two elements co-occur (say, AB) would theoretically allow the learner to use the predictive relationship during a subsequent encounter (that A predicts B)." By the same logic, encoding the relationship between A and B could also allow for the above-chance endorsement of items that contain AB over items containing a weaker relationship.

Both recognition performance and facilitation through target detection reflect different outcomes of statistical learning. While they may reflect different aspects of the learning process and/or dissociable forms of memory, they may best be viewed as measures of statistical learning, rather than mechanisms in and of themselves.

(2) The key manipulation between experiments 1 and 2 is the length of the words in the syllable sequences, with words either constant in length (experiment 1) or mixed in length (experiment 2). The authors show that similar facilitation levels are observed across this manipulation in the current experiments. By contrast, they argue that previous findings have found that performance is impaired for mixed-length conditions compared to fixed-length conditions. Thus, a central aspect of the theoretical interpretation of the results rests on prior evidence suggesting that statistical learning is impaired in mixed-length conditions. However, it is not clear how strong this prior evidence is. There is only one published paper cited by the authors - the paper by Hoch and colleagues - that supports this conclusion in adults (other mentioned studies are all in infants, which use very different measures of learning). Other papers not cited by the authors do suggest that statistical learning can occur to stimuli of mixed lengths (Thiessen et al., 2005, using infant-directed speech; Frank et al., 2010 in adults). I think this theoretical argument would be much stronger if the dissociation between recognition and facilitation through RTs as a function of word length variability was demonstrated within the same experiment and ideally within the same group of participants.

(3) The authors argue for an "anticipation" mechanism in explaining the facilitation effect observed in the experiments. The term anticipation would generally be understood to imply some kind of active prediction process, related to generating the representation of an upcoming stimulus prior to its occurrence. However, the computational model proposed by the authors (page 24) does not encode anything related to anticipation per se. While it demonstrates facilitation based on prior occurrences of a stimulus, that facilitation does not necessarily depend on active anticipation of the stimulus. It is not clear that it is necessary to invoke the concept of anticipation to explain the results, or indeed that there is any evidence in the current study for anticipation, as opposed to just general facilitation due to associative learning.

In addition, related to the model, given that only bigrams are stored in the model, could the authors clarify how the model is able to account for the additional facilitation at the 3rd position of a trigram compared to the 2nd position?

(4) In the discussion of transitional probabilities (page 31), the authors suggest that "a single exposure does provide information about the transitions within the single exposure, and the probability of B given A can indeed be calculated from a single occurrence of AB." Although this may be technically true in that a calculation for a single exposure is possible from this formula, it is not consistent with the conceptual framework for calculating transitional probabilities, as first introduced by Saffran and colleagues. For example, Saffran et al. (1996, Science) describe that "over a corpus of speech there are measurable statistical regularities that distinguish recurring sound sequences that comprise words from the more accidental sound sequences that occur across word boundaries. Within a language, the transitional probability from one sound to the next will generally be highest when the two sounds follow one another within a word, whereas transitional probabilities spanning a word boundary will be relatively low." This makes it clear that the computation of transitional probabilities (i.e., Y | X) is conceptualized to reflect the frequency of XY / frequency of X, over a given language inventory, not just a single pair. Phrased another way, a single exposure to pair AB would not provide a reliable estimate of the raw frequencies with which A and AB occur across a given sample of language.

(5) In experiment 2, the authors argue that there is robust facilitation for trisyllabic and disyllabic words alike. I am not sure about the strength of the evidence for this claim, as it appears that there are some conflicting results relevant to this conclusion. Notably, in the regression model for disyllabic words, the omnibus interaction between word presentation and syllable position did not reach significance (p= 0.089). At face value, this result indicates that there was no significant facilitation for disyllabic words. The additional pairwise comparisons are thus not justified given the lack of omnibus interaction. The finding that there is no significant interaction between word presentation, word position, and word length is taken to support the idea that there is no difference between the two types of words, but could also be due to a lack of power, especially given the p-value (p = 0.010).

