This reminds me of today's political situation. Lawmakers seem to be doing their jobs, however the executive fails to put it into effect. Loopholes are found within laws and yet again nothing changes. This also reminds me of the emancipation proclamation. A big "change" is proposed to take effect, such as the freeing of slaves, yet nothing actually changes. This seems to be a common theme within the civil rights movement that Black people head.

Essentially what this figure is trying to exemplify is that when individuals are "endowed" greater assets or finance than others, it creates an income inequality. For example, people from wealthy families have a head start over those who aren't, forcing the ones born in poverty to be trapped in that cycle. Furthermore, people with more access to educational services have a higher potential of generating increased income for themselves, furthering the economic gap.

This is interesting, often times the familiar norm for a household would always be that the man is deemed as the head. My guess is that the father was not as progressive an is a traditional. I wonder if there is any other reason.

This is interesting, shows how the Native people had their own ways of healing and their knowledge of herbal medicine is probably better than even ours now

Typically refers to an outlaw, which was stereotypical in the ‘Wild West’ of America in the twentieth century. It is associated with the stereotypical criminal costume of a cowboy hat and scarf covering his face. It is also possible that this could be referring to the second meaning of desperado which comes from the word desperate, which was just a noun at the time and did not have the same connotation that it has now. So, ‘the face of a desperado’ could also be referring to someone who is in a clear desperate situation and would, on the American frontier, be someone who would head out West to mine for gold.

Again, explanation

0:24 "what does rebellion look like?" -- answering the question "who are my friends?" -- the system hates my answer so much that cops are threatening to throw me in jail for distributing my book for free in public here in germany...

effectively, my solution is tribalism, secession, small states, "nationalism", groups of 150 people (dunbars number) im permanent competition to each other, including permanent tribal wafare, because many small wars are better than few large wars, and because "pacifism" is a lie, pacifism is only playing for time and always leads to large wars.

Goblin mode? china calls this "tang ping" (lying flat) or "guo re tze" (just pass the day, survive this day) (via serpentza on youtube) -- aka: escapism, second life, mentalism, mind over matter, knowledge is power, living in your head, idealism, high life, city life, depression, apathy, passive resistance, pessimism, nihilism, ignorance, "i dont care", Hikikomori, NEET, MGTOW, hedonism, stupid and happy, ...

Lying flat - China's Silent Revolution<br /> by serpentza<br /> https://www.youtube.com/watch?v=uWl7njLlXLU

ps: only faggets wear socks without shoes

Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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Reply to the reviewers

Manuscript number: RC-2024-02335

Corresponding authors: Pöhlmann, Stefan & Karsten, Christina B.

1. General Statements

We would like to express our gratitude to Reviewers 1, 2 and 3 for dedicating their time to assess this manuscript and for sharing their invaluable expertise on the subject matter. We have incorporated most of the suggestions made by reviewers but regrettably we were unable to conduct any additional experiments. This is because we chose to work with a single pooled virus stock for both CD4+ T cell and macrophage-derived simian immunodeficiency virus (SIV, T-SIV, M-SIV) throughout the whole study. While this heightened our data quality by omitting donor-induced variations into our virus productions, accurately estimating the total amount of viruses needed for this project was difficult, and at this point we have depleted our reserves of M-SIV and T-SIV. Nevertheless, we are confident that our manuscript has been substantially improved in response to the reviewer’s feedback, and we firmly believe that this study holds considerable implications for the development of new biomedical interventions against the human immunodeficiency virus (HIV).

Please see below our point-by-point responses to the reviewer’s comments and concerns. All manuscript references refer to the revised manuscript, in which the key changes have been tracked.

2. Point-by-point description of the revisions

Reviewer #1:

Major comments:

1 - As noted above, the differences in glycosylation are difficult to understand without more background and perhaps a figure, but it is also not clear that the changes described between lines 119 and 137 are biologically or statistically meaningful. For example, does it matter that more M-SIV virions have glycans with four antennae than T-SIV? Are there other data that show this or could experiments be done to specifically cleave these glycans at certain points to reduce their complexity and show that the infectivity differences between M-SIV and T-SIV disappear? Further, it is difficult to confirm the statement on lines 124-125 that "profiles of complex-type N-glycans differed between the two viruses (Fig. 2C)", as no statistical tests were done to compare the glycosylation being detailed in the M-SIV and T-SIV. It is more appropriate to make note that there are minor between M-SIV and T-SIV or run specific statistical tests on the data.

These are very good remarks. We have introduced a new figure (Fig. 1A) to illustrate the various glycan types, moieties, and structures discussed in the paper. Additionally, we have modified Fig. 1D-G with visualizations of the investigated N-glycans and adjusted and clarified the text to enhance accessibility for experts not specializing in glycobiology (line 62-66, 204-210, 269-273). With our current dataset, we are unable to establish a direct correlation between glycosylation and functional outcomes. Consequently, we can only speculate about the potential impact of certain glycan characteristics on SIV viral functions, a field that remains largely unexplored. Furthermore, due to the absence of remaining virus samples, we are unable to conduct experiments to validate any potential direct relationship between glycosylation patterns and viral functions. It's important to note that no statistical tests were applied to the glycan analysis data, we have now emphasized this in the revised text (line 13-16, 145-149, 250-254).

2 - On line 161, the authors note that the results showing that "the virus-producing cell has a broader impact on SIV infectivity beyond its influence on Env incorporation." This is certainly one possibility that is suggested by these and prior data, there are also other possibilities. For example, the impact of Env is not linear and perhaps a certain number of Env need to be engaged, creating some kind of threshold effect that means that the virions with fewer Env just have less infectivity. Given that there is significant data that virions are generated in different locations in macrophages and T-cells, this could also be a function of which specific membrane areas in different cell types that Env embeds in, or it could be something else associated with Env that is not cell type specific.

We agree and have adapted the text to emphasize that our interpretation is just one possible interpretation, which assumes a linear relationship between Env incorporation and SIV infectivity (line 176-178).

*3 - For the studies in Figure 5, looking at the direct vs. indirect infectivity, it is not clear why CEMx174 R5 cells (a T-cell/B-cell hybrid line) were used instead of primary macrophages or T-cells, or macrophage or T-cell lines or a fully agnostic cell type. This would be more convincing tested on primary cells, or at least comparing in a myeloid lineage line as well. *

In this experiment, we followed a previously published protocol, which utilizes the CEMx174 R5 indicator cell line as target cell for an easy read-out of the results. We agree that the use of the suggested target cell types would be a useful extension of our existing work. Regrettably, due to the lack of remaining viruses, we are unable to fulfil this request.

*4 - In Figure 6, it is not clear that VSV-G pseudotyped virus is an appropriate control, as it enters via the acidified endosome pathway and not via similar processes as the T- and M-SIV derived virions. While this may show that the glycans can bind to CBA to inhibit entry, it could also mean that the general process of endocytosis is not as susceptible to CBA inhibition and this difference in pathways should be noted as a caveat. *

We acknowledge this caveat and have incorporated a statement into the results section to inform readers about the potential impact of differences in the viral uptake pathways between VSV and HIV/SIV (line 219-223).

*5 - A very large number of cell lines were used, and it is not clear why experiments were done using so many different indicator or target lines, instead of performing most assays in a single line or set of lines so that they are comparable across experiments. Some discussion of the rationale for this would be helpful. *

Thank you for bringing your perspective to our attention. By selecting the specific cell lines for our experiments, we have adhered to established norms within our research domain. Specifically, 293T cells, C8166, and TZM-bl cells are standard choices for virus production via transfection, SIV titration, and infectivity assays, respectively. Moreover, in conducting the transmission assay, we followed a previously published protocol. We have revised the text to elucidate the rationale behind our selection of cell lines for different assays, omitted the potentially perplexing reference to the C8166 cell line and included references to support our cell line choices (lines 160-163, 187-188, 215-217, 458-459, 476).

Minor comments

*1 - Inclusion of the p27 data characterizing the amount of virus in M-SIV and T-SIV stocks (line 95) should be shown as at least a supplemental figure or could easily be added to figure 1. *

Agreed. We have included the information about the p27-concentration, and additionally the information about the infectious units and RNA copy numbers of M-SIV and T-SIV into the results section (line 98-101).

3 - The figures are relatively thin and could be combined with other figures to better connect the experiments. For instance, Figure 1 could serve as panel A for what is currently listed as Figure 2 because it is a preliminary data to the experiments in Figure 2.

As suggested by the reviewer, we have combined Fig. 1-2 (now Fig. 1), and additionally Fig. 3-5 (now Fig. 2), and 6-7 (now Fig. 3) to enhance the connections between the experiments.

3 - The authors should include quantitation of the Western blot data in Figure 1 in an adjoining graph.

We appreciate the suggestion. However, the purpose of Fig. 1B (formerly Fig. 1) was to visually represent gp120 of M-SIV and T-SIV following all treatment conditions, which produce bands of varying intensities and widths. Consequently, the bands for PNGaseF-digested gp120 appear relatively thick, which typically hampers accurate quantification. Therefore, we made the decision not to quantify the results of these blots.

