Reviewer #2 (Public review):

Summary:

Price et al. present new work providing insight into the function and mechanisms of mitochondrial-derived compartments (MDCs) in yeast. The Hughes lab previously established that these large ~micron-sized structures are formed under a variety of conditions including amino acid stress (rapamycin, conA, cycloheximide), alterations in mitochondrial metabolites and lipids, or acute expression of specific outer membrane proteins. These stressors lead to the sequestration of outer membrane proteins (that can include mistargeted inner membrane proteins) that extend or tubulate into large multilamellar structures that ultimately target the vacuole in an ATG5/Dnm1 dependent autophagy related pathway for degradation. Initially reported in aging yeast a decade ago, it has now been accepted as a mechanism to remove excess mitochondrial proteins as a pathway distinct from mitophagy or the extraction of stalled precursors from the import translocon.

In this study, the authors examined additional metabolic transitions they suspected would drive increased mitochondrial protein expression and promote MDC formation. Indeed, they show that glucose-restricted conditions (or a switch to galactose or incubation with 2DG) induced MDCs within 2 hours. This correlated with increased transcription/translation of mitochondrial precursors porin and OM45. Similar results were seen with osmotic shock, a process previously shown to induce mitochondrial gene expression. The metabolic or osmotic shift was shown to activate a yeast AMPK-type kinase called Snf1, which phosphorylates a key substrate Mig1 - an established repressor of mitochondrial gene expression. Loss of these pathways abolished the generation of MDCs under these conditions. As the key novel finding in the study, the authors explored the relationship/requirement for Snf1 and Mig1 using multiple approaches in different backgrounds and employing auxin-inducible degron tools for acute depletion. These data further support the hypothesis that excess mitochondrial outer membrane proteins result in MDC formation to facilitate their removal, at least transiently until the import machinery can adapt to the increased import demand. To test this more directly, they generated an inducible yeast strain to express a canonical transcription factor Hap4 that induces mitochondrial gene expression. In this system, induction of Hap4 expression also resulted in MDC formation. While not all previously reported MDC inducers act through Snf1/Mig1, the common feature is the transcriptional induction of mitochondrial protein expression.

Strengths:

The important aspect of this work is that the authors dissected the transcriptional signaling pathway that induces MDCs in a much more physiological metabolic transition, which complements the more common use of chemical compounds. They had previously shown that overexpression of individual outer membrane proteins could lead to MDCs, but here the Hap4 expression offers a new condition to show that the canonical induction of mitochondrial biogenesis leads to MDC shedding. Overall, the data are of high quality, the findings are clear, and the work provides important new insights into the regulation of MDC formation.

Weaknesses:

There are a few points that should be addressed.

(1) MDCs are almost exclusively monitored through GFP-tagged TOM70, and the authors do not show the inclusion of any endogenous cargo. The evidence for their fate in the vacuole is through the appearance of cleaved, free GFP after 6 hours that is dependent on ATG5, Dnm1, Pep4, etc. Can the authors demonstrate the appearance of MDCs without expressing any GFP tags and instead monitor known outer membrane cargoes? In the case of Hap4 expression, the proteomics identifies some very highly induced mitochondrial proteins, and there surely must be some with antibodies that can detect the protein by IF and Western blot.

(2) There is a very unexpected ~10X increased in a sporulation factor SPO21 upon induction of Hap4. I see no evidence of sporulation, and it's not long enough for stationary phase. Is the increased mitochondrial biogenesis driving a specific metabolic state of these cells that is signaling to other biology?

(3) It is important to understand the kinetics and stoichiometry of outer membrane loading that drives MDCs, and their transit to the vacuole. This is why it would be highly informative to monitor some endogenous cargoes (previous point). In the review the authors cite (NRMBC, Pfanner lab 2019), it was stated that the import machinery is not generally increased upon metabolic induction of mitochondrial gene expression. Therefore, (pre-MDCs) the field concluded that the import machinery has a very high capacity for the rapid biogenesis of newly synthesized proteins, along with regulation through the phosphorylation of import receptors (ie; the work of Meisenger). Consistent with this, the Hap1 proteomics did not show any increases in the core import machinery, while ETC subunits and a large swath of mitochondrial proteins were elevated over 2-fold (I looked carefully through the Excel sheet). Since MDCs are induced transiently about 2 hours after glucose deprivation, and fully dependent on de-repression of Mig1, the authors are right to imply that this is coupled to the import of newly synthesized proteins.

However, it seems to me that MDCs are being formed at very early stages of mitochondrial protein expression, not after they have necessarily "overloaded" the outer membrane. The Hap4 proteomics after 3.5hr of induction would suggest that the bulk of the mitochondrial proteins have been successfully inserted (no import failure) and are likely already functional (metabolizing). I'm trying to understand the percentage of the proteins that would be incorporated within MDCs, as the mitochondria appear to handle the bulk of their newly inserted proteins without issue. How can the authors adapt their "free GFP" assay to understand the stoichiometry of the transport of endogenous, newly imported outer membrane proteins to the vacuole?

(4) As a last theoretical point for discussion: Can the authors exclude that MDCs are not functional or play a signaling role? Given the emerging work on SPOTs (Lena Pernas), and from the new evidence from Craig Thompson's lab that there can be very specific functional mitochondria (oxidizing vs reducing), it is possible that MDCs are not simply there to be degraded. They last at least 3 hours, which is a long time for yeast (budding cycle 90 min, 3 hours in glucose deprivation). Taking the data presented here very objectively, there is no direct evidence that the cargoes within MDVs reflect any failure to import, or that they are damaged in any way. The deletions of Tom70/71 have way too many pleotropic effects and essentially demonstrate only that the MDC cargoes came from the mitochondria. It could be helpful if the discussion also positioned these MDC mechanisms within the context of other aspects of selective mitochondrial-related compartments that have been emerging in the literature.

Reviewer #2 (Public review):

The manuscript describes a numerical analysis of the domains of the T. cruzi cell surface containing different proteins. It has the potential to be of great interest.

I do not have the expertise necessary to comment on the image collection or analysis.

I have one concern: the amount of manipulation of the cells prior to fixation; these were clearly stated in the methods, which is good.

My concern is whether these manipulations prior to fixation alter the observations. The 'Labelling sialic acid acceptors' involves >6 centrifugations and >90 minutes incubation in PBS prior to fixation, and the 'immunostaining' protocol involves cells 'extensively washed with PBS' prior to fixation. I would like to suggest that the authors do controls in which they compare the pattern of anti-SAPA staining under four conditions.

(1) Cells fixed in culture by the addition of paraformaldehyde to 4%, followed by blocking and PBS washes.

(2) Cells fixed in culture by the addition of paraformaldehyde to 4% and glutaraldehyde to 0.2% followed by blocking and PBS washes.

(3) Cells fixed by the 'labelling sialic acid acceptors' protocol.

(4) Cells fixed by the 'immunostaining protocol'.

Reviewer #2 (Public review):

Summary:

In the submitted manuscript, Akter et al use a series of ferroptosis inhibitors in mesenchymal-like ovarian cancer cells and discover that the ferroptosis inducers induce cell death that is inhibited by pyroptosis inhibitors, namely YVAD-fmk and disulfiram, which inhibit pore formation by gasdermin D (GSDMD). Remarkably, the authors also saw the release of IL-1β in response to ferroptosis inducers. Unexpectedly, they did not observe the involvement of caspase-1 but rather observed that caspase-5 was activated in response to the ferroptosis inducers. Moreover, they found that caspase-5 directly cleaves GSDME in response to the ferroptosis inducers, establishing CASP5/GSDME as downstream executors of ferroptosis.

Strengths:

These findings are interesting because only CASP1 is known to induce IL-1β maturation, and their data suggest that CASP5 rather than CASP1, is responsible for IL-1β activation in the context of ferroptosis inducers. Notably, CASP3 is the only caspase reported to be able to cleave GSDME, so the identification of CASP5 as a driver of ferroptosis in this context is a significant finding. They genetically show that loss of CASP5 and GSDME knockdown inhibits cell death in response to the ferroptosis inducers ML162 and Erastin, which is evidence that they play a role in this context.

Weaknesses:

The major findings in this paper are interesting, but the data presented do not robustly support the claims made in this paper. For example, they claim that CASP5 is responsible for the activation of GSDME by cleaving it directly to induce cell death. They try to rule out the involvement of CASP1, ASC, and CASP4 using siRNA targeting these genes, but the knockdowns are incomplete, and the loading controls are inconsistent. They also claim they do not see GSDMD or CASP3 cleavage and activation but use negative data to make that claim. It is unclear if the antibodies used can detect cleaved GSDMD or CASP3 as they do not include a positive control to show that they can indeed detect these activation events if they were occurring. This needs to happen in the same experiment - they need to show in the same experiment with the same lysates that they can detect CASP5, GSDME and IL-1β activation but not CASP1, GSDMD, CASP4, or CASP3 activation. Of course, they should include agonists for positive controls of CASP1, CASP4 and GSDMD activation, which are lacking in the current manuscript.

Notably, the major evidence supporting a direct role for CASP5 cleavage of GSDME is one Coomassie gel using recombinant CASP5 and GSDME, but there were too many non-specific bands, and the full-length uncleaved protein could not be detected even in the untreated lanes. The authors need to show a gel where the protein can easily be identified and should also include a positive control protein like GSDMD to show the relative cleavage efficiency of GSDME compared to a known substrate. It would also be great to compare this to CASP3-mediated cleavage of GSDME. With recombinant proteins, calculating the catalytic efficiencies would be the best way to ascertain if this is biologically similar to other known substrates.

The way that ferroptosis is defined, it is caspase-independent, and pyroptosis is defined as gasdermin-mediated cell death. Given that these agents lead to activation of CASP5/GSDME, it would be more accurate to say that these ferroptosis inducers also induce CASP5/GSDME-dependent pyroptosis, as opposed to them being the executors of ferroptosis. This can be a distinct mechanism/pathway from the ferroptosis pathway, as multiple cell death pathways can be initiated in cells. Consistent with this, ferrostatin-1 also inhibited cell death, likely due to inhibition of the ferroptosis signaling cascade. It is unclear if this pathway is upstream of the caspases. How these ferroptosis triggers selectively activate CASP5 and not CASP4 to induce GSDME cleavage is a major unresolved question. Notably, it is also unclear if this biology is specific to the mesenchymal-like cells used in this study or if it expands to other cells.

Reviewer #2 (Public review):

This study examines the evolutionary context of the emergence of human speech. The authors address the widely held hypothesis that the expansion of the human vocal space, resulting from modifications of the vocal tract, was a key prerequisite for the evolution of spoken language.

To test this hypothesis, the authors quantified the acoustic space of human speech, non-linguistic vocalizations, and musical vocalizations and compared it with that of nonhuman primates, chimpanzees, bonobos, and chacma baboons.

The authors found that speech and song occupied significantly less volume in the acoustic space than human non-linguistic vocalizations. In addition, the acoustic-feature volume of speech and song was not statistically distinct from that of non-human primates. Accordingly, the authors conclude that the evolution of human speech did not depend on an expansion of the human vocal acoustic space.

I find the analysis presented in this manuscript highly convincing. It is conducted at a contemporary scientific standard, and the results provide strong support for the authors' conclusions. I particularly appreciate that the authors explicitly discuss the limitations of their approach. For example, they acknowledge that MFCCs cannot capture all aspects of acoustic structure.

I have only three minor comments:

First, the authors may wish to briefly summarize the main findings of the study by Anikin et al., as it represents the central reference for the present work. A concise summary in two or three sentences would help readers who are not familiar with that study.

Second, I would appreciate a brief explanation of why the authors chose this particular statistical approach.

Third, the authors could briefly mention that the Chacma baboon dataset provides a very comprehensive representation of the vocal repertoire of this species, although a small number of rare vocalizations are not included. I am not sure whether a similar limitation also applies to the chimpanzee and bonobo datasets, but if so, it would be useful to mention this as well.

Reviewer #2 (Public review):

Summary:

The aim of the authors was to measure starvation-induced and basal autophagy in vivo across several tissues and developmental stages. For this, they developed a novel mouse model expressing the GFP-LC3-RFP reporter. They also aimed to provide a more high-throughput method for autophagy flux measurements than assessment by imaging and developed an assay based on a microplate reader.

Strengths:

(1) Good validation of the mouse model. The knock-in strategy is well explained and illustrated.

(2) The model has potential to be applied to a wide range of research questions. The Cre-dependent expression allows for customization of KO timing, which will be beneficial in developmental studies.

(3) The authors presented consistent findings using two different methods to quantify autophagy, strengthening the robustness of their results.

(4) The authors demonstrated the validity of the high-throughput method (microplate reader).

Weaknesses:

(1) The comparison of neuronal populations in different areas of the brain is not ideal. In the cerebellum, Purkinje cells were chosen, which are rare and not representative of this tissue, as well as functionally very different from the neurons in the hippocampus and cortex that they were compared to.

(2) The explanation of the GFP-LC3-RFP construct and specifically if/how autophagosome formation can be measured and distinguished from flux could be clearer.

Conclusion:

The work presented is thorough, and the authors achieved their goals for this study. The effort used to further investigate unexpectedly high basal levels of autophagy in the brain is well appreciated and adds value to this paper. The conclusions of the authors are mostly very well supported by the data provided. The well-structured description of the results, along with clear figures, allows the reader to comprehend the authors' reasoning in reaching their conclusions.

The presented mouse model has great potential for a lasting positive impact on the research field of in vivo study of autophagy. The method of utilizing a microplate reader will also benefit future research where semi-high throughput is an advantage. Together, the information provided in this study not only presents new methodology that will allow the investigation of new research questions, but also provides novel information about in vivo autophagy flux at the selected developmental stages that opens up new follow-up research questions.

EP.99 故事线A: 预计 2026 年底达到 1000-1200 亿年化收入，对应的 IPO 估值预期超过 2 万亿美元——这将是历史上规模最大的 IPO。AI 公司的财务规模正在超越大多数传统行业巨头，速度令人咋舌。

Reviewer #2 (Public review):

In this study, Serrano et al. employed a combination of cell biological and molecular approaches to investigate the localization and regulation of Casein Kinase CK1 during the cell cycle using U20S cells. They show that CK1 dynamically localizes between the centrosomes and the nucleus but can be sequestered away from the centrosomes upon overexpression of its binding partner PER2. They provide evidence that CK1 WT but not a phospho-null mutant strongly accumulates in a hyperphosphorylated form upon inhibition of phosphatases (using Calyculin and Okadaic Acid) and thus conclude that CK1 tail phosphorylation protects the kinase from degradation. Using synchronized cells, they show that CK1 accumulates unphosphorylated in S-phase (APC/Cdh1 inactive) but phosphorylated at the G2-M transition. Immunostaining shows that CK1 localizes to the centrosomes during mitosis.

The manuscript has improved overall, but some sections are still inconclusive and require clarification.

Major comments:

Figure 1 is inconclusive. CK1 nuclear staining is highly similar in untreated cells and in cells treated with CHX + PF670462. The reduction in centrosomal staining in these cells is barely significant. However, the authors draw very strong conclusions from these data sets. In panel B, the cells appear to have been fixed incorrectly, and the anti-PCNT shows a strong background signal. Not convinced that immunofluorescence is the best approach to look at protein dynamics in vivo.

In Figure 2, panel B, the authors should co-stain the centrosomes of cells that co-express CRY1 and CK1, as some of these dots may represent the centrosomes.

Figures 3B, please provide information on the non-phosphorylable CK1a mutant (it is mentioned as a variant in which all serine and threonine residues in the C-terminal tail were replaced by alanine). Specify the number of sites mutated and their exact position. Is this non-phosphorylable CK1a version catalytically active? Treatment of samples with inactivated PPase should be used as a control.

Strengths:

The authors reveal that the activity and abundance of dephosphorylated and phosphorylated CK1δ are regulated in a cell cycle-dependent manner. This suggests that these different pools are associated with distinct physiological functions.

Weaknesses:

Unfortunately, some of the data are inconclusive, and there is no data/information linking the cell cycle regulation of CK1δ to its function during the cell cycle.

Reviewer #2 (Public review):

This study focuses on revealing the essential divergent function of the Acyl Carrier protein (ACP) in the deadliest human malaria parasite, Plasmodium falciparum. More precisely, using inducible KO, cellular and biochemical approaches, the authors determined that instead of a canonical role for ACP allowing the de novo synthesis of fatty acids in the apicoplast (essential relict plastid) of the parasite, the enzyme couples with pyruvate kinase II to generate nucleoside triphosphate to maintain parasite survival during blood stages. The study is novel, well-designed, providing interesting new data on Plasmodium and apicomplexa biology. The results convincingly support the major claim of the study. However, it is currently incomplete to support some claims on the essentiality of some apicoplast pathways.

In this study, Geher et al. focused on deciphering the role of the Acyl Carrier Protein (ACP) present in the relict non-photosynthetic plastid, i.e. the apicoplast of the most lethal human malaria parasite, Plasmodium falciparum. More particularly, they determined an essential function of ACP independent of its usual/typical function as the central protein for the normal function of the apicoplast Type II fatty acid synthesis (FASII) pathway. Rather, the protein seems to associate with the apicoplast Pyruvate Kinase II, together generating an essential nucleoside triphosphate (NTPs) source to fuel the apicoplast and parasite survival instead.

By generating a TetR-DOZY-based inducible KD line for ACP, they confirmed that the protein is indeed essential to maintain apicoplast integrity and parasite survival during asexual blood stages, as previously predicted and experimentally shown. They showed that ACP requires a biochemical modification, typically activating the protein for its function in the FASII pathway, i.e. binding of the 4-PP group by holoACP synthase. Then, they showed that the other enzymes of the FASII pathway are likely dispensable during the blood stage, as they were able to generate a KO line of the first enzyme of the pathway, FabD (which was predicted to be essential in P. falciparum). Based on a cell culture approach in a controlled culture medium, they further claimed that, unlike current evidence-based hypotheses, the FASII pathway (and thus a potentially FASII-linked ACP) has no role/activity during blood stages. Using a proximity biotinylation approach, they determined that ACP associates with the apicoplast pyruvate Kinase II (PKII), previously shown to generate NTPs in the apicoplast for energy and DNA/RNA maintenance (Xia et al. 2019), and not to fuel the FASII pathway as its main function in blood stages. Finally, they showed that the disruption of ACP induces the reduction of the presence/content in PKII in the parasite, as well as the drastic reduction of the apicoplast DNA and RNA content. Together, they concluded that the main function of ACP is indeed the NTP formation via its association with PKII, rather than its canonical role for the generation of fatty acids in the apicoplast.

This study is novel and focuses on a topic of particular interest in malaria biology, but also for most of the apicomplexa-related diseases, and beyond for plastid bearing orgnaisms and this unusual role for ACP. The study is well thought out with proper biochemical approaches that convincingly point to this association of ACP with PKII for NTP synthesis as a major function during P. falciparum blood stages.

Reviewer #2 (Public review):

Summary:

In the manuscript "Primordial Cardiomyocytes orchestrate myocardial morphogenesis and vascularization but are dispensable for regeneration", Sun et al. identify a novel marker of primordial cardiomyocytes and use it to visualize and ablate the population during development and regeneration. The role of the primordial layer has not been investigated because the tools to manipulate this population have not existed. The manuscript is straightforward, easy to understand, and addresses an important question that has not been explored.

While the manuscript provides important insights into the role of primordial CMs, backed by a convincing methodology, the authors should clarify their requirements for heart development and maturation. Specifically, is the primordial layer required for the fish to survive? Do primordial CMs regenerate when ablated during development, and do the defects observed (in trabecular and compact CMs and coronary vessels) resolve after 10 days post-treatment when they were detected?

Strengths:

The major strengths are the identification of a marker that enables manipulation of primordial cardiomyocytes and the tools generated by the team.

Weaknesses:

The major weakness is not considering the longer-term consequences of primordial layer ablation during development, as it is unclear whether the animals succumb to the acute cardiac defects observed or fully recover.

Reviewer #2 (Public review):

Summary:

As a member of DspB subfamily, PRRT2 is predominantly expressed in CNS and has been associated with various paroxysmal neurological disorders. Previous studies have shown that PRRT2 interacts with Nav and Cav channels, modulating channel properties and neuronal excitability.

In this manuscript, Lu et al. demonstrate that PRRT2 is a potent regulator of Nav channel slow inactivation, promoting the development of Nav slow inactivation and impeding the recovery from slow inactivation. This effect is highly conserved in PRRT2s across species as well as among DspB family members (TRARG1 and TMEM233). The authors further confirmed the interaction between Nav channels and PRRT2 in heterologous expression systems as well as in Prrt2-V5 knock-in mice. Prrt2-mutant mice, which lack PRRT2 expression, require lower stimulation thresholds for evoking after-discharges when compared with WT mice.

Overall, this is a well-executed and methodologically comprehensive study. This work offers valuable insight into the physiological functions of PRRT2 and reveals a potential pathogenic mechanism underlying PRRT2-associated neurological disorders.

The revised manuscript has addressed most of the concerns raised by the reviewers and has been substantially strengthened, although I still have several concerns regarding the discussion section.

Strengths:

(1) Overall, this is a well-executed and methodologically comprehensive study. The electrophysiological data strongly support the conclusion that PRRT2 is a potent regulator of Nav channel slow inactivation. The observation that this regulation is conserved in PRRT2 across species and among DspB family members raises the possibility that altered regulation of Nav channels may also contribute to the pathogenesis of TRARG1- or TMEM233-associated disorders.

(2) Co-immunoprecipitation assay performed using brain tissue from genetically modified Prrt2-V5 knock-in mice provides convincing in vivo evidence for the interaction between PRRT2 and Nav1.2 channels.

(3) Prrt2-V5 KI mice show markedly reduced PRRT2 protein expression and display phenotypes similar to those observed in Prrt2-mutant mice, supporting an important role of PRRT2 in regulating neuronal and network excitability.

Weaknesses:

(1) Nav1.6 is also highly expressed in cortical neurons and is widely regarded as a major contributor to action potential initiation and sustained high-frequency firing. Given that PRRT2 similarly regulates the fast and slow inactivation of Nav1.6 and Nav1.2 channels, the potential contribution of Nav1.6 regulation to neuronal and network excitability should be discussed.

(2) Slow inactivation is generally considered to develop over timescales ranging from hundreds of milliseconds to seconds or longer. Therefore, the statement in Discussion (Page 13, line 381-382) that "slow inactivation develops on a timescale of tens of milliseconds to seconds" may not accurately reflect the conventional kinetic definition of slow inactivation and should be clarified.

(3) Page 14, line 417-430: "question about how Nav channel slow inactivation is regulated in cells that do not express PRRT2".<br /> PRRT2 is unlikely to be the sole regulator of Nav channel slow inactivation. Other molecules and signaling pathways may regulate Nav channel and contribute to neuronal excitability. In addition, neuronal excitability can also be regulated through modulating other Nav properties, such as long-term inactivation or slow recovery from inactivation, as well as through modulating the activity of other ion channels, for example, Kv7.2 and Kv7.3 channels. Therefore, PRRT2-negative cells may utilize alternative mechanisms to fine-tune neuronal excitability. In its current form, this paragraph somewhat overstates the role of PRRT2 and would benefit from a more balanced discussion.

(4) Page 50, Figure 7-figure supplement 2: It would be helpful to include representative traces of the 1st and the last (20th) compound APs in panels B and C.

Reviewer #2 (Public review):

Summary:

In this paper, the authors describe the results of a longitudinal study of pertussis infection in mother/infant dyads in Lusaka, Zambia. Unlike many past studies, the authors assessed the infection status of individuals independently of whether they were symptomatic for a respiratory infection. As a result, this work represents one of the first studies specifically designed to assess asymptomatic transmission of pertussis. Using qPCR, the authors find strong evidence for the role of asymptomatic transmission from mothers to infants and also evidence for long-term bacterial carriage. This work represents an important contribution to our understanding of the global burden of pertussis. Also, it highlights the still under-appreciated role of asymptomatic transmission across many infectious diseases (including vaccine-preventable ones).

Strengths:

Unlike many past studies, the authors assessed the infection status of individuals independently of whether they were symptomatic for a respiratory infection. As a result, this work represents one of the first studies specifically designed to assess asymptomatic transmission of pertussis. Using qPCR, the authors find strong evidence for the role of asymptomatic transmission from mothers to infants and also evidence for long-term bacterial carriage.

Comments on revised version:

I appreciate the authors' attention to my comments during the revision process and still believe that their work represents an important contribution to our understanding of pertussis epidemiology. In most cases, the authors have done a thorough job of either addressing or responding to my comments. However, I do not believe the authors engaged sufficiently with two of the queries raised in my previous round of comments. The two queries were about the vaccination status of the mothers and engagement with literature on asymptomatic transmission. I still think they matter and ask the authors to consider them again.

I do not think the authors can rule out two alternative explanations: (1) recent introduction of pertussis and low vaccination coverage amongst study mothers, or (2) recent introduction of a breakthrough strain (either w.r.t. the vaccine or prior infection) and higher vaccination coverage/infection-derived immunity amongst study mothers. Depending on which mechanism was mostly driving the observed patterns in Zambia, i.e.,

a. long-running, widespread, unreported transmission;<br /> b. transmission started recently, and vaccination was low amongst study mothers;<br /> c. a breakthrough strain is causing the current rise (here we'd still want to know about vaccination status); and<br /> d. something else that I have not considered

would have implications for how the results are interpreted, and potentially far-reaching implications for the broader pertussis community. All of that is to say, I think the authors were too quick to dismiss these concerns (even if they disagree with my assertions).

In their reply, the authors largely dismissed concerns about not knowing the mother's vaccination status, stating in their reply that, "our findings strongly suggest ongoing pertussis transmission in this population. Based on this, we expect that mothers in our study who were not vaccinated would likely have some degree of infection-derived immunity."

However, they also stated that, "Zambia offers an evocative example of pertussis surveillance, where no cases have appeared in official WHO reports since 2009" and "As we noted above (and now address in our Discussion), widespread genomic surveillance and microbiological characterization of pertussis are sorely lacking across Africa."

I don't disagree with the authors' conclusion that pertussis is clearly spreading in Zambia. I also don't disagree that there's clearly evidence for minimally symptomatic, infectious mothers spreading infections to children. Both of these findings matter for Zambia and for our broader understanding of pertussis. However, I don't see how the authors can so confidently conclude that low vaccination rates, coupled with a recent introduction, high vaccination rates, coupled with a breakthrough strain, or high infection-derived immunity, coupled with a breakthrough strain, couldn't be what's driving the increase. The authors do hedge in places and also state in the discussion that their findings don't line up with expectations related to WP/infection-derived immunity, "This corresponds to a mean return frequency of one infection per 14.8 years, which is much shorter than the presumed duration of immunity from natural infection or the whole-cell pertussis vaccination used in Zambia (70, 71)." But, my read of the paper is that the authors are pushing way to ward for a preferred hypothesis that is not more favored than other alternatives.

Secondly, I asked about placing this work in the context of other studies on asymptomatic transmission, but realize that I did not list any specific papers. Two worth considering are Warfel et al. 2014 and Althouse and Scarpino 2015. Restating for the editor, the Warfel study found that WP facilitated rapid clearance in a non-human primate experimental infection study (admittedly with small sample sizes and many other caveats). Many took that as evidence that WP would also block transmission (admittedly experiments Warfel did not run). If the mechanism underlying the results in Zambia is that either WP or natural infection does not block transmission (in the absence of a breakthrough strain), that would upend many of the assumptions in pertussis research. While not incompatible with the Warfel et al. results, it would negate most of the importance of their finding that WP blocked transmission. From what I can see, the authors do not even cite Warfel et al. 2014, which is a serious gap regardless of whether the authors agree or disagree with the findings. A quick sidebar, the authors seem to duplicate Craig et al. 2020 10.1093/cid/ciz531, listing it as both citation 9 and 38.

In Althouse and Scarpino, they found evidence of a rise in asymptomatic/underreported/subclinical transmission following the switch from WP to AP. While not as directly relevant to the current study as the Warfel paper (so I leave it to the authors to decide whether citing this paper is important), Althouse and Scarpino discuss asymptomatic transmission at length and also assume that WP conferred strong protection against transmission, so their results (along with dozens and dozens of other studies assuming similar WP/infection-induced immunity protection and durability) would also need to be reinterpreted in the context of this study. The authors should engage with the implication of their results in the context of past modeling studies and what we think we know about vaccine-/infection-derived immunity.

Going back to my earlier points, unvaccinated mothers and the recent introduction of pertussis, or vaccinated/infection-induced immune mothers with a breakthrough strain, would both explain the current results and be compatible with Warfel et al., Althouse and Scarpino, and a sizable number of other studies. Instead, if transmission from WP- or naturally infected mothers is common (in the absence of a breakthrough strain), that would really change the landscape of pertussis epidemiology. The authors have not convinced me that they can make this conclusion. Hence, why I think it's important that the authors engage more actively with those hypotheses and with relevant debates in the pertussis literature on asymptomatic transmission. I think it's appropriate for the authors to present their preferred hypothesis, but, absent other data, they should also present plausible alternatives that are consistent with past publications.

References:

Althouse, B. M., & Scarpino, S. V. (2015). Asymptomatic transmission and the resurgence of Bordetella pertussis. BMC medicine, 13, 1-12.

Warfel, J. M., Zimmerman, L. I., & Merkel, T. J. (2014). Acellular pertussis vaccines protect against disease but fail to prevent infection and transmission in a nonhuman primate model. Proceedings of the National Academy of Sciences, 111(2), 787-792.

Reviewer #2 (Public review):

Summary:

The authors use an Evolve-and-Resequence approach in Drosophila to study the genomic basis of adaptation to long-term starvation. Replicated selection lines and control populations are sequenced and analyzed to identify signals of selection, which are then related to starvation-related phenotypes. The general experimental design is appropriate, and the combination of genomic and phenotypic data is a clear strength of the study.

Strengths:

The strongest aspect of the work is the experimental evolution framework combined with population genomic inference across replicate populations. The observed parallelism across replicates supports the robustness of at least a subset of the detected selection signals. However, several key methodological details are either unclear or insufficiently justified. In particular, both the maintenance of control populations and demographic assumptions are not fully described, and the treatment of structural variation (e.g., segregating inversions) is not sufficiently addressed. The phenotypic analyses are broadly appropriate and replicated but would benefit from access to raw data.

Weaknesses:

The human ortholog enrichment analysis is an interesting component of the study, but it should be interpreted more cautiously. As currently presented, it is based on correlational signals of differentiation and is therefore sensitive to potential confounding factors. While the analysis may point to intriguing patterns consistent with conserved genetic architecture, the evidence is not sufficient to support strong claims of conserved starvation/malnutrition-related polygenic adaptation in humans. Framing this component more explicitly as exploratory would strengthen the manuscript. In its current form, this analysis is somewhat less conclusive than the experimental evolution results in flies.

Overall, the study provides a useful dataset and a reasonably solid analysis of starvation adaptation in experimental Drosophila populations, but several methodological clarifications and a more balanced framing of the cross-species comparisons would strengthen the manuscript.

Reviewer #2 (Public review):

Summary:

Lee et al. is a comprehensive conservation genomics study that combines a chromosome-level genome assembly (sex-specific, too), population resequencing, coalescent species delimitation, and simulations to reassess the evolutionary status and conservation outlook of the Formosan landlocked salmon, Oncorhynchus formosanus. The authors showed a distinctive genome structure, replete with chromosome fusions and an unusual placement of the sex-determining gene sdY. Across sampling sites, they observed variable levels of genetic diversity, but in a way that was surprising given previous census numbers and conservation history. In particular, the authors report a previously unrecognised native population in Hehuan Creek, and conclude that Hehuan is more resilient to typhoon disturbance than the long-protected Qijiawan population - motivating stream-specific rather than range-wide conservation.

Overall, this is a well-written paper that combines a number of elements that are timely and relevant. It uses state-of-the-art techniques to reach its conclusions and is generally performed to a high standard. It describes a critically endangered species that poses its unique conservation challenges. There are a number of things to like, as well as some substantial shortcomings in this paper.

Strengths:

The genomic resource is excellent. The assembly is well validated (97.3% anchored to 25 scaffolds, 95.7% BUSCO), and the authors generated a separate male assembly specifically to resolve the sex-determining region, allowing XY-shared and Y-specific contigs to be distinguished on coverage rather than inference. This is truly well done, and at a high standard. The synteny evidence for telomere-to-telomere fusions involving at least 14 ancestral chromosomes, against two in O. m. masou, is convincing.

The Hehuan Creek result is the paper's most valuable contribution. Elevated heterozygosity, short and infrequent runs of homozygosity, and private alleles absent from the Qijiawan broodstock are difficult to reconcile with a purely reintroduced origin. The contrast with Luoyewei is a clean and useful cautionary case for hatchery supplementation.

Weaknesses:

(1) The species-rank claim is featured in the abstract, but it is made with any level of rigour in the paper. "New species" appears once, in the abstract (l. 32). The Results conclude only that O. formosanus is a distinct evolutionarily significant unit (ll. 188-191), which itself can be well-justified, but it's far from a taxonomic rank (see author's own ref 10). No species concept is explicitly named anywhere, and the taxon is referred to across the manuscript as a subspecies (l. 68), a "new species" (l. 32), and an ESU (l. 189) in turn.