(6) The results plotted in Figure 2 seem to suggest that RTs to the first syllable of a trisyllabic item slow down with additional word presentations, while RTs to the final position speed up. If anything, in this figure, the magnitude of the effect seems to be greater for 1st syllable positions (e.g., the RT difference between presentation 1 and 4 for syllable position 1 seems to be numerically larger than for syllable position 3, Figure 2D). Thus, it was quite surprising to see in the results (p. 16) that RTs for syllable position 1 were not significantly different for presentation 1 vs. the later presentations (but that they were significant for positions 2 and 3 given the same comparison). Is this possibly a power issue? Would there be a significant slowdown to 1st syllables if results from both the exact replication and conceptual replication conditions were combined in the same analysis?

(7) It is difficult to evaluate the description of the PARSER simulation on page 36. Perhaps this simulation should be introduced earlier in the methods and results rather than in the discussion only.

Reviewer #2 (Public Review):

Summary:

This valuable study investigates how statistical learning may facilitate a target detection task and whether the facilitation effect is related to statistical learning of word boundaries. Solid evidence is provided that target detection and word segmentation rely on different statistical learning mechanisms.

Strengths:

The study is well designed, using the contrast between the learning of words of uniform length and words of variable length to dissociate general statistical learning effects and effects related to word segmentation.

Weaknesses:

The study relies on the contrast between word length effects on target detection and word learning. However, the study only tested the target detection condition and did not attempt to replicate the word segmentation effect. It is true that the word segmentation effect has been replicated before but it is still worth reviewing the effect size of previous studies.

The paper seems to distinguish prediction, anticipation, and statistical learning, but it is not entirely clear what each term refers to.

Reviewer #1 (Public Review):

Summary:

The authors introduce two preparations for observing large-scale cortical activity in mice during behavior. Alongside, they present intriguing preliminary findings utilizing these methods. This paper is poised to be an invaluable resource for researchers engaged in extensive cortical recording in behaving mice.

Strengths:

Comprehensive methodological detailing:<br /> The paper excels in providing an exceptionally detailed description of the methods used. This meticulous documentation includes a step-by-step workflow, complemented by thorough workflow, protocols and list of materials in the supplementary materials.

Minimal of movement artifacts:<br /> A notable strength of this study is the remarkably low movement artifacts, with specific strategies outlined to attain this outcome.

Insightful preliminary data and analysis:<br /> The preliminary data unveiled in the study reveal interesting heterogeneity in the relationships between neural activity and detailed behavioral features, particularly notable in the lateral cortex. This aspect of the findings is intriguing and suggests avenues for further exploration.

Weaknesses:

Clarification about the extent of the method in title:<br /> The title of the paper, using the term "pan-cortical", may inadvertently suggest that both the top and lateral view preparations are utilized in the same set of mice, while the authors employ either the dorsal view (which offers limited access to the lateral ventral regions) or the lateral view (which restricts access to the opposite side of the cortex).

Despite the authors not identifying qualitative effects, tilting the mouse's head could potentially influence behavioral outcomes in certain paradigms.

Reviewer #2 (Public Review):

Summary:

The authors present a comprehensive technical overview of the challenging acquisition of large-scale cortical activity, including surgical procedures and custom 3D-printed headbar designs to obtain neural activity from large parts of the dorsal or lateral neocortex. They then describe technical adjustments for stable head fixation, light shielding, and noise insulation in a 2-photon mesoscope and provide a workflow for multisensory mapping and alignment of the obtained large-scale neural data sets in the Allen CCF framework. Lastly, they show different analytical approaches to relate single-cell activity from various cortical areas to spontaneous activity by using visualization and clustering tools, such as Rastermap, PCA-based cell sorting, and B-SOID behavioral motif detection.

The study contains a lot of useful technical information that should be of interest to the field. It tackles a timely problem that an increasing number of labs will be facing as recent technical advances allow the activity measurement of an increasing number of neurons across multiple areas in awake mice. Since the acquisition of cortical data with a large field of view in awake animals poses unique experimental challenges, the provided information could be very helpful to promote standard workflows for data acquisition and analysis and push the field forward.

Strengths:

The proposed methodology is technically sound and the authors provide convincing data to suggest that they successfully solved various challenging problems, such as motion artifacts of large imaging preparations or high-frequency noise emissions, during 2-photon imaging. Overall, the authors achieved their goal of demonstrating a comprehensive approach for imaging neural data across many cortical areas and providing several examples that demonstrate the validity of their methods and recapitulate and further extend some recent findings in the field. A particular focus of the results is to emphasize the need for imaging large population activity across cortical areas to identify cross-area information processing during active behaviors.