*4 - The legend states that the results in Figure 7 were obtained from two independent experiments (line 778), each with 3 technical replicates. As this represents only 2 biological replicates, and the experiments were performed in easily accessible cells (TZM-bl), they should be performed 1 - 3 more times to provide a more appropriate and robust data set for statistical analysis. *

We agree with the reviewer that this might further improve the results but unfortunately, due to the lack of remaining pooled virus from this study, we are unable to fulfill this request.

Reviewer #2:

Major comments:

*It appears to this assessor that some of the supplementary data can be brought to the front as part of the main figures for presentation. *

We appreciate that you consider our supplementary data worthy enough to be part of the main figure set. We have now included Table S1 into the main figure set as Table 1.

CURRENT figures 3, 5, and 7 can be combined into one figure. Similarly, CUREENT Figure 4, and 6 can also be grouped. Alternatively, incorporating additional approaches in each set of figures to tighten the claims.

Agreed. To address this suggestion, we have combined Fig. 1-2 (now Fig. 1), 3-5 (now Fig. 2), and 6-7 (now Fig. 3).

*Karsten et al pitched their story as glycosylation of SIV from different primary cells are linked to different functionality in its title and abstract, yet the authors then declared in discussion (line 318) that establishing a direct link between Env glycosylation and viral functions is technically challenging and beyond the scope of the study. This assessor feels that authors need to decide whether current manuscript should be a descriptive study (which is more fitting for a less impactful journal) or a study with further mechanistic insights. *

Thank you for bringing this to our attention. We have modified the text in the introduction, results, and discussion section to underscore that our work is only suggesting but not directly proving differential glycosylation as cause for functional differences between M-SIV and T-SIV (lines 71-75, 155-157, 211-215, 251-256, 320-322).

*Table S1 is highly important and should be part of the main figure. Specifically, authors took the opportunity to highlight the differential % of sialic acid terminal glycans in line 133. The charge of the sialic acids would be simple mechanism for these M-SIV particle to attach. Authors should consider some of the described nano-luciferase based viral particle attachment assays used in HIV-glycan biology. Authors should be able to treat SIV (or SIV VLPs) with sialidase to quantify the role of sialic acids on binding. *

Thank you for appreciating the details of our glycan analysis. We have now included Supplementary table 1 into the main figure set as Table 1. Due to the lack of remaining virus, we are unable to address the interesting suggestions for further experiments.

*As authors carefully pointed out (throughput the manuscript) that the identity (and biology) of the producer cells can have profound impacts on glycosylation events of viral particles that are being produced. This assessor was then interested to understand precisely how their simian PBMCs and monocytes derived macrophages were prepared. Additional details in M&M would be very helpful. *

We realized that indeed experimental details appeared to be missing in this section since it was not obvious that kits for magnetic bead isolation have been used to isolate the cells, and adapted the text to make this more clear (395-413).

*With the emphasis of cell type and glycosylation relationship, it is puzzling that authors would have chosen to use TZM-bl (artificially engineered cell line) and spinoculation (2hr to push the viruses down to cell surface with 870 x G force) in Figure 3 for comparison of M-SIV and T-SIV infectivity. To this assessor, this assay neglected the biological roles of SIV glycans. In context, 870 x G is ~150x higher than most human can withstand. *

While we appreciate the reviewer’s feedback, we respectfully disagree. The TZM-bl cell line has long been established as the standard cell line for SIV/HIV infectivity assays and neutralization assays in clinical trials (Sarzotti-Kelsoe et al., 2014). In this project, our initial aim was to conduct infectivity assays on a standard cell line before transitioning to more biologically relevant target cells. However, due to limited virus availability, these studies could not be completed and will be addressed in future studies.

The application of methods to increase virus-cell contact to increase cell infection of cell lines is wide-spread in HIV research. Larger virus quantities could have been used instead of spin infection, which would require the introduction of larger amounts of conditioned cell supernatant from the virus production into the experiment with potential influence on the outcomes. Another option would have been to expose the viruses to even stronger forces during ultracentrifugation to concentrate virus stocks, or to employ "sticky" reagents such as DEAE-dextran, which might generate virus aggregates (Davis et al., 2004). Considering these options, we deemed spin infection to have the smallest overall impact on our experiments, while delivering the most robust results.

Finally, we like to note that sensitivity to force between humans and cells is not comparable and cells can withstand much higher forces than humans. We kindly refer reviewer 2 to the work of Kodaka and colleagues. They carefully assessed the efficiency and impact of spin infection using retroviral constructs on primary human cells, and determined that the best conditions were 2,800xg for 90 min considering important parameter’s such as cell viability, proliferation and in vivo differentiation.

Sarzotti-Kelsoe M, Bailer RT, Turk E, Lin CL, Bilska M, Greene KM, Gao H, Todd CA, Ozaki DA, Seaman MS, Mascola JR, Montefiori DC. 2014. Optimization and validation of the tzm-bl assay for standardized assessments of neutralizing antibodies against hiv-1. J Immunol Methods, 409, 131-146. DOI:10.1016/j.jim.2013.11.022.

Davis HE, Rosinski M, Morgan JR, Yarmush ML. Charged polymers modulate retrovirus transduction via membrane charge neutralization and virus aggregation. Biophys J. 2004 Feb;86(2):1234-42. doi: 10.1016/S0006-3495(04)74197-1. PMID: 14747357; PMCID: PMC1303915.

Kodaka Y, Asakura Y, Asakura A. Spin infection enables efficient gene delivery to muscle stem cells. Biotechniques. 2017 Aug 1;63(2):72-76. doi: 10.2144/000114576. PMID: 28803542; PMCID: PMC5768144.

*Using a single antibody DA6 (in Figure 2, cited Edinger 2000) for Env incorporation estimation via Western seems to be crude and inadequate, even in the context of isogenic virus clone. As authors pointed out, different levels of glycosylation can affect protein folding, therefore affecting Env incorporation. By the same argument, differentially glycosylated Env protein can also impact on the ability of 'epitopes within Env protein' to be recognised by Ab. Therefore, virion incorporation of Env might not be affected, but just the detectability by a specific Ab. Western evaluation with a panel of anti-Env antibodies will help. Furthermore, quantitative proteomics coupling with glycomics would be highly useful. *

We respectfully disagree on some points of your assessment. The antibody DA6 specifically targets a linear epitope in gp120 C1 (amino acids 76 to 99 in SIVmac251, Edinger et al., 2000), and the proteins analyzed by Western blot are denatured. Therefore, changes in protein folding due to differential protein glycosylation of SIV in different target cells should not affect the results. We acknowledge the potential impact of differential N-glycan attachment to gp120 based on the virus-producing cell on the binding of primary antibodies in Western blot analysis and agree that this issue could be mitigated by employing a panel or mixture of primary antibodies. However, please note that in Fig. 1B the input virus of M-SIV and T-SIV was normalized based on the signal received for gp120 removed of N-glycans (PNGase F digested). If the differential glycosylation of M-SIV and T-SIV gp120 would interfere with DA6 binding, we should observed noticeable differences between M-SIV and T-SIV in the signal of the undigested and mannose-reduced gp120 (Endo H) but this is not the case. Thus, we believe it is in this case sufficient to use only the antibody DA6 for gp120 detection.

Edinger AL, Ahuja M, Sung T, Baxter KC, Haggarty B, Doms RW, Hoxie JA. 2000. Characterization and epitope mapping of neutralizing monoclonal antibodies produced by immunization with oligomeric simian immunodeficiency virus envelope protein. J Virol, 74(17), 7922-7935.

*It is understood that T-SIV were pooled from supernatant derived from 9 animals of PBMCs. Levels of p27 production (presumed as particles but including free p27 in reality) from each animal donor should be listed in supplement. Similar types of details should be made available for M-SIV that were derived from 8 animal donors of macrophages. qPCR estimations on the levels of viral particles production in T-SIV and M-SIV from primary cell culture amplifications appear to be already available, such information should be included in supplementary to strengthen the authors' estimated / relationships amongst glycosylation, virion Env incorporation levels, and viral particle productions are carefully controlled. *

Thank you for your suggestion. We opted to include only supernatants containing more than 10 ng p27/ml in the pooled virus that constituted M-SIV and T-SIV. Consequently, we did not determine the p27 concentrations of each virus harvests below this threshold. As a result, we are unable to present replication curves for every virus production. However, we are able to provide additional information on the pooled viruses and now included the information about the p27 concentration, infectious units, and genome copy number of M-SIV and T-SIV (line 98-101).

*Non-glycan biologists generally do not appreciate some of the fine details in glycan biology. The T-SIV and M-SIV system is a great model system to decode some of the functionality of glycan biology. The current team should have (in my opinion) a clear graphic representation on describing what types of different glycans in T-SIV and M-SIV are likely to contribute to the potential differences in biological outcomes. Such incorporation will guide non-glycan biologists to better appreciate the focus and the directions of authors, thereby further improving the citation of this work when it is published after peer reviewed. Importantly, focusing a specific question to be addressed may help to consolidate effort to accelerate publication of this work. A beautiful story line, just need to cross many 't' and dot a few 'i' in my view. *

Thank you for sharing the excellent suggestion. We have now incorporated a new figure (Fig-1A) to help the reader with understanding the glycan biology in our manuscript. We have further adapted Fig. 1D-G to include glycan structures to provide a visual representation of the assessed N-glycan subgroups. Finally, we adapted the text throughout the manuscript to improve the reader’s comprehension of our work (line 62-66, 204-210, 269-273).