(2) Gene flow is asserted, not tested, and two divergence estimates disagree twentyfold. The abstract reports "no detectable gene flow for ~50,000 years." That figure is a divergence time from BPP under the A00 model, which contains no migration parameter; a model that cannot fit gene flow cannot report its absence. Separately, Figure 1b shows a split at 1.15-5.09 Mya (Figure 1b), while the ddRAD coalescent places the same split at ~50 kya (Figure 1d). The explanation offered (ll. 417-421, "differing temporal sensitivity of genomic markers") is not a mechanism.

(3) The placement of sdY is unresolved, and the paper's own figures conflict with its text. Figure S10 and Table S6 both make O. formosanus chr13 homologous to O. m. masou chr32, whereas reference 28 - on which the authors rely - places the sdY contig on O. m. masou chr7, whose O. formosanus homologue is chr5 (Table S6). These cannot both be correct, and Figure S10's caption compounds the confusion by attributing chr13 to masou and omitting the chr32 track entirely.

(4) The population-viability model's stated mechanisms are contradicted by the authors' own supplementary tables. The Discussion attributes Qijiawan's vulnerability to "lower juvenile survival, decreased fecundity, and narrower terminal age class representation" (ll. 522-525). Table S10 gives Qijiawan higher age-0 survival (0.202/0.616 vs 0.184/0.615); Table S11 gives it higher fecundity at every reproductive age (7.68/19.27/7.86 vs 6.10/8.95/4.14); Table S9 gives it a broader terminal age class (5.0% vs 0.8% age-3 in November). The only parameter favouring Hehuan is age-1 survival - 0.087 (95% CI 0.000-0.180) versus 0.131 (0.093-0.187) under typhoon, and 0.054 (0.000-0.167) versus 0.087 (0.047-0.149) at baseline. Both Qijiawan intervals include zero and overlap Hehuan's, yet a reported extinction odds ratio of 4.48 rests on this difference.

(5) The two streams were not measured equivalently, and every asymmetry favours the conclusion.

Reviewer #2 (Public review):

In this manuscript, the authors dissect how Gβγ potentiates PLCβ3 signaling in cells. Using engineered crosslinking to stabilize a Gβγ-PLCβ3 complex, single particle cryo-EM, and cell-based functional assays, they identify map multiple putative Gβγ interaction surfaces on PLCβ3, including a previously unrecognized binding mode. Structure-guided mutagenesis supports the functional relevance of these interactions and suggests that Gβγ potentiation is not primarily mediated by PLCβ3 membrane recruitment, but instead enhances PLCβ3 activity after the lipase is already at the membrane.

Previous reconstitution work on membrane surface (Falzone & MacKinnon, 2023) proposed a recruitment/partitioning-centric model in which Gβγ increases PLCβ3 output largely by elevating its membrane surface concentration, whereas Gαq primarily increases catalytic turnover; under those reconstitution conditions, the two inputs can combine approximately multiplicatively. In receptor-driven cellular signaling, however, PLCβ3 is robustly recruited to the plasma membrane upon Gαq activation, which raises the question of whether Gβγ contributes mainly through additional recruitment or through a post-recruitment mechanism once PLCβ3 is already at the membrane.

This manuscript helps address that gap by using membrane-anchored PLCβ3 and complementary cellular readouts to separate "getting PLCβ3 to the membrane" from "boosting activity once PLCβ3 is already there." Their results argue that, in cells, membrane recruitment is largely dominated by Gαq·GTP, while Gβγ can further potentiate PIP2 hydrolysis after membrane association, consistent with a modulatory role at the membrane rather than primary recruitment.

Overall, the work provides a structural and mechanistic framework for Gβγ-PLCβ3 cooperation and helps clarify the basis of Gq pathway amplification.

Comments on revised version.

The authors have reasonably addressed my comments.

Reviewer #2 (Public review):

This manuscript, "Nerve Injury-Induced Protein 2 preserves lysosomal membrane integrity to suppress ferroptosis", identifies a previously unrecognized function of NINJ2 as a regulator of lysosomal membrane integrity and iron homeostasis, thereby suppressing ferroptosis. The authors demonstrate that NINJ2 localizes to lysosomes, interacts with LAMP1, limits lysosomal membrane permeabilization (LMP), stabilizes ferritin, and protects cells from ferroptotic cell death. They further extend these mechanistic findings to human cancer datasets, showing co overexpression and positive correlation of NINJ2 with ferritin genes in iron addicted cancers.

Overall, the study is conceptually interesting, technically solid, and integrates cell biology, iron metabolism, and ferroptosis in a coherent framework. The work expands the functional repertoire of the Ninjurin family beyond plasma membrane rupture and inflammation, which will be of interest to researchers in cell death, lysosome biology, and cancer metabolism.

Strengths:

(1) The identification of NINJ2 as a lysosome-associated protein that suppresses ferroptosis represents a meaningful advance beyond its previously described roles in inflammation, pyroptosis, and tumorigenesis.

(2) The work distinguishes NINJ2 functionally from NINJ1, reinforcing the idea that structurally related Ninjurins have divergent membrane-related roles.

(3) The study presents a logically connected pathway:<br /> NINJ2 loss → LMP → labile iron increase → ferritin degradation → ferroptosis sensitization, which is well supported by the data.

(4) The link between LAMP1, ferritin turnover, and ferroptosis is particularly compelling and timely given recent interest in lysosomal contributions to ferroptotic signaling.

(5) The authors use confocal microscopy, proximity ligation assays, biochemical IPs, iron measurements, protein half-life analyses, ferroptosis assays, and TCGA-based analyses, providing convergent evidence for their model.

(6) Use of two distinct cell lines (MCF7 and Molt4) strengthens generalizability.

(7) The integration of cancer expression datasets linking NINJ2 with ferritin expression in hepatocellular and breast carcinomas enhances translational relevance.

(8) Assigning NINJ2 a lysosomal protective function, distinct from NINJ1-mediated plasma membrane rupture is novel.

(9) Linking NINJ2 to ferroptosis regulation via lysosomal iron handling, rather than canonical GPX4 or system Xc⁻ pathways is also novel, along with proposing a NINJ2-LAMP1-ferritin axis as a buffering mechanism against iron-driven lipid peroxidation.

(10) These insights are not incremental; they reframe how NINJ2 may function at the intersection of membrane biology, iron metabolism, and regulated cell death.

Reviewer #2 (Public review):

Summary:

This study identifies IR20a-expressing gustatory neurons in Drosophila as a multimodal sensory population integrating amino acid (arginine) and low-salt signals through combinatorial IR20a/IR25a/IR76b receptor assemblies. The proposed model of peripheral-level signal integration and synergistic enhancement of feeding preference is potentially significant, as it expands current understanding of gustatory coding beyond single-modality labeled lines.

Strengths:

Overall, the findings are conceptually interesting and suggest a novel framework for multimodal taste integration, but some mechanistic interpretations remain incompletely supported by direct evidence.

Weaknesses:

(1) Although the authors demonstrate co-expression of IR20a, IR25a, and IR76b in the same GRN population, this evidence is insufficient to support the proposed model of distinct receptors coexisting within individual neurons. Additional molecular or structural data would be required to distinguish whether these subunits assemble into complexes.

(2) Given that IR76b has already been established as a sodium/salt sensing channel, the novelty of this study relies on the proposed role of IR20a in conferring multimodal integration and synergy. However, it remains unclear whether this represents a fundamentally new sensory mechanism or a re-interpretation of known IR76b-dependent salt responses in a different neuronal context.

(3) Line 127:<br /> -The statement that there is no overlap between IR20a-GAL4 and GR64f-LexA or GR66a-LexA is not sufficiently supported by the presented imaging data. In particular, the resolution and clarity of the confocal images in Figure 1 appear suboptimal, making it difficult to confidently assess co-localization. The authors are encouraged to provide higher-resolution images or additional quantitative co-localization analysis to substantiate this conclusion.<br /> -In addition, the images shown in Figure 1 F1-F2 suggest possible partial overlap between IR20a and GR66a signals, which appears inconsistent with the authors' statement of no co-expression. This discrepancy should be clarified.

(4) Lines 138-141:<br /> There appears to be a discrepancy between imaging and behavioral data: IR20a is reported as dispensable for arginine-evoked neural responses, yet IR20a mutants show significantly reduced attraction to arginine in behavioral assays. The authors should clarify how behavioral deficits arise in the absence of detectable changes in calcium imaging,

(5) The manuscript proposes that IR20a functions in combination with IR25a to mediate multimodal detection of arginine and low NaCl. However, the specific role of IR25a in this context remains unclear.

(6) The authors report that co-expression of IR20a and IR25a confers synergistic responses to combined arginine and NaCl stimulation, whereas the inclusion of IR76b abolishes this response (Figures 5E-K). This is an intriguing and potentially important finding; however, the mechanistic basis for this suppression is not clearly explained.

(7) The authors propose that IR56b mediates state-dependent modulation of low-salt preference. However, the current data do not clearly distinguish whether IR56b acts as a real nutrient state sensor or just functions as a downstream modulatory component within a broader feeding circuit. Additional evidence linking IR56b activity changes to upstream metabolic state signals would be necessary to support the interpretation that IR56b functions as a primary state sensor.

(8) The manuscript suggests that IR20a and IR56b define two parallel and functionally independent pathways mediating nutrient detection and state-dependent preference, respectively. However, this conclusion is not fully supported by the current dataset. While the two receptors are shown to be expressed in distinct neuronal populations, the possibility of indirect interactions or convergence at downstream circuit nodes has not been excluded. Given that both pathways ultimately influence feeding behavior, it remains possible that they converge at higher-order interneurons or shared neuromodulatory circuits.

(9) In the state-dependent feeding assays (Figure 6), using H2O as a control introduces a severe masking effect. Salt-deprived flies actively suppress pure water intake to avoid osmotic shock, which artificially inflates the Preference Index (P.I.) for salt due to the denominator effect. To cleanly isolate salt preference from the thirst/osmotic drive, the authors will need to utilize an "isosmotic sucrose vs. isosmotic sucrose + salt" paradigm (Jaeger et al., 2018, eLife; Puri et al., 2026, PNAS).

Reviewer #2 (Public review):

Summary:

This review constructs a novel theoretical framework to elucidate incomplete postmenopausal age-related lobular involution (ARLI) in the breast. Differing from the conventional view of persistent lobules as passive residual structures, the work innovatively defines them as an actively maintained senescence-immune reserve niche. It comprehensively integrates multidisciplinary evidence from breast epidemiology, stromal biology, cellular senescence and immune surveillance, as well as cross-tissue research findings, and identifies menopause as a core biological turning point regulating ARLI and relevant breast cancer risk, providing a new theoretical perspective for subsequent breast cancer risk assessment and preventive intervention research.

Strengths:

This study presents an original, logically rigorous, and well-organized research hypothesis. It innovatively breaks through the traditional cognitive perspective of ARLI and adopts a multidisciplinary and cross-tissue analytical approach to sort out relevant biological mechanisms systematically. The proposed theoretical framework is insightful, with good theoretical innovation and potential translational value for guiding breast cancer risk evaluation and targeted prevention strategies.

Weaknesses:

The manuscript currently serves primarily as a conceptual framework rather than a rigorously evidenced synthesis. Its central argument relies heavily on cross-sectional correlations and theoretical analogies to other organ systems, lacking operational definitions for the reserve state in human breast tissue.

Reviewer #2 (Public review):

Summary:

The authors identify KIN-G as an in vitro substrate for phosphorylation by TbPLK and show that several of the in vitro P-ated sites, including T310, overlap with P-ation sites seen in live cells. The authors further show that PLK-mediated P-ation inhibits KIN-G binding to microtubules in vitro, as does a KIN-G-T301D mutant, and that expression of a KIN-G-T301D Phospho-mimic in T. brucei phenocopies KIN-G RNAi knockdowns, producing defects in cell division, morphogenesis of the centrin arm, FAZ and other cellular structures, as well as misplaced cytokinesis furrow.

Understanding cytoskeletal rearrangements that drive cell division in T. brucei is an important and unresolved problem, so the work addresses important questions that are of great interest. PLK and KIN-G have previously been shown to be important for cell division and morphogenesis of cytoskeletal structures that drive cell division in T. brucei. The current work advances our understanding by suggesting a potential mechanism by which PLK and KIN-G might participate, namely through PLK-dependent P-ation to control KIN-G MT binding activity.

Strengths:

The authors use a rigorous combination of biochemistry, phosphoproteomics, cell biology, and mutant analysis to support their conclusion that PLK-mediated P-ation of KIN-G negatively regulates KIN-G microtubule binding and this may explain the observation that a KIN-G T301 phosphomimic mutant blocks cell division and perturbs biogenesis of cytoskeletal structures that drive cell division and morphogenesis. Combining rigorous and informative in vitro studies with mutant analysis in live cells is a great strength. The work is solid and important, though a few pieces are needed to fully connect the in vitro findings with the in vivo observations.

Reviewer #2 (Public review):

Summary:

This is an interesting study that explores how human RPE could be used as a source for new retinal neurons. This is a welcome addition to the field of retinal regeneration, which is currently focused almost exclusively on the regenerative capacity of Müller glia cells. The line of inquiry is firmly rooted in findings from amphibian and embryonic chick model systems and advances a fetal human retina RPE-based screening system as a rich resource for insights into human RPE biology, including as a potential stem cell source.

The authors investigate the potential of fetal human RPE cells to be reprogrammed into retinal neurons using overexpression of pro-neural factors. While this is a critical knowledge gap in the field of retinal regeneration with significant promise for developing regenerative therapies, several methodological concerns impact the interpretation of results. Firstly, while the authors sought to evaluate factors that enhance RPE reprogramming when co-expressed with ASCL1, nearly all co-expression constructs tested failed to achieve appreciable expression of ASCL1, leaving a central hypothesis of this study largely untested (Major concern 1). Second, although the authors were able to detect a cluster of photoreceptor-like cells in their screen, they were unable to identify which reprogramming construct generated this cluster (Major concern 2). Finally, an essential control that definitively demonstrates the value of combinatorial transcription factor reprogramming is missing (Major concern 3).

In summary, the authors establish a valuable new paradigm for culturing and reprogramming fetal human RPE, and even more importantly, demonstrate successful reprogramming to neural fates. However, the discussion and interpretation of results needs to be modified significantly to make it clear that (i) the outcome of many co-expression paradigms remains effectively unknown/untested due to failed over-expression of ASCL1, and that (ii) the reprogramming construct giving rise to photoreceptor-like cells could not be conclusively identified from their initial screen.

Strengths:

(1) Powerful new screening system advanced for exploring the regenerative potential of human fetal RPE cells.

(2) Co-expression vector system for testing additive effects of proneural transcription factors.

Weaknesses:

Major concerns:

(1) The authors executed a screen for combinations of factors that can enhance ASCL1-mediated reprogramming of RPE into retinal neurons. However, the expression level of ASCL1 was remarkably low in virtually all co-expression paradigms (see Figure 3C). Notably, the reprogramming combination with the highest potency (ASCL1 + NEUROD1) was also the one exhibiting the highest level of ASCL1 expression. The "failed" reprogramming of most of the co-expression constructs (ASCL1+LMO1, ASCL1+EZH2, and ASCL1+RAX2) is potentially a false negative resulting from low transgenic expression of ASCL1.

(2) The authors' interpretation is that the overexpression of NeuroD1 and Ascl1 generated a new cluster that expressed markers of photoreceptors such as RXRG and RCVRN (see Figure 3D). However, there does not actually appear to be any overlap between the ASCL1+NEUROD1 cluster (orange dots, left panel) and the cells expressing markers of photoreceptors (yellow/green/purple?/black? dots, right panel; yellow being ASCL1-EZH2, green being ASCL1, purple being ASCL1-and black being control - though color coding here is admittedly somewhat confusing). Thus, the photoreceptor-like cluster of interest actually seems to correspond to gray cells that were unmapped/exposed to an unknown programming cocktail. So, it remains completely unknown which reprogramming construct generated this cluster.

(3) To conclusively establish the additive role of NEUROD1 in reprogramming, it would be prudent to compare ASCL1 + FA directly to ASCL1+NeuroD1+FA. This control was not included but is needed for a more complete interpretation of results.

Biểu đồ phân tán (Scatter Plot) Khái niệm: Biểu diễn tập hợp các điểm dữ liệu "phân tán" trên mặt phẳng tọa độ.

Cách sử dụng: Đánh dấu các điểm bất thường (outliers), có thể thêm đường xu hướng (trendline) hoặc dùng màu sắc/kích thước điểm khác nhau để biểu diễn các nhóm đè lên nhau.

Sử dụng khi nào: Khi muốn khám phá mối quan hệ, mô hình giữa 2 biến liên tục (continuous variables).

Biểu diễn điều gì: Biểu diễn mối tương quan (Correlation), quan hệ và sự tập trung/phân cụm (Clusters/Outliers) giữa 2 biến.

Reviewer #2 (Public review):

Summary:

The authors investigated whether neurofeedback (NFB) training targeting spontaneous gamma oscillations (30-60 Hz) at the parieto-occipital region (Pz electrode) could reduce experimental pain perception. They randomized 88 healthy participants to active or sham NFB groups across two cohorts (44 each). Active NFB consisted of real-time feedback based on participants' own gamma power; sham NFB consisted of the preceding participant's gamma power. Participants completed three ~16-min sessions, and approximately 52% of active NFB participants showed increased gamma power in session 3 and were considered responders. Analyses restricted to these 23 responders (matched with 23 sham controls) showed reduced pain intensity, unpleasantness, and laser-evoked potential (LEP) amplitudes, with a significant negative correlation between gamma power and pain intensity after session 3.

Strengths:

(1) The distinction between spontaneous and stimulus-evoked gamma oscillations in pain processing is theoretically important.

(2) The rationale for targeting spontaneous gamma via NFB is clearly articulated.

(3) The study was sham-controlled, and the blinding was adequate.

(4) The authors commendably ran a second cohort (n=44) with simultaneous posterior neck EMG recording to address the critical concern of muscle artifact contamination of gamma, in response to a previous review

Weaknesses:

(1) The most critical issue is about the exclusion of non-responders from the analysis. I find this problematic, as the reasoning becomes circular (selecting the participants who managed to increased gamma and then asking whether gamma NFB influenced pain), effect sizes are inflated, and the selection itself may introduce biases. For example, the responders may differ from the non-responders with respect to other characteristics (better attention skills, better self-regulation, etc). It would be more principled to present the results for the entire sample and only present the responder analysis as a secondary analysis. In the preregistration, the responder-only analysis was not mentioned.

(2) Another critical point is about the causal claims made in the abstract, introduction, and discussion. Given that the current results provide only correlational evidence in a subsample, the language should be revised to avoid overinterpretation. If the authors can demonstrate a significant mediation effect (NFB group -> gamma change -> pain change), they may be able to argue that increases in gamma activity mediate the observed reduction in pain.

Minor points:

(1) For the sham procedure, the authors used the preceding participant's gamma data for feedback. This raises two questions: How was this handled for the first participant? Did the authors check the discrepancy between actual gamma and presented gamma in the sham NFB group?

(2) Was baseline gamma power comparable between groups?

Reviewer #2 (Public review):

Many insects possess extremely sensitive olfactory systems that can detect chemical signals from distances of several kilometers. For decades, the arms race between bats and insects has served as a prime example of acoustic co-evolution. The auditory adaptations of insects to echolocation have been well documented. Cricket has a multi-sensory predator recognition system with keen olfactory, tactile, and auditory senses. However, whether crickets can use the scent of bats to avoid them remains unknown at present. The authors hypothesized that cricket prey (Loxoblemmus equestris) might eavesdrop on predator bat (Scotophilus kuhlii) VOCs as an early warning. L. equestris is one of the prey species of S. kuhlii, and the authors demonstrated that the body odor of the insectivorous bat S. kuhlii triggers robust avoidance and electrophysiological responses in the cricket L. equestris, and that a single compound, (-)-limonene, is sufficient to elicit this avoidance in the laboratory and suppress calling in the field. Overall, this paper has a complete chain of evidence and should be a highly praised study.

Reviewer #2 (Public review):

Summary:

The authors introduce a K-mer-based method for profiling repeat content within a species, applied here to 1,142 A. thaliana genomes sequenced with short reads. This approach allowed them to bypass the challenges of genome assembly, particularly for repetitive regions, while still quantifying copy number variation. Their analysis identified >50 trans-acting loci regulating repeat abundance, enriched for genes involved in DNA repair, replication, and methylation. They also speculate on the role of selection in shaping genome repeat content, arguing that purifying selection tends to suppress alleles that promote repeat expansion.

The work presents a scalable way to extract meaningful insights from the large quantities of short-read datasets available. However, I have several concerns regarding the methodology, scope of claims, and interpretation of results.

Strengths:

The authors leverage a large dataset, >1100 samples, of A. thaliana. The scale of the study is impressive and clearly bolsters their findings. Additionally, this provides a framework for future, large-scale studies and offers a solid foundation for hypothesis generation. The k-mer-based method is generally practical for large-scale analysis and should be transferable to other datasets. Finally, the authors are commendably upfront about many of the project's limitations.

Weaknesses:

The decision to use k=12 is loosely justified. While the authors performed a sweep of k-mer lengths (from 5-20) and noted computational constraints, the choice is highly dataset-specific. Benchmarking across different k values with additional datasets (especially including other species) would strengthen confidence in the robustness of the method.

All analyses rely exclusively on the TAIR10 reference genome, which is incomplete and known to collapse certain repetitive regions. This dependence raises concerns that some repeats (especially recently expanded or highly variable ones) are systematically undercounted. With improved A. thaliana assemblies now available, testing the method against a more complete reference would alleviate these concerns.

The manuscript's conclusions are framed in very broad terms (e.g., "shaping genome evolution in plants"). However, the study is restricted to a single species, A. thaliana, which may not represent other plants. While the findings may suggest general principles, the claims in the abstract and conclusion should be moderated to reflect the study system more accurately.

The identification of >50 trans-acting loci enriched for DNA repair and replication genes is compelling, but the conclusions remain correlational.

Reviewer #2 (Public review):

Summary:

The authors aimed to determine the molecular mechanisms by which nuclear pore component NPP-3/NUP205 regulates chromosome localization in C. elegans embryos. Previous studies had shown that depletion of NPP-3 caused premature chromosome condensation and movement of chromosomes to the nuclear periphery. Peripheral location of chromosomes is also observed under respiratory stress conditions, suggesting that peripheral chromosome positioning could act as a protective response to stress conditions. How NPP-3 affects chromosome positioning was unknown. Here, the authors conduct a screen to identify factors that promote chromosome relocation to the periphery in npp-3-depleted embryos, identifying an important role for spindle assembly checkpoint components in this process.

Strengths:

Using cytological tools to visualise chromosomes and nuclear envelope markers, the authors show that, in addition to the peripheral location of chromosomes, NPP-3 depletion causes partial rupture of the nuclear envelope and premature chromosome condensation. By systematically co-depleting NPP-3 and factors required for heterochromatin association with nuclear lamina (CEC-4), telomere binding to nuclear envelope (SUN-1 and POT-1), proteins required for the nuclear rupture repair machinery (BAF-1 and LEM-2), kinetochore proteins and components of the spindle assembly checkpoint (SAC) (MDF-1 and MDF-2), the authors convincingly show that SAC components are required for peripheral relocation of chromosomes in absence of NPP-3. The study also provides convincing evidence that peripheral relocation of chromosomes in the absence of NPP-3 has functional implications as it causes transcriptional deregulation and premature relocation of SAC components from the nuclear envelope to chromosomes. Co-depletion of NPP-3 and SAC components accelerates progression through miotic prophase and increases the incidence of defects in chromosome segregation during mitosis. These findings demonstrate that SAC proteins play an important role in regulating chromosome positioning during prophase (at least in the absence of NPP-3) and that they can regulate cell cycle progression at earlier stages than previously thought.

Weaknesses:

The authors also propose that NPP-3 depletion causes DNA damage; however, the evidence presented to support this claim is not as strong as that presented for the effects mentioned above. Also, the premature condensation of chromosomes appears as a clear consequence of NPP-3 depletion, but this intriguing phenotype remains unexplored.

Reviewer #2 (Public review):

Summary:

STX is a non-steroidal, CNS-selective estrogenic compound with neuroprotective effects in stroke and Alzheimer's disease models, but its molecular target has remained unknown for nearly 20 years. In this study, the authors identify VDAC proteins as the direct mitochondrial targets of STX using chemoproteomics, single-cell qPCR, electrophysiology, and metabolic flux analyses. They further show that VDAC2 is the primary functional target in female POMC neurons, linking STX-mediated VDAC modulation to enhanced mitochondrial bioenergetics and neuroprotection.

Strengths:

This study is strengthened by its innovative chemoproteomic approach, in which the authors developed a novel bifunctional STX probe (BF-STX) containing a photo-crosslinkable diazirine group and an alkyne handle to capture transient STX-protein interactions in living cells. The experimental design is further reinforced by rigorous controls, including no-UV negative controls and competition assays with excess unlabeled STX, which provide convincing evidence that VDAC1, VDAC2, and VDAC3 are genuine STX-binding targets rather than nonspecific artifacts. Finally, the authors validate the STX-VDAC interaction using multiple complementary approaches, including chemoproteomics, single-cell qPCR, planar lipid membrane electrophysiology, and Seahorse metabolic flux analyses, providing strong mechanistic support for their conclusions.

Weaknesses:

While the study provides convincing evidence that STX directly modulates VDAC function, several limitations remain. Most experiments were performed in immortalized cell lines rather than primary neurons or in vivo models, limiting their physiological relevance. In addition, the exact structural binding site of STX on VDAC remains unresolved, and no loss-of-function experiments (e.g., VDAC2 knockdown) were performed to establish a direct causal link between VDAC2 and STX's bioenergetic and neuroprotective effects. The non-linear dose-response at higher STX concentrations also requires further investigation.

Reviewer #2 (Public review):

This manuscript addresses an important and timely question in TDP-43 biology by systematically identifying regulators of TDP-43 anisosome formation, with a particular focus on nuclear export via XPO1. Using a combination of unbiased chemical screening, genetic perturbation, and advanced imaging approaches, the authors propose that inhibition of nuclear export modulates the abundance and biophysical properties of TDP-43 anisosomes. They further strengthen their findings by introducing an additional model system, a semi-permeabilized in vitro assay, which provides mechanistic evidence that XPO1 activity prevents anisosome dissolution by retaining nuclear RNAs. The study is conceptually innovative and has potential relevance for neurodegenerative diseases characterized by TDP-43 pathology. Some minor concerns remain, mostly about experimental design of the newly added data.

Strengths:

(1) The study employs an unbiased, hypothesis-free compound screen to identify regulators of TDP-43 anisosome formation, which is a major strength and reduces confirmation bias.

(2) The authors combine chemical and genetic screening approaches, providing orthogonal validation of key pathways and increasing confidence in the biological relevance of top hits.

(3) The focus on biophysical properties of TDP-43 assemblies, assessed through imaging and FRAP, moves beyond simple presence/absence of aggregates and provides mechanistic insight into the biophysical states of TDP-43.

(4) The use of multiple experimental modalities, including live-cell imaging, FRAP, pharmacological perturbation, and transcriptomic analysis, reflects a technically sophisticated and ambitious study design.

(5) The authors attempt to extend findings beyond immortalized cancer cell lines by incorporating organoid models, demonstrating awareness of disease relevance and translational importance.

(6) The authors extend their study by incorporating a semi-permeabilized in vitro system, which provides compelling evidence that inhibition of nuclear export promotes the retention of nuclear anisosomes, an effect driven by the accumulation of nuclear RNAs.

Overall, the manuscript is clearly written and logically structured, making complex experimental workflows accessible and the central hypotheses easy to follow.

Weaknesses:

(1) The manuscript has significantly improved with the revisions. Some experimental procedures and method details, as well has statements remain incompletely described:<br /> a) What is the smear in Figure S1 after VLX treatment?<br /> b) The authors state that "The reduction in TDP-43 signal was not due to protein elimination.", however no data is provided to support that statement.<br /> c) The authors state that "TDP-43 shifts from phase-separated state to a soluble state ...", however no data is provided to support that statement.<br /> d) Why did the authors choose cow lover cytosol for this study?<br /> e) The experimental setup for supplementing with cytosol/ATP/GTP is unclear. A more detailed schematic would be helpful to understand at what stage in the experiment these factors were added. Which step of the protocol was performed at 37 {degree sign}C, which is indicated in the figure schematic but not described in the methods.<br /> f) In the organoid model, the authors mention that they observe similar levels of total TDP-43, however they do not provide quantification. Instead, they provide a graph that shows highly significant changes in nuclear TDP-43, which was not addressed in the text.

Additionally, some questions remain unclear:

(1) The anisosomes induced by ATP/GTP or cytosol are insufficiently characterized. It remains unclear whether these structures correspond to canonical ring-shaped anisosomes, and whether they exhibit dynamic (liquid-like) or more static (gel-like) properties.

(2) The contribution of the cytosol and ATP/GTP supplementation experiments to the overall narrative is unclear. While the findings are intriguing, their interpretation within the context of the study is not well articulated. In particular, the rationale for including cytosol is not sufficiently justified, given that ATP/GTP alone induces a pronounced effect, whereas cytosol alone does not.

(3) The authors should address why endogenous XPO1 does not co-localize with anisosomes, whereas overexpressed XPO1 does. This raises the possibility that the observed co-localization may be an artifact of non-physiological protein levels, which should be discussed.

(4) The iPSC-based model remains insufficiently characterized. While the authors propose that this system recapitulates the accumulation of liquid and solid aggregates resembling anisosomes, it is unclear whether this phenotype is robustly observed and whether KPT treatment effectively modulates it.

(5) The rationale for the selected treatment durations is unclear, and the timing appears inconsistent across experiments (ranging from 3 to 16 hours), including within experiments involving the same compound. This variability should be justified or standardized.

(6) Several figure legends require clarification:<br /> a) In the section stating "Collectively, our results suggest that the stability and dynamics of anisosomes are modulated by XPO1-mediated nuclear export ...", the cited figure appears to be incorrect. This should refer to Figure 5L rather than Figure 5J.<br /> b) Figure 1B: Please specify the number of replicates per concentration, the number of cells analyzed, and the model used for regression analysis. Additionally, the legend indicates a treatment duration of 15 hours, whereas Figure 1A states 24 hours.<br /> c) Figure 2G: The authors state "7 anisosomes per condition," but the graph displays only 4-6 data points. Please clarify what each data point represents.<br /> d) Figures 3B and 3G: Please clarify whether a defined threshold was used to determine a "reduction in anisosome number."<br /> e) Figure 4B: These do not represent biological replicates, as all samples derive from a single cell line; rather, they constitute independent experimental replicates.<br /> f) Figures 5B and 5H: The legend states "n = 3 biological repeats," but the number of data points shown appears higher. Please clarify.<br /> g) Figures 5K, 6C, and 6E: "Mean Fluorescence Intensity (MPI)" should be corrected to "MFI."<br /> h) Figure 6C: Please include the number of cells analyzed and provide relevant statistical measures (e.g., R², p-value).<br /> i) Figure 6D: The experimental timeline is unclear. Please specify the duration of incubation and the timing of each step.<br /> j) Figure 7B: Improved labeling is needed (e.g., clarification of "mean spot volume") to better align with the figure legend.

Reviewer #2 (Public review):

Summary:

The authors have made a convincing argument that the current system of in vitro translation using E. coli extracts can be significantly optimized to work with much lesser components, while maintaining activity. They have showcased their improved activity using not only physical but also functional readouts.

Strengths:

The experiments are designed in a very logical and easy to understand manner, which makes it easier not only to follow the paper, but also reproduce the results. Functional assays with the synthesized proteins are a good way to demonstrate functionality and applicability of the system. They also benchmark their system against a commercial kit to show superior performance of their system.

Weaknesses:

The production of the lysate requires special instrumentation, limiting accessibility.

Comments on previous version:

Thank you to the authors for addressing the concerns both textually and experimentally. This work has significant value.

Reviewer #2 (Public review):

Summary:

Chapman, Determan et al. investigate how pathogenic mutations in DNMT3A which cause of Tatton-Brown-Rahman Syndrome (TBRS) disrupt human cortical developmental processes using a comprehensive panel of human pluripotent stem cell models spanning DNMT3A loss-of-function severity. The authors aim to identify the cellular and molecular mechanisms underlying TBRS-associated brain overgrowth and intellectual disability, and to test whether mechanistic convergence exists between TBRS and other overgrowth-intellectual disability disorders (OGIDs) caused by mutations in EZH2 (Weaver syndrome) or PIK3CA pathway components. Their central conclusion is that GABAergic interneuron development is selectively vulnerable to DNMT3A mutation where reduced DNA methylation causes premature de-repression of neuronal and synaptic genes, driving precocious neuronal maturation and hyperactivity sufficient to disrupt neuronal network synchrony. This report adds to a growing literature supporting the vulnerability of GABAergic interneurons in NDDs and further provides a mechanistic view of this vulnerability potentially convergent across OGIDs. The mechanistic claims around H3K27me3 compensation and mTOR-based therapeutic convergence, while promising, rest on more preliminary evidence and would benefit from the distinction between correlation and mechanism being made more explicit in the text. Overall, this is a compelling study with rigorous experimental design and novel findings with potential impact across better understanding OGID pathophysiology.