Weaknesses:

The manuscript contains a lot of technical details and might be challenging for readers without previous experimental experience. However, the different paragraphs illuminate a large range of technical aspects and challenges of large-scale functional imaging. Therefore, the work should be a valuable source of solutions for a diverse audience.

Reviewer #3 (Public Review):

Summary

In their manuscript, Vickers and McCormick have demonstrated the potential of leveraging mesoscale two-photon calcium imaging data to unravel complex behavioural motifs in mice. Particularly commendable is their dedication in providing detailed surgical preparations and corresponding design files, a contribution that will greatly benefit the broader neuroscience community as a whole. The quality of the data is high and examples are available to the community. More importantly, the authors have acquired activity-clustered neural ensembles at an unprecedented spatial scale to further correlate with high level behaviour motifs identified by B-SOiD. Such an advancement marks a significant contribution to the field. While the manuscript is comprehensive and the analytical strategy proposed is promising, some technical aspects warrant further clarification. Overall, the authors have presented an invaluable and innovative approach, effectively laying a solid foundation for future research in correlating large scale neural ensembles with behavioural. The implementation of a custom sound insulator for the scanner is a great idea and should be something implemented by others.

This is a methods paper, but there is no large diagram (in the main figures) that shows how all the parts are connected, communicating and triggering between each other. This is described in the methods and now supplemental figure, but a visual representation would greatly benefit the readers looking to implement something similar as a main figure but I guess they can find it in the methods. No stats for the results shown in Figure 6e, it would be useful to know which of these neural densities for all areas show a clear statistical significance across all the behaviors. While I understand that this is a methods paper, it seems like the authors are aware of the literature surrounding large neuronal recordings during mouse behavior. Indeed, in line 178-179 the authors mention how a significant portion of the variance in neural activity can be attributed to changes in "arousal or self-directed movement even during spontaneous behavior." Why then did the authors not make an attempt at a simple linear model that tries to predict the activity of their many thousands of neurons by employing the multitude of regressors at their disposal (pupil, saccades, stimuli, movements, facial changes, etc). These models are straightforward to implement, and indeed it would benefit this work if the model extracts information on par with what it's known from the literature. We also realize such a model could be done in the future.

Reviewer #1 (Public Review):

Summary:

The manuscript examines the contribution of the dorsal and intermediate hippocampus to goal-directed navigation in a wide virtual environment where visual cues are provided by the scenery on the periphery of a wide arena. Among a choice of 2 reward zones located near the arena periphery, rats learn to navigate from the center of the arena to the reward zone associated with the highest reward. Navigation performance is largely assessed from the rats' body orientation when they leave the arena center and when they reach the periphery, as well as the angular mismatch between the reward zone and the site rats reach the periphery. Muscimol inactivation of the dorsal and intermediate hippocampus alters rat navigation to the reward zone, but the effect was more pronounced for the inactivation of the intermediate hippocampus, with some rat trajectories ending in the zone associated with the lowest reward. Based on these results, the authors suggest that the intermediate hippocampus is critical, especially for navigating to the highest reward zone.

Strengths:

_ The authors developed an effective approach to study goal-directed navigation in a virtual environment where visual cues are provided by the peripheral scenery.

_ In general, the text is clearly written and the figures are well-designed and relatively straightforward to interpret, even without reading the legends.

_ An intriguing result, which would deserve to be better investigated and/or discussed, was that rats tended to rotate always in the counterclockwise direction. Could this be because of a hardware bias making it easier to turn left, some aspect of the peripheral landscape, or a natural preference of rats to turn left that is observable (or reported) in a real environment?

_ Another interesting observation, which would also deserve to be addressed in the discussion, is the fact that dHP/iHP inactivations produced to some extent consistent shifts in departing and peripheral crossing directions. This is visible from the distributions in Figures 6 and 7, which still show a peak under muscimol inactivation, but this peak is shifted to earlier angles than the correct ones. Such change is not straightforward to interpret, unlike the shortening of the mean vector length.