To address your concerns regarding the clarity of the research question, we revised the text to become more specific (line 155-157, 277-283, 294-300, 317-319, 320-322, 329-338, 364-365).

Most primate centres often incorporate transcriptomic studies in their animal works. It will be helpful for the audience if the authors could provide additional transcriptomic data (with a focus on glycosylation related genes) of simian CD4+ T cells, simian macrophages, SIV infected simian CD4+ T cells, and SIV infected simian macrophages. These data will improve the comprehensiveness of this study (and should not require any major wet-lab studies) and add weight on the arguments of the authors.

This is an interesting suggestion and should be considered in future studies. Here, we choose to focus exclusively on the investigation of the viruses but not the host cell itself. Nevertheless, we discuss the existing transcriptomics data of glycosylation relevant genes in simian CD4+ T cells and macrophages published by Gaskill and colleagues (line 277-287) and find that their results provide explanations for the results of our N-linked glycan analysis of M-SIV and T-SIV.

Gaskill PJ, Zandonatti M, Gilmartin T, Head SR, Fox HS. 2008. Macrophage-derived simian immunodeficiency virus exhibits enhanced infectivity by comparison with t-cell-derived virus. J Virol, 82(3), 1615-1621.

Reviewer #3:

Major comments *1) Line 85 "These substitutions facilitate efficient utilization of CCR5 in the absence or at very low levels of CD4 expression (Puffer et al.2002). This makes the molecular clone studied rather unique and the authors should aim to address this throughout. It does not take away from the results presented but should be addressed. *

Thank you for this suggestion. We included the information about the M-tropism of our viral strain two more times into the manuscript to emphasize this information in the discussion and the limitations of the study (lines 247-249, 345-347).

*2) (Figure 1) State the predicted size differences between T-SIV and M-SIV stocks with EndoH digestion (and similar for all 3 runs?). *

We would have liked to address this suggestion but despite corresponding with other experts and literature research; we were unable to identify a tool, which would allow us to make such predictions.

*3) Line 95 Data should be shown. This describes infectivity and could incorporated within Figure 3 along with infection of the TZM-bl cells. Infectivity of T-SIV and M-SIV on primary CD4 T-cells and macrophages is of importance. This would only be possible I assume if p27 levels were measured at each time-point collected. *

We agree that the manuscript could be extended by virus replication curves on primary cells. However, we chose to include only supernatants with p27 concentrations exceeding 10 ng/ml in the pooled virus comprising M-SIV and T-SIV. Consequently, we did not determine p27-concentrations for virus harvests below this threshold in all cases, preventing us from presenting replication curves for every virus production. We have updated the results section to incorporate the total p27-concentration of M-SIV and T-SIV (lines 98-101). Prior to the submission of this manuscript, we had initiated replication assays of M-SIV and T-SIV on primary rhesus CD4+ T cells and macrophages were initiated but these could not be completed due to the depletion of available virus.

4) There is a lack of statistical difference in the results shown in Figure 2. I assume this is due to a single measurement, but can comment be made on likelihood of biological significance with such difference between values.

Indeed, we did not conduct statistical analysis on this dataset because, given that a single pooled virus for M-SIV and T-SIV was utilized, only one measurement exists. Although we agree with the assessor on the importance of discussing the potential biological significance of the identified glycosylation differences, we are of the opinion that there is currently insufficient evidence in the literature to make scientifically grounded arguments on this matter.

*5) (Figure 3) On TZM-bl cells the T-SIV stock shown 55-fold lower infectivity compared to M-SIV. This is the reverse as to what was found on macaque CD4 T-cells where T-SIV showed a 6.5-fold higher infectivity than M-SIV? Needs addressing. Again, this should be considered in context of the results with CEMx174 R5 cells where infection between the 2 stocks appears to be similar (Figure 6). *

Thank you for raising these points. We like to remark that p27-content and infectivity are not absolutely linked (Narayan et al. 2023). Virus productions also contain empty or non-functional virions and the proportions can differ depending on the virus producer cell. Thus, T-SIV having a lower infectivity per ng 27 is likely a result of cell type dependent variation in the proportion of non-functional virions and does not represent an inconsistent result.

Kedhar Narayan, Jeongpill Choi, Shreyas S. Gujar, Aidan McGraw, Hasset Tibebe, Lilia Mei Bose, Caroline N. Arnette, Taisuke Izumi, Identifying Discrepancies in HIV Infectivity and Virion Maturation Using FRET-Based Detection and Quantification, bioRxiv 2023.12.25.573317; doi: https://doi.org/10.1101/2023.12.25.573317

*6) (Figure 5) The result may look cleaner if No Lectin value is subtracted from the cell lines carrying the lectin expression? *

Agreed. We have adapted the figure (Fig. 2D) as suggested.

*7) A much clearer introduction to CBA's would be beneficial. *

We agree that this would improve our manuscript and have expanded the introduction on carbohydrate binding agents (lines 204-210).

8) A concern I have is the presentation of data in Figures 6 and 7, especially given that the cell line used is the TZM-bl cell which has been shown to be 55-fold less infectible with T-SIV. Plotting the results as % infectivity on the same graph could be somewhat misleading. Two graphs one panel for M-SIV and one for T-SIV may be easier to follow. The CEMx174 cell line may have been a better choice as similarity to infection was found? But assume those experiments were not performed?

We kindly ask reviewer 3 to note that the virus input in these experiments has been normalized for equal infectivity, as described in the figure legend. An example demonstrating the comparability of results obtained using this method can be observed in Figure 2A, right panel, which justifies our approach. While we agree that conducting neutralization assays on additional cell types might be a valuable extension of the existing work, we chose here to use the TZM-bl cell line, the standard cell line for neutralization assays in the field of HIV research (Sarzotti-Kelsoe, 2013).

Sarzotti-Kelsoe M, Bailer RT, Turk E, Lin CL, Bilska M, Greene KM, Gao H, Todd CA, Ozaki DA, Seaman MS, Mascola JR, Montefiori DC. 2014. Optimization and validation of the tzm-bl assay for standardized assessments of neutralizing antibodies against hiv-1. J Immunol Methods, 409, 131-146. DOI:10.1016/j.jim.2013.11.022.

*9) I do feel the Discussion is extremely long and could be stream-lined to make it clearer and to the point. *

To follow your valuable suggestion, we reduced the length of the discussion by approximately one-third and eliminated sections that were less directly related to our results.

10) Materials and Methods section. Is the first section on Animal studies required. Could this not just be cited if it has been previously published.

While we agree that a manuscript should be as compact as possible, we decided to include this information to ensure complete transparency regarding our animal experiments. Additionally, many journals request this information prior to publication. Consequently, we opt to retain the text in its current form.

Minor comments *1) A) needs to be removed from Figure legend 1. *

Please note that we have not addressed this suggestion since Fig. 1 is now a multi-graph figure.

*2) Line 160 I assume this the result from (Fig 3A). *

That is correct. We have included the figure reference to make this line of text more clear.

*3) Line 255-257 Difficult sentence to understand. *

Thank you for making this point. This sentence has been removed in our efforts to shorten the discussion.

Reviewer #1 (Public Review):

Summary:

The study investigates the role of cylicin-1 (CYLC1) in sperm acrosome-nucleus connections and its clinical relevance to male infertility. Using mouse models, the researchers demonstrate that cylicin-1 is specifically expressed in the post acrosomal sheath-like region in spermatids and plays a crucial role in mediating acrosome-nucleus connections. Loss of CYLC1 results in severe male subfertility, characterized by acrosome detachment and aberrant head morphology in sperm. Further analysis of a large cohort of infertile men reveals CYLC1 variants in patients with sperm head deformities. The study provides valuable insights into the role of CYLC1 in male fertility and proposes CYLC1 variants as potential risk factors for human male infertility, emphasizing the importance of mouse models in understanding the pathogenicity of such variants.

Strengths:

This article demonstrates notable strengths in various aspects. Firstly, the clarity and excellent writing style contribute to the accessibility of the content. Secondly, the employed techniques are not only relevant but also complementary, enhancing the robustness of the study. The precision in their experimental design and the meticulous interpretation of results reflect the scientific rigor maintained throughout the study. Furthermore, the decision to create a second mouse model with the exact CYLC1 mutation found in humans adds significant qualitative value to the research. This approach not only validates the clinical relevance of the identified variant but also strengthens the translational impact of the findings.

Weaknesses:

There are no obvious weaknesses. While a few minor refinements, as suggested in the recommendations to authors, could enhance the overall support for the data and the authors' messages, these suggested improvements in no way diminish the robustness of the already presented data.

Reviewer #2 (Public Review):

Summary:

* To verify the function of PT-associated protein CYLC1, the authors generated a Cylc1-KO mouse model and revealed that loss of cylicin-1 leads to severe male subfertility as a result of sperm head deformities and acrosome detachment.

* Then they also identified a CYLC1 variant by WES analysis from 19 infertile males with sperm head deformities.