Strengths:

(1) A major strength of this work is the breadth and rigor of the disease modeling approach. Four independent TBRS model systems are used in tandem: a patient-derived iPSC line with isogenic CRISPR-corrected control (R882H), a knock-in hESC model (P904L) with its wild-type isogenic, patient deletion iPSC lines (Del1/2), and CRISPRi knockdown models (G1/G2), collectively spanning a range of DNMT3A loss-of-function that correlates with phenotypic severity. This allelic series design substantially strengthens causal inference beyond what any single isogenic pair could provide.

(2) The multi-omic integration across matched developmental stages provides a strong mechanistic foundation for the cellular phenotyping and provides significantly enhanced novelty. RNA-seq, whole-genome bisulfite sequencing, and H3K27me3 CUT&Tag are combined in the same cell types and timepoints show that DNMT3A loss reduces CG methylation at neuronal and synaptic gene loci, leading to premature transcriptional activation.

(3) The selective vulnerability of ventral (GABAergic) versus dorsal (glutamatergic) progenitors is one of the study's most important findings. This lineage specificity is consistently observed across all model systems and in both 2D and organoid formats, where ventral NPCs show increased proliferation, premature neuronal gene expression, and increased neurogenesis, while dorsal NPCs are largely unaffected at the transcriptomic and cellular level despite exhibiting comparable DNA methylation changes. This adds to a body of emerging work showing GABAergic interneuron vulnerability in NDDs where ubiquitously expressed genes such as chromatin modifiers are perturbed and provides additional molecular insights into potential mechanisms of "resilience" of dorsal populations.

(4) The functional characterization follows a logical progression from single-neuron electrophysiology (demonstrating GABAergic hyperactivity with increased action potential amplitude and firing rate) to network-level analysis using high-density multi-electrode arrays. The HD-MEA experimental design - pairing TBRS or control GABAergic neurons with a constant background of control iGlut neurons - cleanly isolates GABAergic dysfunction as the driver of network hypersynchrony.

Weaknesses:

(1) The concomitant induction of proliferation and differentiation in TBRS V-NPCs is conceptually striking, since these are generally considered antagonistic developmental programs. The authors clarify that neuronal and synaptic gene de-repression is the more prominent direct consequence of mCG loss, while PIK3/AKT/mTOR pathway upregulation is not itself directly linked to differentially methylated regions, suggesting an indirect relationship between DNMT3A LOF and increased proliferative signaling. This framing is reasonable, but the mechanism linking DNMT3A mutation to mTOR activation remains unresolved, and the manuscript would benefit from being explicit about this gap. Relatedly, the rapamycin rescue, while demonstrated across multiple models including 904 and Del1 (Supplementary Fig. S3e-f), remains limited to proliferation readouts. Whether mTOR inhibition also rescues the downstream neurogenesis, maturation, or network phenotypes is an important open question that the authors appropriately frame as motivation for future work.

(2) The claim that H3K27me3 compensates for mCG loss is supported by prior work (Lii et al. 2022), which demonstrated increased PRC2 component expression and H3K27me3 gain at sites of DNA methylation loss in Dnmt3a knockout mouse neurons, and by data showing that PRC2 subunits (SUZ12, EED, EZH2) are significantly more highly expressed in D-NPCs than V-NPCs. Together, these findings provide a plausible molecular basis for why dorsal progenitors may be better equipped to maintain repression when DNA methylation is lost, and they make the EZH2 overexpression rescue in V-NPCs more interpretable. Yet, a formal distinction related to two competing, potentially underlying mechanisms, between active compensation, in which EZH2 is recruited to specific loci in response to methylation loss, and functional redundancy, in which higher baseline Polycomb occupancy in dorsal cells simply becomes the dominant repressive mark once mCG is reduced, has not been resolved.

Reviewer #2 (Public review):

Summary:

This work presents a spiking network model of traveling waves at the whole-brain scale in mouse neocortex. The authors use data from the Allen Institute to re-construct connectivity between different neocortical sites. They then quantify macroscopic traveling waves following stimulation of all layer 4 neurons in neocortex.

Strengths:

Overall, the results are interesting and shed new light on the dynamic organization of activity across neocortex of the mouse. The paper uses realistic neuron models specifically fit to intracellular recordings, demonstrating that traveling waves occur in the mouse neocortex with both realistic connectivity and realistic single-neuron dynamics. The paper is also well-written in general. For these reasons, the authors have generally achieved their aims in this work.

Weaknesses:

(1) Description of Algorithm 1: While the Methods section clearly explains the density parameter \rho, the statement on line 358 concerning the "ideal" average number of connections is a little unclear. The authors should explicitly clarify that \rho is a free parameter that can be adjusted to balance computational feasibility (for a given set of computational resources) and biological fidelity.

(2) Lines 102-103: The \rho parameter used here results in approximately 300 connections per neuron on average. The authors should state clearly that the number of connections per cell is the key determinant of computational feasibility (cf. Morrison et al., Neural Computation, 2005). The authors should also review neuronal density and synaptic connectivity in mouse neocortex and clearly reference density and connectivity in their model to the biological scales found in the mouse.

(3) Line 131: From the plots in Figure 2, it is not clear that the stimulus response is necessarily a rhythmic oscillation, in the sense of a single narrowband frequency.

(4) Line 217: Can the authors clarify how these findings relate to the results from Mohajerani et al. (Nature Neuroscience, 2013), or differ from them?

(5) Line 230: Because higher temporal frequency activity also tends to be more spatially localized, a correlation between PGD and temporal frequency could be an inherent consequence of this relationship, rather than a meaningful result.

(6) Line 247-248: It is not clear that the algorithm for generating connections between neurons presented here really relates to those for community detections. For example, in the case of the Allen Institute data, the communities are essentially in the data already.

(7) Line 284-285: The relationship between conduction delay is more direct than this sentence suggests. Conduction delay is fundamentally determined by the time required for action potentials to propagate along axons, making it intrinsically linked to anatomical distance.

(8) Line 287-288: The authors suggest at this point that they do not have enough information to estimate time delays due to axonal conduction along white matter fibers. However, experimental data from white matter connections typically includes information about fiber length, which does enable estimating conduction delays. These estimations have been previously implemented for Allen Institute connectome data in the mouse (Choi and Mihalas, PLoS Comput Biology, 2019) and human connectome data (Budzinski et al., Physical Review Research, 2023).

(9) Lines 294-295: Several methods do exist for detecting and characterizing wave dynamics in three-dimensional data (Budzinski et al., Physical Review Research, 2023).

Comments on revised version.

In this response and revised manuscript, the authors have addressed all points raised in the first round of review. In response to Point 2.7, however, is it not the case that the Allen dataset has the axonal lengths?

Reviewer #2 (Public review):

Summary and Strengths:

This in-depth genetic analysis of Zasp52 function in Drosophila indirect flight muscle (IFM) provides an interesting perspective regarding the role of a partially disordered region (IDR) in exon 15e. This exon seems to be exclusively present in IFM and contributes to the prevention of myofibril disintegration during aging, likely due to interactions of this region with Z-disc insertion and/or stability. The addition of an isoform (PR) that lacks exon 15e serves as a nice control to illustrate the necessity of exon 15e in muscle structure and function. Overall, the manuscript is exceptionally well-written, logical, with nicely controlled experiments and detailed statistical analysis that largely support the conclusions drawn by the authors. While exon 15e is clearly involved in preventing muscle degeneration, a solid role for thin filament stability is not clearly shown (as mentioned in the abstract). In addition, which regions/how the proteins of the IDR may contribute are unclear.

Reviewer #2 (Public review):

Summary:

This manuscript examines how the statistical properties of others' charitable donations shape subsequent giving using four preregistered experiments and computational modelling. The authors find that both the average level and variability of observed donations influence donation behaviour, and that individual differences in social information use are associated with psychopathic traits.

Strengths:

This is a well-executed paper on the important question of how social information shapes charitable giving. In my view, the combination of preregistered experiments, large sample sizes, computational modelling, and a multi-paradigm approach makes for convincing evidence. The progression across experiments, the use of real donation data rather than deception, the incentivized experiment 4, and the generalization to a second paradigm are all notable strengths. The introduction is clearly written and well-motivated - an enjoyable read. The experimental paradigm is thoughtfully designed, and the methods and supplementary materials are described in considerable detail. The computational modelling provides useful additional insights beyond the behavioural analyses.

As far as I could tell, the manuscript also adheres closely to the preregistrations. The primary hypotheses, experimental designs, exclusion criteria, and key analyses are all consistent with the preregistered plans. Deviations seem to consist of methodological improvements (e.g., mixed-effects models replacing ANOVAs), additional computational and robustness analyses, and therefore strengthen rather than weaken the manuscript. (NB: for transparency, I would appreciate a clearer distinction between preregistered and post hoc analyses, as well as a brief explanation for why some preregistered secondary analyses are no longer reported; see minor comments below).

Overall, I enjoyed reading this paper. I believe it will make a valuable contribution. My comments below are intended to further strengthen an already solid manuscript.

Weaknesses:

(1) The rationale for the social-information phase could be clarified further. Given the research question, I wondered why participants observed the five donations sequentially (and only briefly) rather than simultaneously. In particular, variance is arguably more difficult than the mean to encode and remember, and a sequential presentation may both obscure distributional differences and introduce primacy or recency effects. It would be helpful if the authors could better motivate this design choice, and indicate whether they examined possible order effects.

Relatedly, I felt somewhat uncertain about the purpose of asking participants to predict each donation before observing it. The prediction phase appears to play an important role in the computational model, but its theoretical role is not clearly introduced. Is it intended as a measure of participants' evolving beliefs about the descriptive norm, or primarily as a modelling device? Finally, were these predictions incentivized (e.g., for accuracy), and if not, how should readers interpret them?

(2) I would appreciate having the full experimental materials reproduced in the Supplementary Information. This would make it easier to understand what participants experienced during the task, including what they were told about the "other participants" whose donations they observed.

Minor points:

(1) The interpretations around domain-generality would be strengthened by reporting the association between social information use in the charitable giving task and in the BEAST. Currently, both measures are shown to correlate with psychopathy, but it remains unclear whether individuals who rely strongly on social information in one task also do so in the other. Reporting this correlation (or explaining why it cannot be meaningfully computed) would provide a nice and direct test of a domain-general tendency to use social information.

(2) It would help to explain more explicitly why the standard deviation of donations is theoretically interesting in its own right. The motivation for studying the mean seems immediately intuitive, whereas the motivation for focusing on variability could be elaborated on further in the Introduction.

(3) As I said above, I think the manuscript follows the preregistrations closely. Maybe I missed it, but it seems that prediction accuracy and reaction-time analyses were omitted. It would improve transparency further if the authors would briefly mention the preregistered secondary analyses that are no longer reported (and explain why they were omitted).

Reviewer #2 (Public review):

Summary:

The manuscript by Lau et al. investigates the mechanisms underlying IRF4 and BLIMP1 transcriptional activities during antibody-secreting cell fate decision. Both master regulators of plasma cell differentiation, these two transcription factors have distinct targets and non-overlapping roles. The authors used an in vitro culture system to generate antibody-secreting cells from human naïve B cells, and scRNA-seq, Crispr Cas9 editing, and Cut&Run to dissect the molecular mechanisms defining their specificity.

Strengths:

The experiments are overall well executed, and the manuscript is well written. The in vitro culture model appears to generate genuine human antibody-secreting cells. The identification of non-conserved nucleotides within the binding motifs that induce the specific binding of IRF4 or BLIMP1 is convincing, novel, and exciting.

Weaknesses:

The authors need to correct some overstatements and flaws to improve the manuscript.

In Figure 1f, the authors aimed to determine whether in their culture system the plasma cells emerged from the plasmablasts or directly from the activated B cells. First, it is noticeable that the distinction between plasmablasts and plasma cells relies here only on the expression of CD138. It does not include a higher capacity to secrete antibody or their proliferative state. In Figure 1e, the authors could have strengthened their distinction by showing the Ki67 staining at day 21 for both subpopulations. Second, this question does not seem to be related to IRF4 or Blimp1 activity, and thus one could wonder if it is relevant to this study. Finally, and most importantly, the design of the experiment appears flawed to me. The authors sorted cells at day 7 of culture based on their expression of CD20 and put the two subpopulations back for 14 more days. This culture system is a stepwise system, and it is not specified if the CD20+ cells were put back in the day 7 condition or the day 0 condition with the CD40L stimulation. Have both conditions been tested? This experiment also assumes that all B cells have equal potential to differentiate into antibody-secreting cells. What if it is not the case and some are anergic or have committed to the memory B cell fate during the first 7 days? Then the day 7 CD20+ fraction would be enriched in these cells. Moreover, this experiment didn't show that the plasma cell derived from the plasmablasts in the strict sense of the term, as the CD138+CD20- cells could be a mix of proliferative plasmablasts and immature plasma cells.

In Figure 3a and thereafter, the authors claimed that IRF4 acted earlier than BLIMP1, but both deletions strongly affected differentiation at day 7. IRF4 might have a stronger effect, but it does not mean that it had an earlier effect. To substantiate their claim, the authors would need to demonstrate that, at an earlier time point, deletion of IRF4, but not BLIMP1, results in defective differentiation.

In Figure 3b, the authors stated that in each individual KO the expression of the other transcription factor was lower. Given that there were no cells in the gate, it is puzzling to figure out how these expressions were compared.

In Figure 3c, on the UMAP the bottom right part of the activated B cell cluster does not appear to be attributed to any condition. How can it be? Besides, it is highly surprising that at D9 we cannot see any plasmablast on these UMAP, even in the control. Based on the G1/S and G2/M scores, none of the ASC represented were proliferating. Could the authors explain this strong discrepancy with Figure 1?

Another discrepancy exists between Figure 3b and c: Figure 3b depicted no IRF4- or BLIMP1-expressing cells in either KO, so what were the stunted PC and the BLIMP-KO PC reported in Figure 3c? What are the signature genes defining pre-PC and the score depicted in Supplementary Figure 3d, as the materials and methods only state that they are intermediate between PC and B cells? Could the authors show IRF4, BLIMP1 and some of their known target expression in these populations?

The authors claim that BLIMP1 is not needed to initiate the transition from pre-PC to PC, but in Figure 1, the intracellular staining showed that at day 7 the antibody secreting cells already expressed BLIMP1. This would rather suggest that BLIMP1, unlike IRF4, does not need to be maintained once the cell reaches a certain point.

Reviewer #2 (Public review):

Summary:

The authors tested whether the olfactory cues that drive attraction or avoidance behavior have diverged between surface‑dwelling and cave‑adapted strains of the Mexican cavefish Astyanax mexicanus. They use high‑throughput odor‑discrimination assays between known attractants and repellents by calculating an "odor index" per fish (=the difference in time spent in an odor zone versus a control zone). Further, hybrid crosses to probe heritability, starvation experiments to assess plasticity of odor perception, and whole‑brain pERK detection/mapping to link behavioral changes with known localized neural activity. The results support the hypothesis that the extreme cave environment has selected for an approach response to stimuli that are ancestrally aversive (like alarm or death odors) but in harsh environments can be used as guidance to the rare food sources in this ecosystem.

Strengths:

The odor index analysis is convincing, and the experiments for odor attraction/avoidance are robustly performed. The light-to-darkness shift reflected by avoidance to attraction in cavefish towards skin odors is compelling and carefully analyzed. The analysis of odor indices of three cave-dwelling populations in comparison to surface fish highlights a similar regime, yet with differences among the different populations, suggesting population-specific genetic variation.

Another strength of the paper is exactly this genetic inheritance study by generating F2 hybrids of cave-dwelling and surface-living individuals. The hybrids displayed a continuous range of odor indices for social, alarm, and death odors, indicating that these traits are heritable and likely based on additive genetic markers. Further, the authors uncovered a sexual dimorphism: only female cavefish exhibited approach behavior to social odors, whereas males remained neutral. This result aligns with known differences in olfactory organ morphology between sexes of other species from harsh environments.

Although limited in number, the neurophysiological correlation using whole‑brain pERK mapping after 10 min of odor exposure is convincing. The data revealed overlapping activation in the thalamus and pre‑optic region for food and decay odors, suggesting that these brain areas mediate the evolved attraction response to previously repellent stimuli.

Overall, the manuscript presents a concise story: cavefish have evolved attraction to alarm and death odors as a result of shifting from ancestral avoidance-driven to attraction by genetic changes and physiologically similar activation of specific neural circuits. The evidence is robust, with multiple independent experiments (behavioral assays, hybrid genetics, starvation experiments, and brain mapping) that collectively support the conclusions.

Furthermore, exposure to unpleasant odors can not only be tolerated but can even serve as a trigger for foraging. This plasticity demonstrates that genetic predispositions can be put into practice through active changes in physiology in species or organisms confronted with (drastically) changing environmental conditions.

Weaknesses:

I value that the authors are critical of their own data, indicating low numbers in the pERK/brain experiments. Yet this is a weak point as the statistical power is thus limited. However, their reasoning is careful, based on the results and not over-interpreting.

The layout/design of the ethograms (bout category plots) for both individual and population-wise are not easy to follow. Reworking these display items to convey the information is necessary.

Taken together, the manuscript uses odor perception and attraction/avoidance behavior studies to show that environmental changes (light-to-darkness) have an immediate impact on smell perception and behavior. Attraction to otherwise repellent odors is used by cavefish to likely adapt to harsh environments with low food sources. The manuscript convincingly demonstrates this plasticity, which is an interesting idea to follow up for other traits spreading among a population. This also underlines that a genome may be fixed and the blueprint for behavioral traits, but extrinsic cues can readily be adapted to change wired behavior even to the extreme as reported here: changing avoidance to attraction.

Reviewer #2 (Public review):

Summary:

In this short paper, a clever single-cell Strand-seq method was used to study the number and location of sister chromatid exchange events (SCEs) in cells after CRISPR/Cas9-induced DNA double-strand breaks (DSBs). Unique as well as multiple genomic loci were targeted. Cas9-induced cuts at unique genomic locations led to statistical enrichment of SCEs at the target site, whereas Cas9 targeted at repetitive targets revealed only mild enrichment of on-target SCEs unless analysis was restricted to a subset of cells with >8 SCEs per cell. Interestingly, reciprocal daughter-cell pair analysis revealed large-scale structural alterations on some chromosomes. Whereas disruption of DNA repair genes, including LIG3, LIG4, XRCC1, and XRCC4, did not measurably alter SCE frequency per cell within 24 hrs, consistent with delayed functional loss following editing and selection against essential genes. Together, these findings demonstrate that Cas9-induced DSBs are potent local triggers of SCE at unique loci and can be associated with structural alterations, highlighting the influence of lesion type and genomic context on recombination outcomes during genome editing.

Strengths:

The data in this paper represent a very rich resource of how parental DNA template strands are distributed in paired daughter cells after various treatments. Abnormalities observed in only one of such paired daughter cells provide a novel and exciting approach to study mechanisms of DNA instability and DNA repair at a genome-wide level in general and following Cas9-induced DSB in particular.

Weaknesses:

The effect of Cas9-induced DSBs in the cells that are used will depend on the cell cycle stage of the cells that are targeted, as well as the number of times cuts are made. The latter could happen before, during, and after DNA repair reactions on one or both alleles in a diploid cell. As a result, it is very difficult to extrapolate the mechanisms of DNA instability and DNA repair from the observed genomic rearrangements. Novel approaches are needed to limit the number and timing of Cas9-induced breaks to overcome some of these limitations. The language and logic in the paper can be improved, and some of the claims seem incorrect. For example, the abstract reads "A single Cas9 cut at a unique genomic locus led to strong local enrichment of SCE at the break site, reaching up to 41% in the same cell cycle and 17% in the subsequent division, indicating that DSB repair frequently engages non-local inter-sister repair." The evidence that only a single Cas9 cut was made is lacking (see my earlier comment); it is not clear how local enrichment or non-local inter-sister repair are defined.

Reviewer #2 (Public review):

Summary:

The authors use DRL to train a C. elegans connectome-based ANN to control stepping in a D. melanogaster body model. The resulting system can walk. This shows that one needs further constraints to derive biologically meaningful results from this approach.

Strengths:

The authors perform a very simple experiment with a clear outcome. The interpretation (or lack of interpretation) is a striking cautionary tale.

Weaknesses:

There is little analysis of precisely how robust this result is to parameter variation and network wiring. The worm also undulates in an oscillatory fashion. Thus, it is possible that the network is tapping into biologically meaningful motifs to generate oscillations for walking. As well, it would be useful to examine which heuristics one can use to determine whether modeling efforts are sufficiently constrained (i.e., how much biological data will be necessary to start obtaining fruitful, interpretable outcomes from DRL task optimization). For example, their "solution" using the worm connectome is not sparse (i.e., it uses many neurons). Perhaps a signature of a biologically-meaningful, interpretable result is one that is sparse?

Reviewer #2 (Public review):

Summary:

The authors showed the expression of TGR5 in hematopoietic compartments and that loss of TGR5 doesn't impair steady-state hematopoiesis. Notably, TGR5 knockout significantly decreases BMAT, increase the APC population and accelerate the recovery upon bone marrow transplantation.

Strengths:

The role of TGR5 is interesting.

Weaknesses:

Additional mechanistic studies would further strengthen the work and provide deeper insight into how TGR5 regulates the bone marrow microenvironment.

Reviewer #2 (Public review):

Summary:

Ma and colleagues presented a study on the characterization of brain-wide spatio-temporal impact of olfactory cortical outputs. They take advantage of multi-modal techniques on rats: fMRI, optogenetics and electrophysiology. In addition, they used cutting-edge analytical techniques and modeling to support and interpret their data. The main findings of the study are:

(1) Neurons in Olfactory Bulb (OB) predominantly activate primary olfactory network regions, while stimulation of OB afferents in Anterior Olfactory Nucleus (AON) and Piriform Cortex (Pir) primarily orthodromically activates hippocampal/striatal and limbic networks, respectively.<br /> (2) Non-specified adaptation or habituation mechanisms may play a significant role in modulating olfactory outputs over subsequent fMRI sessions.

(3) Artificially induced aging in rats induces profound modification in the functional interaction between olfactory cortices and multiple brain regions.

The results on AON are of particular interest because of the lack of functional information on this region, despite its recognized importance in shaping OB output and behavior (odor localization tasks).

Strengths:

The manuscript is very accurate. The figures are well-crafted, clear and provide much information with the most appropriate plots and graphics. The study's amount and data quality are remarkable, and the experimental size adequately addresses the scientific questions. I particularly appreciated the details in the description of the methods regarding the missing data and the size of the different animal groups. The supplementary data complete the leading figures and provide information at a single animal level.

Weaknesses:

(1) One of the main reasons the Piriform Cx is understudied in rodents is because of the proximity to air, which creates artifacts in fMRI images. This issue becomes more critical at ultra-high magnetic fields, but I would expect it also at 7T. One main achievement of this study is, indeed, the acquisition of fMRI data from Piriform, and this point should be highlighted by showing raw functional data from a rat. The best would be if an fMRI data sample for a rat, no matter which stimulation, is shared on a public repository, like Zenodo or similar. I am curious to check the quality of the BOLD data from such an 'enormous' field of view, particularly in the OB, with a single-shot sequence. Also, the visual inspection of raw data is essential to appreciate how many 0.5 x 0.5 x 1 mm voxels fit into AON, and others analyzed small brain structures, like the amygdala, etc. Was the amygdala entirely visible in BOLD, or did the air in the ear channel make an artifact partially shadowing it?

(2) Surprisingly, the only information missing in the methods is the post-surgery period and the time between two consecutive fMRI sessions. How much time was accorded to rats to recover from the surgeries, and what time interval between two scans? This information is crucial for interpreting the decrease in most BOLD responses in subsequent recordings. The supposed adaptation should fit into the known time frames for odor adaptation. Usually, fast adaptation does not last for days (and it should be measured within a single experiment: is it the case?), while for long-lasting adaptation the stimulus (odor or opto) should be maintained constantly ON. This does not seem to be the case in this study. The hypothesis, alternative to adaptation, of a less efficient light activation, for example, due to gliosis around the fiber tips, should be discarded with more evidence than the preservation of OB > Pir responses or acknowledged in the manuscript.

(3) The D-galactose experiments were conducted only after administering the aging molecule, with no baseline/reference data on the same animals. Then, comparisons were made with healthy rats, but the two groups not only can be discriminated with respect to D-galactose administration but also with age (10 VS 18 weeks). A control group for 18-weeks-old rats with no D-galactose treatment would better compare the D-galactose effect and avoid any potential bias from group comparisons of rats at different ages. Do you confirm that D-galactose was injected into each rat 56 times/days in a raw, or am I mistaken?

The updated version of the manuscript partially addresses the flaws of the original submission. Here are my general concerns:

(1) Overall, the revised version comes with a few modifications/additions and no new data. Apart from a new correlation analysis, the improvements are mainly discursive, often non-convincing, justifications of the authors' choices. This may reflect a lack of interest in a publication that, in the meantime, lost its original peer-review value. However, it should be acknowledged that the Authors made an effort to partially address the concerns raised by the reviewers.

(2) My main concern was the quality of fMRI recordings. In the revised version, the Authors provided a new figure with an example single-mouse fMRI data. However, the depicted regions of interest (ROIs) mostly cover the brain spots that I expected to be the most impacted by the BOLD artifacts caused by the proximity of the air and the big field-of-view. In addition, these ROIs do not appear to match the mouse anatomy shown above the functional data. As an example, the EPI images in the OB are almost entirely covered by the colored mask. The feeling is that the fMRI data was indeed poor, as I worried, and the lack of any public repository of raw data reinforces that feeling. To make this point clear: I do not think the findings are not true, but poor fMRI data quality might have hidden more insightful results and does not foster the use of fMRI to monitor the olfactory pathway, which lowers the impact of this article.

Reviewer #2 (Public review):

Summary:

Overall, the authors aimed to provide evidence that clarifies two debates within metacognition research concerning subjective confidence reports:

(1) Does the post-decision confidence report arise from the same process that drives the initial decision, or does a separate, independent process support confidence computation?

(2) How do we stop accumulating evidence for the post-decision confidence report? Is it based on a self-imposed time limit, or on accumulated evidence crossing a boundary?

For the investigation, the authors constructed four models (2 × 2 factorial) to compare each combination of processes to account for random-dot motion tasks data with speed/accuracy manipulations. The models are generally embedded in the drift diffusion model framework, retaining basic parameters such as drift rate, boundary separation, starting point, and non-decision time, while adding linearly collapsing boundaries to model the initial choice. For the single vs. distinct process dimension, the difference lies in whether post-decision evidence accumulation is referenced to the endpoint of the initial decision process or restarts from a new, freely estimated starting point. For the time- vs. boundary-based stopping rule dimension, the key difference is that post-decision evidence accumulation stops either at a deadline sampled from a normal distribution or when the accumulated evidence hits a collapsing boundary.

Based on model comparison, the boundary-based stopping rule clearly outperformed the time-based stopping rule. However, models with the boundary-based stopping rule performed similarly regardless of whether a single or distinct process was used. Here, the authors drew additional insights from EEG recordings during the task, focusing on the centro-parietal positivity (CPP), which has been proposed as a neural correlate of the evidence accumulation process. By simulating evidence accumulation trajectories (with additional assumptions) and comparing the patterns of those trajectories with observed ERP waveforms, the authors argued that the single-process model provided a better match to the CPP findings and was therefore preferred. This was specifically demonstrated by the model's superior ability to match the pre-response CPP amplitude differences conditioned on the post-decision confidence-related variables.

Strengths:

(1) The authors translated existing theories into computational models of decision-making and systematically compared different cognitive processes by assessing model fits to the data. This provides strong evidence supporting the idea that post-decision confidence reports could be better explained by boundary crossing rather than a self-imposed deadline to respond.

(2) Beyond model evidence, an important result is that CPP amplitude predicted confidence before the initial choice was reported, which is a unique prediction of the single-process model. The use of EEG as an independent validation measure provided additional evidence in favour of this model.

(3) Combining points 1 and 2, this study successfully addressed the two key debates with solid evidence to favour one theory over another.

(4) Another strength of this study is the data quality. The high number of trials provided a strong foundation for model inference as well as ERP analysis. The experiment also contained a speed-accuracy manipulation to evaluate model performance across diverse situations.

Weaknesses:

I have two main concerns around the modelling work and neural analyses, which in my opinion could have limited the interpretation of the findings. My responses here will be lengthier, but this reflects the nature of the modelling work rather than implying stronger criticisms than those suggested by the strengths discussed above.

(1) There are a few assumptions in the models that lack psychologically meaningful interpretations, and this study placed more effort into model comparison while lacking discussion of the cognitive processes inferred from parameter estimates.

To start, I think some of the parameterisations were not properly justified. For the boundary models, it is not very clear why the upper and lower boundaries were different and collapsed at different rates for confidence decisions, given that a single boundary parameter and collapse rate were used for the initial decision. This allows more flexible shifts in the model's predictions of confidence ratings without strong justification. Specifically, it is unclear why the boundary-single model has such an implementation while the boundary-distinct model was only equipped with one boundary parameter (a2, compared to a2up and a2down).

Similarly, the inclusion of metacognitive noise creates another layer of flexibility in the predictions of confidence ratings. In most existing evidence accumulation models with a diffusion process, noise comes from two sources: within-trial noisy evidence accumulation and across-trial variability (e.g., drift rate variability). Beyond these, such models almost always assume that the decision is made deterministically once the evidence reaches a specific boundary. The inclusion of metacognitive noise here sounds more like a noisy decision-to-action mapping.

I also have similar doubts about allowing the non-decision time parameter for confidence accumulation in the distinct model to be negative. The authors argued that confidence accumulation may begin during initial evidence accumulation. However, this is a flawed implementation, as the non-decision time was simply added to the evidence accumulation time rather than being incorporated within it. Allowing negative non-decision times may achieve similar predictions, but it is ad hoc.

The inclusion of a collapsing boundary mechanism in the post-decision confidence accumulator helped the model reach more diverse levels of accumulated evidence and ultimately improved predictions of confidence ratings. However, no strong argument is presented for this implementation beyond the observation that the model performs worse without it. The collapsing boundary mechanism has traditionally been interpreted as reflecting a sense of urgency. For the boundary models, I noticed that the collapse rate of the upper boundary differed significantly between speed and accuracy conditions, which is consistent with the urgency interpretation. Overall, I would like to see more discussion of the specific model mechanisms included by the authors, interpreted in light of parameter estimates.

(2) While the ERP findings provided external evidence and validation of the modelling results, I find the simulation practices not particularly useful and potentially misleading for naive readers. Specifically, the authors attempted to draw a parallel between patterns of simulated evidence accumulation traces and observed CPP waveforms. While the CPP has received support as a correlate of the evidence accumulation process, the DDM is by no means a neural model capable of generating predictions of neural observations. To my understanding, the superior fit of the boundary-single model was primarily due to the fact that pre-response CPP amplitude predicts post-decision confidence ratings. Therefore, as the boundary-distinct model did not connect the two phases of evidence accumulation, it would fail to account for this observation. I think this point could be clearly demonstrated without the need to introduce additional assumptions into the model simulations in order to directly compare averaged trajectories with averaged ERP waveforms. While the authors did not explicitly claim otherwise, this approach creates an illusion that the model can mechanistically account for ERP data. I would like the authors to provide explicit clarification on this point.

Appraisal:

Overall, the authors have provided solid evidence in support of their research aims. The findings contribute to longstanding debates with insights from model mechanisms and neural findings that should not be overlooked by future studies on this topic. This study also offers a good starting point for future model development and refinement in broader contexts of confidence reporting, such as paradigms involving simultaneous initial decisions and confidence judgements. The high quality of the behavioural and EEG data will make a valuable contribution to future research.

Reviewer #2 (Public review):

Summary:

The authors studied cognitive control and attention in response to mnemonic prediction errors (MPEs): situations in which the external reality violates internal memory-based predictions. The behavioral task first established strong versus weak predictions, and then either confirmed or violated these predictions. The authors examined markers of cognitive control (frontal theta) and attention (posterior alpha suppression, pupil response) while strong and weak predictions were confirmed or violated. They found increased cognitive control (frontal theta) for strong MPEs, which correlated with subsequent memory. Markers of attention (alpha suppression, pupil response) also accompanied strong MPEs but did not correlate with subsequent memory. Pupil response was investigated using an interesting approach that decomposes the response into different components, finding that different components respond earlier or later and show different correlations with MPEs and their strength. The authors also investigated how EEG, reaction time, and pupil responses correlated with one another, providing further insight into the mechanism underlying the response to MPEs. Together, the study points toward multiple control and attention mechanisms involved in MPE response and memory.

Strengths:

The study has a clear behavioral paradigm with multiple measures - behavioral, EEG, and pupillometry that offer an investigation into different aspects of MPE response and memory.

The study is also very comprehensive in looking at multiple phases in processing MPEs: the prediction phase (prior to the violation), the response to MPEs, and subsequent memory of MPEs, all within one study. Specifically, the link between neural mechanisms and subsequent memory is a major advancement, as most prior studies did not include this component. Mechanisms underlying subsequent memory of MPEs are theoretically important, as a primary function of MPEs is to promote learning and memory. As the authors mention, the different neural and pupillary signals are not robustly correlated, suggesting multiple mechanisms underlying MPE detections, which is interesting, offers avenues for future research, and can facilitate a better theory of how MPEs are processed in the brain. Finally, the decomposition of pupil response into different components and their correlation with behavior (RT during match/MPE detection) is interesting.