Maybe rats under muscimol could navigate simply by using the association of reward zone with some visual cues in the peripheral scene, in brain areas other than the hippocampus, and therefore stopped their rotation as soon as they saw the cues, a bit before the correct angle. While with their hippocampus is intact, rats could estimate precisely the spatial relationship between the reward zone and visual cues.

Weaknesses:

_ I am not sure that the differential role of dHP and iHP for navigation to high/low reward locations is supported by the data. The current results could be compatible with iHP inactivation producing a stronger impairment on spatial orientation than dHP inactivation, generating more erratic trajectories that crossed by chance the second reward zone.

To make the point that iHP inactivation affects the disambiguation of high and low reward locations, the authors should show that the fraction of trajectories aiming at the low reward zone is higher than expected by chance. Somehow we would expect to see a significant peak pointing toward the low reward zone in the distribution of Figures 6-7.

Reviewer #2 (Public Review):

Summary:

The aim of this paper was to elucidate the role of the dorsal HP and intermediate HP (dHP and iHP) in value-based spatial navigation through behavioral and pharmacological experiments using a newly developed VR apparatus. The authors inactivated dHP and iHP by muscimol injection and analyzed the differences in behavior. The results showed that dHP was important for spatial navigation, while iHP was critical for both value judgments and spatial navigation. The present study developed a new sophisticated behavioral experimental apparatus and proposed a behavioral paradigm that is useful for studying value-dependent spatial navigation. In addition, the present study provides important results that support previous findings of differential function along the dorsoventral axis of the hippocampus.

Strengths:

The authors developed a VR-based value-based spatial navigation task that allowed separate evaluation of "high-value target selection" and "spatial navigation to the target." They were also able to quantify behavioral parameters, allowing detailed analysis of the rats' behavioral patterns before and after learning or pharmacological inactivation.

Weaknesses:

Although differences in function along the dorsoventral axis of the hippocampus is an important topic that has received considerable attention, differences in value coding have been shown in previous studies, including the work of the authors; the present paper is an important study that supports previous studies, but the novelty of the findings is not that high, as the results are from pharmacological and behavioral experiments only.

Reviewer #3 (Public Review):

Summary:

The authors established a new virtual reality place preference task. On the task, rats, which were body-restrained on top of a moveable Styrofoam ball and could move through a circular virtual environment by moving the Styrofoam ball, learned to navigate reliably to a high-reward location over a low-reward location, using allocentric visual cues arranged around the virtual environment.

The authors also showed that functional inhibition by bilateral microinfusion of the GABA-A receptor agonist muscimol, which targeted the dorsal or intermediate hippocampus, disrupted task performance. The impact of functional inhibition targeting the intermediate hippocampus was more pronounced than that of functional inhibition targeting the dorsal hippocampus.

Moreover, the authors demonstrated that the same manipulations did not significantly disrupt rats' performance on a virtual reality task that required them to navigate to a spherical landmark to obtain reward, although there were numerical impairments in the main performance measure and the absence of statistically significant impairments may partly reflect a small sample size (see comments below).

Overall, the study established a new virtual-reality place preference task for rats and established that performance on this task requires the dorsal to intermediate hippocampus. They also established that task performance is more sensitive to the same muscimol infusion (presumably - doses and volumes used were not clearly defined in the manuscript, see comments below) when the infusion was applied to the intermediate hippocampus, compared to the dorsal hippocampus, although this does not offer strong support for the authors claim that dorsal hippocampus is responsible for accurate spatial navigation and intermediate hippocampus for place-value associations (see comments below).

Strengths:

(1) The authors established a new place preference task for body-restrained rats in a virtual environment and, using temporary pharmacological inhibition by intra-cerebral microinfusion of the GABA-A receptor agonist muscimol, showed that task performance requires dorsal to intermediate hippocampus.

(2) These findings extend our knowledge about place learning tasks that require dorsal to intermediate hippocampus and add to previous evidence that, for some place memory tasks, the intermediate hippocampus may be more important than other parts of the hippocampus, including the dorsal hippocampus, for goal-directed navigation based on allocentric place memory.

(3) The hippocampus-dependent task may be useful for future recording studies examining how hippocampal neurons support behavioral performance based on place information.