* To prove the pathogenicity of the identified mutation site, they further generated Cylc1-mutant mice that carried a single amino acid change equivalent to the variant in human CYLC1. The Cylc1-mutant mice also exhibited male subfertility with detached acrosomes of sperm cells.

Strengths:

* The phenotypes observed in the Cylc1-KO mice provide strong evidence for the function of CYLC1 as a PT-associated protein in spermatogenesis and male infertility.

* Further mechanistic studies indicate that loss of cylicin-1 in mice may disrupt the connections between the inner acrosomal membrane and acroplaxome, leading to detached acrosomes of sperm cells.

Weaknesses:

* The authors identified a missense mutation (c.1377G>T/p. K459N) from 19 infertile males with sperm head deformities. The information for the variant in Table 1 is insufficient to determine the pathogenicity and reliability of the mutation site. More information should be added, including all individuals in gnomAD, East Asians in gnomAD, 1000 Genomes Project for allele frequency in the human population; MutationTaster, M-CAP, FATHMM, and more other tools for function prediction. Then, the expression of CYLC1 in the spermatozoa from men with CYLC1 mutation should be explored by qPCR, Western blot, or IF staining analyses.

* Although 19 infertile males were found carrying the same missense mutation (c.1377G>T/p. K459N), their phenotypes are somewhat different. For example, sperm concentrations for individuals AAX765, BBA344, and 3086 are extremely low but this is not observed in other infertile males. Then, progressive motility for individuals AAT812, 3165, 3172, 3203, and 3209 are extremely low but this is also not observed in other infertile males. It is worth considering why different phenotypes are observed in probands carrying the same mutation.

Reviewer #3 (Public Review):

Summary:

In this study, Wang et al. have demonstrated that TMC7, a testis-enriched multipass transmembrane protein, is essential for male reproduction in mice. Tmc7 KO male mice are sterile due to reduced sperm count and abnormal sperm morphology. TMC7 co-localizes with GM130, a cis-Golgi marker, in round spermatids. The absence of TMC7 results in reduced levels of Golgi proteins, elevated abundance of ER stress markers, as well as changes of Ca2+ and pH levels in the KO testis. However, further confirmation is required because the analyses were performed with whole testis samples in spite of the differences in the germ cell composition in WT and KO testis. In addition, the causal relationships between the reported anomalies await thorough interrogation.

Strengths:<br /> The microscopic images are of great quality, all figures are properly arranged, and the entire manuscript is very easy to follow.

Weaknesses:<br /> Tmc7 KO male mice show multiple anomalies in sperm production and morphogenesis, such as reduced sperm count, abnormal sperm head, and deformed midpiece. Thus, it is confusing that the authors focused solely on impaired acrosome biogenesis. Further investigations are warranted to determine whether the abnormalities reported in this manuscript (e.g., changes in protein, Ca2+, and pH levels) are directly associated with the molecular function of TMC7 or are the byproducts of partially arrested spermiogenesis. Please find additional comments in "Recommendations for the authors".

HE WILL HE WILL

fck him

wait noo you're supposed to hit his HEEL

thats so real

this is so sad, saying all that you wish to say before you pass

they make a fun trio

UGH I LOVE HIM

NO NO NO

omgg he crafted him

wait why can i feel the chemistry

oh-

Emoticons, traditonal puppet shows, animation, and manga all use signals to indicate emotions or experiences to other others

This sections speaks into how green plays into how even the most "honorable" people in high positions all fell to the sin of greed. Some scholars define greed as "Greed begins in the mind and it ends as a corruption of the qualities which the mind values most" (Freedman, 171). This can be interpreted by how people in these high religious positions, like a clerk or a pope, can be corrupted with power and end up as greedy people. Furthermore, greed as a sin can be a harder one to overcome since it is a harder one to recognize, as most people (especially religious people), end up negating the fact that they, too, are affected by greed.

Freedman, L. (2009). The Narrative of Consumption: Greed and Literature. In: Brassey, A., Barber, S. (eds) Greed. Palgrave Macmillan, London. https://doi.org/10.1057/9780230246157_12

Charon is the ferryman of the underworld who leads the dead down into Hell. In this line, Dante is telling Charon not to be angry because his and Virgil's presence has been ordained and approved by those who rank higher than Charon. He instructs Charon not to question them anymore, as the issue is over Charon's head in terms of authority. https://www.theoi.com/Khthonios/Kharon.html https://danteworlds.laits.utexas.edu/gate.html

The Green Knight is a complex character. His duality is conveyed during the time spent as Bernlak, versus his first appearance as the Green Knight in the grand hall. Although his true identity is not revealed until the end, Bernlak is perceived as a supporting character to Gawain, whilst his Green alter ego is considered the antagonist to Gawain. When analyzing both of his personas, one might deduct that he dons the Green Knight figure for a purpose. Not solely to carry out the whims of Morgan Le Fay, but to proctor the capabilities of King Arthur's Knights and their valor. To see whether or not they are worthy enough to serve the land of Camelot.

“Who Is the Green Knight?” Character Analysis of the Green Knight, Pace, Accessed 8 Mar. 2024. https://csis.pace.edu/grendel/projs2002d/CHARACTERESSAY.htm

This line sparked. my attention because of the word choice "Yet more precious". To me, the specific details and elements of the knight's armor hold more symbolism than just armor. The text explains that the knight's helmet was covered in diamonds, which happen to be a precious part of Earth’s nature. Based on my research if a diamond crystal’s "surrounding conditions change, its impurity content may change as well, perhaps yielding a diamond with zones of different types” (Harlow, Page 21). What’s interesting is this is what the helmet is clocked with diamonds. Of all parts of the knight to be protected, the helmet of diamonds is what protects the head. Further, I would suggest that there is hidden symbolism here explaining that the mind is a fighter’s most important asset and should be protected at all costs.

Harlow, George E. The Nature of Diamonds. Cambridge University Press, 1998.

Here, we see the bravery that the Green Knight possesses, and this could be interpreted in two ways based on how the reader views the Green Knight. If they see him as the "devil" or some kind of evil figure, this could be cockiness because he knows that he will be ok. If he is viewed in a more positive light by the reader, this is an act of courage by the Green Knight. Either way, he is so calm when being threatened that an ax being swung is compared to him being brought a glass of wine because of how small of a reaction he had.

https://www.jstor.org/stable/25642113?seq=1

During medieval times, the axe was used as a representation of an executor. The image of the Green Knight holding an axe paints him as a figure of death. however, in the text, "Suffers himself to be beheaded first, unfortunately, after having bound his victim to submit to a like operation at the end of a stipulated term, then picks up his head and walks off with it' (208)." The idea that the Green Knight offers to be executed first makes him a more complex and unusual character.

Carnicella, Bobby. “The Green Knight: A Symbol of Life, Death and Rebirth?” The Green Knight, vault.hanover.edu/~battles/arthur/greenknight. Accessed 8 Mar. 2024.

Gawain in this text considers shrinking in the past and makes the decision to never shrink again, no matter what the consequences are. He emphasize that even if their head were to fall, it cannot be recovered acknowledging the irreversible nature of certain actions. Still trust the knight to carry out their destiny, so they beg him to go quickly. Gawain's unwavering will to face their destiny head-on and withstand whatever may come his way is evident in the determination.

It was brave for Gawain to take the king's place in the Green Knight's challenge. "Medieval chivalric literature certainly celebrates this pursuit of knightly honour, but as Sir Gawain and the Green Knight makes abundantly clear, the threat of shame is ever-present".(Trigg) I am curious though if by "strike" the Green knight meant decapitate. It was a bold move for Gawain to try to kill the Green Knight considering the deal was he'd face the exact same blow one year later. It could be debated whether this is honorable, cocky, or careless. I feel this choice was one of the lessons Gawain learned through this journey as a knight since it left him feeling uneasy when the Green Knight left and the party resumed.

Professor Stephanie Trigg, University of Melbourne. “The Poem behind the Green Knight.” Pursuit, The University of Melbourne, 4 Mar. 2024, pursuit.unimelb.edu.au/articles/the-poem-behind-the-green-knight.

All throughout the poem, the author used duality to remind the audience that life is not black and white, but rather complex. This can be seen in the Green Knight being beheaded and surviving as "the poet calls attention to a binary of an impermanent world and a world of renewal [...]" (Martinez 116). Though, this is not the only instance of a dualistic symbol being brought to light as Sir Gawain later battles both internal and external conflicting circumstances.

Martinez, Ann M. “Bertilak’s Green Vision: Land Stewardship in sir Gawain and the green knight.” Arthuriana, vol. 26, no. 4, 2016, pp. 114–129, https://doi.org/10.1353/art.2016.0052.

When reading this I was thinking it meant that he was not pained or affected by his actions of cutting the Green Knight's head off. As if it were normal he was carrying a head by the hair freely.

This description continues on in representing the attire of the green knight, starting off by stating how a lace was twinned about it and looped at the end. This is describing a ribbon or string of some sorts, giving the sword a very medieval feel when imagining it like that. As stated by the poem, the handle was clasped with tassels and buttons of bright green richly broidered on, giving a sense of identity to the sword, something very important to knights. According to Knights Templar, "for a knight, his sword was not just a weapon—it was a symbol of honor, valor, and duty. The medieval knight’s sword was more than just a piece of metal; it was an embodiment of a warrior’s soul and a testament to his commitment to the chivalric code" (Oksana).