Weaknesses:

The methods are rigorous, and the data support the claims. The weaknesses are minor and are offered here as avenues for future research.

(1) The relationships the authors find between brain measures and pupil components were largely not specific to mismatches/matches. Thus, the specificity of this relationship is untested.

(2) The results with subsequent memory are important and address a major gap in the field that largely did not relate neural effects of MPE to subsequent memory. However, one major limitation of the study is that the authors did not test memory for matches. I understand the logic of avoiding testing matches. Because matches were repeated more times in the study, it's not a fair comparison and could change participants' overall criterion for old/new decisions. Future research could address this, e.g., by testing weak matches or potentially using a between-subject design.

Comments on revised version.

The authors addressed all my concerns. I appreciate the authors' thoughtful and detailed response.

Reviewer #2 (Public review):

The authors investigate the contribution of dorsal CA1 hippocampal dysfunction to cognitive impairments in the Cntnap2 knockout mouse model of autism spectrum disorder. Building on previous evidence implicating the hippocampus in episodic and relational memory processes, they combine trace fear conditioning, fiber photometry, optogenetic manipulation, a relational/declarative memory radial maze task, and cFos mapping to test whether altered CA1 function contributes to deficits in temporal binding and memory flexibility.

The study has several important strengths. First, the work addresses a relatively understudied aspect of autism-related cognition, namely hippocampal-dependent memory processes, whereas much of the literature has focused on social behavior, cortical circuits, or striatal dysfunction. Second, the authors employ multiple complementary approaches that converge on a coherent mechanistic hypothesis. The behavioral data demonstrate a reduced ability of Cntnap2 knockout mice to retain associations across long temporal gaps. Fiber photometry recordings reveal reduced dorsal CA1 activity during conditions that challenge temporal binding, and optogenetic activation of dorsal CA1 neurons during the trace interval is sufficient to rescue memory performance. Together, these findings provide strong support for a causal contribution of dorsal CA1 activity to temporal binding deficits in this model.

The second major strength of the manuscript is the extension of these findings to a more complex hippocampus-dependent memory task. The radial maze experiments indicate that Cntnap2 knockout mice show impaired memory flexibility and a greater reliance on egocentric learning strategies. The accompanying cFos analyses suggest altered recruitment of hippocampal and striatal networks during learning, providing a systems-level framework that may explain the observed behavioral phenotype.

Overall, the main conclusions regarding impaired temporal binding and reduced dorsal CA1 engagement are well supported by the data. The optogenetic rescue experiments are particularly compelling because they move beyond correlation and directly test causality. The manuscript therefore makes a meaningful contribution to our understanding of how hippocampal dysfunction may contribute to cognitive abnormalities associated with autism.

Weaknesses:

Some conclusions are necessarily more inferential than others. In particular, the interpretation that the observed behavioral phenotype reflects a broader shift from hippocampal-dependent declarative memory toward striatum-dependent procedural learning is supported primarily by cFos activity patterns and behavioral strategy measures. While the data are consistent with this interpretation, they do not directly demonstrate a causal reorganization of memory systems. Similarly, although the findings identify a mechanism in the Cntnap2 model, caution is warranted when extrapolating these conclusions to autism spectrum disorder more broadly; but I believe this caution is addressed in the discussion.

Despite these limitations, the study presents a coherent and well-executed body of work that provides novel mechanistic insight into hippocampal contributions to cognitive dysfunction in a widely used autism model. The findings should be of considerable interest to researchers studying hippocampal function, memory systems, and neurodevelopmental disorders.

Reviewer #2 (Public review):

Summary

This manuscript by Schilling et al. presents an important advancement in our understanding of how mTOR signaling regulates organismal aging. While the longevity-promoting effects of reduced mTOR activity have been extensively documented across species, the mechanisms by which mTOR communicates systemic metabolic information to regulate lifespan remain unclear. In this study, the authors provide strong evidence that longevity induced by reduced TORC1 signaling requires the bile acid-like steroid hormone dafachronic acid (DA) and its cognate nuclear receptor DAF-12. Furthermore, through a combination of transcriptomics and functional genomics, they identify the conserved short-chain dehydrogenase DHS-26/DHRS1 as a previously unrecognized downstream effector of this pathway. The work integrates genetics, lifespan analyses, sterol measurements, transcriptomics, proteomics, endogenous genome engineering, and comparative mammalian datasets. The resulting model, in which mTOR influences lifespan through regulation of endocrine steroid signaling, represents a conceptual advance that links nutrient sensing, metabolism, and organismal aging. Although several mechanistic questions remain unresolved, the study is comprehensive, technically rigorous, and likely to be of broad interest to investigators studying aging, metabolism, endocrine signaling, and cellular stress responses.

Strengths:

One of the major strengths of this manuscript is its conceptual novelty. Rather than reinforcing the well-established role of mTOR as a longevity regulator, the study proposes a specific endocrine mechanism that links reduced mTOR activity to increased lifespan through steroid hormone signaling. This advances the field beyond descriptive observations of mTOR-dependent longevity and introduces a model in which bile acid-like hormones function as systemic mediators of nutrient-sensing pathways. The idea that endocrine steroid signaling may serve as a downstream effector of mTOR provides a new perspective on how longevity signals are coordinated at the organismal level.

The genetic evidence supporting this model is particularly strong. In Figure 1, the authors use a series of epistasis experiments to demonstrate that mutations in daf-36, daf-9, and daf-12 suppress lifespan extension in raga-1 mutants. The DA supplementation experiments further strengthen the pathway ordering by rescuing longevity in hormone-deficient backgrounds while failing to restore lifespan in receptor-deficient animals. Importantly, the direct quantification of endogenous DA levels elevates the study by providing biochemical support for the proposed model.

The transcriptomic analyses presented in Figure 2 provide a valuable systems-level perspective on the interaction between mTOR and steroid signaling pathways. The observation that DAF-12 profoundly reshapes the RAGA-1 transcriptional program highlights the importance of steroid signaling in mediating the physiological consequences of reduced mTOR activity. The enrichment of metabolic, lysosomal, and peroxisomal pathways is consistent with established longevity-associated programs and generates a valuable resource for future mechanistic studies.

Figure 3 effectively integrates discovery-driven and hypothesis-driven biology. The authors use transcriptomic information to prioritize candidate genes and then perform a functional genomic screen to identify factors required for RAGA-1-mediated lifespan extension. This approach converges on DHS-26, which subsequently emerges as a central mechanistic component of the study. The progression from transcriptomics to functional validation is well executed.

In Figure 4, the generation of CRISPR-engineered dhs-26 deletion mutants and endogenous tagged reporter strains provides strong validation for DHS-26 function. The demonstration that dhs-26 deletion selectively abolishes RAGA-1-dependent longevity without substantially affecting wild-type lifespan strongly supports its role as a context-dependent mediator of mTOR signaling. Furthermore, the conservation analyses linking DHS-26 to mammalian DHRS1 provide biological context and enhance the broader significance of the findings.

In Figure 5, multiple independent experimental approaches converge on the conclusion that DHS-26 participates in DA-dependent lifespan regulation. The rescue of lifespan by DA supplementation, reductions in DA levels in raga-1;dhs-26 mutants, reporter-based analyses of DAF-12 activity, and proteomic profiling collectively support a mechanistic model. The proposed positive feedback relationship between DA/DAF-12 signaling and DHS-26 is intriguing and offers a plausible explanation for how endocrine signaling may amplify longevity-promoting responses. Finally, the incorporation of mammalian datasets showing regulation of DHRS1 by rapamycin and FXR signaling provides a promising avenue for future studies investigating conservation of this pathway.

Weaknesses:

Despite the many strengths of the study, important mechanistic questions remain unresolved. The most significant limitation is that the precise molecular connection between reduced mTOR activity and increased DA production remains unclear. While the genetic and biochemical data convincingly place DA/DAF-12 signaling downstream of mTOR, the study does not establish whether mTOR regulates DA biosynthesis, degradation, intracellular trafficking, sterol uptake, or hormone availability. The observed increase in endogenous DA levels is statistically significant but relatively modest, and the mechanistic basis for this increase remains speculative. Additional experiments examining sterol flux, enzyme activity, or intracellular sterol trafficking would substantially strengthen the proposed model.

The transcriptomic analyses in Figure 2 are informative but correlative. Because the RNA-sequencing was performed at a single adult time point, it remains difficult to distinguish primary transcriptional responses from secondary adaptive changes. Similarly, while pathway enrichment analyses identify plausible processes, they do not establish direct regulatory relationships. Additional temporal analyses or direct assessment of DAF-12 occupancy at candidate loci would strengthen mechanistic interpretations and help distinguish direct from indirect targets.

A major unresolved question concerns the biochemical function of DHS-26 itself. While the genetic evidence clearly establishes DHS-26 as an important regulator of RAGA-1-mediated longevity, its endogenous substrate and enzymatic activity remain unknown. The manuscript presents evidence linking DHS-26 to sterol metabolism, but direct biochemical characterization is lacking. Thus, the mechanistic model remains somewhat incomplete. Defining the substrates and products of DHS-26 activity would greatly strengthen the study and provide important insight into how this enzyme influences DA availability.

Another area requiring additional clarification is the proposed neuroendocrine role of DHS-26. The expression of DHS-26 in canal-associated neurons is interesting and raises the possibility that these cells participate in systemic longevity regulation. However, the current data do not establish whether DHS-26 functions autonomously within these neurons or whether expression in other cell types contributes to the observed phenotypes. Tissue-specific rescue or depletion experiments would strengthen the neuroendocrine model and help establish physiological sites of action.

Finally, the mammalian data presented in Figure 5 are supportive and suggestive of evolutionary conservation, but they remain correlative. While regulation of DHRS1 expression by rapamycin and FXR signaling is interesting, these observations do not yet demonstrate functional conservation of the longevity mechanism itself. Additional studies directly testing DHRS1 function in mammalian systems will be required before stronger conclusions regarding conservation can be drawn.

In summary, this manuscript provides a significant contribution to the aging field and introduces a model linking mTOR signaling, endocrine steroid hormones, and longevity. The study is comprehensive, technically sophisticated, and supported by multiple complementary approaches. Although some mechanistic questions remain open regarding the precise regulation of DA production, the biochemical function of DHS-26, and the extent of conservation, these limitations represent opportunities for future investigation. Overall, the work substantially advances our understanding of how nutrient-sensing pathways regulate aging and is likely to stimulate considerable interest within the fields of aging biology, metabolism, and endocrine signaling.

Reviewer #2 (Public review):

Summary:

The authors investigate chemical strategies to disrupt the interaction between the SARS-CoV-2 accessory protein Orf9b and the host mitochondrial receptor Tom70, an interaction implicated in suppression of type-I interferon responses. They employ two discovery approaches: a crystallographic fragment screen against the Orf9b homodimer and a high-throughput fluorescence polarization screen for compounds that compete with Orf9b binding to Tom70. The study identifies fragment-binding hotspots on Orf9b, develops lipidated analogs that stabilize the Orf9b homodimer, and discovers Tom70-binding compounds with low micromolar activity that inhibit Orf9b binding in vitro.

Strengths:

An impressive amount of work using a variety of complementary approaches and methods to validate binding (FP, SPR, and computational modelling and SAR). The combination of crystallographic fragment screening on Orfb9 and HTS on Tom70 provides two independent routes for perturbing the Orf9b-Tom70 interaction. The structural work seems to be of very high-quality. The fragment campaign is extensive, yielding a substantial number of fragment-bound structures and identifying biologically meaningful binding hotspots on Orf9b.

Finally, the screen results in reporting useful chemical starting points. Although potency remains modest, the study provides tractable scaffolds and a clear framework for future optimization.

Weaknesses:

General comment:

(1) Although there is already an incredible amount of data presented, one limitation of this study is the lack of cellular validation - do these drugs enter cells, restore interferon signalling, reduce viral loads, or alter Orfb9 localization?

(2) The logic of locking Orfb9 as a dimer is that the monomer binds Tom70 - thus, a more stable dimer means less monomer. In Figure 2, the Orfb9 homerdimer stabilization by compounds should reduce binding affinity to Tom70. A direct binding experiment measuring reduced Tom70 binding with compound treatment would better strengthen this claim.

Reviewer #3 (Public review):

Summary:

The manuscript takes a dynamical systems perspective on emotion regulation, meaning that rather than a simplistic model conceptualising regulation as applying to a single emotion (e.g. regulation of sadness), emotion regulation could cause a shift in the dynamics of a whole system of emotions (which are linked mathematically to one another). This builds on the idea that there are 'attractor states' of emotions between which people transition, governed by both the system's intrinsic characteristics (e.g. temporal autocorrelation of a particular emotion/person) and external driving forces (having a stressful week). Conceptually this is a very useful advance because it is very unlikely that emotions are elicited (or reduced) singly, without affecting other emotions. This paper is a timely implementation of these ideas in the context of a psychotherapeutic intervention, distancing, which participants were trained (randomised) to perform while watching emotion-inducing videos.

The authors' main conclusion is that distancing both stabilises specific emotional patterns and reduces the impact of external video clips. I would consider these results strong and believable, and to have the potential to impact models of emotion regulation as well as the field's broader views on the mechanisms of psychological therapies.

Strengths:

This paper has very many strengths: I would especially note the authors' very-well-matched active control condition and the robustness of their model comparison approach. One feature of the authors' approach in is that they explicitly add noise - not what you typically see in an emotion time-series analysis - which allows for participants to make errors in their own subjective ratings (a reasonable thing to assume); this noise can then be smoothed during filtering. In their model comparison approach, they explicitly test whether a true dynamical system explains emotion change/emotion regulation effect on emotions - demonstrating that both intrinsic dynamics and external inputs were needed to explain subjective emotion. Powerfully, they also used this approach to test the differential effects of the treatment groups (see below).

The main result seems quite robust statistically. Verifying the effects of the distancing intervention on emotion, the authors found an interaction between time (pre- to post-intervention) and intervention group (distancing vs. relaxation) suggesting that distancing (but not relaxation) reduced ratings of almost all emotions. Participants allocated to the distancing intervention also showed decreased variability of emotion ratings compared to those in the relaxation intervention (though note this interaction was not significant).

Using a model comparison approach, the authors then demonstrated that whilst the control group was best-explained by a model that did not change its dynamics of emotions, the active intervention (distancing) group was best-explained by a model that captured both changing emotion dynamics and a changing input weights (influence of the videos) - results confirmed in follow-up analyses. This is convincing evidence that emotion regulation strategies may specifically affect the dynamics of emotions - both their relationships to one another and their susceptibility to changes evoked by external influences.

The authors also perform analyses that suggest their result is not attributable to a demand effect (finding that participants were quicker during the control intervention, which one would expect if they had already decided how to respond in advance of the emotion question). I personally also think a demand effect is unlikely given the robustness of their control intervention (which participants would be just as likely to interpret as a mental health-enhancing training as distancing) and am convinced by the notion that demand effects would be unlikely to elicit their more specific effects on the dynamic quality of emotions.

Weaknesses:

The authors use an active control - a relaxation intervention - which is extremely closely matched with their active intervention (and a major strength). However, there was an additional difference between the groups: "in the group allocated to the distancing intervention, the phrasing of the question about their feelings in the second video block reminded participants about the intervention, stating: "You observed your emotions and let them pass like the leaves floating by on the stream." Therefore, some of the effects of distancing may have also been driven by different emotion regulation strategies, i.e. reappraisal, since this reminder might have evoked retrospective changes in ratings.

An unanswered question is exactly how distancing is producing these effects. As the authors point out, there is a possibility that eye-movement avoidance of the more emotionally-salient aspects of scenes could be changing participants' exposure to the emotions somewhat, which could vary by emotion, as the authors now discuss in their limitations.

Comments on revised version.

The authors have addressed my concerns.

Reviewer #2 (Public review):

Okray et al. identify a novel form of multisensory memory in Drosophila, where pairing reward with a color+odor together gives a stronger memory than color alone or odor alone. Remarkably, this multisensory enhancement occurs even if only one modality is used during testing (i.e. training color+odor, then testing odor alone gives a stronger memory than training odor alone, then testing odor alone), showing that the two modalities are persistently linked following training. The manuscript presents compelling behavioural genetic evidence that the normally visual-selective gamma-d Kenyon cells acquire a functional role in the retrieval of odor memories following odor+color training, and that this occurs via transfer from gamma-main KCs via the serotonergic interneuron DPM.

The key pieces of evidence supporting this conclusion are that olfactory retrieval of multisensory memories requires:

(1) synaptic output from gamma-d KCs during retrieval (but not training);

(2) synaptic output from gamma-main KCs during training and retrieval (whereas it's only required during retrieval, not training, for pure-olfactory memory);

(3) synaptic output from DPM during training and retrieval, and expression of the serotonin receptor 5HT2A in gamma-d KCs.

In the absence of physiological data, the exact nature of the gamma-d KCs' participation in olfactory retrieval following odor+color training remains unclear. For example, do the gamma-d KCs encode the odor identity (i.e., is there an odor-specific pattern of gamma-d KCs activated for a particular odor+color combination), or does their activity provide a general activity boost to other neurons (e.g. gamma-m) that encode odor identity? This will be interesting to address in future studies.

That being said, the behavioural data are clear and back up the authors' conclusion that signaling between KC subtypes via DPM underlies multisensory integration for multimodal memories in the fly mushroom body.

Reviewer #2 (Public review):

Summary:

Using the 5xFAD model in combination with GPR34 mice, the authors explore the function of microglia in the context of neurodegeneration. Using a broad spectrum of methodology, they show that DAM signatures are increased in KO 5xFAD mice. Using several KO clones of GPR34 KO iMGLs and another set of broad methodologies, the authors show that GPR34 is important for microglia homeostasis,<br /> phagocytosis, specifically of myelin. GPR34 KO iMGLs also show a distinct transcriptional response to myelin. Together, they propose that GPR34 limits microglial activation in neurodegeneration.

Strengths:

All methods are state-of-the-art, and the combination of mouse and human microglia responses is a particular strength.

Weaknesses:

No weaknesses were identified by this reviewer.

Reviewer #2 (Public review):

Summary:

The authors set out to test the extent to which differences in learning capacity and experience contribute to behavioural variation in a genetically identical population under identical environmental conditions.

Strengths:

The authors developed and used a scaled-up version of a simple two-choice behavioural paradigm allowing them to test thousands of individuals across multiple genotypes. They then deployed clever and powerful statistical analysis methods and provided compelling evidence for a role of variability in learning in the expression of behavioural variation.

Weaknesses:

There are no major weaknesses, although some level of longitudinal analysis to strengthen the evidence for a strict definition of individuality would be a welcome extension of a future study. In addition, it would have been very interesting, although understandably beyond the current scope, to delineate a potential source of learning variability in the brain.

Reviewer #2 (Public review):

This study uses a combination of field sampling and manipulative experiments to test for facilitative impacts of pikas on yaks via suppression of a poisonous forb. The authors found that, when Stellera forbs were present, yak weight increases over the growing season were greater in the presence of pikas compared to in their absence. This occurred because, although pikas do not consume Stellera, they clip it and use it in nest/burrow construction, thereby decreasing its relative abundance in the plant community. Thus, overall, the study contributes to our understanding of how herbivores of different size classes indirectly affect each other via use of shared resources.

It is well known that large herbivores on grasslands impact smaller animals, but the reciprocal interaction is rarely tested. Thus, this study asks a valuable question, and the experiment is well-designed to test it. The authors also do a good of demonstrating the potential conservation impacts of their research.

Reviewer #2 (Public review):

Summary:

The authors identify KIN-G as an in vitro substrate for phosphorylation by TbPLK and show that several of the in vitro P-ated sites, including T310, overlap with P-ation sites seen in live cells. The authors further show that PLK-mediated P-ation inhibits KIN-G binding to microtubules in vitro, as does a KIN-G-T301D mutant, and that expression of a KIN-G-T301D Phospho-mimic in T. brucei phenocopies KIN-G RNAi knockdowns, producing defects in cell division, morphogenesis of the centrin arm, FAZ and other cellular structures, as well as misplaced cytokinesis furrow.

Understanding cytoskeletal rearrangements that drive cell division in T. brucei is an important and unresolved problem, so the work addresses important questions that are of great interest. PLK and KIN-G have previously been shown to be important for cell division and morphogenesis of cytoskeletal structures that drive cell division in T. brucei. The current work advances our understanding by suggesting a potential mechanism by which PLK and KIN-G might participate, namely through PLK-dependent P-ation to control KIN-G MT binding activity.

Strengths:

The authors use a rigorous combination of biochemistry, phosphoproteomics, cell biology, and mutant analysis to support their conclusion that PLK-mediated P-ation of KIN-G negatively regulates KIN-G microtubule binding and this may explain the observation that a KIN-G T301 phosphomimic mutant blocks cell division and perturbs biogenesis of cytoskeletal structures that drive cell division and morphogenesis. Combining rigorous and informative in vitro studies with mutant analysis in live cells is a great strength. The work is solid and important, though a few pieces are needed to fully connect the in vitro findings with the in vivo observations, as detailed below.

Weaknesses:

Overall, I find this work to be solid, and to provide an important addition to our understanding of mechanisms controlling cell division in T. brucei. The biochemistry, in particular, is rigorous and convincingly demonstrates PLK can P-ate KIN-G, altering its MT-binding ability. Analysis of phospho-mutants of KIN-G in live T. brucei support the conclusion that P-ation of KIN-G at T301 negatively affects KIN-G function in vivo. I think, however, that the results fall short of supporting the title, because, although the data convincingly show that PLK can phosphorylate KIN-G at T301 in vitro, and that T301 is P-ated in vivo, they do formally demonstrate (nor even test) whether PLK is the kinase responsible for this phosphorylation in vivo (experiments to address this seem quite feasible). I also do not see where the authors try to reconcile the absence of phenotype for KIN-G-T301A with the implied importance of KIN-G phosphorylation by PLK in cell division, which calls into question the need for P-ation of KIN-G-T301 in cell division. Suggestions for addressing these concerns are provided below.

My two main questions are:

(1) What is the biological relevance of KIN-G P-ation at T301?<br /> a. The authors report no defect for the KIN-G-T301A mutant, so what then is the need for T301 P-ation, if the cell gets along fine without it? One step toward addressing this would be to ask what fraction of KIN-G shows P-ation at T301. Although published studies indicate P-ation at T301, it isn't known what percentage of KIN-G in the cell is P-ated. One might anticipate, for example, that T301-P is a small minority of the population in asynchronous cultures and that T301 P-ation increases at specific cell cycle stages.<br /> b. Published work links PLK to cell division, FAZ elongation, etc... The current work suggests that one role of PLK is to P-ate KIN-G at T301. In contrast, however, the current work also indicates that P-ation of KIN-G at T301 is unnecessary for normal cell division, FAZ elongation, etc....<br /> c. Some experiments or at least commentary on points a and b above would strengthen the paper.<br /> - The authors have now addressed this question by assessing what % of KING is phosphorylated at T301 and adding commentary on this point in the revised paper.<br /> - I would suggest that the model (new figure 8) include a dephosphorylation step, as that is proposed by the authors in the text. Also include in the legend some commentary on the role of phosphorylation, which is the center point of this paper, but not currently mentioned.

(2) Is PLK the kinase that P-ates Kin-G T301 in vivo?<br /> a. The authors show PLK P-ates T301 (and other residues) in vitro, and that T-301 is P-ated in vivo. To bring the analysis full circle, it would be informative to examine KIN-G P-ation in a PLK mutant or upon inhibition of PLK with published inhibitors. This seems to be a very doable experiment with the tools available.<br /> - The authors have addressed this question by demonstrating that T301 phosphorylation is reduced upon treatment with a PLK inhibitor, thus supporting that PLK phosphorylated T301 in vivo. It is noted that one might consider an alternate kinase is also able to phosphorylate T301 in absence of PLK activity, as that could explain the relatively low (~27%) reduction in phosphorylation by PLK inhibitor treatment.

Reviewer #2 (Public review):

Summary:

The study finds that nutrient resorption efficiency in Phragmites australis shows no plastic response to salinity stress but is canalized by phylogeographic lineage, ecotype, and latitude. In a common garden with 110 genotypes, salinity induced stress, yet no plastic change occurred for N, P, or K resorption. The authors conclude that intraspecific variation is historical and geographic; thus, predictions of wetland nutrient cycling need to account for phylogeographic composition.

Strengths:

The core finding that NuRE shows no plastic response to salinity, but is instead evolutionarily canalized by lineage and latitude, challenges a key assumption of broad trait plasticity. This conclusion is firmly supported by a robust common garden design with 110 genotypes, rigorous multi-level stress validation, and element-specific resorption analyses. The work provides compelling evidence that intraspecific variation in this critical nutrient cycling trait is shaped by phylogeographic history rather than short-term acclimation. The implications for predicting wetland responses to salinization are significant, as ecosystem-level nutrient dynamics may be constrained by the genetic composition of plant populations.

Weaknesses:

The experiment covers only one growing season, with salinity applied in June and measurements in December. While the stress is clearly effective, longer-term or multi-year stress might reveal acclimation or epigenetic effects that are not captured. Given the author team's expertise in parental and transgenerational effects in clonal plants, this limitation is particularly relevant and warrants more thorough discussion in the manuscript.

The salinity treatment uses a single moderate level of 10 ppt, which does not allow assessment of whether more extreme stress might trigger a plastic response. A dose-response design across a gradient would have provided stronger inference about the threshold at which NuRE canalization might be overcome. Additionally, the ecotype analysis in Figure 4 applies only to Chinese populations, as classification was not available for non-Chinese populations, which should be stated more explicitly in the Results.

The variation partitioning shows latitude as a significant predictor, but the R² values are relatively low, indicating that much variance remains unexplained. The manuscript should avoid overinterpreting latitude's explanatory power and more openly acknowledge the role of unmeasured factors. The interpretation of slopes greater than 1 for the resorbed N:P versus green N:P relationship, labeled as "inverted limitation", also needs further explanation regarding its functional significance.

Reviewer #2 (Public review):

Summary:

The authors aim to address a major problem in brain network modeling: the high computational cost of simulating and fitting brain activity models, particularly for large samples, individualized models, and broad parameter searches. They introduce cuBNM, an open software package that uses graphics processing units to accelerate model simulation, fitting, and calculation of simulated brain activity features.

The manuscript is primarily a methods and software contribution, rather than a paper providing novel neurobiological insights. The authors demonstrate the tool using human imaging data, showing examples of group-level and individualized model fitting, comparisons between homogeneous and heterogeneous model parameterizations, and analyses of repeated-measurement stability and genetic influences of simulated features. They also provide speed and scaling tests to support the claim that the software can make large-scale and individualized brain network modeling more practical for the field.

Strengths:

A major strength of this work is that it addresses a clear computational bottleneck in brain network modeling. The authors provide an open software package that combines a user-friendly Python interface with an accelerated back-end, making large numbers of simulations and model fits more practical for other researchers.

The demonstrations are broad and relevant to real use cases. The authors show group-level and individualized model fitting, different optimization strategies, and comparisons between homogeneous and heterogeneous models, rather than limiting the paper to a narrow technical benchmark. The benchmarking and openness of the work further increase its value. The comparisons across hardware and network sizes give readers a practical sense of the tool's speed and scalability, while the availability of code, documentation, tutorials, and containers should make the method easier for the community to test and adopt.

Weaknesses:

(1) The benchmarking provides solid evidence for substantial speed improvements within the authors' implementation, but the generality of the performance claims is more limited. The largest reported speed-ups are measured relative to a single central processing unit thread, and the study does not fully benchmark cuBNM against other optimized brain modeling frameworks. This makes the results useful as evidence of strong acceleration in the tested setting, but less definitive as a general comparison across available implementations.

(2) The comparison between homogeneous and heterogeneous models is informative, but it is not fully controlled for model complexity. The best-fitting node-based heterogeneous model has more free parameters than the homogeneous and map-based alternatives, so its improved fit may partly reflect greater flexibility rather than a more biologically valid parameterization. As a result, the model comparison supports the conclusion that this parameterization fits better under the current setup, but not necessarily that it is generally superior or more biologically realistic.

(3) The reliability and heritability analyses are valuable demonstrations of what scalable individualized modeling can enable, but they do not establish the simulated features as validated biological mechanisms. Because these simulated features are derived from individualized structural and functional imaging data, their stability across repeated measurements and genetic influences may partly reflect information already present in the empirical inputs or fitting targets. These results therefore support a more cautious conclusion: the simulated features retain stable and genetically structured variation, but their biological interpretation remains model dependent.

(4) The empirical demonstrations are narrower than some of the broader claims made in the manuscript. Most analyses rely on one human imaging dataset, one cortical parcelation, one main brain model, and a specific fitting objective, while broader claims refer to diverse populations, dense networks, high-dimensional models, and biological applications. The current results show that cuBNM is a useful and scalable tool in the tested setting, but the extent to which the findings generalize across datasets, model classes, network resolutions, or clinical contexts remains to be established.

Reviewer #2 (Public review):

Summary:

In vivo glia-to-neuron conversion emerges as a potential regeneration-based therapeutic strategy for neural injuries and diseases. However, controversies exist in this exciting field, largely arising from the non-stringent methods employed for analyzing in vivo neuronal conversions. The study by Li et al. directly addressed this controversy regarding Neurod1-mediated microglia-to-neuron conversion. They took advantage of two transgenic mouse lines to specifically express Neurod1 in the microglia of adult mouse brains. Results from immunohistochemistry, in vivo live-cell imaging, and scRNA-seq convincingly demonstrate that microglia cannot be converted in vivo to neurons by ectopic Neurod1 expression under both normal and injury conditions. Instead, it induces microglia death, consistent with their earlier findings. These solid results, though negative, are critical additions to the field and further support that stringent lineage tracing methods are essential for studying in vivo cell reprogramming. Overall, the studies are rigorously designed and executed. Only minor issues need to be dealt with.

Reviewer #2 (Public review):

Summary:

In this study, the authors set out to determine how a contact-dependent bacterial antagonistic system contributes to the ability of specific bacterial strains to persist within a complex, native gut community derived from wild animals. Rather than focusing on simplified or artificial models, the authors aimed to examine this system in a biologically realistic setting that captures the ecological complexity of the gut environment. To achieve this, they combined controlled laboratory experiments with animal colonization studies and sequencing-based tracking approaches that allow individual strains and mobile genetic elements to be followed over time.

Strengths:

A major strength of the work is the integration of multiple complementary approaches to address the same biological question. The use of defined but complex communities, together with in vivo experiments, provides a strong ecological context for interpreting the results. The data consistently show that the antagonistic system is not required for initial establishment but plays a critical role in long-term strain persistence, an insight that moves beyond traditional invasion-based views of microbial competition. The observation that transferable genetic elements can confer only temporary advantages, and may impose longer-term costs depending on community context, adds important nuance to current understanding of microbial fitness.

Weaknesses:

Overall, the study is not a lack of evidence, but a deliberate trade-off between ecological realism and mechanistic resolution, which leaves some causal pathways open to interpretation.

Comments on revised version.

The authors have addressed all previous concerns thoroughly and satisfactorily.

Reviewer #2 (Public review):

This study by Jaykumar and colleagues seeks to expand the field's appreciation of insulin responses in the brain, specifically by implicating WNK kinase function in various neuronal responses, ranging from behavioral / memory changes to GLUT4 trafficking to the cell surface with subsequent glucose uptake. This revised study is now comprehensive and presents a logical and reasonably documented cascade of molecular interactions responsible in part for GLUT4 trafficking under the regulation of WKK and insulin. Additional data allow the authors to dissect a plausible WNK/OSR1/SPAK-sortilin pathway for the modulation of GLUT4 trafficking, in part by capitalizing on an overlay of various techniques and systems. The data - much of it in vivo or ex vivo - showing a potential role for WNK function in brain glucose utilization remains a compelling part of the story, with the dissection of the signaling cascade and a potential role for sortilin in mediating WNK function via effects on GLUT4 cellular localization now more convincing.

Initially, the group shows that oral WNK463 treatment - an inhibitor of WNKs broadly - in mice augments a number of memory readouts. These findings fit within the context of the overall story the authors present: that WNK function is critical to brain glucose utilization, which impacts learning. Multiple approaches are used to show that WNK463 treatment, i.e. inhibition of WNKs, increases glucose uptake, including labeled 2-deoxyglucose uptake in vivo in the brain and in isolated synaptosome, and uptake in ex vivo hippocampal slices. These findings are solid and consistent. With the exception of some relatively minor comments regarding the data presentation made to the authors and now fully addressed, the findings showing that WNK463 treatment increases GLUT4-mediated glucose uptake and surface localization of GLUT4 are reasonable, with the hippocampal slice data being particularly relevant.

While the details of the WNK signaling cascade is dense, in the revised application one clearly appreciates the molecular interrogation and interactions the group is dissecting, supported by the use of multiple models. With the additional findings, these systems and the data now reinforce each other, presenting a strongly documented overall story.

A limitation of the study with the initial submission was the authors' reliance upon a single pharmacological tool (WNK463) to inhibit WNK kinases. WNK463 apparently has substantial specificity for WNKs and WNK463 treatment lessened OSR1 phosphorylation (a WNK substrate). Nevertheless, the cohesiveness of the findings in terms of the broader pathway engagement (GLUT4 trafficking, glucose uptake) is consistent with the author's proposed mechanisms and conclusions. The authors have additionally addressed this concern in the revised manuscript with more information supporting the specificity of WNK463 as well as the multiple approaches to confirm the effect of WNK463 on the WNK signaling pathway of interest.