Weaknesses:<br /> (1) The new findings do not strongly support the authors' suggestion that the dorsal hippocampus is responsible for accurate spatial navigation and the intermediate hippocampus for place-value associations.

The authors base this claim on the differential effects of the dorsal and intermediate hippocampal muscimol infusions on different performance measures. More specifically, dorsal hippocampal muscimol infusion significantly increased perimeter crossings and perimeter crossing deviations, whereas dorsal infusion did not significantly change other measures of task performance, including departure direction and visits to the high-value location. However, these statistical outcomes offer only limited evidence that dorsal hippocampal infusion specifically affected the perimeter crossing, without affecting the other measures. Numerically the pattern of infusion effects is quite similar across these various measures: intermediate hippocampal infusions markedly impaired these performance measures compared to vehicle infusions, and the values of these measures after dorsal hippocampal muscimol infusion were between the values in the intermediate hippocampal muscimol and the vehicle condition (Figures 5-7). Moreover, I am not so sure that the perimeter crossing measures really reflect distinct aspects of navigational performance compared to departure direction and hit rate, and, even if they did, which aspects this would be. For example, in line 316, the authors suggest that 'departure direction and PCD [perimeter crossing deviation] [are] indices of the effectiveness and accuracy of navigation, respectively'. However, what do the authors mean by 'effectiveness' and 'accuracy'? Accuracy typically refers to whether or not the navigation is 'correct', i.e. how much it deviates from the goal location, which would be indexed by all performance measures.

So, overall, I would recommend toning down the claim that the findings suggest that the dorsal hippocampus is responsible for accurate spatial navigation and the intermediate hippocampus for place-value associations.

(2) The claim that the different effects of intermediate and dorsal hippocampal muscimol infusions reflect different functions of intermediate and dorsal hippocampus rests on the assumption that both manipulations inhibit similar volumes of hippocampal tissue to a similar extent, but at different levels along the dorso-ventral axis of the hippocampus. However, this is not a foregone conclusion (e.g., drug spread may differ depending on the infusion site or drug effects may differ due to differential expression of GABA-A receptors in the dorsal and intermediate hippocampus), and the authors do not provide direct evidence for this assumption. Therefore, a possible alternative account of the weaker effects of dorsal compared to intermediate hippocampal muscimol infusions on place-preference performance is that the dorsal infusions affect less hippocampal volume or less markedly inhibit neurons within the affected volume than the intermediate infusions. I would recommend that the authors briefly consider this issue in the discussion. Moreover, from the Methods, it is not clear which infusion volume and muscimol concentration were used for the different infusions (see below, 4.a.), and this must be clarified.

(3) It is good that the authors included a comparison/control study using a spherical beacon-guided navigation task, to examine the specific psychological mechanisms disrupted by the hippocampal manipulations. However, as outlined below (4.b.), the sample size for the comparison study was lower than for the main study, and the data in Figure 8 suggest that the comparison task may be affected by the hippocampal manipulations similarly to the place-preference task, albeit less markedly. This would raise the question as to which mechanisms that are common to the two tasks may be affected by hippocampal functional inhibition, which should be considered in the discussion.

(4) Several important methodological details require clarification:<br /> a. Drug infusions (from line 673):<br /> - '0.3 to 0.5 μl of either phosphate-buffered saline (PBS) or muscimol (MUS) was infused into each hemisphere'; the authors need to clarify when which infusion volume was used and why different infusion volumes were used.<br /> - I could not find the concentration of the muscimol solution that was used. The authors must clarify this and also should include a justification of the doses used, e.g. based on previous studies.<br /> - Please also clarify if the injectors and dummies were flush with the guides or by which distance they protruded from the guides.<br /> b. Sample sizes: The authors should include sample size justifications, e.g. based on considerations of statistical power, previous studies, practical considerations, or a combination of these factors. Importantly, the smaller sample size in the control study using the spherical beacon-guided navigation task (n=5 rats) limits comparability with the main study using the place-preference task (n=8). Numerically, the findings on the control task (Figure 8) look quite similar to the findings on the place-preference task, with intermediate hippocampal muscimol infusions causing the most pronounced impairment and dorsal hippocampal muscimol infusions causing a weaker impairment. These effects may have reached statistical significance if the same sample size had been used in the place-preference study.<br /> c. Statistical analyses: Why were the data of the intermediate and dorsal hippocampal PBS infusion conditions averaged for some of the analyses (Figure 5; Figure 6B and C; Figure 7B and C; Figure 8B) but not for others (Figure 6A and Figure 7A)?