Reference: https://knightstemplar.co/medieval-knights-swords-blades-that-shaped-battles/

is milliseconds loading time?

Setting

https://web.archive.org/web/20240307125758/https://www.smithsonianmag.com/history/what-is-the-dominant-emotion-in-400-years-of-womens-diaries-180983834/

Women's diaries from 17th till now have frustration as recurring theme, analysis shows. Not a big surprise. I think journaling often is emerging when frustration rears its head. And women have had ages of deeply systemic reasons to be very frustrated by.

I've only ever journaled when there was something wrong with me or my context, when I was frustrated, sad, depressed etc. Perhaps except for those who treat their being as action research and make daily notes for later data mining, or those in a public role journaling to maintain first hand observations before spin gets invovled (keep a journal is a sound advice for anyone getting politically active).

So these sanctions on Russia following the Russo-Ukraine war have led to some pretty substantial supply shocks. If the recent COVID supply shocks are any indicator, governments will feed money into the economy to compensate...But this leads to undue inflation. On top of increasingly unaffordable energy prices the more vulnerable won't be able to hedge themselves against the inflation with real assets etc. This has global implications. I wonder what the trade off is, if it's a necessary evil or if there are other ways to essentially suffocate Russia (seeing as the US has a history of avoiding head-on military engagement with them and for good reason). At what point does it stop?

Think the value prop can be better here - 1. Data privacy 2. Team/ department based workflows - approvals from head of teams/ departments and reporting managers

Author Response

The following is the authors’ response to the original reviews.

eLife assessment

This study presents valuable findings characterising the genomic features of E. coli isolated from neonatal meningitis from seven countries, and documents bacterial persistence and reinfection in two case studies. The genomic analyses are solid, although the inclusion of a larger number of isolates from more diverse geographies would have strengthened the generalisability of findings. The work will be of interest to people involved in the management of neonatal meningitis patients, and those studying E. coli epidemiology, diversity, and pathogenesis.

Public Reviews:

Reviewer #1 (Public Review):

Summary:

This study uses whole genome sequencing to characterise the population structure and genetic diversity of a collection of 58 isolates of E. coli associated with neonatal meningitis (NMEC) from seven countries, including 52 isolates that the authors sequenced themselves and a further 6 publicly available genome sequences. Additionally, the study used sequencing to investigate three case studies of apparent relapse. The data show that in all three cases, the relapse was caused by the same NMEC strain as the initial infection. In two cases they also found evidence for gut persistence of the NMEC strain, which may act as a reservoir for persistence and reinfection in neonates. This finding is of clinical importance as it suggests that decolonisation of the gut could be helpful in preventing relapse of meningitis in NMEC patients.

Strengths:

The study presents complete genome sequences for n=18 diverse isolates, which will serve as useful references for future studies of NMEC. The genomic analyses are high quality, the population genomic analyses are comprehensive and the case study investigations are convincing.

We agree

Weaknesses:

The NMEC collection described in the study includes isolates from just seven countries. The majority (n=51/58, 88%) are from high-income countries in Europe, Australia, or North America; the rest are from Cambodia (n=7, 12%). Therefore it is not clear how well the results reflect the global diversity of NMEC, nor the populations of NMEC affecting the most populous regions.

The virulence factors section highlights several potentially interesting genes that are present at apparently high frequency in the NMEC genomes; however, without knowing their frequency in the broader E. coli population it is hard to know the significance of this.

We acknowledged the limitations of our NMEC collection in the Discussion. We agree the prevalence of virulence factors in our collection is interesting. The limited size of our collection prevented further evaluation of the prevalence of these virulence factors in a broader E. coli population.

Reviewer #2 (Public Review):

Summary:

In this work, the authors present a robust genomic dataset profiling 58 isolates of neonatal meningitis-causing E. coli (NMEC), the largest such cohort to be profiled to date. The authors provide genomic information on virulence and antibiotic resistance genomic markers, as well as serotype and capsule information. They go on to probe three cases in which infants presented with recurrent febrile infection and meningitis and provide evidence indicating that the original isolate is likely causing the second infection and that an asymptomatic reservoir exists in the gut. Accompanying these results, the authors demonstrate that gut dysbiosis coincides with the meningitis.

Strengths:

The genomics work is meticulously done, utilizing long-read sequencing.

The cohort of isolates is the largest to be sampled to date.

The findings are significant, illuminating the presence of a gut reservoir in infants with repeating infection.

We agree

Weaknesses:

Although the cohort of isolates is large, there is no global representation, entirely omitting Africa and the Americas. This is acknowledged by the group in the discussion, however, it would make the study much more compelling if there was global representation.

We agree. In the Discussion we state this is likely a reflection of the difficulty in acquiring isolates causing neonatal meningitis, in particular from countries with limited microbiology and pathology resources.

Reviewer #3 (Public Review):

Summary:

In this manuscript, Schembri et al performed a molecular analysis by WGS of 52 E. coli strains identified as "causing neonatal meningitis" from several countries and isolated from 1974 to 2020. Sequence types, virulence genes content as well as antibiotic-resistant genes are depicted. In the second part, they also described three cases of relapse and analysed their respective strains as well as the microbiome of three neonates during their relapse. For one patient the same E. coli strain was found in blood and stool (this patient had no meningitis). For two patients microbiome analysis revealed a severe dysbiosis.

Major comments:

Although the authors announce in their title that they study E. coli that cause neonatal meningitis and in methods stipulate that they had a collection of 52 NMEC, we found in Supplementary Table 1, 29 strains (therefore most of the strains) isolated from blood and not CSF. This is a major limitation since only strains isolated from CSF can be designated with certainty as NMEC even if a pleiocytose is observed in the CSF. A very troubling data is the description of patient two with a relapse infection. As stated in the text line 225, CSF microscopy was normal and culture was negative for this patient! Therefore it is clear that patient without meningitis has been included in this study.

We have reviewed the clinical data for our 52 NMEC isolates, noting that for some of the older Finish isolates we relied on previous publications. This data is shown in Table S1. To address the Reviewer’s comment, we have added the following text to the methods section (new text underlined).

‘The collection comprised 42 isolates from confirmed meningitis cases (29 cultured from CSF and 13 cultured from blood) and 10 isolates from clinically diagnosed meningitis cases (all cultured from blood).’

Patient 2 was initially diagnosed with meningitis based on a positive blood culture in the presence of CSF pleocytosis (>300 WBCs, >95% polymorphs). We understand there may be some confusion with reference to a relapsed infection, which we now more accurately describe as recrudescent invasive infection in the revised manuscript.

Another major limitation (not stated in the discussion) is the absence of clinical information on neonates especially the weeks of gestation. It is well known that the risk of infection is dramatically increased in preterm neonates due to their immature immunity. Therefore E. coli causing infection in preterm neonates are not comparable to those causing infection in term neonates notably in their virulence gene content. Indeed, it is mentioned that at least eight strains did not possess a capsule, we can speculate that neonates were preterm, but this information is lacking. The ages of neonates are also lacking. The possible source of infection is not mentioned, notably urinary tract infection. This may have also an impact on the content of VF.

We agree. In the Discussion we now note the following (new text underlined):

‘… we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants.’

Submission to Medrxiv, a requirement for review of our manuscript at eLife, necessitated the removal of some patient identifying information, including precise age and detailed medical history.

Sequence analysis reveals the predominance of ST95 and ST1193 in this collection. The high incidence of ST95 is not surprising and well previously described, therefore, the concluding sentence line 132 indicating that ST95 E. coli should exhibit specific virulence features associated with their capacity to cause NM does not add anything. On the contrary, the high incidence of ST1193 is of interest and should have been discussed more in detail. Which specific virulence factors do they harbor? Any hypothesis explaining their emergence in neonates?

We compared the virulence factors of ST95 and ST1193 and summarized this information in Figure 4. We also discussed how the K1 polysialic acid capsule in ST95 and ST1193 could contribute to the emergence of these STs in NM. Specifically, we stated the following: ‘We speculate this is due to the prevailing K1 polysialic acid capsule serotype found in ST95 and the newly emerged ST1193 clone [22, 37] in combination with other virulence factors [15, 28, 29] (Figure 4) and the immature immune system of preterm infants.’

In the paragraph depicted the VF it is only stated that ST95 contained significantly more VF than the ST1193 strains. And so what? By the way "significantly" is not documented: n=?, p=?

We compared the prevalence of known virulence factors between ST95 and ST1193, and showed that ST95 strains in our collection contained significantly more virulence factors than the ST1193 strains. The P-value and the statistical test used were included in Supplementary Figure 3. To address the reviewers concern, we have now also added this to the main manuscript text as follows (new text underlined):

‘Direct comparison of virulence factors between ST95 and ST1193, the two most dominant NMEC STs, revealed that the ST95 isolates (n = 20) contained significantly more virulence factors than the ST1193 isolates (n=9), p-value < 0.001, Mann-Whitney two-tailed unpaired test (Supplementary Table 1, Supplementary Figure 3).’

The complete sequence of 18 strains is not clear. Results of Supplementary Table 2 are presented in the text and are not discussed.