The final few paragraphs of the discussion that weave the author's findings into the field more broadly, including Sortilin function and neurological disorders, are appreciated. Additional clarity in the Methods section is also helpful.

Reviewer #2 (Public review):

Summary:

This study is quite thorough, tackling this NO-dependent UV avoidance circuit with both breadth and depth. There are several novel discoveries throughout, but the whole package represents perhaps even more than the sum of these parts.

Strengths:

The presentation of the work is compelling. The introduction sets up the question and the state of the field very nicely. The discovery of the non-canonical NO receptor pathway in the ciliary photoreceptors is fascinating and will likely open up new avenues for future research into NO-pathways in different species. The use of genetic and pharmacological manipulations of circuit components was well thought-out. The authors applied different experimental techniques expertly throughout the study so that they could develop a comprehensive view from the molecular to the behavioral levels.

Weaknesses:

The authors have done an excellent job revising and explaining their model. No important weaknesses remain, in my opinion.

Reviewer #2 (Public review):

Summary:

The manuscript "Quantifying microbial fitness in high-throughput experiments" provides a comprehensive analysis of the various approaches to quantifying fitness in microbial evolution, focusing on three primary factors: encoding of relative abundance, time scale of measurement, and the choice of reference subpopulation. The authors systematically explore how these choices impact fitness statistics and provide recommendations aimed at standardizing practices in the field. This manuscript aims to highlight the impact of differing fitness definitions and the methodologies utilized for analysis and how that can significantly alter interpretations of mutant fitness, affecting evolutionary predictions and the overall understanding of genetic interactions in the experiments.

Strengths:

The choices for quantifying fitness in evolution experiments are critical and highly relevant given the increasing prevalence of high-throughput experiments in evolutionary biology. The authors methodically categorize fitness statistics and their implications, providing clarity on a complex subject. This structured approach aids in understanding the nuances of fitness measurement. The manuscript effectively highlights how different choices in fitness measurement can influence fitness rankings and the understanding of epistasis, which is important for modeling evolutionary dynamics.

Comments on revisions:

The authors have comprehensively addressed all previous comments and suggestions. In particular, the addition of the new methods section: 'A guide to calculate pairwise relative fitness under the logit encoding from bulk competition data' - significantly improves the clarity of the implementation and helps in the overall interpretation of the framework.

Reviewer #2 (Public review):

This paper describes application of the "GLM-Spectrum" mass univariate approach to examine the effects of age on M/EEG power spectra. Its strengths include promotion of the unbiased approach, suitable for future meta/mega-analyses, and the provision of effect sizes for powering future studies. These are useful contributions to the literature. What is perhaps lacking is discussion of limitations of this approach, in comparison to other methods.

An analogy is the mass univariate approach to spatial localisation of effects in fMRI/PET images. This approach is unbiased by prior assumptions about the organisation of the brain, but potentially also less sensitive, by ignoring that prior knowledge. For example, a voxelwise univariate approach is less sensitive to detecting effects in functionally homogeneous brain regions, where SNR can be increased by averaging over voxels. In the context of power spectra, the authors' approach deliberately ignores knowledge about the dominant frequency bands / oscillations in human power spectra. This is in contrast to approaches like FOOOF and IRASA, that explicitly parametrise frequency components. I am not saying these methods are better; I just think that the authors should acknowledge that these approaches have advantages over their mass univariate approach (in sensitivity and interpretation; see below). I guess it is a type of bias-sensitivity trade-off: the authors want to avoid bias, but they should acknowledge the corresponding loss of sensitivity, as well as loss of interpretation compared to model-based approaches (i.e., models that parameterise frequency; I don't mean the statistical models for each frequency separately).

An example of the interpretational loss can be seen in the authors' observation of opposite-signed effects of age around the alpha peak. While the authors acknowledge that this pattern can arise from a reduction in alpha frequency with age, this is an indirect inference, and a direct (and likely much more sensitive) approach would be to parametrise and estimate the peak alpha frequency directly for each participant, as done with FOOOF for example (possibly with group priors, as in Medrano et al, 2025, EJN). The authors emphasise the nonlinear effects of age in Fig 2A, but their approach cannot test this directly (e.g. in terms of plotting effects of age on frequency, magnitude, width for each participant), so for me, this figure illustrates a weakness of their approach, not a strength.

Then I think the section "Two dissociable and opposite effects in the alpha range" in the Discussion section is confusing, because if there is a single reduction in alpha peak frequency and magnitude with age, then there is only one "effect", not "two dissociable" ones. If the authors do want to claim that there are two dissociable age effects within the alpha range, then they need to do a statistical test, e.g., that the topographies of low and high alpha are significantly different. This then reveals another limitation of the mass univariate approach - that space (channel) is not parametrised either - so one cannot test for significant channel x effect interactions within this framework, as necessary to really claim a dissociation (e.g., in underlying neural generators).

While the authors show that normalisation of each person's power spectra by the sum across frequencies helps improve some statistics, they might want to say more about disadvantages of this approach, e.g., loss of sensitivity to any effects (e.g. of age) that are broadly distributed across majority of frequencies, loss of real SI units (absolute effect sizes) (as well as problems if normalisation were used for techniques like FOOOF, where the 1/f exponent would be affected).

Please give more information how artifactual ICs were defined. This may be important for cardiac artefacts, since Schmidt et al (2004, eLife) have pointed out how "standard" ICA thresholds can fail to remove all cardiac effects. This is very important for effects of age, given that age affects cardiac dynamics (even though the focus of Schmidt et al is the 1/f exponent, could residual cardiac effects cause artifactual age effects in current results, even above ~1Hz?).

Please could the authors clarify the precise maxfilter arguments, and explain what "reference" was used for the "trans" option - e.g., did the authors consider transforming the data to match a sphere at the centre of the helmet, which might not only remove some of the global power differences due to different head positions, but also be best for generalisation of the effect sizes they report to future studies (assuming the centre of the helmet is the most likely location on average)? And on that matter, did head positions actually differ by age at all?

Comments on the latest version:

I am happy with their revised version.

Reviewer #2 (Public review):

Summary:

The authors train E-I recurrent networks with short-term synaptic plasticity on a sequential delayed match-to-sample task, comparing regular versus jittered sample timing. They report a small accuracy gain under rhythmic input, a more separable population geometry during encoding, organization of internal oscillations around the dominant input frequency, a preference for temporal order over feature encoding, and improved decodability and persistence of stimulus information in both activity and synaptic efficacy. A delay-period perturbation shows synaptic efficacy contributes more than activity to maintenance.

Strengths:

The model is well-specified. Dale's law, the STSP formulation, the training objective, and the hyperparameters are all reported clearly enough to reproduce, and code is shared. The statistical machinery is appropriate, with cluster-permutation tests for the spectral analyses and across-network sign-flip tests rather than naive pooling. The temporal-order versus stimulus-direction dissociation in Figure 4C is the most interesting result. The negative association between phase locking and direction selectivity is non-trivial and argues against a simple global-gain reading, and it connects to Liebe et al. 2025. The serial-position decoding curves and the synaptic-versus-neuronal perturbation are well-motivated tests of the maintenance claim.

Weaknesses:

The behavioral effect is very small. Match accuracy is 0.991 versus 0.987, and non-match is 0.973 versus 0.969, on networks already at the ceiling. The entire mechanistic analysis is built to explain a roughly 0.4 percentage point difference, and the paper does not establish that this difference is functionally meaningful rather than a marginal byproduct of the timing manipulation. The IOI-dependence result meant to support it is weak, with an R-squared of 0.071 at a p-value of 0.029 on n of 67.

The core spectral and phase results are close to definitional and should be framed that way. The regularity index R is computed from IOI variability, the dominant frequency f0 is computed from the same IOIs, and the oscillatory metrics in Figures 3 and 4 are then measured relative to f0 and correlated against R. This shows that more regular input produces internal phase progression closer to the input-derived reference frequency, partly restating the input statistics rather than uncovering an independent network mechanism. The phase-locking-increases-with-regularity finding is the clearest case. This does not invalidate the analyses, but the manuscript currently reads them as a mechanism when much of the signal is built into the measurement.

The only genuinely causal manipulation is the delay-period shuffle, and it is underpowered at n of 15. Its main conclusion, that synaptic efficacy matters more than activity for maintenance, largely recovers prior STSP results (Mongillo et al. 2008, Masse et al. 2019) rather than establishing something specific to rhythm. The result the authors most want, that disrupting synaptic state removes the rhythmic advantage, is predicted in the Discussion but not tested.

The authors should add a control that breaks the circularity (a held-out f0/phase reference, or shuffling R against the metric) and run the causal STSP-disruption test that is mentioned in the Discussion.

The oscillatory framing is stronger than the model supports. Phase locking to a periodic input can reflect temporal predictability or repeated preparation without self-sustained entrainment, and the authors acknowledge this once but then use entrainment-style language throughout. The signals are extracted from firing-rate units and should not be read as LFP or EEG oscillations.

The authors should show raw single-unit and population activity so readers can verify the oscillations before the filtered pipeline. The delay perturbation largely recovers Mongillo 2008 / Masse 2019 rather than anything rhythm-specific, and the relationship to Liebe et al. 2025 should be addressed in the Results.

Appraisal and impact:

The authors largely achieve their stated aim of describing how temporal regularity constrains recurrent dynamics in this model, and the temporal-order preference is a useful prediction. The reach of the conclusions exceeds the evidence in two places: the functional importance of the behavioral effect and the degree to which the phase results are independent of the input construction. With the framing corrected and one causal test added, this would be a useful contribution to the modeling literature on timing and working memory rather than a definitive account.

Reviewer #2 (Public review):

Summary:

This work investigated differences in the temporal dynamics of neural populations in frontal orienting fields (FOF) and anterior dorsal striatum (ADS) in rodents during an auditory change detection task. The relative roles of these two regions have been studied previously and have been shown to play a role in the accumulation of evidence, with FOF converting this evidence into a categorical decision. By focusing on the temporal dynamics of neurons in these regions, the authors identified a subpopulation of neurons within FOF that displayed an abrupt ramping of activity near the time of decision commitment. Both FOF and ADS contained subpopulations exhibiting ramping activity aligned to stimulus onset. This is an interesting finding, suggesting that FOF contains a subpopulation of neurons that transforms accumulating evidence from other subpopulations in ADS and FOF into an action.

Strengths:

The conclusions of this paper are mostly well supported by data.

Weaknesses:

(1) In the neural analysis, the authors use a technique in which the weights of a linear decoder are used to define a feature vector for each neuron. These weights are used to measure the overall contribution of a neuron in decoding time (from stimulus or decision commitment). Interpreting decoding weights in this way is technically not correct (Kriegeskorte and Douglas, "Interpreting encoding and decoding models"), as a large weight in a decoder is not necessarily indicative of a large effect. Weights in decoding models can become large in order to cancel noise. Alternative analyses, for instance, treating the time series of each neuron as a feature vector, could have supported the conclusions from this technique.

(2) In this same analysis, it appears that the abrupt change in response in FOF at the time of decision commitment is coming from a single subpopulation of about 130 neurons. In the example session (Figure 8J), there is a clear outlier (the neuron in the top right corner). A closer inspection of the single neuron responses in this group would strengthen the results to confirm the abrupt change in mean population response is not coming from a relatively small number of neurons and sessions.

(3) The significance of the dynamical motif corresponding to transient bumps was unclear. For example, when looking at Figure 6K-L, I do not see any neuron groups that exhibit a clear transient bump. I would characterize all groups as ramping, with some groups showing steeper ramps. It would be helpful if the figure displayed the fraction of variance explained by PC2 so that it would be clear how much variance the bump motif is contributing. Given that there was no discussion of the functional relevance of this second motif, interpretation of this result is unclear.

(4) The finding that FOF contains subpopulations which slowly ramp during the trial as well as a subpopulation which acts like a switch that abruptly turns on at the time of decision commitment is interesting and significant and presents several computational questions. For example, is this subpopulation a non-linear readout of the more slowly ramping populations? The approach based on constructing a feature vector for each neuron, projecting these vectors into a low-dimensional subspace, and partitioning into subpopulations is insightful and allowed distinguishing these different computational functions within a single region (FOF). However, I found this particular result to not be clearly stated and obscured by other seemingly less significant results (e.g., existence of the transient bump motif) and other less interpretable analyses (e.g., subspace re-alignment).

Reviewer #2 (Public review):

Summary:

The authors investigated the role of hypothalamic CRH neurons in social behavior. They performed fiber photometry recordings in mice from CRH neurons and showed that novel conspecifics trigger stronger and more prolonged responses compared to familiar conspecifics and objects. The activity of CRH neurons appears to be related to risk assessment, as interactions with juvenile unfamiliar mice (lower-risk conspecifics) trigger responses similar to those of familiar adult mice. Behaviorally, CRH neurons were linked to increased anogenital investigation of unfamiliar compared to familiar mice. Optogenetic suppression of CRH neurons decreased anogenital sniffing of unfamiliar conspecifics.

Strengths:

The manuscript is elegant, and the results are compelling. The approaches are well justified, and the methods are validated (eg: Arch inhibition).

The findings substantiate the role of CRH neurons in responses to stress and uncover the involvement of these neurons in the assessment of social risk.

Weaknesses:

These are not weaknesses, just some observations: It is somewhat surprising that CRH neurons respond similarly to familiar and unfamiliar objects; it would be good to have more insights into that aspect.

Similarly, the novel context by itself is expected to lead to increased activity of CRH neurons (based on data from the last author's lab as well as other labs in the field). It is somewhat surprising (and interesting) that the novel environment did not affect the magnitude of CRH responses to unfamiliar conspecifics.

Reviewer #2 (Public review):

Summary:

Shimogawa et al. studied the effect of lysine acetylation at different sites in the alpha-synuclein (aS) sequence on the protein-membrane affinity, seeding capacity in the test tube and in cells, and on the structure of fibrils, using a range of biophysical methods. They use non-canonical amino acid (ncAA) mutagenesis to prepare aS lysine acetylated variant at different sites.

Strengths:

The major strength of this paper is the approach used for the production of site-specific lysine acetylated variants of aS using ncAA mutagenesis, as well as the combination of a range of biophysical methods together with cellular assays and structure biology to decipher the effect of lysine acetylation on aS-membrane binding, seeding propensity, and fibril structure. This approach allowed the author to find that lysine acetylation at positions 12, 43, and 80 led to lower seeding capacity of aS in the test tube and in cells, but only acetylation at lysine 80 did not affect aS-membrane interaction. These results suggest that lysine acetylation at position 80 may be protective against aggregation without perturbing the proposed functional role of aS in synaptic plasticity.

Weaknesses:

SDS is not a good membrane model to investigate the effect of lysine acetylation on aS membrane-binding because it is a harsh detergent and solubilizes membranes. Negatively charged vesicles or vesicles made of a mixture of lipids mimicking the lipid composition of synaptic vesicles are more accepted in the field to study aS-membrane interactions. The authors used such vesicles for the FCS experiments, and they could be used for the initial screening of the 12 lysine acetylated variants of aS.

Reviewer #2 (Public review):

Summary:

In this study, the authors propose the existence of an AQP4-positive tanycyte-associated canal system in the hippocampus and suggest that this system participates in waste clearance and contributes to Alzheimer's disease pathology. Using histological, ultrastructural, immunohistochemical, and RNA-based approaches, the manuscript attempts to reinterpret amyloid-β plaques and tau-associated structures as components of a tanycyte-derived waste-internalization system. The work is conceptually ambitious and raises observations that may stimulate discussion regarding glial organization and waste clearance in the diseased brain.

Strengths:

A strength of the manuscript is the combination of imaging modalities and anatomical observations across mouse and human tissue. Some of the reported morphological features are intriguing and may warrant additional investigation. The study also attempts to integrate structural observations with broader hypotheses regarding neurodegeneration and Alzheimer's disease.

Weaknesses:

The central interpretation depends almost entirely on identifying the observed hippocampal structures as tanycytes, and the evidence supporting this conclusion remains insufficient. Tanycytes are classically associated with ventricular regions in circumventricular organs, particularly in the third ventricle and median eminence region, yet the manuscript does not provide sufficiently specific anatomical or molecular evidence to convincingly distinguish the described structures from astrocytic, ependymal, radial glial-like, oligodendroglial, myelin-associated, vascular-associated, or degenerative elements. The marker profile used throughout the study, particularly the reliance on AQP4 labeling and Luxol-positive structures, is not sufficiently selective to establish tanycyte identity, especially in pathological tissue where reactive glial changes may occur.

This becomes particularly important because the manuscript repeatedly interprets Luxol-positive and myelin-associated structures as tanycytic processes or "myelin-derived tanycyte protrusions," despite tanycytes not being known to produce myelin. Alternative explanations are not sufficiently explored. Some of the canal-like structures shown in Figure 4 also resemble vascular profiles, and additional vessel markers would be necessary to exclude this possibility.

Several of the proposed structures and mechanisms are also difficult to reconcile with established cell biology and neuroanatomy. The introduction of new terminology such as "tanysomes," "waste receptacles," and "toroids" further extends the interpretation beyond what is currently demonstrated experimentally.

The discussion and integration of the existing literature on tanycytes are also insufficient. Tanycytes themselves are not clearly introduced; the manuscript does not adequately discuss what is currently established regarding tanycyte anatomy, ventricular localization, morphology, and function. Foundational literature defining tanycyte biology, including work from the Prévot group or others, is largely absent despite its central importance to the field. Because the manuscript proposes a substantial departure from established neurobiological concepts, it is particularly important that previous literature be discussed comprehensively and critically. The current version does not sufficiently contextualize the proposed model within the existing literature on tanycyte, AQP4, glymphatic, and Alzheimer's disease, making it difficult to evaluate what is genuinely novel versus what is merely being reinterpreted. It is also not entirely clear what is genuinely new here compared with the authors' previous work, particularly reference 11, which appears to present a highly similar conceptual framework.

More broadly, several of the manuscript's mechanistic conclusions extend well beyond the available evidence. The proposal that amyloid-β plaques and tau pathology represent hypertrophic tanycyte-derived waste structures is provocative and potentially interesting, but currently remains largely correlative and speculative. At several points, it becomes difficult to distinguish direct observations from broader mechanistic interpretation. The manuscript itself acknowledges that the proposed glial-canal hypothesis contradicts the current understanding of nervous system organization and states that ultrastructural serial-section analysis would be required to unambiguously determine the origin of the myelinated profiles described. This point is critical because the study's central conclusions depend on the assumption that these structures are tanycyte-derived. At present, this interpretation remains insufficiently demonstrated, which substantially limits the strength of the broader pathological and mechanistic conclusions proposed throughout the manuscript.

Although access to human material is understandably limited, the study appears to include only one male and one female AD patient, making it difficult to assess the reproducibility or frequent these structures are across individuals and pathological conditions. The manuscript would benefit from clearer characterization of prevalence, reproducibility, and variability across samples.

Overall, the manuscript presents an unconventional and thought-provoking model that may stimulate discussion. However, the evidence currently provided does not convincingly establish tanycyte identity for the described hippocampal structures, and several of the broader disease-related interpretations would require substantially stronger anatomical and molecular evidence before the proposed model can be convincingly supported.

Reviewer #2 (Public review):

Summary:

The study introduces an innovative device designed to collect non-invasive saliva samples from animals using disposable cassettes with odor attractants and filter paper. The authors aimed to validate this tool for pathogen monitoring, specifically by detecting pathogen RNA in animal models. While the concept is compelling and the problem statement well-framed, the validation of the device for pathogen detection was not achieved. For example, the rabies virus was not detected in the chosen model, and results were limited primarily to FeLV. The work highlights the potential of saliva-based sampling for microbiota analysis, but the rationale for virus selection and the experimental design require further clarification. Overall, the study presents a novel approach with promise, though its current scope is better suited to microbiota monitoring rather than pathogen surveillance.

Strengths:

The innovative design of the device, which enables non-invasive saliva collection through disposable cassettes with odor attractants, represents a creative and practical advance in sampling methodology. The authors undertook an extensive experimental effort, generating a substantial amount of data that highlights the feasibility of saliva-based monitoring. The rationale for exploring saliva as a medium is valid, and the work successfully shows that the device can be applied to microbiota profiling, where the strongest results were obtained. This methodological innovation could be valuable for expanding non-invasive approaches to animal health monitoring.

The authors acknowledge that metabarcoding sequencing has limitations; however, the study could be refocused on the microbiota in general rather than on pathogen detection. They could give greater prominence to the taxonomic composition of microorganisms in saliva using high-throughput sequencing. That is where they obtained the most results.

Weaknesses:

Despite the enormous experimental effort undertaken, the results fall short of the expected success of the proposed test. The rationale and criteria for virus selection are not clearly explained, leaving the experimental design insufficiently justified.

The central aim of validating the device for pathogen detection was not achieved, particularly in the case of the rabies virus. The mouse infection model used for the rabies virus does not seem to adequately replicate the natural course of the disease. This could explain, at least in part, the negative results obtained.

Of the three viruses evaluated, satisfactory results were obtained only for FeLV, and the sample size remains limited. According to the literature reviewed, this virus is not common in wild cats, so the applicability of the results would appear to be limited primarily to domestic cats.

The collected samples were stored at −80 {degree sign}C for later analysis, which likely contributed to the high Ct values observed with the device. The need to store samples at low temperatures may be a limitation to applying this technique in wildlife sampling scenarios where access to dry ice or liquid nitrogen tanks may be difficult.

Stating that the device can be used for pathogen monitoring in wild animals is not desirable, since the viruses for which results were obtained are not relevant in wild animals. On the other hand, claiming that this is a tool for monitoring diseases in endangered species is also misleading. Endangered species are typically scarce and therefore would not be the reservoirs that these surveillance efforts should target. In fact, groups such as wild rodents would be a better target for monitoring zoonotic pathogens.

Reviewer #2 (Public review):

This study examines how curl in the retinal flow field can be used as a control variable for estimating and controlling the heading of a moving observer. The basic idea (which is not entirely new, see Matthis et al. 2022) is that translation along a path with eccentric gaze (meaning that the subject is not heading toward the point they are looking at) produces a pattern of optic flow on the retina with a rotational component around the point of fixation (which can be captured by the mathematical "curl" operator). The sign and magnitude of retinal curl varies with heading relative to the point of fixation, such that curl can be used as a control variable to steer rightward or leftward to move toward the fixated target. The authors perform behavioral experiments and show that there are biases in perceived heading that seem to be largely governed by retinal curl. They also show that a simple controller model can use curl to steer toward a target, and they provide a neural network model that provides a biologically-plausible implementation of the controller (although there are some questions about that).

There is a core of interesting work here that I think can be important to the field. However, there is a lack of clarity on several important fronts, including design of the behavioral experiments, presentation of the behavioral data, conceptual framing of what curl can and cannot do, etc. Equally importantly, the manuscript is not written in a manner that will make it accessible to most vision scientists. I consider myself to be pretty knowledgeable about optic flow, and I had to read most of the manuscript 3 or 4 times to be able to understand the bulk of it. And my experience is that most vision scientists do not understand optic flow well, so I fear that most of the readers that the authors should want to reach would struggle to understand the work. As written, this is mainly going to make an impact on a handful of optic flow gurus. Thus, this manuscript is going to need a major overhaul to clarify important issues and make this more accessible.

Major issues:

(1) The manuscript contains inconsistent, if not misleading, messaging about what information retinal curl does, and does not, provide regarding heading estimation. In the Abstract, the authors state: "We propose an alternative: the visual system utilizes retinal curl directly to estimate heading, rendering the explicit recovery of the FOE unnecessary." Based on my understanding of the rest of the manuscript, I find this statement to be a misrepresentation for two main reasons:<br /> a. To "directly estimate heading" relative to what? When not qualified, most people interpret "heading" to mean an observer's heading relative to the world (or some allocentric reference frame). But retinal curl only gives information about an observer's heading relative to the point on which their eyes are fixated. Moreover, that point of fixation will change every few hundred milliseconds in natural viewing, so the retinal curl will change with each new fixation even as heading relative to the world remains unchanged. So, I think most readers would grossly misinterpret the claim that retinal curl can be used "directly to estimate heading". Indeed, in the authors' controller model, the initial heading needs to be given and then the controller can work. But from where does the visual system get the initial heading, since it does not come from curl? These issues are left hanging. Thus, while curl can provide a very useful input for steering toward a fixated target, other signals are needed to estimate heading relative to the world. This has to be made much clearer early on, and a conceptual schematic diagram might help. Also, the authors generally do not specify the reference frame of the variables they are talking about, leaving lots of room for misinterpretations. It should be clear each time they are talking about a variable, such as heading, whether it is relative to the fixation target, body, world, etc.<br /> b. It seems to me that retinal curl will depend on other variables, in addition to heading relative to the fixation target. For example, it seems to me that the magnitude of retinal curl will depend on self-motion speed, the depth structure of the scene, the angle of elevation of the fixated target, and perhaps others. This is not discussed at all, and many readers would get the misguided impression that there is a 1:1 mapping from curl to heading (relative to fixation). If I am right that this is not correct, it means that retinal curl can tell the observer whether to steer right or left to move toward the fixated target, but it cannot tell them how much to steer. Indeed, in the authors' controller model, there is a free parameter that calibrates curl to angle. It makes sense that this works to fit trajectory data that are given from a fixed environment, but it is unclear how the brain would use retinal curl to control steering when these other variables are uncertain or changing unpredictably. Moreover, how does the system change the mapping from curl to steering command as the location of fixation changes relative to the current heading? These are issues that need to be brought up in framing the problem and discussed at some length. If the authors can show mathematically that retinal curl is only dependent on heading (relative to fixation) and not any of these other variables, it would be very valuable to show the equations for this relationship.

(2) The description of the behavioral experiment and presentation of behavioral data leaves a lot to be desired.<br /> a. First, it is stated (line 158) that "Participants continuously reported their perceived direction of self-motion while maintaining fixation on the yellow dot." Again, reference frame is completely unspecified. Participants were reporting their perceived heading relative to what? The fixation target? The world? What exactly were the instructions given to the subjects to perform the task? Based on the description of how perceived paths are computed (line 166-), it seems to be presumed that subjects are reporting their heading relative to the world because those angles are then converted into x and z coordinates in what I presume is a world-centered reference frame. But how do we know that subjects are accurately reporting their heading relative to the world? What if they are biased in their reports by the location of the fixation target relative to the scene, or by some other reference signal? Is it possible for the authors to rule out the possibility that perceptual biases seen in the unaltered curl condition result from observers not fully adopting the assumed reference frame of the task? If this cannot be firmly excluded, it seems to create problems for the rest of the study.<br /> b. I also feel that there is a mismatch between what the behavioral task requires and what the controller model does. Subjects are apparently asked to report their heading relative to the world, but the controller model only controls their heading relative to the point that they are fixating. I understand how this is resolved in the model, but I think this type of distinction is buried and will not be apparent to most readers. Again, the reference frames of what is being measured and controlled need to be specified explicitly in all parts of the paper, and the authors needs to explain how the system would combine curl-based control with some other measures of (at least initial) heading for world-centered heading to be computed. All of the assumptions need to be clearly specified.<br /> c. Second, I found it frustrating that the authors never present raw perceptual data from the observers. Rather, in Figure 2, we see reconstructed trajectories that are perfectly smooth with no indications of noise whatsoever. Since these paths are computed from the perceptual reports, there must be some noise inherent in them. The figures should represent this uncertainty somehow, and it should be explained how these perfectly smooth trajectories are obtained.

(3) "...the magnitude of retinal curl in the fovea can specify the body trajectory relative to gaze (Matthis et al., 2022)." The main idea put forward by the authors here seems to overlap heavily with this statement that they attribute to Matthis et al. 2022. While I think this paper still adds importantly to the topic, the authors do not discuss how their findings are different from those of Matthis et al. 2022, why they are an important extension, etc. Readers should not have to go read this other paper to have any idea how the present findings are placed in importance relative to the literature.

(4) The analysis and treatment of eye movements is extremely weak. The authors discarded trials for which gaze deviated from the fixation point by more than 3 degrees (which is a LOT given that the eye speeds are generally in the neighborhood of 0.5 deg/sec), and they provide basic stats on the distribution of positions. But this largely misses the point: it is not small position errors that are likely to matter, but rather velocity errors. Even a small amount of retinal slip of the target while it is being pursued will cause image motion that is going to alter the optic flow field around the fixation target. So, for example, the retinal curl field may no longer be centered on the fixation target. How do we know that some of the perceptual biases are not influenced by image motion resulting from imperfect tracking of the fixation target? This needs to be analyzed and discussed.

(5) I found the sections of text comparing the separate and joined fits (starting line 287) to be a bit too rosy. The authors show the separate fits in the main text, and it is not very surprising that these fits are good given that the model has 30 parameters, and these data are pretty low dimensional. The authors only show the joined fits in the supplement, and they say that they are almost as good as the separate fits (indeed they are better in a model comparison sense, but this is 30 parameters vs. 2 parameters). However, when I look at the fits of the joined model in the supplement, I don't find them to be very impressive. In particular, the model grossly misses the data for the straight paths for several subjects (e.g., id5, id6, id8, id10). And fitting the straight paths would presumably be easiest. This implies that the joined model is really missing something and that fitting the curved paths interacts strongly with fitting the data for different fixation target locations on the straight path. I think that the authors should discuss the results a bit more soberly and tone down their conclusions here.

(6) The section of the paper on neural simulations (starting line 387) has a few weaknesses. First, why are only straight paths simulated here? This does not seem to provide a very rigorous test of the model. Second, it is awkward that the simulation results are presented in units of pixels, rather than degrees. Third, the authors seem to downplay the fact that the neural estimates of heading seem to oscillate rather wildly (over a range of hundreds of pixels, whatever that means, see especially Fig. S16). It was far from clear to me how an estimate of heading with these large oscillations is useful. It would seem to require that heading estimates are integrated over substantial lengths of time to be reliable. It was therefore unclear how the model produces such smooth paths from these oscillating estimates.

Comments on revised version.

Overall, the authors have done a responsible job of responding to the comments of my previous review, and the manuscript is substantially improved. There are a few points on which I still do not completely agree with the authors, and I think these are important to document for the record:

(1) Introduction: "Pure visual decomposition should function regardless of 3D depth or whether the rotation stems from an active eccentric fixation." Perhaps in a world of noiseless perfect computation, this might be true. But I generally disagree. When there is more depth structure in an environment, then translation of the observer is generally going to create greater motion parallax. That is a fact that I don't think can be disputed. And greater motion parallax should help to decompose optic flow into components related to translation and rotation (the latter of which is not depth dependent), especially when there is noise in estimating location motion vectors.

(2) Related to point #9 of my previous review: I had asked why the authors believed that retinal curl was computed in area MSTd. Their response is that previous studies (i.e., Graziano et al. 1994) show selectivity to spiral motion stimuli in MSTd. That is true, but those studies typically placed the spiral stimulus centered on the MSTd receptive field, hence they were not presenting something like retinal curl as defined here. So, I think it is still an open question as to where in the brain retinal curl is encoded, and from which areas it would be possible to decode retinal curl from population responses.

(3) Related to point #10 of my previous review: I had asked about biological plausibility of the gaze-centered inhibition signal in the model. The authors' response is that parietal neurons show gain fields in which response depends (usually monotonically) on eye position. This is true, but it is not a trivial jump from gain fields in individual neural responses to a gaze-centered inhibition signal, and I think the authors should have been more forthcoming about the lack of an established neural signal that directly signals what they want in their model.

(4) The authors point out that the perceptual biases they measure take a few seconds to emerge and they attribute this to temporal integration. But in their curl manipulations, they temporally average over a 2.4 second window in computing the curl signals that they use to cancel or over-cancel curl. So, it is not clear whether some of the delay in the behavioral effects might result from their computations.

(5) Related to point #13 of my previous review: I had asked about empirical evidence for the assumption of a relationship between the heading preferences of MSTd neurons and their receptive field locations. In response, the authors state that such a relationship is built into the Layton and Browning (2014) model. While that is a precedent, citing another model as a response to a question about empirical evidence is not a convincing response. If there is no empirical evidence to support such a relationship, it would have been better for the authors to acknowledge this.<br /> Given the way that the eLife review model works, it is not necessary for the authors to address these comments, but I think they should be included in the public review record.

Reviewer #2 (Public review):

Here, the authors record dopamine release using fast-scan cyclic voltammetry in the nucleus accumbens/ ventromedial striatum (VMS) while rats perform variants of a go/no-go task. Two versions are self-paced, in that the rat can initiate a trial by nosepoking at the odor port at any time once the ITI had elapsed, whereas the other two require the rat to wait for a cue-light before responding. Two "long" variants also require either more lever-presses on go trials, or a longer nosepoke time for no-go trials, and also incorporate "free" trials in which the rat is rewarded for just heading straight to the food tray. The authors find that dopamine levels increase more during the response requirement for go than no-go trials, indicating a role for invigorating to-be-rewarded actions. Dopamine levels also steadily increased as rats approached the site of reward delivery, and the authors demonstrate quite elegantly that this was not due to orientation to the food tray, or time-to-reward, or action initiation, but instead reflects spatial proximity to the rewarded location. Contrary to previous reports, the authors did not discern any differences in dopamine dynamics depending on whether the trials were cue- or self-paced, and dopamine release did not scale with effort requirements.<br /> The manuscript is well-written and the authors use figures to great effect to explain what could otherwise be a hard-to-parse set of data. The authors make good use of the richness of their behavioral data to justify or negate potential conclusions.