Reviewer #1 (Public Review):

Summary:

This work describes a simple mechanical model of worm locomotion, using a series of rigid segments connected by damped torsional springs and immersed in a viscous fluid. It uses this model to simulate forward crawling movement, as well as omega turns.

Strengths:

The primary strength is in applying a biomechanical model to omega-turn behaviors. The biomechanics of nematode turning behaviors are relatively less well described and understood than forward crawling, and the increase in power during omega turns is one of the more novel results. The model itself may be a useful implementation to other researchers, particularly owing to its simplicity.

Weaknesses:

The strength of the model presented in this work relative to prior approaches is not well supported, and in general the paper would be improved with a better description of the broader context of existing modeling literature related to undulatory locomotion. This paper claims to improve on previous approaches to taking body shapes as inputs. However, the sole nematode model cited aims to do something different, and arguably more significant, which is to use experimentally derived parameters to model both the neural circuits that induce locomotion as well as the biomechanics and to subsequently compare the model to experimental data. Other modeling approaches do take experimental body kinematics as inputs and use them to produce force fields, however, they are not cited or discussed. Finally, the overall novelty of the approach is questionable. A functionally similar approach was developed in 2012 to describe worm locomotion in lattices (Majmudar, 2012, Roy. Soc. Int.), which is not discussed and would provide an interesting comparison and needed context.

In some sense, because the model takes kinematics as an input and uses previously established techniques to model mechanics, it is unsurprising that it can reproduce experimentally observed kinematics, however, the forces calculated and the variation of parameters could be of interest, but other methods derived from kinematics could provide similar results. It is unclear what the predictive power of the model is.

Relatedly, a justification of why the drag coefficients had to be changed by a factor of 100 should be explored. Plate conditions are difficult to replicate and the rheology of plates likely depends on several factors, but is for example, changes in hydration level likely to produce a 100-fold change in drag? or something more interesting/subtle within the model producing the discrepancy?

Finally, the language used to distinguish different modeling approaches was often unclear. For example, it was unclear in what sense the model presented in Boyle, 2012 was a "kinetic model" and in many situations, it appeared that the term kinematic might have been more appropriate. Other phrases like "frictional forces caused by the tension of its muscles" were unclear at first glance, and might benefit from revision and more canonical usage of terms.

Reviewer #2 (Public Review):

Summary:

Developing a mechanical model of C. elegans is difficult to do from basic principles because it moves at low (but not very small) Reynolds number, is itself visco-elastic, and often is measured moving at a solid/liquid interface. The ElegansBot is a good first step at a kinetic model that reproduces a wide range of C. elegans motility behavior.

Strengths:

The model is general due to its simplicity and likely useful for various undulatory movements. The model reproduces experimental movement data using realistic physical parameters (e.g. drags, forces, etc). The model is predictive (semi?) as shown in the liquid to solid gait transition. The model is straightforward in implementation and so likely is adaptable to modification and addition of control circuits.

Comments on revised version:

This is a revised manuscript. I'm happy with the changes made, including the specific responses to my previous concerns.

Reviewer #3 (Public Review):

A mechanical model of C. elegans, embedded in a resistive force environment, is used to calculate input torque patterns required to generate output curvature patterns and coordinates, corresponding to a number of different locomotion behaviors in C. elegans.

Strengths:

The use of a mechanical model to study a variety of locomotor sequences and the grounding in empirical data are strengths. The matching of speeds (though requiring adjusted drag coefficients) is a strength.

Weaknesses:

The paper lacks evidence of numerical validation or comparison with the results and tools in the literature. E.g. is it surprising that the uniform torque distribution yields maximal speed? What is the relation between input and output data? How does the input-output relation depend on the parameters of the model? What novel model predictions are made?

In particular, if validated, the breakdown of drag forces and torque distributions during forward locomotion and turning behaviors may be interesting to compare to predictions by other tools, and to empirical measurement. One caveat is that the worm touches itself during such turns, and even crosses over itself in delta turns, and so the estimated drag coefficients and the resultant mechanical forces are likely incorrect.