NMEC isolates that were completely sequenced in this study are indicated in bold and marked with an asterisk in Figure 1. This information is indicated in the figure legend and was provided in the original submission. All information regarding genomic island composition and location, virulence genes and plasmid and prophage diversity is included in Supplementary Table 2. This information is highly descriptive and thus we elected not to include it as text in the main manuscript.

46 years is a very long time for such a small number of strains, making it difficult to put forward epidemiological or evolutionary theories. In the analysis of antibiotic resistance, there are no ESBLs. However, Ding's article (reference 34) and other authors showed that ESBLs are emerging in E. coli neonatal infection. These strains are a major threat that should be studied, unfortunately, the authors haven't had the opportunity to characterize such strains in their manuscript.

We agree 46 years is a long time-span. The study by Ding et al examined 56 isolates comprised of 25 different STs isolated in China from 2009-2015, with ST1193 (n=12) and ST95 (n=10) the most common. Our study examined 58 isolates comprised of 22 different STs isolated in seven different geographic regions from 1974-2020, with ST1193 (n=9) and ST95 (n=20) the most common. Thus, despite differences in the geographic regions from which isolates in the two studies were sourced, there are similarities in the most common STs identified. The fact that we observed less antibiotic resistance, including a lack of ESBL genes, in ST1193 is likely due to the different regions from which the isolates were sourced. We acknowledged and discussed the potential of ST1193 harbouring multidrug resistance including ESBLs in our manuscript as follows:

‘Concerningly, the ST1193 strains examined here carry genes encoding several aminoglycoside-modifying enzymes, generating a resistance profile that may lead to the clinical failure of empiric regimens such as ampicillin and gentamicin, a therapeutic combination used in many settings to treat NM and early-onset sepsis [35, 36]. This, in combination with reports of co-resistance to third-generation cephalosporins for some ST1193 strains [22, 34], would limit the choice of antibiotic treatment.’

Second part of the manuscript:

The three patients who relapsed had a late neonatal infection (> 3 days) with respective ages of 6 days, 7 weeks, and 3 weeks. We do not know whether they are former preterm newborns (no term specified) or whether they have received antibiotics in the meantime.

As noted above, patient ages were not disclosed to comply with submission to Medrxiv, a requirement for review of our manuscript at eLife.

Patient 1: Although this patient had a pleiocytose in CSF, the culture was negative which is surprising and no explanation is provided. Therefore, the diagnosis of meningitis is not certain. Pleiocytose without meningitis has been previously described in neonates with severe sepsis. Line 215: no immunological abnormalities were identified (no details are given).

We respectfully disagree with the reviewer. The diagnosis of meningitis is made unequivocally by the presence of a clearly abnormal CSF microscopy (2430 WBCs) and an invasive E. coli from blood culture. This does not seem controversial to the authors. We had believed it unnecessary to include this corroborative evidence, but have added the following to support our assertion:

‘The child was diagnosed with meningitis based on a cerebrospinal fluid (CSF) pleocytosis (>2000 white blood cells; WBCs, low glucose, elevated protein), positive CSF E. coli PCR and a positive blood culture for E. coli (MS21522).’

On the contrary, the authors are surprised by the statement that CSF pleocytosis occurs in neonatal sepsis ‘without meningitis’ and do not know of any definitions of neonatal meningitis that are not tied to the presence of a CSF pleocytosis. Furthermore, the later isolation of E. coli from the CSF during the relapsed infection re-enforces the initial diagnosis.

Patient 2: This patient had a recurrence of bacteremia without meningitis (line 225: CSF microscopy was normal and culture negative!). This case should be deleted.

In a similar vein to the previous comment, we respectfully assert that this patient has clear evidence of meningitis (330 WBCs in the CSF, taken 24h after initiation of antibiotic treatment). In this case, molecular testing was not performed as, under the principle of diagnostic stewardship, it was not considered necessary by the clinical microbiologists and treating clinicians following the culture of E. coli in the bloodstream. We agree that this is not a case of recurrent meningitis, but our intention was to highlight the recrudescence of an invasive infection (urinary sepsis requiring admission to hospital and intravenous antibiotics) which we hypothesise has arisen from the intestinal reservoir. We did not state that all patients suffered from relapsed meningitis.

Despite this, to address this reviewers concern, we have changed all reference to ‘relapsed infection’ to now read ‘recrudescent invasive infection’ in the revised manuscript.

Patient 3: This patient had two relapses which is exceptional and may suggest the existence of a congenital malformation or a neurological complication such as abscess or empyema therefore, "imaging studies" should be detailed.

This patient underwent extensive imaging investigation to rule out a hidden source. This included repeated MRI imaging of head and spine, CT imaging of head and chest, USS imaging of abdomen and pelvis and nuclear medicine imaging to detect a subtle meningeal defect and CSF leak. All tests were normal, and no abscess or empyema found.

We have modified the text to include this information:

Text in original submission: ‘Imaging studies and immunological work-up were normal.’

New text in revised manuscript (underlined): ‘Extensive imaging studies including repeated MRI imaging of the head and spine, CT imaging of the head and chest, ultrasound imaging of abdomen and pelvis, and nuclear medicine imaging did not show a congenital malformation or abscess. Immunological work-up did not show a known primary immunodeficiency. At two years of age, speech delay is reported but no other developmental abnormality.’

The authors suggest a link between intestinal dysbiosis and relapse in three patients. However, the fecal microbiomes of patients without relapse were not analysed, so no comparison is possible. Moreover, dysbiosis after several weeks of antibiotic treatment in a patient hospitalized for a long time is not unexpected. Therefore, it's impossible to make any assumption or draw any conclusion. This part of the manuscript is purely descriptive. Finally, the authors should be more prudent when they state in line 289 "we also provide direct evidence to implicate the gut as a reservoir [...] antibiotic treatment". Indeed the gut colonization of the mothers with the same strain may be also a reservoir (as stated in the discussion line 336). Finally, the authors do not discuss the potential role of ceftriaxone vs cefotaxime in the dysbiosis observed. Ceftriaxone may have a major impact on the microbiota due to its digestive elimination.

We addressed the limitations of our study in the Discussion, including that we did not have access to urine or stool samples from the mother of the infants that suffered recrudescence, and thus cannot rule out mother-to-child transmission as a mechanism of reinfection. We have now added that we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants. The limitations of our study are summarised as follows in the Discussion (new text underlined):

‘This study had several limitations. First, our NMEC strain collection was restricted to seven geographic regions, a reflection of the difficulty in acquiring strains causing this disease. Second, we did not have access to a complete set of stool samples spanning pre- and post-treatment in the patients that suffered NM and recrudescent invasive infection. This impacted our capacity to monitor E. coli persistence and evaluate the effect of antibiotic treatment on changes in the microbiome over time. Third, we did not have access to urine or stool samples from the mother of the infants that suffered recrudescence, and thus cannot rule out mother-to-child transmission as a mechanism of reinfection. Finally, we did not have clinical data on the weeks of gestation for all patients, and thus could not compare virulence factors from NMEC isolated from preterm versus term infants.’

Recommendations for the authors:

Reviewer #1 (Recommendations For The Authors):

It would be useful to mention the sample size (number of genomes analysed, n=58) in the abstract to give readers a sense of the scale of the analysis.

We have added the number of genomes in the abstract as suggested (new text underlined).

‘Here we investigated the genomic relatedness of a collection of 58 NMEC strains spanning 1974-2020 and isolated from seven different geographic regions.’

The term 'strain' is used throughout, it would be clearer to use 'isolates' to describe the biological material and 'genomes' when the unit being referred to is genome sequences. For example, lines 108-111 use 'strain' to mean the collection of 52 isolates but also uses 'strain' to mean the collection of 58 genomes including those of the 52 isolates that the authors sequenced plus a further 6 genomes of isolates that they do not have in their isolate collection.

We have changed the term ‘strain’ to ‘isolate’ or ‘genome’ as suggested.

Figure 1 (annotated phylogeny) is hard to read and interpret, as so much data is presented. It would assist readers if the authors could provide an interactive form of the phylogeny and metadata/genomic feature data discussed in the text, e.g. using microreact.org, so that details can be explored more easily.

This is an excellent suggestion, and we created a project on microreact.org. This information has been added to the Figure 1 legend.

https://microreact.org/project/oNfA4v16h3tQbqREoYtCXj-high-risk-escherichia-coli-clones-that-cause-neonatal-meningitis-and-association-with-recrudescent-infection.

It would be useful to provide information on the frequency and/or distribution of the virulence factors in the broader E. coli population, to provide context for readers and to better understand the importance/significance of the high frequency of the reported virulence factors within NMEC.

As noted above, we agree the prevalence of virulence factors in our collection is interesting. We discussed the prevalence of these virulence factors in our collection, and the detailed data is presented in Table S1. However, we also note a limitation in our study is the number of isolates, and thus we would prefer to avoid evaluation of the prevalence of these virulence factors in the context of a broader E. coli population. There are other studies that have examined NMEC virulence factors in the past; some examples are noted below, and we have now referenced these in our manuscript (note Ref 15 was suggested by Reviewer 3 in a comment below; PMID: 11920295).