Reviewer #2 (Public review):

Summary:

The manuscript from the Rice lab by Gangadharan et al., submitted to eLife, investigates the polymerization mechanism of the yeast microtubule polymerase Stu2. The lab has published a number of articles demonstrating the structural basis by which the two TOG domains of Stu2 each bind free tubulin heterodimers and has developed a tethered polymerization model by which the TOG domains drive polymerization by shuttling those tubulin subunits onto the microtubule plus end. A second model was proposed by Nithianantham et al. (eLife, 2018) based on a closed - to - open transitional state in which Stu2 unfurls and loads two longitudinal associated tubulin heterodimers onto the microtubule plus end. While the second model is not directly tested, the current work aims to further characterize/model the tethered polymerization model using a kinetic framework developed by developed by Breitsprecher et al. for Ena/VASP actin polymerization activity, using a model that is enzymatic (EMBO J., 2011). The general architecture and function of Ena/VASP on actin polymerization versus Stu2 on microtubule polymerization is a reasonable relation and hits upon, as the authors note, potential convergent mechanistic evolution across distinct cytoskeletal networks. The model effectively treats tubulin as the substrate, and the polymerized microtubule plus end as the product. If Stu2 is "enzymatic" in this framework, the model predicts it would behave with Michaelis-Menten kinetics, that there would a Vmax, and polymerase activity would either be "affinity limited" by TOG:tubulin affinity (KD) and/or "kinetically limited" by TOG:tubulin association (Kon) and transfer of tubulin to the microtubule plus end (Kt). The authors find that the Brietsprecher model works well for Stu2 activity, and that Stu2 best aligns with a "kinetically limited" model. The work is interesting and adds to the growing elucidation of the Stu2 microtubule polymerase model. While yeast microtubule polymerases are somewhat distinct in their architecture, there is significant overlap that findings from the manuscript can be utilized to inform the mechanisms of larger, more complex microtubule polymerases such as human ch-TOG.

Strengths:

The manuscript invokes the enzymatic model of Breitsprecher et al. used for Ena/VASP and conducts an elegant series of (mostly established) experiments to determine whether Stu2 microtubule polymerase activity aligns with the model - which they conclude does align, supported by the data/results obtained.

Weaknesses:

The authors used biolayer interferometry to measure TOG:tubulin affinity. The affinities obtained were significantly higher affinities than the lab obtained in an earlier publication using analytical ultracentrifugation. While differences in buffer and salt conditions may underlie these differences, additional runs using comparable buffer systems, or use of a third independent assay to measure affinities would have added rigor.

The discussion could be expanded to better compare and contrast the results with both existing polymerase models introduced in the introduction, as well as expanded to look at reversible enzymatic activity (microtubule depolymerization at low to zero tubulin concentrations) and microtubule plus versus minus end activity.

Comments on revised version.

The revised submission has addressed these comments adequately.

Reviewer #2 (Public review):

Summary:

In this manuscript, Gracia-Alvira et al. investigated how environmental temperature affects competition among members of the microbiome, with a focus on intraspecific diversity, using the Drosophila model.

Notably, the authors identified three clades of Lactiplantibacillus plantarum from a natural population of Drosophila simulans collected in Florida. They tracked the dynamics of these three bacterial clades under two temperature conditions over the course of more than ten years. Using comparative genomics and phylogeny, they showed that these three bacterial clades likely adapted to their host independently in a temperature-specific manner. Further, by combining in vitro culture and in vivo mono-association assays, they demonstrated the functional divergence of these three bacterial clades phenotypically, including their growth dynamics and effects on host fitness. Lastly, they performed pathway analysis and speculated on key genomic variance supporting such functional divergence.

Strengths:

The laboratory evolutionary experiment in response to cold or hot environmental temperature is impressive, given its more than ten years of experimental time period. This collection of achieved microbiome samples paired with the fly host data can be a valuable resource for the field.

Comments on revised version:

The revised version has addressed my major points raised in the original review.

Reviewer #2 (Public review):

Uphoff and colleagues present the results of a study focused on characterizing the binding of SVEP1 to TIE1 along with Angiopoietin-2. Starting with computational prediction of SVEP1 binding to TIE1, the authors identify the region of SVEP1 that serves as a high-affinity ligand for TIE1. Advanced studies identify a weak secondary binding site within SVEP1 that appears to be sufficient but not necessary for its interaction with TIE1 based on in vivo rescue experiments. The most novel contribution of the manuscript seems to be the identification of angiopoietin-1 and -2 as co-factors that seem to enhance the binding of SVEP1 with TIE1 and impact downstream AKT signaling. They propose a complex in which SVEP1 binds to TIE1 and ANG2.

Although the first set of results is essentially confirmatory, the identification of ANG-2 as a "co-factor" enhancing the binding of SVEP1 to TIE1 and associated downstream signaling (i.e., Figures 3 and 4) is novel and is of interest. However, the manuscript and its conclusions would greatly benefit from some clarifying details and additional experiments to ensure rigor and support specific claims.

Comments on revised version:

I have no further comments. The authors have addressed my concerns.

Reviewer #2 (Public review):

Summary:

This study aims to test the hypothesis that microsaccades are linked to the shifting of spatial attention, rather than the maintenance of attention at the cued location. In two experiments, participants were required to judge an orientation change at either a validly cued location (80% of the time) or an invalidly cued location (20% of the time). This change was presented at varying intervals (ranging from 500 to 3,200 ms) after cue onset. Accuracy and reaction times both showed attentional benefits at the valid versus invalid location across the different cue-target intervals. In contrast, microsaccade biases were time-dependent. The authors report a directional bias primarily observed around 400 ms after the cue, with later intervals (particularly in Experiment 2) exhibiting no biases in microsaccade direction towards the cued location. Noteworthy, it would have been interesting to observe whether directional biases in microsaccades are also evident when compared to a neutral condition. The authors argue that this finding supports their initial hypothesis that microsaccade biases reflect shifts in attention, but that maintaining attention at the cued location after an attention shift is not correlated with microsaccade direction.

Strengths:

The results are straightforward given the chosen experimental design. The manuscript is clearly written, and the presentation of the study and its visualisations are of a high standard.

Weaknesses:

The link between attention and microsaccades has been the subject of extensive research over the past two decades. The authors present a potential solution to the conflicting past findings, arguing that attention should be considered a dynamic process that can be broken down into an attention shift and a sustained attention phase. To differentiate between the two components, the authors varied the interval between the onset of the attention cue and the test stimulus. It would have been nice to use a theory-driven criterion (or an independent measure), in addition to their data-driven approach, to distinguish between these components of a dynamic attention concept. Moreover, it is important to note that the current experiments take a purely correlational approach.

Reviewer #2 (Public review):

Summary:

This manuscript addresses an important and mechanistically interesting question: whether plasma membrane glutamate transporters contribute only to slow clearance of ambient glutamate or whether they can rapidly shape synaptic signaling during high-frequency auditory activity. This manuscript provides important evidence that EAAT-mediated glutamate uptake is not merely a slow background clearance mechanism but is essential for maintaining reliable synaptic transmission and linear stimulus-intensity coding in ventral cochlear nucleus T-stellate cells during sustained auditory nerve activity.

Strengths:

The finding that EAATs may be required for rapid, local control of glutamate during high-frequency auditory nerve activity is interesting and could have broad relevance to auditory processing. The electrophysiological evidence is generally strong, particularly the use of patch-clamp recordings, stimulus trains, partial versus complete EAAT blockade, and comparison with bushy cell/endbulb synapses. The comparison between T-stellate cells and bushy cells/endbulb synapses strengthens the manuscript. The authors demonstrate that EAAT blockade disrupts coding in T-stellate cells but has little effect on bushy cell spike transmission, supporting a cell-type- and synapse-specific role of glutamate uptake.

Weaknesses:

However, some mechanistic conclusions, especially the specific contribution of neuronal versus glial EAATs and the absence of glutamate crosstalk between auditory nerve inputs, rely mainly on pharmacological and indirect electrophysiological inference and would be strengthened by additional anatomical, genetic, or direct glutamate-sensing evidence.

(1) Clarification of DL-TBOA concentration.

The authors used bath application of 200 µM TBOA and 25-50 µM in the other experiments, stating that "sub-maximal concentrations (25-50 µM)". The authors should provide a clearer rationale for why different concentrations were used across experiments rather than a fixed concentration.

The reversibility of DL-TBOA effects should be demonstrated by washout experiments. In addition, potential off-target effects of DL-TBOA on postsynaptic receptors, intrinsic membrane excitability, or presynaptic release (e.g., PPR measurement) should be carefully considered. It would also be useful to test the effects of the submaximal DL-TBOA concentrations (25-50 µM) on membrane potential and inward currents, shown in Figure 1, to determine whether these concentrations depolarize the membrane potential in current-clamp mode or induce inward currents under voltage-clamp conditions.

(2) Potential contribution of altered intrinsic excitability.

In Figures 3B and 3C, DL-TBOA appears to induce additional action potentials even immediately after the first stimulation, whereas Figures 6 and 7 suggest that the first EPSC is not substantially altered. This raises the possibility that the enhanced firing may partly result from a modest depolarization caused by background glutamate accumulation or from other changes in intrinsic membrane properties after drug treatment. To address this, the authors should provide a quantitative analysis of physiological parameters under submaximal DL-TBOA conditions, including spontaneous action potential frequency, resting membrane potential, input resistance, and spike threshold.

(3) Spillover/ crosstalk between AN-fiber-synpases.

The authors should provide more explanation of how altering the number of active auditory nerve fibers demonstrates the absence of glutamate spillover/crosstalk between bouton synapses. Strong stimulation likely recruits more AN fibers, but it may also change release probability, axonal synchrony, or stimulation spread. The authors should more clearly justify the interpretation that strong stimulation recruits additional independent AN fibers rather than altering release probability or activating fibers with different intrinsic properties.

(4) Interpretation of glial versus neuronal EAAT contributions.

The authors claim that both neuronal and glial transporters contribute to rapid uptake using pharmacological approaches. The pharmacological data demonstrate that glial EAATs play a major role in glutamate clearance at T-stellate cell synapses. The strong increase in EPSC decay time and synaptic charge after UCPH-101/DHK application supports the conclusion that glial transporters contribute substantially to limiting glutamate accumulation during sustained auditory nerve activity. However, the conclusion that neuronal EAATs contribute directly should be stated with some caution. The evidence for neuronal EAAT involvement is indirect and depends on the pharmacological specificity and completeness of glial EAAT blockade. The conclusion would be strengthened by additional evidence, such as EAAT subtype expression/localization in T-stellate cells or auditory nerve terminals, transporter current recordings, immunohistochemistry, or genetic manipulation of neuronal EAATs. In addition, fitting the decay phase with a double-exponential model may help determine whether glial and neuronal EAATs contribute over distinct temporal windows.

Reviewer #2 (Public review):

This manuscript describes the fascinating phenomenon of growth hormone (GH)-independent growth occurring in the mother during pregnancy. This growth was most pronounced in dwarf mice that are lacking the receptor for growth hormone-releasing hormone (GHRH) and therefore showing isolated GH deficiency. However, the pregnancy-induced growth could also be observed in wild-type mice, suggesting that it is a normal part of the maternal adaptation to pregnancy. The study falls short of identifying the mechanism(s) driving this pregnancy-induced growth response, but it certainly reveals a novel insight into maternal physiology. The authors have completed a range of experiments in mice to prove that, as well as being GH independent, the pregnancy-induced growth also did not require GH signaling in the liver (i.e. not another pregnancy-specific ligand operating through the GHR to promote IGF). They also provided complementary data from a population of humans with untreated isolated GH deficiency that are broadly consistent with the hypothesis. While it is important to consider the significant species differences between rodents and humans, both in terms of growth physiology and also in terms of evolution of placental somato-mammotrophic hormones, this unique population are a valuable resource and adds credence to the study. Overall, I find this a compelling research story, but disappointingly unfinished. There are some areas where additional information could improve the ability to interpret the data, and some additional concepts that could be considered in the discussion. There are also areas where additional experiments might provide important insights. However, I think that such suggestions can be considered as appropriate for future research, rather than delaying consideration of the current manuscript.

Main comments:

(1) Data in Figure 1 are remarkable - not so much the growth in pregnancy in the wildtype mice, because while elevated GH is well known in pregnancy, but growth in the dwarf mice is indicative of GH-independent growth. From these data, it seems that there is good evidence that growth in pregnancy is an adaptive function. However, it is possible that growth is achieved in dwarf mice and that in wildtype mice may have been mediated through different mechanisms. The dwarf mice showed an increase in liver and plasma IGF1, suggestive of an additional ligand driving IGF in pregnancy. One could hypothesize that such an effect could be mediated by an additional pregnancy-specific ligand activating the GH receptor. In humans, placental growth hormone could be such a ligand, but as far as we know, there is no placental GH in mice. In contrast, the wildtype animals showed suppression of liver and circulating IGF1, and low levels of pSTAT5 in the liver during pregnancy. These data (in Figure 5) are very surprising. Given the high circulating GH in pregnancy, as well as high placental lactogen (which would be expected to activate STAT5 in the liver through the Prlr), the low levels of pSTAT5 are unexpected and would seem to indicate some sort of acquired insensitivity to GH. Is this entirely driven by down-regulation of STAT5b protein, or could there be activation of other, negative regulators of STAT signalling, such as SOCS? What is causing such a profound suppression of STAT5? Regardless of the mechanism, this suggests that pregnancy-induced growth in wildtype mice is independent of circulating IGF1 (potentially a different mechanism or in addition to that seen in IGHD mice).

The data shown in Figure 6 are a major strength of the study, showing that the pregnancy-induced changes are not specific to one particular transgenic model, but still occur in a variety of models affecting GH through different approaches. Given the pregnancy-specific nature of the changes, however, it seems an oversight not to have evaluated the role of placental lactogens. Prlr is highly expressed in the liver, but the function of this hormone in the liver is not well established. Could the extremely high levels of PL be mediating this growth response? Given the low expression of STAT5 in the liver and the fact that plasma IGF1 is not markedly elevated, it seems more likely that this growth response may be mediated by locally produced IGF1 in target tissues.

I think these possibilities could be addressed by an expanded discussion of species variation in placental hormones, to highlight that humans have expansion of the GH locus, but rodents have expansion of the prolactin axis (see Soares, M. J. The prolactin and growth hormone families: pregnancy-specific hormones/cytokines at the maternal-fetal interface. Reprod Biol Endocrinol 2, 51, 2004). Importantly, placental GH and chorionic somatomammotropins (CSM) in humans are all variants of the GH gene, but CSM have preferential activity at Prlr. This seems to be a fundamental species difference in pregnancy biology, but has been interpreted as an example of convergent evolution, with conservation of prolactin and GH-like functions at the maternal-fetal interface, mediated by different mechanisms, likely contributing to the metabolic adaptations of the mother (see Newbern D, Freemark M. Placental hormones and the control of maternal metabolism and fetal growth. Curr Opin Endocrinol Diabetes Obes. 2011; 18: 409-416). While the preceding function has focused on explaining the evolution of placental lactogens (either prolactin or GH variants), the present data suggest that there are also mechanisms to maintain growth in pregnancy, independent of GH (even in the absence of a placental GH).

(2) The human data are very interesting, and my initial impression was that it seemed unlikely to be the same phenomenon. Was there any real evidence for "growth" in pregnancy? Pubertal maturation of long bone growth might be expected to prevent further growth in adulthood. However, these issues were appropriately discussed, and it seems well justified to evaluate this unique population of women with IGHD who underwent pregnancy. It would be very interesting to know if these women experienced elevated IGF1 during pregnancy, indicative of placental GH contributing to growth. Mechanistically, this might be more like the dwarf mouse situation of IGHD, that the situation in wildtype mice (associated with liver insensitivity to GH and low IGF1).

(3) It would be useful to include investigations that isolate the effects of pregnancy and the placental hormones. Such studies could include evaluating growth in pseudopregnant mice with IGHD (pregnancy-like changes in hormones but lacking the placental contribution) and in IGHD animals that experience pregnancy but not lactation (pups removed at birth). I accept that this might be too large an additional study to add for the present manuscript.

(4) It is an important and translationally relevant observation that pregnancy increased the risk of long-term weight gain, and that after the first pregnancy, the pregnancy-induced growth response was more directed to promoting fat deposition. Does this provide any mechanistic insight? Could a metabolic adaptation result in growth?

Reviewer #2 (Public review):

Summary:

This study uses neurofeedback to modulate alpha-band activity and examines how this influences pain-related processing. The question is timely and methodologically elegant, because it addresses whether noninvasive modulation of ongoing oscillatory activity can causally shape pain perception and/or expectation-related processes.

Strengths:

The use of neurofeedback as a tool to modulate alpha activity is a major strength, because it provides a noninvasive and conceptually clean approach to probing the functional role of oscillatory brain activity. The design is also attractive because it links neurophysiological regulation to a psychologically meaningful outcome, namely pain processing. Further, the induced changes were also related to different EEG microstates and ERP components during the processing of the pain stimulus, and therefore the authors demonstrate a clear relation between preparatory prestimulus states and stimulus processing.

The manuscript appears to address an important and clinically relevant question, and the idea of testing whether alpha regulation can alter pain-related responses is of high interest for systems neuroscience and pain research.

Weaknesses:

Methodologically, it is unclear what alpha values were used in the analyses. It is stated that alpha was extracted within 2s windows of the 16s long feedback period. However, the values change across this period. Which value is used for the correlation with the pain ratings and all other analyses? Using the average across the 16s could reflect large values in the first half and low values in the final half, but for the relationship between alpha and pain, the last segments should be more relevant. If the initially elevated alpha activity subsides several seconds before the onset of the pain stimulus, it is difficult to see how it could influence subsequent pain processing.

Related, after the 16s feedback period, a fixation period is used with a 3-5s length. If alpha band activity is relevant for the consecutive pain processing, the amount of alpha in this period should be relevant. The authors should demonstrate that the induced alpha change during the feedback period remains stable during the fixation period and that the activity in this period is related to pain processing.

Further, it should be noted that the alpha band modulations related to alpha band training were accompanied by significant effects in other frequencies. Therefore, a clear relationship between alpha and behavioral pain ratings is not the only interpretation. Correlations with other frequencies or combinations of frequency band modulations should be incorporated to allow a more precise interpretation. Furthermore, in the sham feedback group, an increase in alpha band activity was observed (p=0.06), and the small difference in the pain intensity rating may be related to a clear outlier in the Sham group (Figure 4a).

In both groups, a main effect of training, regardless of sham or real feedback, was reported with a small difference between groups. But the main modulator seems to be related to the instruction to modulate the neural activity, and this large effect should be discussed in more detail regarding, for example, possible attentional processes.

A further central concern is that the visual feedback signal (the ball movement) may generate expectations that are not specific to alpha activity and that these expectation processes modulate the pain processing (ball down may indicate more pain). It is well known that intensity cues can generate expectations about upcoming perceptions, and the used feedback signal with an increasing or decreasing visual curve clearly signals what intensity should be expected. Therefore, it is important to show that the amount of positive (ball up) and negative visual displays is matched between the sham and real feedback group. Further, the authors should report whether the final ball position can predict the latter pain rating in both groups or differentially. Following this interpretation, alpha band activity is not directly related to pain processing but only serves as a signal that is transformed to a visual stimulus that then generates expectations.

Finally, the manuscript would benefit from a more explicit analysis of whether individual alpha changes are related to pain ratings within each subject. If higher alpha is truly linked to reduced pain perception, this should be visible at the participant level during learning of the neurofeedback procedure. Relatedly, there is no learning period incorporated, and usually participants are not able to regulate their alpha activity from the first trial on. The authors should include an analysis of the development of alpha band activity over learning and a relation of these individual alpha values and the corresponding pain ratings.

I cannot find a link to the preregistration in the current manuscript.

In summary, a "causal" relation of alpha activity with pain perception -that is mentioned several times in the manuscript- is not fully supported by the present results

Reviewer #2 (Public review):

Summary:

The study tests whether male/female-related information is represented in a form that generalizes across faces, bodies, and gender-associated objects. Using within- and cross-category MVPA, regression RSA, comparisons with fine-tuned CNNs, and connectivity analyses, the authors identify a right middle temporal gyrus region whose patterns generalize across the three stimulus classes. They conclude that this region provides a category-general, mid-level representation of gender and acts as a neural hub.

Strengths:

The question is novel and important, while the logic of the study is straightforward. Examining faces, bodies, and objects within the same participants provides a useful extension beyond the predominantly face-based literature. Cross-category decoding is also a stronger test of shared information than simple anatomical overlap between within-category maps. The combination of MVPA, RSA, computational modelling, and connectivity analysis is ambitious, and the replication of the CNN layer profile with both AlexNet and VGG16 is a useful characterization of relevant information.

Weaknesses:

(1) The construct labelled "gender" is not equivalent across stimulus classes. For faces and bodies, the male/female label is intended to track a property of the depicted person, albeit one inferred imperfectly from appearance; for objects, masculinity or femininity is not an intrinsic property of the object but a culturally contingent association that may vary across observers and contexts. Treating both as levels of a single binary factor risks conflating person-category information with gender-stereotypic object associations and interpreting their common neural discriminability as evidence for one abstract concept of gender. The term "object gender" could also be confused with grammatical gender in some languages (e.g., French or German).

(2) The CNN analysis does not isolate the shared male/female component. The authors correlate the complete six-condition neural RDM with the complete CNN RDM. However, rMTG also carries substantial information about whether an image is a face, body, or object. Consequently, the peak correspondence with Conv4 may reflect category structure rather than the representation that supports cross-category male/female decoding. The current analysis does not establish that shared gender-related information specifically depends on mid-level features.

(3) The connectivity interpretation is overstated. PPI measures task-dependent covariance; it does not establish information transmission, directionality, or an upstream-to-downstream processing sequence. The reported face-body connectivity similarity is also small (r=.08). Also, describing rMTG as a "hub" is not justified without network-centrality measures, lesion evidence, or causal perturbation.

The authors partly achieve their aims. The results provide credible evidence that patterns in rMTG contain information that generalizes across binary male/female-labelled faces and bodies and masculine/feminine-associated objects. They do not yet establish a genuinely abstract representation of gender, a specifically gender-related correspondence with intermediate CNN layers, or a neural hub that transmits information through a directed network. With more precise framing and targeted reanalysis, the study could make a useful contribution to research on social vision and cross-category representation.

Reviewer #2 (Public review):

Summary:

The authors extend the ORGaNICs framework (a recurrent circuit that dynamically implements divisive normalization) to connected cortical areas with explicit top-down feedback. Because the network has a known analytical fixed point that coincides with (or closely approximates) the normalization equation, the authors can linearize about that fixed point and derive closed-form expressions for the power spectral density, inter-areal coherence, and communication subspaces. Using a two-area instantiation (V1 & V2) with a single fixed parameter set and no data fitting, they show the model reproduces: (i) contrast-response functions with steeper slope V2; (ii) gamma-band power and coherence peaks that shift to higher frequency with contrast; and (iii) a low-dimensional inter-areal communication subspace that is lower-dimensional than the within-area subspace. They derive parallel predictions of what happens by changing model parameters: feedback gain enhances inter-areal and suppresses within-area communication, and normalization is necessary for both the oscillatory dynamics and the reduced subspace dimensionality. A three-area extension (V1&V4, V1&V5/MT) is used to argue that differential top-down feedback can dynamically route functional connectivity.

Strengths:

(1) Analytical tractability: Deriving power spectra, coherence, and communication-subspace structure in closed form from a known fixed point is genuinely valuable.

(2) Conceptual unification: Framing coherence and communication subspaces as arising from the same normalization-driven dynamics is an elegant and useful contribution.

(3) Breadth from few assumptions: A large range of phenomena (contrast gain, gamma dynamics) emerges from normalization-based model assumptions.

(4) Biological grounding: The mapping of model variables onto identified cell types connects the abstract computation to known cortical microcircuitry.

(5) The prediction that input-gain versus feedback-gain modulation produce distinct spectral signatures gives experimentalists a clear way to test the framework.

Weaknesses:

(1) Comparisons are qualitative, not quantitative: The theory/experiment panels are visual side-by-side comparisons. There is no quantitative goodness-of-fit for any predictions.

(2) The simulations use τ ≈ 1 ms for all cell types, which the authors acknowledge is unrealistically short; realistic values would shift the gamma peaks to lower frequencies.

(3) Divisive normalization is a special case and is recovered exactly only for the identity recurrent matrix (self-normalization). Some statements that the circuit implements divisive normalization exactly need softening.

(4) The element-wise (multiplicative) interaction in the modulator dynamics is not tied to a specific cellular mechanism.

Reviewer #2 (Public review):

Summary:

The authors provide the first thorough profiling of neurons in Tribolium characterized by the expression of the transcription factor foxQ2, which will be useful for developmental neurobiology. They use state-of-the-art methods convincingly to not only identify the neurons, but also to further characterize them anatomically and neurochemically.

Strengths:

Thorough and meticulous application of state-of-the-art anatomical methods in a non-standard laboratory organism.

Weaknesses:

No weaknesses were identified by this reviewer.

Comments:

I don't really have any major suggestions at all. Loved the work.

There is only one tiny nitpicking aspect:

P21: "Biogenic amines are involved in learning and memory and setting arousal threshholds (Davis, 2023), which are functions performed by the mushroom bodies and related to the function of the central complex in goal directed navigation, respectively."

MBs mainly process olfactory memory. At least in Drosophila, most other kinds of memories are being supported elsewhere.

https://pubmed.ncbi.nlm.nih.gov/10454381/

such as, e.g., visual pattern learning in the CX

https://pubmed.ncbi.nlm.nih.gov/16452971/

or motor learning in motor neurons

https://pubmed.ncbi.nlm.nih.gov/38779314/

or ventral ganglion, antennal lobes, and median bundle for place learning:

https://pubmed.ncbi.nlm.nih.gov/10706599/

If the authors focus on MBs, this sentence ought to reflect the fact that the function of the MBs is much narrower than the current sentence appears to suggest.

Reviewer #2 (Public review):

Summary:

This work provides an open-source, Python-based, graphical user interface for curating the detection and classification of dentate spikes (DSs) from hippocampal local field potential (LFP) recordings. The tool may also be used to detect, but not classify, sharp wave-ripples (SPW-Rs). The tool utilizes previously published Python packages for loading LFP files and creating experiment-specific probe objects. Detection and classification parameters are clearly defined and logged in a parameter file before starting processing. Once LFP data has been mapped to the probe object, event detection occurs across all channels. DSs are detected as qualifying peaks in the filtered DS band LFP, while SPW-Rs are detected as qualifying peaks in the filtered ripple band amplitude envelope. An initial curation step allows visualization of the LFP, instantaneous current source density (CSD), and depth-by-frequency band power plots for determining the approximate channel locations of key anatomical regions (i.e., CA1, the hippocampal fissure, and the hilus of the dentate gyrus). The optimal channel for detection is further refined in the next step by comparing event waveforms and quality metrics across channels. Artifacts and noisy waveforms can also be manually excluded during this step. Finally, DSs detected from the optimal channel are classified by computing the CSD profile around events and then clustering the first two principal components of all CSDs. The authors claim that this customizable tool will standardize DS detection and classification.

Strengths:

Toothy's detection and classification algorithms are appropriate and well-validated in the literature. The ability to change many parameters, the CSD calculation method, and clustering algorithm is helpful for precise replication of methodology that has varied previously. Default parameters optimized for mouse recordings provide a standardized starting point for rodent researchers.

The authors' commitments to transparency and user-friendliness are to be commended (e.g., clear instructions, defined and logged parameters, multiple visualization options, etc.) and are likely to be appreciated by new users. Researchers with little-to-no coding experience should find this tool especially powerful for jumpstarting their own DS analyses.

While not the focus of the paper, the capability to detect SPW-Rs provides an additional use case for Toothy and streamlines simultaneous analysis of SPW-Rs and DSs.

Weaknesses:

I encountered unexpected errors while trying to load LFP data into Toothy for testing, indicating that the "data ingestion" stage of Toothy requires minor code revision.

Toothy's utility for recordings that do not produce an LFP depth profile is unclear. According to the authors, Toothy allows probe designs with irregular spatial sampling (e.g., tetrodes) to be used. However, recording from a linear probe with electrodes spanning from approximately the hippocampal fissure to the hilus of the dentate gyrus is required for Toothy's full functionality. For example, Toothy uses a DS type classification algorithm that relies on sufficiently sampled CSD depth profiles that tetrode recordings cannot provide. As such, usage is currently restricted to detection only for certain recording setups.

The documentation on Toothy's output could be improved. Specifically, the work does not state which files different data are saved to or list the properties saved per detected event. Furthermore, the work does not discuss the potential importance of DS properties that are saved besides those related to the timing of the DS and its type.

Reviewer #3 (Public review):

In this manuscript, the authors investigate the role of attention in foveal processing during a naturalistic task. They record neural activity from extrastriate visual areas V4 and inferotemporal cortex, as well as from the lateral prefrontal cortex, in macaques performing a free-gaze visual search task. In this task, animals searched for a face or house target among multiple complex stimuli, with no constraints on eye movements. Unlike classic studies of visual attention, which often rely on controlled fixation, this work examines neural activity in both foveal and peripheral receptive fields during naturalistic eye movements.

The main question addressed by the authors is how feature-based attention is distributed and coordinated across foveal and peripheral visual fields during active search, and how this attentional processing influences saccade behavior. The authors show that foveal units in visual areas exhibit feature-based attentional enhancement, with stronger responses when a fixated stimulus is a target compared to when the same stimulus serves as a distractor. Peripheral units in visual and prefrontal areas show both feature-based and spatial attentional modulation, consistent with prior work. Finally, the authors show that attentional modulation depends primarily on stimulus category rather than response magnitude, with neurons showing similar enhancement for all images within the target category regardless of how strongly individual images drive the cell.

There are several notable strengths of this paper including:

(1) Disentangling feature-based and spatial attention during naturalistic vision remains a central challenge. This paper tackles both simultaneously, parsing neural populations by object selectivity (face-selective, house-selective, non-selective) and RF position (foveal vs. peripheral).

(2) The unconstrained search task (Fig. 1A) moves beyond the dominant fixed-gaze, cued-attention designs (Zhou & Desimone, 2011) to study attention as it operates during natural behavior, with sequential fixations and voluntary saccades.

(3) The scale of the multi-area recordings is a major strength and is well aligned with current trends in primate and human neuroscience toward large-scale, multi-area recordings. Simultaneous recordings from visual and prefrontal areas, comprising over 4,900 foveal units and more than 1,500 peripheral units, enable meaningful cross-area latency comparisons and area-specific analyses of attentional modulation. This study builds on the authors' previous analyses of this dataset by expanding the scope to show that feature-based attention generalizes across neuronal classes and operates on categorical identity rather than response magnitude.

(4) The combination of simultaneous multi-area recordings and a rich behavioral paradigm provide a dataset that is well suited for population decoding, cross-area interaction analyses, and trial-by-trial prediction of saccade choices, which could substantially deepen mechanistic understanding beyond the largely univariate comparisons presented here.

While the data broadly support the paper's main conclusions, several issues limit the strength of the mechanistic interpretation and should be taken into consideration:

(1) Receptive field size is not explicitly quantified and may confound foveal-peripheral comparisons. Units are classified as foveal or peripheral based on responsiveness to the cue versus the search array (Methods, p. 17), but the manuscript lacks essential information about receptive field sizes, eccentricities, and the number of search stimuli falling within each receptive field and related proper controls. This is critical because receptive fields in visual area V4 at foveal eccentricities are relatively small (Gattass et al., 1988; Desimone & Schein, 1987), whereas receptive fields in inferotemporal cortex can span several degrees to tens of degrees and often include the fovea (Op de Beeck & Vogels, 2000; DiCarlo & Maunsell, 2003; Zoccolan et al., 2007). Given the 2{degree sign} × 2{degree sign} stimulus size, multiple search items could potentially fall simultaneously within peripheral receptive fields. This introduces a potential confound, as attentional modulation is known to be strongest when multiple stimuli appear within a single receptive field (Reynolds et al., 1999). Although the authors acknowledge this issue for visual area V4 (p. 17), it is neither quantified nor controlled for. Without explicit receptive field mapping relative to the search array, comparisons between foveal and peripheral units, as well as between visual areas, are difficult to interpret cleanly.

(2) Attentional modulation is difficult to dissociate from saccade planning and decision-related signals. The free-gaze paradigm enhances ecological validity but introduces a temporal confound: mean distractor fixation durations are approximately 156 ms (p. 9), while attentional effects emerge between 137 and 170 ms after fixation onset (Fig. 2). As a result, the reported attentional modulation coincides with preparation of the subsequent saccade. Neural activity measured in the primary analysis window (150-225 ms; p. 19) therefore likely reflects a mixture of visual, attentional, motor planning, target recognition, and behavioral relevance signals, all of which are known to modulate responses in visual areas at similar latencies (e.g., Chelazzi et al., 1998). Moreover, target fixations (~257 ms) and distractor fixations (~156 ms) occur on fundamentally different behavioral timescales, which may inflate apparent foveal attentional effects. While the authors suggest that these timing differences support the idea that foveal feature-based attention facilitates prolonged fixation on target stimuli, this interpretation is not fully supported by the current analyses. That said, the saccade-aligned analyses of peripheral units (Fig. S3) partially mitigate this concern by demonstrating that feature-based modulation persists through saccade execution.