Reviewer #2 (Public Review):

Summary:

Laham et al. investigate how the projection from adult born granule cells into CA2 affects the retrieval of social memories at various developmental points. They use chemogenetic manipulations and electrophysiological recordings to test how this projection affects hippocampal network properties during behavior. The study is of relevant interest for the neuroscience community and the results are important for our understanding of how social memories of different nature (remote or immediate) are encoded and supported by the hippocampal circuitry. The behavioral experiments after abGC projections to CA2 are compelling as they show clearly distinct behavioral readout. While the electrophysiological experiments are difficult to interpret without more single cell responses quantifications, they clearly show that more than one region in the hippocampus is involved in the formation of social memories.

Reviewer #3 (Public Review):

Laham et al. present a manuscript investigating the function of adult-born granule cells (abGCs) projecting to the CA2 region of the hippocampus during social memory. It should be noted that no function for the general DG to CA2 projection has been proposed yet. The authors use targeted ablation, chemogenetic silencing and in vivo ephys to demonstrate that the abGCs to CA2 projection is necessary for the retrieval of a remote social memories such as the memory of one's mother. They also use in vivo ephys to show that abGCs are necessary for differential CA2 network activity, including theta-gamma coupling and sharp wave-ripples, in response to novel versus familiar social stimuli.

The question investigated is important since the function of DG to CA2 projection remained elusive a decade after its discovery. Overall, the results are interesting but focused to the social memory of the mother and their description in the manuscript and figures is too cursory. For example, raw interaction times must be shown before their difference. The assumption that mice exhibit social preference between familiar or novel individuals such as mother and non-mother based on social memory formation, consolidation and retrieval should be better explained throughout the manuscript. Thus, when describing the results, the authors should comment on changes in preference and how this can be interpreted as a change in social memory retrieval. Several critical experimental details such as the total time of presentation to the mother and non-mother stimulus mice are also lacking from the manuscript. The in vivo e-phys results are interesting as well but even more succinct with no proposed mechanism as to how abGCs could regulate SWR and PAC in CA2.

The manuscript is well-written with the appropriate references. The choice of behavioral test is somewhat debatable however. It is surprising the authors chose to use a direct presentation test (presentation of the mother and non-mother in alternance) instead of the classical 3-chamber test which is particularly appropriate to investigate social preference. Since the authors focused exclusively on this preference, the 3-chamber test would have been more adequate in my opinion. It would greatly strengthened the results if the authors could repeat a key experiment from their investigation using such test. In addition, the authors only impaired the mother's memory. An additional experiment showing that disruption of the abGCs to CA2 circuit impairs social memory retrieval in general would allow to generalize the findings to social memories in general. As the manuscript stands, the authors can only conclude as to the importance of this circuit for the memory of the mother. Developmental memory implies the memory of familiar kin as well.

The in vivo ephys section (Figure 3) is interesting but even more minimalistic and it is unclear how abGCs projection to CA2 can contribute to SWR and theta-gamma PAC. In figure 1, the authors suggest that abGCs project preferentially to PV+ neurons in CA2. At minima, the authors should discuss how the abGCs to PV+ neurons to CA2 pyramidal neurons circuit can facilitate SWR and theta-gamma PAC.

Finally, proposing a function for 4-6-week-old abGCs projecting to CA2 begs two questions: What are abGCs doing once they mature further and more generally, what is the function of the DG to CA2 projection? It would be interesting for the authors to comment on these questions in the discussion.

Revision:

The authors have followed my recommendations except for the ones suggesting new experiments. As a result, the clarity of the manuscript and the links between evidence and claims have improved by the message is quite reduced. Many important questions remain open such as: What makes mother's memories so special they require the abGC projection to CA2 unlike other types of social memories? Do abGCs truly connect CA2 PV+ interneurons and how does this connection shape sharp-wave ripples in CA2?

Reviewer #1 (Public Review):

Summary:

In this study, Diana et al. present a Monte Carlo-based method to perform spike inference from calcium imaging data. A particular strength of their approach is that they can estimate not only averages but also uncertainties of the modeled process. The authors then focus on the quantification of spike time uncertainties in simulated data and in data recorded with a high sampling rate in cerebellar slices with GCaMP8f.