Ref 15: Johnson JR, Oswald E, O'Bryan TT, Kuskowski MA, Spanjaard L. Phylogenetic distribution of virulence-associated genes among Escherichia coli isolates associated with neonatal bacterial meningitis in the Netherlands. J Infect Dis 2002; 185(6): 774-84.

Ref 28: Wijetunge DS, Gongati S, DebRoy C, et al. Characterizing the pathotype of neonatal meningitis causing Escherichia coli (NMEC). BMC Microbiol 2015; 15: 211.

Ref 29: Bidet P, Mahjoub-Messai F, Blanco J, et al. Combined Multilocus Sequence Typing and O Serogrouping Distinguishes Escherichia coli Subtypes Associated with Infant Urosepsis and/or Meningitis. J Infect Dis. 2007; 196(2):297-303.

I suggest avoiding the term 'global' to describe the collection, given that there are only seven countries included in the collection and two of the most populous continents (Africa and South America) are not represented at all.

We agree, and now refer to our collection as ‘an NMEC strain collection from geographically diverse locations.’

Reviewer #2 (Recommendations For The Authors):

This is a suggestion regarding discussion/food for thought: This study sheds information on genomic features and indicates the presence of a reservoir in the infected infant. Previous studies have demonstrated the presence of a reservoir in the vaginas of women with recurrent UTIs. Is there any information as to whether the mothers of these infants, especially the three with recrudescent infection, had a UTI or recurrent UTI in their life? It may be worthwhile discussing the potential of testing for E. coli in expecting mothers, if they have a history of UTI.

We do not have such data, and as indicated above we note this as a limitation of our study.

It is unclear as written in the main text, as to whether all three cases of recrudescent infection come from the same geographical location. It would be easier to have this information in the corresponding main text, in addition to the supplement.

The three cases of recrudescent invasive infection were from 3 different locations. We have added the information as following (new text underlined):

‘These patients were from different regions in Australia.’

Reviewer #3 (Recommendations For The Authors):

Line 48 and 67 change the word "devasting".

Changed as suggested.

Line 49 second most in full-term infants.

Changed as suggested.

Line 56 delete the sentence "antibiotic resistance genes occurred infrequently".

We changed the sentence, which now reads (new text underlined):

‘Antibiotic resistance genes occurred infrequently in our collection’.

Line 76 reference 10 is inappropriate.

Reference 10 reported that 5/24 infants treated for neonatal Gram-negative bacillary meningitis over a 10-year period had a relapse of meningitis after the initial course of treatment. Four of the isolates that caused these relapsed infections were E. coli.

To address the reviewers concern, we have altered the text as follows (new text underlined):

‘Moreover, NMEC is an important cause of relapsed infections in neonates [10]’.

Line 83 several references related to serotypes are missing, notably doi.org/10.1086/339343.

We have added this reference.

Line 171 significantly? n=?, p=?

The numbers and P-value were provided in the Supplementary Figure 3 legend. We have now added these to the text as follows:

‘Direct comparison of virulence factors between ST95 and ST1193, the two most dominant NMEC STs, revealed that the ST95 isolates (n = 20) contained significantly more virulence factors than the ST1193 isolates (n = 9); P-value < 0.001, Mann-Whitney two-tailed unpaired test (Supplementary Table 1, Supplementary Figure 3).”

Figure 4 is not necessary.

We respectfully disagree. Figure 4 provides an illustrative comparison of virulence factors between the two most dominant NMEC sequence types, ST95 and ST1193. We believe this will be informative for many readers.

Line 311 "We speculate....of preterm infants" This sentence does not add anything to the discussion.

We respectfully disagree and have kept the sentence. This reflects our opinion.

Line 320 "clear clinical risk factors to explain... ». Term of neonates is missing.

Updated as follows (new text underlined):

‘Although reported rarely, recrudescent invasive E. coli infection in NM patients, including several infants born pre-term, has been documented in single study reports [39, 40]. In these reports, infants received appropriate antibiotic treatment based on antibiogram profiling and no clear clinical risk factors to explain recrudescence were identified, highlighting our limited understanding of NM aetiology.’

I think often people get caught up in ideas by their ability to be great and expanded on. However, as discussed in this book, how it is helpful to society as a whole? What does a great idea actually prompt and what are the consequences? When I watched Jurassic park funny enough I thought about my own current projects in augmented reality and the consequences of utilizing those head sets but also considering the potential good. There are so many nuances.

The concept of designing timelines with both an "at-a-glance" and a "detailed" seems to be important for user engagement. How can digital humanities developers balance these two aspects to cater to both casual browsers and serious researchers?

Such tragic death

I've always thought there had to be some sort of physical damage done to the eye for blindness to occur.. this is interesting

My thoughts on this new highly advanced technology is that this is simply to dangerous for someone to have as it may seem like there might be a lot of side effects to it. For example, let's say if someone was having a very bad day or if they had a mental breakdown, what would happen to the chip in their heads. We're still not to certain about the abilities and skills this has to offer. If anything most people would agree that having this chip implanted into your head isn't the smartness move to go with. Star Wars might see this as the inhibitor chips that were put into all the Clones heads to then execute Order 66 on the Jedi. Mortal of the story is that something like this isn't really good idea given how much both the chip and the surgery will cost you.

Many students initially perceived research courses as unfamiliar and separate from their field of study, finding the material abstract and challenging, contributing to a negative perception fueled by high failure rates. Anxiety was prevalent, stemming from concerns about the course difficulty, workload, and fear of not passing, leading some students to feel unprepared. Additionally, a significant portion of students developed a research self-concept that positioned researchers as different and unrelatable, leading to resistance in learning and adoption of surface learning strategies among those with weak or negative research self-concepts

then we need to stop perpetuating the myth of the child genius, who like Beethoven, laid his ear on a piano and could play something he never heard just by the vibrations on his head.

Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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Reply to the reviewers

Manuscript number: RC-2023-02132R

Corresponding author(s): Halyna, Shcherbata

Point-by-point description of the revisions

We would like to sincerely thank the reviewers for the positive evaluation of our work, careful reading of our manuscript, and helpful suggestions. In the revised version of our manuscript, we have introduced the proposed changes and added the new data based on the suggested experiments to address the reviewers’ concerns. We hope that this modified version of the manuscript is now acceptable for publication.

• *

Reviewer #1 (Evidence, reproducibility and clarity (Required)):

Summary Elucidating the cellular and molecular mechanisms underlying age-related neurodegeneration remains a key challenge for neurobiologists. In this manuscript, Mariana Tsap and colleagues in the team of Halyna Shcherbata focus on the function of the neuropathy target esterase NTE/Swiss Cheese (Sws) in the Drosophila brain. The authors use an elegant combination of genetics, light and electron microscopy, RT-qPCR and GS-MS mass spectrometry to determine the complex role of Sws in cellular blood brain barrier (BBB) integrity, the brain inflammatory response and fatty acid metabolism. The study provides a detailed characterisation as to how the loss of sws affects glial cell morphology in the BBB revealing abnormal membrane accumulations and tight junctions, and in consequence causing permeability issues. Importantly, they observed the upregulation of antimicrobial peptides in the brain, indicative of neuroinflammation, as well as of fatty acids, equally connected with the inflammatory response.

Major comments

The study provides a detailed and comprehensive characterization of the sws mutant phenotype, and in particular the role of this gene in blood-brain barrier forming glia.

The study connects neurodegeneration and inflammation, but also makes a particular point about "inflammaging". However, the age contribution has not been studied in detail. Indeed, the flies analyzed are 15 days old (according to the Material and Methods section, with the exception of Figure 1 where flies are 30 days old), and hence have not been compared with younger or older flies to make a point of age as evoked in the abstract, introduction or discussion. The authors should either add experiments comparing differently aged flies or de-emphasize this point to a brief consideration in the discussion. Instead, it would be very helpful to provide concise information about the current knowledge concerning the inflammatory response in the Drosophila brain. We thank the reviewer for raising this point. The decision to use 15-day-old flies was made due to the high mortality of swsmutants after two weeks and because age-dependent character of sws neurodegeneration has been previously well described. As the reviewer suggested, now we also included old animals in our experiments to show a connection between age-dependent neurodegeneration and inflammation. We measured and compared the mRNA levels of expression of the antimicrobial peptides (AMPs) Attacin A, Cecropin A, and Diptericin in the heads of 15- and 30-day-old sws loss-of-function mutants, in the heads of flies that had sws downregulation only in SPG cells (moody>swsRNAi) and in the heads of flies expressing NTE/SWS in SPG cells in sws mutant background. We found that the expression levels of the antimicrobial peptides are increased in the age-dependent manner in the tested mutants. In addition, we found that the expression of NTE/SWS in SPG in sws mutant background reduces inflammatory response in aging animals (see Figure 5D). Also, as the reviewer suggested, we provide brief information on the current understanding of the inflammatory response in the Drosophila brain in the Introduction and Results sections.