(3) The "attention-out" condition for spatial attention lacks directional control. In the spatial attention analyses (Fig. 4D-F), the "attention-out" condition appears to include all fixations followed by saccades directed away from the receptive field, regardless of saccade direction. This differs from classic spatial attention designs, which typically use controlled anti-saccades or saccades to fixed locations opposite the receptive field (e.g., Moore & Armstrong, 2003; Gregoriou et al., 2009). Saccades directed toward locations adjacent to, but outside, the receptive field may still partially engage spatial attention mechanisms near the receptive field via broad attentional fields or motor preparation gradients (Bisley & Goldberg, 2010). In addition, the "attention-out" condition likely contains a heterogeneous mixture of trials in which the stimulus in the receptive field is either a target or a distractor, since feature-based attention effects are derived from this same pool of trials. As a result, spatial and feature attention effects are not fully orthogonal, and variance related to feature attention may already be embedded in the spatial attention baseline.

[Editors' note: the authors have provided responses to each of these points.]

Reviewer #2 (Public review):

Summary:

Song et al. comprehensively analyzed the SHIV-infected macaque B cell repertoires and commonalities among their antibody responses, despite their diverse genetic background. They suggest these studies would inform HIV-1 vaccine design.

Strengths:

This study is well-designed and used proper analysis methods, and the figures are clear and effectively presented.

Weaknesses:

However, it tends to overstate its novelty and significance, emphasizing points that are relatively obvious (e.g., different classes of antibodies can recognize a common epitope) and appears to have been overwritten and unnecessarily fancy ("conceptually analogous to ecomorph evolution", "epitopic convergence"). Moreover, some limitations of the rhesus macaque model and the differences between bnAbs and nAbs should be discussed. That said, the underlying data are solid and important in their detail, and the manuscript will be a useful resource for HIV-1 vaccine and pathogen studies.

Reviewer #2 (Public review):

Summary:

Foik et al. studied the regulation of the fro operon in response to HOCl, an oxidant derived from immune cells, especially neutrophils. They use a transcriptional fusion of YFP to the froA promotor in an mCherry expressing P. aeruginosa strain to determine fro-induction under the microscope. They use this system to study fro expression in medium, in the presence of neutrophils and macrophages, neutrophil-conditioned medium, and several chemical stimuli, including NaCl, HOCl, hydrogen peroxide, nitric acid, hydrochloric acid, and sodium hydroxide. They also use a corneal infection model to demonstrate that froA is upregulated in P. aeruginosa 20 h post infection and perform transcriptional analyses in WT and a froR mutant in response to HOCl.

Strengths:

Their data clearly shows that HOCl is a strong inducer of the fro Operon. Addition of HOCl-quenching chemicals together with HOCl abrogates the response. They also show that a froR mutant is more susceptible to HOCl than WT. Their transcriptomic data reveals genes under control of the FroR/FroI sigma factor/anti sigma factor system.

Weaknesses:

Although the presented evidence is mostly solid, some of their findings need to be evaluated more carefully; explaining the rationale behind some of the experiments might enhance the article; and some of the models proposed by the authors seem far-fetched, as outlined below:

Unexpected outcomes and open questions for future research:

(1) As outlined above, HOCl seems to be the main inducer of the fro operon. Interestingly, during interaction with immune cells, macrophages and neutrophils seem to induce a reporter gene under fro control in a similar manner, although macrophages are generally thought to produce less HOCl, when compared to neutrophils. May be this view needs to be revised, or another reactive species, produced by macrophages, can activate the fro operon as well.

(2) HOCl is typically unstable in the presence of biomolecules. Nevertheless, medium conditioned by activated neutrophils is a strong inducer of the fro operon. The medium used by the authors for this experiment contains taurine, and, as the authors acknowledge, this taurine will likely react with HOCl to form the more stable taurine N-chloramine. Similarly, the MinA bacterial medium used to treat P. aeruginosa with HOCl directly also contains ammonium ions at mM concentrations, which could potentially react with HOCl to form monochloramine. It could be speculated that taurine N-chloramine and other chloramines are as effective as HOCl in activating the fro-operon.

(3) The fro operon was originally described to be activated by shear stress ("flow-regulated operon"). How shear stress and HOCl-stress are related, or if fro activation by both stimuli is a coincidence, remains unclear. The authors propose a model, in which flow transports oxidizing molecules, which ultimately activate the fro operon. However, the initial work by Sanfilippo et al. (2019, Nat Microbiol) used plain LB medium in a fluidic chamber to induce the shear stress, which should be free of oxidants, and certainly of HOCl.

Comments on revised version:

The authors have addressed my concerns appropriately.

Reviewer #2 (Public review):

Summary:

Sleep plays a critical role in memory consolidation, but the neural mechanisms underlying this relationship remain incompletely understood. The authors examined a specific subset of PAM dopaminergic neurons, PAM-α1, and DPM neurons in Drosophila. These neurons have previously been implicated in memory, and DPM neurons have also been linked to sleep. The study explores whether this circuit provides a mechanistic link between sleep and memory consolidation.

Strengths:

The authors report several novel findings. Brief activation or inhibition of PAM-α1 neurons, or brief inhibition of DPM neurons during the first few hours after training, impairs 24-hour LTM. Notably, these brief manipulations disrupt sleep for many hours afterward, particularly during the night. The authors further show that perturbation of PAM-α1 and DPM neurons impairs sleep and appetitive memory consolidation under starvation conditions, and that pharmacological sleep induction during the night rescues the LTM defects. Together, these findings suggest that PAM-α1 and DPM neurons are involved in sleep regulation and LTM consolidation under starvation. These are important observations that advance our understanding of the circuits regulating sleep and memory consolidation.

Weaknesses:

Some claims require additional evidence or clarification.

(1) Previous studies linking impaired memory to reduced sleep have primarily examined conditions involving severe sleep deprivation. In contrast, this manuscript argues that relatively modest decreases in total sleep, accompanied by sleep fragmentation, are sufficient to impair memory consolidation. It remains unclear whether sleep fragmentation of this magnitude is itself critical for LTM consolidation. An independent method for inducing comparably mild sleep loss and fragmentation would be needed to directly test this interpretation.

(2) It is unclear why both activation and inactivation of PAM-α1 neurons produce similar effects on sleep and memory. In addition, MB299B-labeled neurons exert stronger effects on memory than MB043B-labeled neurons, whereas MB043B-labeled neurons have stronger effects on sleep. If sleep disruption is the primary driver of impaired memory consolidation, a stronger correspondence between the sleep and memory phenotypes might be expected. The authors speculate that MB043B may affect sleep through non-PAM neurons, but without identifying the relevant neurons, this remains speculative.

(3) The complex schematic model (Fig. 12), with parallel circuits and unidentified neuronal groups, underscores the difficulty of interpreting the current data. In the "less activity" arm of the model, distinct circuits are proposed to regulate sleep and LTM, respectively, and DPM neurons are not included. This makes it difficult to reconcile the model with the central claim that the PAM-α1-to-DPM microcircuit links sleep and LTM consolidation.

(4) The TRIC-LUC reporter system is not ideal for resolving dynamic changes in neuronal activity. Activity-dependent Ca²⁺ signaling must first reconstitute the TRIC transcriptional system, which then drives luciferase transcription, translation, and accumulation. The original characterization of TRIC indicates that TRIC signals accumulate and decay over several hours. Thus, the kinetics of the TRIC-LUC reporter should be interpreted cautiously, particularly when inferring transient or precisely timed changes in neuronal activity.

(5) Including data from training under fed conditions would provide a more complete understanding of state-dependent neural activity and would help distinguish starvation-specific effects from more general circuit mechanisms.

Reviewer #2 (Public review):

Summary:

The authors set out to compare functional encoding in the tuft dendrites and somata of a specific cortical cell type during motor planning and learning.

Strengths:

The investigation of a specific projection type (L5 ET) is a strength that aids reproducibility and interpretation. The elegant approach to increasing the depth of field of dendritic imaging is another strength. The data analyses are largely clear in their methods, scope, and interpretation. The writing is extremely clear and appropriately referenced, with an excellent Introduction, in particular.

Weaknesses:

This work is largely observational, describing signals that might reflect computational transformations and/or instruct plasticity, but those possibilities have not yet been deeply investigated. The manuscript does a good job of laying out these as future directions.

Reviewer #2 (Public review):

Summary:

In this paper Drs. Kercmar, Murko and Bombek make a series of observations related to the role of AVP in pancreatic islets. They use the pancreatic slice preparation that their group is well known for. The observations on the slide physiology are technically impressive. However, I am not convinced by the conclusions of this manuscript for a number of reasons. At the core of my concern is perhaps that this manuscript appears to be motivated to resolve 'controversies' surrounding the actions of AVP on insulin and glucagon secretion. This manuscript adds more observations, but these do not move the field forward in improving or solidifying our mechanistic understanding of AVP actions on islets. A major claim in this manuscript is the beta cell expression of the V1b Receptor for AVP, but the evidence presented in this paper fall short of supporting this claim. Observations on the activation of calcium in alpha cells via V1b receptor align with prior observations to this effect and can explain the effects of beta cell calcium and insulin secretion better than an explanation where beta cells express functional V1BR, for which direct evidence is lacking.

I have focused my main concerns below. I hope the authors will consider these suggestions carefully - please be assured that they were made with the intent to support the authors and increase the impact of this work.

Strengths:

The main strength of this paper is the technical sophistication of the approach and the analysis and representation of the calcium traces from alpha and beta cells.

Weaknesses:

(1) There are excellent data that indicate that the actions of AVP are mediated via V1bR on alpha cells and that V1bR is 1) not expressed by beta cells and 2) does not activate beta cell calcium at all at 10 nM - which is the same concentration used in this paper (Figure 4G) for peak alpha cell Ca2+ activation (see https://doi.org/10.1016/j.cmet.2017.03.017; cited as ref 30 in the current manuscript). Any published stimulatory actions of AVP on insulin secretion can be explained by the potentiating effects of glucagon, released in response to AVP stimulation of alpha cells.

(2) The RNAscope data offered in the revision as a second line of evidence for the expression of the V1bR in beta cells do not convince. I applaud the authors for trying as these are hard experiments to do well, as evidenced from the Gcg RNAscope signal that is not at all concentrated in the islet periphery, and in fact both color puncta occur outside of the islet at similar density. Absent a convincing concentration of Gcg signal (which is a very abundant transcript in alpha cells), it is hard to depend on these results. They certainly do not substitute experiments to determine cell autonomous activation of isolated beta cells by AVP. Claim of beta cell expression of V1br, require a more direct demonstration by staining (if appropriate antibodies exist), by beta cell-specific deletion of V1br, or by documenting the direct calcium activation in isolated beta cells in the absence of alpha cells. This should include a demonstration of Gaq-dependence in isolated beta cells.

(3) We know from bulk RNAseq data on purified alpha, beta, and delta cells from both the Huising and Gribble groups that there is no expression of V2a. I will point you to the data from the Huising lab website published almost a decade ago (http://dx.doi.org/10.1016/j.molmet.2016.04.007) - which is publicly available and can be used to generate figures (https://huisinglab.com/data-ghrelin-ucsc/index.html). They indicate the absence of expression of not only AVP2 receptors anywhere in the islet - but the lack of expression of V1bra, V1brb, and Oxtr in beta cells. These AVP/OXT receptor expression data are largely and helpfully confirmed by the efforts in this paper that involved the generation of the V1aR agonist and V2R antagonist.

(4) Importantly, the lack of V1br from beta cells does not invalidate observations that AVP affects calcium in beta cells, but it does indicate that these effects are mediated 1) indirectly, downstream of alpha cell V1br or 2) via an unknown off-target mechanism (less likely). The different peak efficacies in Figure 4G would also suggest they are not mediated by the same receptor. The recent work by Huixia Ren and colleagues (PMID: 41916313) that demonstrates that glucagon accelerates the frequency of beta cell calcium is in line with such a scenario.

(5) The use of forskolin across almost all traces complicates the interpretation of the results. The design does not account for the elevation of cAMP in alpha cells and subsequent release of glucagon - particularly upon co-stimulation with AVP which permits glucagon release by activating a calcium response in alpha cells. This glucagon then could activate beta cells. If resolving the mechanism of action is the goal, often less is more. The activation of Gaq-mediated calcium is not cAMP dependent (although the downstream hormone secretion clearly often is). As was shown, AVP does not activate calcium in beta cells in the absence of cAMP. The experiments should have been completed in the absence of cAMP/forskolin, which would likely have had different outcomes on the beta cell responses and to the hormone secretion.

(6) It is motivated by a desire to 'study the AVP dependence of both alpha and beta cells at the same time'. As best as I can determine, the design choice to conduct most studies under sustained forskolin stimulation is related to the permissive actions of AVP on hormone secretion in response to cAMP-generating stimuli. The permissive actions by AVP that are cited are on hormone secretion - which in many cell types requires activation of both calcium and cAMP signaling. Whether the activation of V1br and subsequent calcium responsive is permitted by cAMP is unclear. I believe the argument the authors are making here is that the activation of beta cell calcium by AVP is permitted by forskolin. i.e. the cAMP stimulated by it in beta cells.

(7) Figure 9 suggests a pharmacological activation of beta cell V1bR in the low pM range. How do the authors reconcile this compare with the apparent absence of an effect of AVP stimulation at low pM to low nM doses in beta cells (Figure 5A). I note that there are changes over time with sustained beta cell stimulation with 8 mM glucose, but these changes are relatively subtle, gradual and quite likely represent the progression of calcium behaviors that would have occurred under sustained glucose irrespective of these very low AVP concentrations. I will note that the Kd of the V1bR for AVP is around 1 nM, with tracer displacement starting around 100 pM according to the data in figure 6B, which is hard to reconcile with changes in beta cell calcium by AVP doses that start 10-100-fold lower than this dose at 1 and 10 pM (Figure 9).

Reviewer #2 (Public review):

Summary:

The authors first introduce a framework to understand how different phenotypic drivers of viral evolution, i.e., changes in transmissibility versus immune escape, complicate epidemic forecasting using only genetic data. To overcome these complications, they advance an evolutionary "selective pressure" metric to predict population-wide epidemic growth from genetic data alone. Separately, they introduce a latent space model to infer a "pseudo" population immune structure from geographic variation in viral lineage dynamics, and find that the inferred pseudo-structure predicts human serological data.

Strengths:

This paper begins with a useful pedagogical exposition on the connection between fitness-driven frequency dynamics and underlying mechanisms of viral-immune co-evolution. A major contribution of this paper - a method to infer variant-specific escape properties from geographically non-uniform variant frequency dynamics alone - is an interesting and potentially timely one, given the advance of sequencing-based surveillance.

Weaknesses:

The logical flow of the pedagogy part of the text works against the reader, which is problematic since it motivates the rest of the text. Moreover, some important modelling choices and procedures, particularly with respect to the selective pressure metric, are only cursorily described in the methods section. The lack of explanation and detail, especially relative to more simple choices that are seemingly motivated by the authors' own theory, makes it difficult to understand and therefore assess their validity and/or necessity.

Reviewer #2 (Public review):

Summary:

dbGIST appears to be the first dedicated multi-omics resource worldwide that is specifically focused on GIST.

Strengths:

The main value of the paper is not simply that the authors collected datasets, but that they built a usable resource around them, with cohort-aware analyses, curated clinical labels, interactive visualizations, downloadable results, selected API access, and an optional LLM-assisted interface. The work is solid, and the database is likely to be useful for GIST researchers interested in target discovery, cross-dataset validation, drug-response hypotheses, and translational follow-up.

The MCM7 analysis is a reasonable use case. It shows how a user can start from one candidate gene and then move across transcriptomic, proteomic, clinical, single-cell, immune-related, drug-response, and experimental evidence. I do not see this as the main discovery of the paper, but rather as a practical demonstration of what the database can do. That is appropriate for a resource manuscript.

Weaknesses:

(1) The authors should make the organization of the platform a little easier to follow. The manuscript refers to five primary omics layers, six omics-focused pages, and eight analytical modules. This structure is understandable after reading the relevant sections, but it may not be immediately obvious to readers. A brief clarification of how the omics layers, web pages, and analytical modules relate to each other would help.

(2) Since dbGIST is a live web resource, the authors should provide a clear versioning statement. The manuscript should indicate which version of the database corresponds to the analyses and figures reported in the paper, and how future updates will be distinguished from the version evaluated here. This is a small point, but it matters for reproducibility.

(3) The API function is a strength of the resource, but it is still described rather generally. The authors should give more concrete documentation of what can be accessed through the API, what inputs are required, and what type of output is returned. This could be placed in the supplementary materials. It would make the database more useful for computational users.

(4) The manuscript should clarify the status of downloadable data. It is clear that figures, source-data tables, and selected derived outputs are available, but it is less clear whether the full processed matrices used internally by the platform are downloadable or only maintained for deployment. This distinction should be stated plainly.

(5) The statistical reporting in the MCM7 clinical-association analyses needs a little more care. Several p-values are shown across different cohorts and clinical variables. The authors should state whether these are nominal p-values or adjusted p-values. If they are nominal, that is acceptable for a resource demonstration, but the exploratory nature of the analyses should be made clear.

(6) The ROC analyses for imatinib response should include sample sizes, and confidence intervals for AUC values would be useful if available. Some of the AUC values are high, and without group sizes, it is difficult to judge how stable those estimates are. The authors should avoid implying that these ROC results are validated predictive models.

(7) The interpretation of MCM7 should be slightly more cautious. MCM7 is a well-known DNA replication and cell-cycle gene, and the single-cell analyses seem to support its association with proliferative cell states. This is biologically consistent, but it also means that MCM7 expression should not be presented as tumour-cell-specific without qualification. The manuscript should frame it mainly as a proliferation-associated signal in the current analysis.

(8) The drug-response section would benefit from a clearer explanation of the response metric. The authors report correlations between MCM7 expression and predicted response to C6-ceramide, but readers need to know whether the predicted value represents IC50, AUC, sensitivity score, or another metric. The direction of interpretation should also be made explicit, since a negative correlation can mean different things depending on the scoring system.

(9) The single-cell annotation would be more convincing if the authors provided a compact marker-gene summary for the major cell types in each single-cell cohort. The current description of annotation by source labels, marker inspection, and manual curation is reasonable, but users of the database would benefit from seeing the marker evidence behind the labels.

(10) The experimental validation section should include a few routine details that are currently not easy to find. The siRNA sequences or target regions, number of biological replicates, statistical tests for the CCK-8 and wound-healing assays, and details of wound-closure quantification should be reported. These additions would make the in vitro part more reproducible.

(11) The wound-healing result should be interpreted with caution. Since MCM7 knockdown reduces proliferation, reduced wound closure could reflect changes in proliferation, migration, or both. Unless proliferation was controlled during the wound-healing assay, the authors should avoid describing this result as purely migratory.

(12) The LLM-related claims should remain conservative. The assistant is a useful feature for navigation, plain-language explanation, and user support, especially for clinicians or wet-lab researchers. However, the strongest statements about the LLM transforming interpretation or automating analysis should be toned down. The important point is that the LLM layer helps users interact with the resource, while the numerical analyses come from predefined dbGIST modules.

Reviewer #2 (Public review):

This is a study of the dynamics of plant volatile emissions, using a curve-fitting approach to describe salient properties of the dynamics of plant volatile chemicals. The study is interesting and unique in taking this approach. Some of the dynamics uncovered (e.g. lagged emission of many sesquiterpenes) are already well known using less sophisticated approaches, while other properties (diurnal cycles in emission dynamics) are newly uncovered. The approach in general is new for the topic of plant volatile emissions, but curve-fitting is widely used to describe the dynamics or function-valued responses of plants and other organisms. The study thus reads as rather methods-focused, giving tidbits of interesting properties of the dynamics of plant VOCs rather than being structured strongly around clear biological hypotheses. The method seems like a logical and robust way to analyze the dynamics of plant VOCs. I believe the impact of the work will largely depend on whether there are substantial and meaningful outcomes (for herbivores, downstream processes of induction, etc) due to the differences in VOC dynamics described via these methods that would be hard to observe in other ways. If so, there will be a need to adopt robust methods such as this to describe the salient features of those dynamics. At present, I do not believe there is evidence one way or another as to whether the subtle differences in VOC dynamics have large consequences.

The paper sells itself as describing a new technique for describing response curves generally across biological systems, but it only uses this technique to look at the dynamics of induced plant volatiles. I believe to show general utility of this approach, a wider range of examples of plastic responses to stimuli across organismal groups would be needed. I am, however, convinced that this approach is both novel and useful within the scope in which the examples are shown (i.e. in describing the dynamics of induced plant responses). Some of the text purporting novelty in uncovering shared and divergent responses across the tree of life seems pretty overstated.

Much of the introductory and discussion text is quite broad, and I wonder if the technique is really meant to be applicable to the specific case that is described (repeated measures of an induced volatile response). Likewise, there has been considerable work in such realms as behavioral science, function-valued traits (e.g. Stinchcombe et al 2012), performance curves (Kingsolver various papers), etc to describe dynamic or variable responses phenomenologically, and there are approaches including GAMs, parametric curve fitting, and other techniques that probably report the same salient features as the approach here. Indeed, there are already statistical techniques to assess the macroevolution of response curves (e.g. Goolsby 2015) and wide discussions as to how to compare function-based responses among organisms (The Functional Phylogenies Group 2012). So in the broad scheme of biology, I am not sure I'm convinced of the novelty of the approach. However, I believe it is novel within the context in which it is used here. The salient part of the methods is that it uses predefined attributes of dynamics (onset, duration, etc) based on a gamma distribution that the researchers (with good reason) believe to be biologically meaningful. This is in contrast to multivariate approaches (e.g. Izem et al 2005) that attempt to find salient dynamic features in a less constrained way.

I would have liked to see a clear description of model fits (e.g., how much of the variation in the real data is described by the fitted model). This seems important because there are quite a number of constraints placed on model fitting - so presumably when a model blind to those constraints picks unrealistic parameters, that would suggest that the constrained model probably does not fit the data all that well.

I am curious about the normalization process in the 'normalized emission' that is analyzed throughout the study. Normalization to leaf size makes sense, though I was less clear about L459: "Additionally, values were normalized to the maximum response observed in each experiment, yielding a range of positive values < 1." Why was this needed? Is the 'maximum response observed in each experiment' across all plants/compounds/treatments or within a single plant? In general, is there a way of reporting VOC emission rates in absolute values (e.g. umol / Liter air)? Normalization would presumably not impact most curve properties very much, but it could have effects on 'integral', and the need for within-experiment normalization would suggest a lack of transferability or comparability among datasets from different experiments (at least as regards 'integral'), which is suggested as a major advantage of this approach in the discussion.

Reviewer #2 (Public review):

Summary:

In this manuscript Zhu, Emanuelli and colleagues describe a novel pharmacological activator of the Integrated Stress Response kinase GCN2. The work is conclusive and biochemically solid. This work significantly adds to the pharmacological arsenal targeting the ISR and in particular GCN2.

Strengths:

Strong biochemistry, novel molecular activator of GCN2 (GCN1 independent).

Weaknesses:

Rationale for the screen not exploited in the results (e.g. pathogenic GCN2 mutants), lots of cell-based read-outs not endogenous.

Comments on revised version.

The authors did a great job at addressing my initial critique on their manuscript and consequently I have no further comment.

Reviewer #2 (Public review):

Summary:

The authors showed the localization pattern of nucleolus components, including Pre-rRNA, a precursor of rRNAs, changes during meiotic prophase I, particularly with the localization of these nucleolar components to the X-Y body, which shows inactivation of RNA polymerase II transcription, during pachynema. The localization of Pre-rRNA depends on ATR kinase and gammaH2AX. The chemical inhibition of rRNA transcription disrupts the binding of pre-rRNA to the X-Y body and suppresses the inhibition of the RNA polymerase II-mediated transcription on the sex chromosomes.

Strengths:

The cytological analysis, combined with the chemical inhibition, provided solid evidence to support the idea that, together with the remodeling of the nucleolus structure, pre-rRNA is an essential component of sex chromosome inactivation in male mouse meiosis. The role of pre-rRNA in sex chromosome inactivation in male meiosis helps our understanding of how the X-Y body, which would be a biological condensate, would be formed; e.g. for example, this Pre-rRNA may promote phase separation.

Weaknesses:

However, there is limited information on how Pre-rRNA is recruited to only sex chromosomes and how the RNA promotes the inactivation of sex chromosomes. Of course, these will be a target of future study. One major weakness of this paper is a poor description of the results, with fair presentation and interpretation of the data.

Reviewer #3 (Public review):

Summary:

In their manuscript, the authors investigate how glutaminolysis (GLS) and mitochondrial pyruvate import (MPC2) jointly shape B cell fate and the humoral immune response. Using inducible knockout systems and metabolic inhibitors, they uncover a "synthetic auxotrophy": When GLS activity/glutaminolysis is lost together with either GLUT1-mediated glucose uptake or MPC2, B cells fail to upregulate mitochondrial respiration, IL 21/STAT3 and IFN/STAT1 signaling is impaired, and the plasma cell output and antigen-specific antibody titers drop significantly. This work thus demonstrates the promotion of plasma cell differentiation and cytokine signaling through parallel activation of two metabolic pathways. The dataset is technically comprehensive and conceptually novel, but some aspects leave the in vivo and translational significance uncertain.

Strengths:

(1) Conceptual novelty: the study goes beyond single-enzyme deletions to reveal conditional metabolic vulnerabilities and fate-deciding mechanisms in B cells.

(2) Mechanistic depth: the study uncovers a novel "metabolic bottleneck" that impairs mitochondrial respiration and elevates ROS and directly ties these changes to cytokine-receptor signaling. This is both mechanistically compelling and potentially clinically relevant.

(3) Breadth of models and methods: inducible genetics, pharmacology, metabolomics, seahorse assay, ELISpot/ELISA, RNA-seq, two immunization models.

(4) Potential clinical angle: the synergy of CB839 with UK5099 and/or hydroxychloroquine hints at a druggable pathway targeting autoantibody-driven diseases.

Comments on revised version.

Authors extensively modified the text with great care and provided new data e.g. Fig. 5. Collectively, this is convincing and hence, I have no further comments.

Reviewer #2 (Public review):

Summary:

The study demonstrates that CRISPR-Sirius provides a powerful approach to investigating chromosome dynamics in living cells during environmental stress. By focusing on serum starvation, the authors show that this process induces global nuclear changes, including a reduction in nuclear area and increased morphological dynamism, while at the same time driving specific reorganization of chromosome 1. Chromosome 1 relocates toward the nuclear periphery and displays distinctive patterns of motion, maintaining overall motility but punctuated by occasional long-distance displacements, particularly near the nuclear envelope. Importantly, the analysis reveals that homologous copies of chromosome 1 do not behave uniformly: peripheral loci become more mobile and responsive to starvation, whereas central homologs remain comparatively stable, often associated with nucleolar subcompartments. By integrating live imaging with machine learning and explainable AI analysis, the study highlights the complexity of nuclear organization and provides valuable insights into how chromosome-specific and locus-specific responses to stress are orchestrated within the three-dimensional nuclear landscape.

Strengths:

The study uses live-cell imaging to investigate the dynamics of loci during starvation. Live-cell tracking and data interpretation are carried out using machine learning and AI models, which is a major strength.

Weaknesses:

The manuscript is at times difficult to follow, partly because the methodological descriptions are highly specialized, especially for non-expert biologists. In addition, the observations are not tested for a mechanistic basis. Experiments that could provide deeper insights are missing, for example, why chromosome 1 moves, why the peripheral homologue dislocates, or why a "long jump" is observed at the periphery even though the speed of the loci does not change. It is also unclear whether a displacement of 0.5 μm is functionally meaningful.

Comments on revised version:

The authors have added some technical information and provided a better discussion of the data, but beyond that, they have not strengthened the conclusions. The observations are not supported by any perturbation assays.

Reviewer #2 (Public review):

Summary:

The Drosophila executioner caspase Dcp-1 has established roles in cell death, autophagy, and imaginal disc growth. This study reports previously unrecognized factors that work together with Dcp-1. Specifically, the authors performed a turboID-based proximal ligation experiment to identify factors associated Dcp-1 and Drice. Dcp-1-specific interactors were further examined for their genetic interaction. The authors report autophagy-related genes, including Debcl and Buffy, to be required for Dcp-1 activation. In addition, the authors present evidence of an interaction between Bruce and Dcp-1. Bruce expression blocks the Dcp-1 overexpression phenotype. Inhibition of effector caspases or overexpression of Bruce commonly reduced wing growth, suggesting a relationship between the two proteins.

Strengths:

The study identifies new Dcp-1-interacting proteins and provides a functional link between Dcp-1 and Sirt1, Fkbp59, Debcl, Buffy, Atg2, and Atg8a. During the revision, the authors have also added convincing new data supporting the interaction between Dcp-1 and Bruce. They further make a strong case regarding the quality of the turboID-proteomics data. Overall, this is a strong manuscript supporting an interesting discovery.

Reviewer #2 (Public review):

Summary:

This study functionally characterizes a single KCNE-like gene, kcne0, from a jawless vertebrate. The authors conducted multiple experiments, including TEVC, VCF, RT-PCR, and RNA-seq to show that KCNQ1 and kcne0 exhibited a broadly overlapping organ distribution in lamprey species, and KCNE0 produced a constitutively active current when co-expressed with lamprey KCNQ1, similar to the effects of human KCNE3 on KCNQ1. This modulation was species-specific, as co-expression of KCNE0 with other species' KCNQ1 was less effective. Moreover, the authors found that truncating the N-terminal had a more significant reduction of the modulatory effects than truncating the C-terminal of KCNE0. Interestingly, the introduction of the tetra-leucine motif from human KCNE4 into KCNE0 conferred KCNE0 with comparable effects of human KCNE4 on KCNQ1.

Strengths:

The authors clearly introduced an early-diverging member of the KCNE family, and convincingly demonstrated the function of this gene, KCNE0. The results are supported by experiments of multiple approaches and are clearly written. The work is significant and will interest readers from the extended research area.

Weaknesses:

No major concerns were identified with the manuscript in general.

Reviewer #2 (Public review):

This manuscript aims to characterize how semantic information is prioritized relative to perceptual details in visual working memory. The central claim is that semantic judgements benefit from faster pre‑decisional access (shorter non‑decision time), and that advantages in evidence accumulation emerge under higher cognitive demands (e.g., when items are outside the focus of attention or must be maintained under interference). Based on this, the paper argues that unattended working‑memory contents are reformatted into more abstract, long‑term‑memory‑like semantic representations that remain more readily accessible than fine‑grained perceptual features.

Strengths:

(1) The question is timely and relevant to current research about the format of visual working memory.

(2) Behaviorally, the semantic advantage is carefully documented in many conditions across datasets.

(3) The use of hierarchical drift-diffusion modelling is helpful to decompose the semantic advantage into cognitive processes such as non‑decision time and drift‑rate components.

Weaknesses:

(1) The strong claims about visual working‑memory representation and "long‑term‑memory‑like" formats rest on an indirect inference from decision‑model parameters to representational content, and this link is not convincingly established. Non‑decision time, as implemented here, bundles many things, such as probe processing, cue processing, retrieval/access, and motor preparation, so reduced non‑decision time for semantic probes could reflect easier question reading, simpler response mapping, or more efficient decision preparation rather than a genuine advantage in accessing semantic memory representations. Although the manuscript acknowledges that non‑decision time includes multiple processes, it nonetheless treats this parameter as primary evidence for a retrieval‑stage semantic advantage, which overstates what the data can uniquely support.

(2) The modelling approach is relatively constrained and does not fully address the underdetermination inherent in mapping latent drift-diffusion parameters onto specific psychological mechanisms. The preferred model that allows multiple parameters (non‑decision time, drift rate, threshold) to vary provides only modest improvements in predictive accuracy over simpler models, and several key drift‑rate effects are present only in particular load or lag conditions. As a result, the theoretical interpretation that semantic prioritization primarily reflects faster access and secondarily more efficient accumulation under high demand appears rather post hoc, and alternative accounts focused on generic task efficiency or strategy differences remain plausible.

(3) The operationalization of "semantic" is narrow and largely categorical, focusing on animacy (animal/object) and a perceptual format dimension (photo/drawing), rather than richer semantic or associative relations among items. This makes it difficult to generalize the conclusions to broader claims about semantic structure and its integration into working‑memory representations. Important recent work on how semantic and associative relationships facilitate the formation, maintenance, and retrieval of visual working memory is not adequately integrated into the theoretical framing. Consequently, the discussion tends to generalize from a specific probe structure to a broader semantic prioritization theory without engaging fully with the existing literature on semantic facilitation and neural decoding of working‑memory content.

(4) The paper contrasts its behavioral/model‑based results with prior neural decoding findings, but the comparison is not fair. Neural decoding provides complementary evidence about the content and format of working memory representations, whereas drift-diffusion parameters reflect downstream decision dynamics given a probe. Because the current work does not include any direct representational or neural measure, its conclusions about representational "reformatting" and long‑term‑memory‑like access remain speculative and, in places, feel like a stretch.