Strengths:

- The authors provide a solid groundwork for sequential Monte Carlo-based spike inference, which extends previous work of Pnevmatikakis et al., Greenberg et al., and others.

- The integration of two states (silence vs. burst firing) seems to improve the performance of the model.

- The acquisition of a GCaMP8f dataset in the cerebellum is useful and helps make the point that high spike time inference precision is possible under certain conditions.

Weaknesses:

- The algorithm is designed to predict single spike times. Currently, it is not benchmarked against other algorithms in terms of single spike precision and spike time errors. A benchmarking with the most recent other SMC model and another good model focused on single spike outputs (e.g., MLSpike) would be useful to have.

- Some of the analyses and benchmarks seem too cursory, and the reporting simply consists of a visual impression of results instead of proper analysis and quantification. For example, the authors write "The spike patterns obtained using our method are very similar across trials, showing that PGBAR can reliably detect single-trial action potential-evoked GCaMP8f fluorescence transients." This is a highly qualitative statement, just based on the (subjective) visual impression of a plot. Similarly, the authors write "we could reliably identify the two spikes in each trial", but this claim is not supported by quantification or a figure, as far as I can see. The authors write "but the trade-off between temporal accuracy, SNR and sampling frequency must be considered", but they don't discuss these trade-offs systematically.

- It has been shown several times from experimental data that spike inference with single spike resolution does not work well (Huang et al. eLife, 2021; Rupprecht et al., Nature Neuroscience, 2021) in general. This limitation should be discussed with respect to the applicability of the proposed algorithm for standard population calcium imaging data.

- Several analyses are based on artificial, simulated data with simplifying assumptions. Ever since Theis et al., Neuron, 2016, it has been known that artificially generated ground truth data should not be used as the primary means to evaluate spike inference algorithms. It would have been informative if the authors had used either the CASCADE dataset or their cerebellum dataset for more detailed analyses, in particular of single spike time precision.

- In its current state, the sum of the current weaknesses makes the suggested method, while interesting for experts, rather unattractive for experimentalists who want to perform spike inference on their recorded calcium imaging data.

Other comments:

- One of the key features of the SMC model is the assumption of two states (bursting vs. non-bursting). However, while it seems clear that this approach is helpful, it is not clear where this idea comes from, from an observation of the data or another concept.

- Another SMC algorithm (Greenberg et al., 2018) stated that the fitted parameters showed some degeneracy, resulting in ambiguous fitting parameters. It would be good to know if this problem was avoided by the authors.

Reviewer #2 (Public Review):

Summary:

Methods to infer action potentials from fluorescence-based measurements of intracellular calcium dynamics are important for optical measurements of activity across large populations of neurons. The variety of existing methods can be separated into two broad classes: a) model-independent approaches that are trained on ground truth datasets (e.g., deep networks), and b) approaches based on a model of the processes that link action potentials to calcium signals. Models usually contain parameters describing biophysical variables, such as rate constants of the calcium dynamics and features of the calcium indicator. The method presented here, PGBAR, is model-based and uses a Bayesian approach. A novelty of PGBAR is that static parameters and state variables are jointly estimated using particle Gibbs sampling, a sequential Monte Carlo technique that can efficiently sample the latent embedding space.

Strengths:

A main strength of PGBAR is that it provides probability distributions rather than point estimates of spike times. This is different from most other methods and may be an important feature in cases when estimates of uncertainty are desired. Another important feature of PGBAR is that it estimates not only the state variable representing spiking activity but also other variables such as baseline fluctuations and stationary model variables, in a joint process. PGBAR can therefore provide more information than various other methods. The information in the GitHub repository is well-organized.

Weaknesses:

On the other hand, the accuracy of spike train reconstructions is not higher than that of other model-based approaches, and clearly lower than the accuracy of a model-independent approach based on a deep network. The authors demonstrate convincingly that PGBAR can resolve inter-spike intervals in the range of 5 ms using fluorescence data obtained with a very fast genetically encoded calcium indicator at very high sampling rates (line scans at >= 1 kHz). It would be interesting to more systematically compare the performance of PGBAR to other methods in this regime of high temporal resolution, which has not been explored much.