(5) Overall, while the data show a semantic advantage in decision‑stage measures and the modelling provides an informative decomposition of this advantage, the manuscript does not fully achieve its stated aim of characterizing the representational format of visual working memory or demonstrating a mechanistic shift toward long‑term‑memory‑like semantic representations. The work primarily informs decision‑process analyses of the conditions under which semantic judgements are faster and more robust, rather than the nature of visual working‑memory representations themselves.

Reviewer #2 (Public review):

Summary:

The authors used Cryo-EM to obtain a complex between MEK1 and ERK2. They used the same method as previously used by the same authors to form a stable complex between MKK6 and p38, an extra-strong KIM replacing the wild-type KIM in MEK1. Three conformers were resolved, with the highest resolution of 3.0 Å. The multiple conformers indicate more flexibility in MEK2 than in ERK2. These data suggest that nucleotide exchange is possible while maintaining MEK1-ERK2 interactions. SAXS and HDX data reinforce the idea of flexibility. They point to interactions between the two N-terminal domains between histidines at the N-terminus of helix C and between the G helices that are maintained in each of the 3 conformers, and sequence and structure suggest these histidines may be a source of specificity in MEK1-ERK2 versus MKK6-p38 interactions. A 2.2 Å structure of a complex between ERK1 (88% identical to ERK2) and the docking peptide used was also presented. Molecular dynamics simulations suggest that the MEK1-ERK2 complex can assume a fully active configuration of MEK1.

Strengths:

This is the first structure of a MEK1-ERK2 complex. The structural data are valuable additions to our understanding of MAP2K-MAPK interactions. The discussion points offered in the results section are palatable. These include the origins of specificity and the idea of flexibility in the MAP2K in support of a processive mechanism for the dual phosphorylation activity of MAP2Ks.

Weaknesses:

(1) This reviewer considers that the abstract is overstated. Specifically, this paper does not reveal the molecular details of phosphoryl transfer, nor does it demonstrate that substrate binding releases the catalytic machinery.

(2) The discussion is in some places not supported by evidence and in others has superfluous text. Examples follow:

- "Once the αG-helix is docked, and the C-lobe histidine triad is in place, the N-lobe interactions must then be fulfilled." The data in this paper does not suggest an order of events.<br /> - "If the substrate MAPK is incorrect, the N-lobe interaction will not be stabilised, preventing alignment of the MAPK A-loop with the MAP2K active site." This statement could be described as obvious.

(3) Much of the discussion is embedded in the results, such that it is difficult to separate new facts offered by the paper from speculation.

Reviewer #2 (Public review):

Summary:

Here, Sutlief et al. use a novel patch-foraging task to investigate the role of dorsomedial striatal (DMS) neurons in determining when animals disengage from a resource. They show that mice, contrary to canonical optimal-foraging predictions, adopt a strategy in which reward receipt resets timing behavior, with decisions further shaped by both cumulative time spent in a patch and the overall quality of the environment. The authors further demonstrate that a subset of DMS neurons exhibits step-like activity patterns during task performance. Importantly, the accumulation of these state transitions across the neuronal population predicts the timing of patch-leaving decisions on a trial-by-trial basis, providing a potential neural mechanism underlying decisions about when to abandon a currently exploited resource.

Strengths:

This study addresses an important question using a well-designed, interesting behavioral task. The finding that mice employ a reward-triggered exit-timing policy is particularly interesting, as it is pertinent to the many patch foraging-style tasks that have been developed for use in mice, where rewards are delivered as discrete events. The identification of step-like activity in DMS neurons is mostly compelling, and the authors' trial-by-trial analysis linking this activity to behavior provides some support for its relevance to patch-leaving decisions.

Weaknesses:

A key interpretational issue is whether the DMS signal reflects timing specifically, rather than movement initiation or other task-related factors. The authors argue that once a sufficient number of neurons transition, the animal exits the time-investment port. However, it remains unclear whether this population threshold reflects a timing computation that determines when to leave in the more abstract sense, or a signal more directly related to movement onset (that may also be initiated after some proportion of the population has changed its activity). An important control would be to examine neural activity while animals are engaged at the context port. In this epoch, animals presumably do not need to time their departure in the same way, but they still eventually initiate movement. If the DMS signal reflects timing rather than movement, one would not expect the same accumulation-to-threshold pattern of step-like transitions at the context port.

It would also be helpful for the authors to clarify the behavioral definition of the leaving decision. Can mice return to the time-investment port after exiting it if they do not subsequently enter the context port? How exactly is "exit" defined: as withdrawal from the time-investment port, entry into the context port, or some other behavioral event? Is there variability in the latency between time-investment port exit and context-port entry, and if so, is this latency related to DMS step-like activity? These details are important for interpreting whether the neural activity is aligned with a timing decision, movement initiation, or the execution of a transition between task states.

The classification approach for identifying step-like activity seems generally reasonable, and the low false-positive rate against homogeneous Poisson controls is reassuring. However, one potential issue is that the identification of trial-by-trial state transitions is not independent of the session-level characterization of each neuron. The algorithm first fits a sigmoid to the pooled session data and then uses the resulting high- and low-firing-rate states to constrain interval-level fits. This may bias the analysis toward finding step-like transitions in neurons whose activity is only approximately step-like at the session level, effectively reducing the space of alternative solutions available to the interval-level fits. As implemented, the approach therefore functions more as a detector of consistency with a session-defined step model than as an unbiased test of whether individual intervals are better described by discrete state transitions versus alternative dynamics such as ramps or gradual drifts. This concern could be addressed by comparing the constrained sigmoid model against alternatives, such as constant-rate or ramping models, on held-out intervals, or by deriving state parameters from an independent subset of trials and testing classification on the remaining trials.

The inclusion threshold for the accumulation analysis is difficult to evaluate. Sessions were included if they contained at least seven simultaneously recorded step-like units, but this number is hard to interpret without knowing the total number of recorded units per session and the fraction classified as step-like. Seven units may be sufficient for fitting a population accumulation trajectory, but because the cutoff is based on an absolute number rather than a proportion of the recorded population, it is unclear whether included sessions reflect robust population-level step-like dynamics or a relatively small selected subset of DMS activity. Reporting the number and fraction of step-like units per session, as well as the sensitivity of the accumulation results across different inclusion thresholds, would help clarify this point.

Reviewer #2 (Public review):

Summary:

This article looks at differences in how the brain entrains to, or tracks, the rhythmic presentation of syllables and words in speech in infants at increased likelihood versus low likelihood for autism. The authors first sought to characterize how brain responses are modulated by learning the statistical probability of a given syllable following the one before it over the first two years of life. They then sought to identify at which stages of word learning infants at increased likelihood for autism showed difficulties, and whether those difficulties worsened over time. Finally, they sought to indicate whether infants' statistical learning and word learning abilities could predict later verbal skills. The authors found similar developmental trajectories of neural entrainment to syllables in infants at high and low likelihood for autism, but infants at high likelihood for autism had overall weaker syllable-level entrainment. Infants at high versus low likelihood for autism showed different developmental trajectories for word entrainment. Lower syllable entrainment in high-likelihood infants corresponded with poorer verbal outcomes, but word entrainment was not associated with verbal outcomes. Event-related potential responses to words and part words were positively associated with verbal outcomes, however, but only in low-likelihood infants.

Strengths:

Overall, the article provides rigorous statistical analysis of longitudinal EEG data to provide strong support for the claims that neural entrainment to syllable and word features of speech may be a useful marker for language development difficulties, particularly in infants at increased likelihood for neurodevelopmental disorders. The EEG data collection and preprocessing procedures are well within standards within the field. Readers should take care to note that authors indexed neural entrainment to speech using phase-locking values instead of spectral power.

Comments on revised version.

While the statistical analyses are rigorous, there are a few potential confounds to the results. The authors now do a nice job addressing these limitations to the work. For example, sleep status may modulate some of the biomarkers relevant for language learning. Exposure to additional languages may influence performance on the verbal assessment, though the authors do clarify that participants came from majority French-speaking households. As a result, readers should be encouraged to interpret that neural entrainment to speech features is likely a useful mechanism to explain differences in language development, while taking this interpretation with some caution.

Reviewer #2 (Public review):

Summary:

In this manuscript, the authors studied transgenic reporter mice to profile Nestin expression in the postnatal mouse cerebellum. They discovered a small population of Nestin+; Atoh1+ granule neuron precursors (GNPs) in the external granule cell layer (EGL). Using immunostaining, qPCR, and RNA-sequencing, the authors showed that these Nestin+ cells are not identical to Sox2+ cells (e.g., the majority of Nestin+ cells are Sox2-). Using various mouse genetic strategies, including an elegant intersectional strategy that specifically targets Nestin+; Sox2+ cells, the authors showed that Nestin+ cells are capable of initiating Sonic hedgehog (SHH) medulloblastoma when they express the SmoM2 allele that drives constitutively active SHH signaling. Lastly, the authors profiled the transcriptomes of these cells and showed that they display enriched stem cell genes and are closer to the transcriptomes of GNP-like cells in medulloblastoma compared to Nestin- GNPs in the developing cerebellum.

Strengths:

(1) The comprehensive mouse genetics experiments, in combination with immunostaining, lineage tracing, and RNA-seq studies, provided compelling evidence that rare Nestin+ cells are present in the EGL, predominantly at the posterior lateral cerebellum in early postnatal mice.

(2) The intersectional genetics experiment unequivocally show that Nestin+; Atoh1+ cells can be oncogenically transformed by SmoM2, leading to SHH medulloblastoma.

(3) The more stem cell-like transcriptomic features of the Nestin+ GNPs compared to Nestin- GNPs provide support for the heterogeneity of this transient progenitor cell population, with implications for development, congenital diseases, and tumors from the cerebellum.

Weaknesses:

Main comments:

My main concern relates to whether these Nestin+; Atoh1+ cells are restrictively localized in the EGL. Both the title "A Rare Nestin-Expressing Granule Cell Precursor Subpopulation Underlies SHH Medulloblastoma Formation" and what the authors described throughout the manuscript propose that Nestin+; Atoh1+ cells in the EGL are the cell-of-origin of SHH medulloblastoma. To definitively conclude this, the authors need to comprehensively analyze all regions of the developing cerebellum.

Most importantly, are Nestin+; Atoh1+ cells present in the rhombic lip? Are there any rhombic lip cells genetically labeled in their intersectional mouse mutants (e.g., the Atoh1Frt-Cre/+; Nes-FlpoER; R26LSL-SsmoM2/+ mice)?

If Nestin+; Atoh1+ cells are present at non-EGL regions in the developing cerebellum, the authors would have to reconsider many of their conclusions and also the title of this paper.

Additional comments:

(1) To investigate Nestin expression, the authors used Nes-CFP transgenic mice expressing CFP from promoter/enhancer sequences from the rat Nes gene (Encinas et al., 2006). Given that Nestin expression is of central importance for this study, it is important to validate that these reporter mice faithfully report Nestin protein expression (e.g., by co-labeling CFP with Nestin antibody and systemically comparing signals throughout the cerebellum, ideally in several developmental stages).

(2) The authors mostly presented immunostaining data of the cerebellum from P1 mice. It is important to systematically profile the appearance and disappearance of these Nestin+, Atoh1+ cells in mouse cerebellum across developmental stages (e.g., embryonic, early, and late postnatal stages).

(3) How different is the proliferative ability of the Nestin+ versus Nestin- GNPs at various developmental stages? Also, the difference between EdU+; Barhl1+; Nestin+ and EdU+; Barhl1+; Nestin- cells is quite small despite statistical difference (Figure 1N). Do the authors think this very small EdU incorporation difference can translate into a biological difference (in developmental and/or disease context)?

(4) Lines 145-147: "Compared to double-negative cells, Atoh1 and Nes were significantly higher in the double-positive fraction, supporting the identity of the cells as a previously unrecognized rare population of GCPs at P1 that expresses both the GCP marker Atoh1 and ventricular zone marker Nes." Nestin is not a ventricular zone marker. This should be rephrased.

(5) In Figure 3, the authors showed mouse survival data and concluded that Nes-driven and Atho1-driven SHH medulloblastoma models show similar tumor penetrance. This is not an entirely accurate description of their data. The Nes-SmoM2 mice displayed significantly longer survival compared to the Atoh1-SmoM2 mice (Figure 3B). This conclusion needs to be revised.

(6) In Figure 5, the authors showed that genes enriched in cluster 10 included Sox2, Nes, Wls, and Wnt1, while Neurod1 and Rbfox3 were preferentially expressed in the other GCP clusters. They conclude that cluster 10 represents a less differentiated, more stem-like GCP state, potentially positioned upstream in the lineage hierarchy. While these few markers are useful, it is more informative to formally support this conclusion by comparing the stem cell transcriptomic signature (using a larger gene list) between cluster 10 and other GCPs.

(7) In Figure 5, the authors performed gene ontology analysis and showed that cluster 10 is enriched for biological processes linked to WNT signaling and proposed that this molecular profile supports their identity as a transient, developmentally plastic population within the GCP lineage related to the rhombic lip. The authors are recommended to use an orthogonal approach (i.e., immunostaining to compare nuclear localization of beta-Catenin) to validate their transcriptome-based finding.

Reviewer #2 (Public review):

Summary:

In this work, the authors investigated the regulation of the transcription factor PPARγ by the post-translational modification lysine methylation The data demonstrate that the lysine methyltransferase SETD6 targets PPARγ for methylation using biochemical and cell-based assays. Methylation of PPARγ occurs in its DNA binding domain, and the authors demonstrate that loss of methylation limits PPARγ chromatin binding, particularly to lipid storage and metabolism genes promoters. As a physiological output, the authors demonstrate that deletion of SETD6 and loss of PPARγ methylation also disrupt lipid droplet accumulation in hepatocytes. In addition, the authors uncover a positive feedback loop in which SETD6 methylation of PPARγ also regulates its binding to the SETD6 promoter and expression of the gene.

Strengths:

One of the key strengths of this manuscript is the novelty of the findings in terms of identifying a new mode of regulation of PPARγ that modulates its chromatin association in cells and thereby regulating lipid metabolism genes. The authors nicely combine biochemical studies of SETD6 activity with cell-based assays investigating PPARγ and SETD6 function in regulating lipid storage. Data supporting this conclusion is largely convincing and frequently, multiple assays are used to provide sufficient support to the conclusions. This work therefore expands regulatory modes of PPARγ and identifies a new target for SETD6, an enzyme that targets a number of other transcription factors. Furthermore, the regulatory loop that controls SETD6 expression via PPARγ methylation is likely important for understanding SETD6 function in different cell types that have high levels of lipid accumulation or regulation. The gene expression and lipid accumulation assays are useful for testing the physiological outcome of loss of SETD6 activity or PPARγ methylation directly. In the revised manuscript, the authors have added useful structural modeling to better define potential roles of methylation of PPARγ in regulating its function, particularly relative to DNA binding, and to better define the physical interaction between PPARγ and SETD6.

Weaknesses:

The revised manuscript substantially improved on the presentation of the data and broadened the discussion to provide more context to both the role of SETD6 and to elaborate on potential mechanisms by which methylation impacts PPARγ function and under what physiological conditions this interaction and regulation is important. This improves and strengthens the manuscript and its impact overall.

Comments on revised version.

The authors addressed all of my major concerns following this round of review and I do not have additional recommendations. The presentation of the manuscript including text and figures is improved compared to the previous version. I have updated my public review to reflect these changes.

Reviewer #2 (Public review):

Summary:

DNA double-strand breaks (DSB) in repeated DNA pose a challenge for repair by homologous recombination (HR) due to the potential of generating chromosomal aberrations, especially involving repeats on different chromosomes. This conceptual caveat led to a long-held notion that HR is not active in repeated DNA, which was disproven in groundbreaking work by Chiolo showing in Drosophila that DSBs in pericentromeric repeats are mobilized to the nuclear periphery for repair by HR. A similar mechanism operates in mouse cells, as shown by the Gautier laboratory, but the mobilization goes to the nucleolar periphery, called nucleolar caps. In this manuscript, the authors reexamine the role of MDC1 in the mobilization of DSBs in rDNA in human cells. Previous work has shown that MDC1 is replaced by Treacle, the gene associated with Treacher Collins syndrome 1, in its role as the main adaptor of the DNA damage response, and these results are confirmed here. The novelty of this contribution lies in the discovery that MDC1 is required downstream in the recruitment of BRCA1 and RAD51 to nucleolar DSBs that were mobilized to the nucleolar cap. Using multiple MCD knockout models and DSBs induced by the nuclease PpoI, which cleaves at nuclear sites as well as in the 28S rDNA, convincingly documents this role of MDC1 and shows that it acts upstream of the RNF8-RNF168 ubiquitylation axis. Using a proxy assay of co-localization of EdU incorporation at DSBs (gammaH2AX), evidence is provided that MDC1 is required for HR in rDNA. MDC1 was not required for RAD51 recruitment to IR-induced foci, but it is unclear whether this is related to the different DSB chemistry (enzymatic versus IR) or to the localization of the DSB (rDNA versus unique sequence genome).

Strengths:

(1) The manuscript is well-written, and the experimental evidence is nicely presented.

(2) Multiple MDC1 knockout models are used to validate the results.

(3) Convincing back-complementation data clarify the relationship between MDC1 and RNF8.

Reviewer #2 (Public review):

Summary:

This manuscript describes the results of an interesting study examining the rate of degradation of extracellular DNA in soil ecosystems using a clever experimental approach. 16S ribosomal RNA genes were amplified from soil samples, and then purified PCR amplicons, containing a 5' linker sequence on the forward primer, were introduced to soils and monitored over time using real-time quantitative PCR and NGS amplicon sequencing. The study was able to measure rates of overall extracellular DNA degradation, but also sequence-specific degradation rates. I like the idea and execution of the study, and the results are interesting. The manuscript needs some help to improve the overall readability. Please see general and editorial comments below.

Strengths:

Innovative experimental design that is well deployed across a large number of soil types, revealing interesting variability in extracellular DNA degradation.

Weaknesses:

(1) The manuscript needs another review to improve the readability of the document.

(2) The authors have used 16S genes to look at sequence-specific degradation. But 16S rRNA genes are actually pretty well conserved, and there isn't as much genetic variation across this gene among organisms as there is for other genes. It might be more relevant to look at metagenomic DNA degradation from high AT, high GC organisms, etc. This would be more generalizable than 16S genes.

(3) Consideration of differential cell lysis during soil DNA extraction needs to be considered as well.

(4) It is not clear why the authors didn't put GAPDH linkers on the reverse primer as well. This would have given an easier amplicon to amplify (no degeneracies at all).

Reviewer #2 (Public review):

Summary:

In this EEG study, Huang et al. investigated the relative contribution of two accounts to the process of conflict control, namely the stimulus-control association (SC), which refers to the phenomenon that the ratio of congruent vs. incongruent trials affects the overall control demands, and the stimulus-response association (SR), stating that the frequency of stimulus-response pairings can also impact the level of control. The authors extended the Stroop task with novel manipulation of item congruencies across blocks in order to test whether both types of information are encoded and related to behaviour. Using decoding and RSA they showed that the SC and SR representations were concurrently present in voltage signals and they also positively co-varied. In addition, the variability in both of their strengths was predictive of reaction time. In general, the experiment has a solid design and the analyses are appropriate for the research questions.

Strengths:

(1) The authors used an interesting task design that extended the classic Stroop paradigm and is effective in teasing apart the relative contribution of the two different accounts regarding item-specific proportion congruency effect.

(2) Linking the strength of RSA scores with behavioural measure is critical to demonstrating the functional significance of the task representations in question.

Weaknesses:

I still have some doubts on the effectiveness of the experimental manipulation on Phase 2: although the ISPC effect is still present, it is much weaker in comparison, suggesting the participants did not learn the contingency statistics in Phase 2 as well as they did in the other phases, due to either the lingering effect of the previous phase or an inherent bias towards one color pairs. Perhaps by separately plotting the earlier and later blocks of Phase 2 any difference can be revealed if it exists. This behavioral difference could result in unequal levels of SC/SR representation across phases, which may raise problems when data were combined for analyses that assume the neural effects are equivalent.

Reviewer #2 (Public review):

Summary:

This manuscript presents a large-scale combinatorial transcription factor overexpression screen in mouse embryonic fibroblasts coupled with single-cell RNA-seq to systematically map the relationship between TF combinations, gene regulatory networks, and transcriptional reprogramming. Using approximately 100 transcription factors, the authors identify TF combinations that shift cells toward diverse transcriptional states, organize TF combinations into "perturbation clusters" with shared transcriptional outputs, infer modular gene regulatory networks, model pairwise TF interactions, and use pseudotime analyses to nominate candidate reprogramming TF combinations. The resulting dataset represents a potentially valuable resource for studying combinatorial TF activity and transcriptional reprogramming.

Strengths:

The primary strength of the study is its experimental scale and the breadth of the generated dataset. The Reprogram-Seq platform enables systematic interrogation of thousands of TF combinations that would be difficult to test individually, and the authors develop several computational frameworks to organize these data and generate biological hypotheses. The epicardial reprogramming analyses, including independent qPCR and protein localization experiments, provide proof-of-principle that the platform can recover biologically relevant TF combinations.

Weaknesses:

Many of the manuscript's central conclusions rely on a complex computational pipeline that is not sufficiently justified or independently validated. Identification of transcriptionally reprogrammed cells depends on co-embedding with reference atlases, yet the robustness of this analysis and the interpretation of cells occupying primary-cell clusters are not explored in depth. Similarly, the conclusions regarding modular gene regulatory networks depend critically on the perturbation clusters defined by MDE embedding and HDBSCAN clustering. These perturbation clusters form the basis for nearly all downstream analyses, including differential expression, gene module identification, gene specificity, and TF modularity, yet little evidence is provided that the clusters are robust to alternative embedding strategies, clustering parameters, or resampling approaches.

The manuscript also provides relatively limited orthogonal validation of its computational predictions. Although the epicardial analyses are validated experimentally, comparable validation is not performed for most other predicted cell fates, TF interaction classes, or perturbation modules. Consequently, many conclusions regarding the generality of modular TF activity, TF cooperativity, and the predicted reprogramming cocktails remain supported primarily by computational inference.

In addition, several aspects of the analytical workflow-including the quality filtering of TF combinations, interpretation of unclustered perturbations, selection of genes for downstream visualization, and robustness of pseudotime analyses across lineages-would benefit from greater methodological transparency.

Overall, this work provides a valuable dataset and introduces analytical approaches that will likely be useful to the community. However, in its current form, I believe the strongest biological conclusions are insufficiently validated. Additional analyses demonstrating the robustness of the computational framework, together with broader orthogonal validation of representative predictions, would substantially strengthen confidence in the proposed principles governing combinatorial transcription factor activity and transcriptional reprogramming.

Reviewer #2 (Public review):

This manuscript introduces DrosoMating, an integrated hardware-software pipeline designed to automate quantification of Drosophila courtship and mating behavior. The authors aim to provide a low-cost, scalable alternative to existing behavioral tracking systems, focusing on extracting key temporal metrics including courtship index, copulation latency, and mating duration from high-throughput video recordings.

A major strength of the work is the clear emphasis on experimental scalability and practical usability. The system is designed for multi-chamber recording and performs robustly under low-quality imaging conditions where conventional pose-tracking pipelines often fail. The revised manuscript substantially improves its scientific positioning through the inclusion of systematic benchmarking against widely used tools (Ctrax and FlyTracker), demonstrating that both fail to complete end-to-end analysis under these recording conditions: Ctrax due to segmentation instability and trajectory fragmentation, FlyTracker due to runtime errors during feature computation. A comparative table (Table 1) summarizes key features across tools, and the authors appropriately qualify that these limitations are specific to the low-quality video conditions tested and should not be interpreted as general shortcomings of those tools. The addition of individual-level behavioral ethograms (Figure S3) further strengthens the evidence by allowing direct assessment of the system's temporal resolution at the single-fly level.

The authors also appropriately address statistical concerns raised in review. The re-analysis using ANOVA frameworks - one-way ANOVA with Tukey's HSD for multi-strain comparisons, two-way ANOVA with Sidak's correction for genotype × training interactions - improves the rigor of the behavioral comparisons and supports the revised conclusions regarding strain and learning effects. The addition of locomotor control analyses (Figure S4) further clarifies interpretation of mutant phenotypes by partially disentangling motor from courtship-specific effects, with the revised text appropriately acknowledging contributions from both general hypoactivity and sensory impairments.

A key limitation remains the conceptual scope of the system. DrosoMating is optimized for state-based temporal segmentation rather than fine-grained behavioral annotation or posture-level decomposition. While the authors now clearly acknowledge this and position the tool appropriately, it inherently restricts its use cases compared to modern pose-estimation and classifier-based frameworks. Additionally, the benchmarking comparison is necessarily asymmetric: DrosoMating is tested on low-quality videos where it excels by design, while Ctrax and FlyTracker are evaluated under conditions outside their intended operating range. A comparison under more favorable conditions for the tracking-based tools, or an evaluation of whether modest improvements in video quality would bring conventional pipelines within functional range, would further contextualize the practical boundary between approaches. The comparison also does not include modern deep-learning-based tools (e.g., DeepLabCut, SLEAP), which may be more robust to low-contrast conditions than classical segmentation-based pipelines. These points do not diminish the demonstrated utility of DrosoMating for its intended niche but would help users make more informed decisions about tool selection.

Overall, the revised manuscript presents a well-validated and clearly positioned contribution. It defines the niche in which DrosoMating provides substantial practical value while appropriately delimiting its limitations relative to more general behavioral analysis frameworks.

Reviewer #2 (Public review):

Summary:

Protein tyrosine kinases are submitted to diverse regulatory mechanisms controling their activity in normal situation. The authors previously identified SLAP (Src-like adaptor protein), a negative regulator of receptor tyrosine kinase (RTK) signaling, as a key suppressor of the cytoplasmic tyrosine kinase SRC in the normal colon and demonstrated that SLAP is downregulated in a majority of colorectal cancers (CRCs).

In this study, the authors further explored slap functions in mouse models using constitutive and inducible epithelial-specific Slap deletion (villin-CreERT2 model). They found that loss of slap augments colonic epithelial cell proliferation and that induction of tumorigenesis by the AOM/DSS protocol mimicking CRC leads to more aggressive tumors in the absence of slap. This effect is apparently cell-autonomous as growth of normal and tumoral colonic organoids is SLAP-dependent in in vitro settings. Finally, the authors define that, in colon, SLAP represses EphB2, an RTK lying upstream of SRC, and show that inhibitors of EphB2 can partially limit tumorigenic development in vitro.

Strengths:

The manuscript is clearly and concisely written, making it easy to follow. Data obtained in the mouse models are very convincing.

Weaknesses:

Direct evidence that EphB2 is activated/phosphorylated in the absence of SLAP is lacking as conclusions are only based on results obtained with inhibitors. Some other issues have to be addressed before acceptance, in particular the relevance of the findings in CRC patients.

Comments on revised version.

The authors have satisfactorily addressed my concerns.

Reviewer #2 (Public review):

In K. Kostanjevec et al., the authors study a possible mechanism for the formation of spiral patterns in the cornea. First the authors analyze an inferred velocity field, which is deduced from images of fixed corneas, and then determine the position-dependent spiral angle of this velocity fields. Next, the authors analysed two possible markers of cell polarity: the direction of the centrosome-nuclei and the axis of mitosis. Then the authors introduce a stochastic agent-based model of self-propelled particles with over-damped dynamics and with aligning interactions to the orientation of the nearest neighbors and to the particle's velocity. The authors claim to be able to reproduce the equal-time autocorrelation function and the velocity Fourier spectrum. Then the authors introduce the geometry of the cornea by constraining the dynamics on a spherical cap and show that their model can reproduce a typical trajectory in experiments. Finally, the authors produce a phase diagram of the states at a fixed time point as a function of the spherical cap radius and the strength of the coupling aligning constant. Finally, the authors propose an interpretation of the cell fluxes based on the equation of mass conservation.

Reviewer #3 (Public review):

Here the Wang et al resubmit their manuscript describing the events in the establishment of polarity in MDCK cells cultured in vitro. As with the original version, the description is throughout and is important to the field to report as it establishes a hierarchy of events in polarization, placing Par3 upstream of centrosome positioning and apical membrane component trafficking. Unfortunately, in the revised version, the authors addressed almost none of my points. They did a cursory job of responding in the rebuttal letter but made little attempt to actually address what was being asked or to incorporate any of my suggestions into the manuscript. The particularly egregious examples are cited below:

Comments on revisions:

(1) My original main experimental concern was not addressed: I had originally asked what role microtubules play in the process of polarization (either centrosomal or non-centrosomal). An obvious model is that Gp135, Rab11, etc. are delivered to the AMIS on centrosomal microtubules. Centrosomes might also be pulled to the AMIS via cortically derived microtubules as is the case in the C. elegans intestine where the centrosome moves apically on apical microtubules via dynein directed transport to the cortically anchored minus ends. The authors do not explore the role of microtubules in the revision, citing that it was not possible to observe the microtubules directly or to perform nocodazole experiments during polarization. Instead, the authors use a relatively new genetic tool to disrupt centrosomal microtubules. They appear to succeed in displacing centrosomal g-tubulin using this tool, but without being able to observe microtubules, a remaining caveat of this experiment is that it is still unclear whether the authors have removed centrosomal microtubules. Compounding this issue is that this tool has never been used in MDCK cells. The authors conclude "we found that cells lacking centrosomal microtubules were still able to polarize and position the centrioles apically.", but they have not shown this, instead the data suggest this conclusion and the authors should acknowledge the caveat that they have no idea whether centrosomal microtubules are abolished. Similarly, the authors also state: "Additionally, although PCNT knockout cells show reduced microtubule nucleation ability, they still recruit a small amount of γ-tubulin". Where are the data that show that microtubule nucleation is reduced in these PCNT knock out cells?

(2) Many of my comments were addressed in the rebuttal, but not in the text.

The non-centrosomal GP135 in Figure 2 is not acknowledged or explained.

That the polarity index does not actually measure polarity, but nuclear-centrosome distance is not acknowledged or explained in the paper.

I still don't believe that the quantification in Figure 3D matches the images I am being shown in Figure 3A. In the centrinone treatment condition, there is certainly an enrichment of GP135 at the AMIS that is not detected in the quantification. The method described in the rebuttal might miss this enrichment if it is offset from line drawn between the centroid of the two nuclei.

Cell height changes in the centrosome depleted cysts are still referenced in the text ("the cell heights of the centrosome-depleted cysts are less uniform"), but no specific data or image is called out. Currently, Figure 3G is referenced, but that is a graph of GP135 intensity.

In my original review, I called on the authors to comment on the striking similarity of the mechanisms they documented in MDCK cells to what has been shown in in vivo systems. The authors did not do this, instead restating in the rebuttal some features of what they found. But the mechanisms shown here are remarkably similar to the polarization of primordia that generate tubular organs in vivo. Perhaps most striking is the similarity to the C> elegans intestine where Par3 localizes to the cortex at the site of an apical MTOC that pulls the centrosome to the apical surface via dynein (Feldman and Priess, 2012). Instead of discussing this similarity, the authors state: "Par3 is likely to regulate centrosome positioning through some intermediate molecules or mechanisms, but its specific mechanism is still unclear and requires further investigation." Given the acetylated tubulin signal emanating from the Par3 positive patch in Figure 5E and F, I suspect similar mechanisms to the C. elegans intestine are at play here. Such a parallel should be noted in the Discussion.

I had originally commented that "I find the results in Figure 6G puzzling. Why is ECM signaling required for Gp135 recruitment to the centrosome. Could the authors discuss what this means?" The authors responded that "The data in Figure 6G do not indicate that ECM signaling is required for the recruitment of Gp135 to the centrosome". In Figure 6G, the localization of GP135 to the centrosome appears significantly delayed compared to its localization to the centrosome in images where cells were cultured in Matrigel. Indeed, the authors argue that the centrosomal localization precedes and contributes to its localization to the AMIS. In the absence of ECM, GP135 localizes to the membrane before it localizes to the centrosome and its localization to the centrosome appears significantly reduced. Thus, my original and current interpretation is that ECM signaling is somehow required for the centrosomal targeting of GP135. One could make a competition argument, i.e. that the cortex in the absence of ECM is somehow a more desirable place to localize than the centrosome, but this experiment also argues that the centrosome does not need to be a source of this material in order for it to end up on the cortex.

(3) There needs to be precision in the language used in many places:

I don't understand this line in the abstract: "When cultured in Matrigel, de novo polarization of a single epithelial cell is often coupled with mitosis." If a cell has divided, it is no longer a single cell.

The authors state in the Introduction "Because of its strong ability to nucleate microtubules, the centrosome functions as the primary microtubule organizing center", but then state ""In polarized epithelial cells, the centrosome is localized at the apical region during interphase, which contributes to the construction of an asymmetric microtubule network conducive to polarized vesicle trafficking". In the latter statement, I assume the authors are describing the well-characterized apical microtubule network in epithelial cells that is non-centrosomal. Thus, the latter sentence is at odds with the former.

The authors continually refer to Par3 as a tight junction protein. "Par3, which controls tight junction assembly to partition the apical surface from the basolateral surface". To my knowledge, PARD3 is an apical protein with similar localization to C. elegans PAR-3 and Drosophila Bazooka. PARD3B is a junctional protein. I assume that the antibody that the authors are using is to PARD3 and not PARD3B? Can the authors please clarify this in the text.