Related to this point, the authors convincingly show that sws is required in surface glia using rescue experiments. Nevertheless, all experiments rely on drivers and mutants that could cause the emergence of phenotypes during development. Thus, to strengthen the causative link between the breakdown of the BBB and the neuroinflammatory response, it would be helpful to consider an acute knock-down in adults after BBB formation has been completed. To strengthen the causative link between the breakdown of the BBB and the neuroinflammatory response during adulthood, we performed qPCR analysis and measured the mRNA levels of the antimicrobial peptides Attacin A, Cecropin A, and Diptericin in the heads of flies with sws downregulation in glia cells induced after the blood-brain barrier was formed using the Gal80ts tool. We found that sws downregulation in glial cells during adulthood, after the BBB is formed, leads to the increased inflammatory response (new Supplementary Figure 4E).

To test the brain permeability barrier, the study uses a 10 KDa dextran permeability assay. Almost 25% of brain in controls show a leaky barrier. It would be helpful to describe the causes for this relatively high occurrence. The observed relatively high occurrence of a leaky barrier phenotype in our control group may be attributed to our experimental procedure. We injected flies peritoneally and waited for over 12 hours before dissecting their brains for the permeability assay. Typically, such analyses are conducted after shorter periods, often around 2 hours. Additionally, we used Dextran with the smallest molecular weight (10kDa). The blood-brain barrier (BBB) is not 100% impermeable, and small molecules can gradually enter the brain over time. Recent studies have shown that this entry could be facilitated by endocytosis (Artiushin et al, 2018), which could partially explain the presence of Dextran 10kDa in control brains. Considering this, using a larger Dextran (70kDa) in our experiments could have been more accurate. Importantly, we always compared mutants and controls that underwent identical treatment, dissection, and analysis. We conducted experiments in multiple biological replicates to accurately assess the significance of the differences between mutants and controls. Therefore, we are confident that the differences we observed between controls and mutant flies in the BBB permeability are significant. We included all relevant numbers and statistics for these experiments in Supplementary Table 4.

An important point in the study concerns the increase of free fatty acids as cause of the inflammatory response. The measurements were based on measurements of whole heads, which could include the hemolymph and fat body within the head in addition to brain. However, the causative relationship remains unclear and the question why a leaky blood brain barrier would increase the free fatty acid levels in the body or brain remains mainly an observation at the descriptive level. Here, it would be helpful to design an experiment, which could test the causative links or to modify the interpretation in scheme 6D and adjust the wording in the text. We agree that the causative relationship between a leaky blood-brain barrier and increased free fatty acid levels in the body or brain is currently an observation at the descriptive level and that it would be important to investigate the correlation between a leaky blood-brain barrier, inflammation, and increased free fatty acid levels in greater detail in future studies. In the modified manuscript, we have changed the scheme in Figure 5G and adjusted the wording in the text.

Related to this, how do the levels of AMP caused by a leaky BBB would compare to an elicited neuroinflammation by the presence of bacteria? The neuroinflammatory response can be accompanied by macrophage entry into the brain following AMP induction. Could the authors detect this response (which could be envisioned as manipulations include pupal development, provided macrophages would persist into adulthood)? This would make a strong point regardless of the outcome. We thank the reviewer for suggesting this excellent experiment. To detect macrophage entry into the mutant brains, we used antibodies (NimC1) and srp(Hemo)>mCherry that label the macrophage cells. We found macrophages in the larval and adult sws mutant brains and also in adult brains upon downregulation of sws in SPG cells (Figure 5E-F and Supplementary Figure 4F-IG. These data additionally support our hypothesis that a leaky BBB in sws mutants induces neuroinflammation, which is accompanied by macrophage entry into the brain following AMP expression.

Expression of sws is determined using sws-Gal4 driving membrane-tethered GFP. As sws is expressed very widely and classical Gal4 lines tend to be active in the BBB, it is important to provide the exact information about the nature of this driver. We appreciate the reviewer for bringing this to our attention. We have now included information about the line we used to express transgenes in a sws-dependent manner. Specifically, we utilized the y*w*P{GawB}swsNP4072/FM7c line (Kyoto Stock Center 104592), which was generated using the Gal4 enhancer trap element P{GawB} insertion strategy.

The Material and Methods section should contain a proper Quantification and Statistical analysis section. In the Figures, it would be helpful to refer to the Table reporting sample numbers. As the reviewer suggested, we have now included a Quantification and Statistical analysis section in the Materials and Methods. Additionally, we ensured that all figure legends include a reference to the corresponding tables reporting sample numbers and statistics.

In Figure 5, it would be important to indicate sample numbers, the nature of the error bar, and show data points together with columns. We agree with the reviewer that it is important to report all sample numbers and statistics. We generated a new Supplementary Table 1 for all qRT-PCT data, and Supplementary Tables 5 containing all "n" values and corresponding p-values. In the Figure Legends, we denoted the type of error bars and deviations, included p-values, and referred to the relevant tables for comprehensive numerical data.

Minor comments

On page 8, cell death is visualized using "the apoptotic marker Cas3". It should be Caspase-3. Moreover, it is not clear whether this antibody (directed against vertebrate Caspase-3) recognizes indeed Caspase-3 in Drosophila? This should be formulated more carefully. As the reviewer correctly noted, the Caspase-3 antibody is designed for human Caspase-3. While it has been employed in Drosophila apoptosis research, its specificity for Caspase-3 in Drosophila is unclear. Given the very well-documented apoptosis in sws mutants (Kretzschmar et al, 1997; Muhlig-Versen et al, 2005) and the non-focus on neuronal cell death in this research, we have opted to exclude this information from the supplementary figure. We appreciate the reviewer for bringing this to our attention and for the valuable suggestion.

On Page 9 (3rd paragraph), the authors report that they "want to understand what signaling pathway is activated." However, the described experiments do not lead to a signaling pathway, but conclude that an antiflammatory response is evoked. This should thus be reworded. Thank you for pointing this out. In the revised version, we state that we wanted to understand whether the compromised brain barrier in sws mutants triggers the activation of any cellular stress pathways, including apoptosis, ferroptosis, oxidative stress, ER stress, and inflammation.

Figure 1 reports the expression pattern and phenotype of sws; thus, the title of the figure should be extended. Thank you for the suggestion. We have updated the title of Figure 1 to more accurately reflect its content. The revised title is now: NTE/SWS is expressed in Drosophila brain and its loss leads to severe neurodegeneration.

Concerning the description of phenotypes, the authors use the term "clumps", but it is not clear what this entails (e.g., Page 6, or Figure 6). For the reader, it is also necessary to refer to original studies of moody to understand the septate junction phenotype represented in the figure. As the reviewer suggested, we changed the word “clumps” to “clusters”. We also agree with the reviewer’s recommendation to cite the original work on Moody to acknowledge previous research and enhance the understanding of moody phenotypes. We have now included the relevant citations in the manuscript.

**Referees cross-commenting**

I fully agree with the comments of the other two reviewers, as they were complementary and overlapping with mine (e.g. the contribution of age).

Reviewer #1 (Significance (Required)):

This study provides a detailed cellular and functional characterization of the swiss cheese phenotype in the blood-brain barrier so far not reported in previous studies, including the team's own earlier publications (e.g., Kretzschmar et al., 1997; Melentev et al., 2021 and Ryabova et al., 2021). Furthermore, it uses cutting-edge technology to provide links to neuroinflammation and neurodegeneration, Previous studies explored neuroinflammation in the brain of Drosophila by challenging the organism with bacteria to mount an inflammatory response (Winkler et al., 2021). Intriguingly, this current study provides evidence, that a leaky blood brain barrier alone could lead to an inflammatory response, and that in turn, treatment with anti-inflammatory agents could reduce the cellular defects in glia and in consequence neurodegeneration. This represents an important conceptual advance that will be of wide interest to neurobiologists interested in glial biology, neuroinflammation and neurodegeneration in Drosophila and in vertebrates. One possible limitation of the study may be that while complex cellular processes have been pinpointed, some of the causative links of the BBB with neuroinflammation remain unexplored, in particular the aspect of elevated free fatty acids/antimicrobial peptides.

We appreciate the reviewer's recognition of the conceptual significance of our study, revealing that a leaky blood-brain barrier alone can induce an inflammatory response, with subsequent treatment using anti-inflammatory agents and the importance of these findings for neurobiologists. We also thank the reviewer for thorough examination and insightful suggestions. Given that prior studies have demonstrated the induction of neurodegeneration by the overactivation of innate immune-response pathways, especially elevated expression of antimicrobial peptides (Cao et al, 2013), our new experimental data showing increased levels of antimicrobial peptides in aging flies with a defective BBB further strengthen the connection between the BBB, AMPs and neuroinflammation. This link is even more enhanced by the rescue experiments and the detection of macrophage entry in the mutant brains. We trust that the implemented revisions, accompanied by supplementary experimental data, enhance the suitability of our manuscript for publication.

Reviewer #2 (Evidence, reproducibility and clarity (Required)):

The manuscript by Tsap et al describes a role of NTE/SWS in forming the BBB in Drosophila. Disruption of the BBB in SWS mutants and knockdown flies results in morphological changes of the glia forming the BBB, increased brain permeability, altered lysosomes, and an upregulation of innate immune genes. The experiments to show a function of SWS in surface glia and the resulting changes in permeability are well supported by the experiments and the statistics appears appropriate.

The authors also show changes in innate immune genes and some fatty acids and that similar changes are found in another mutant affecting the BBB. They discuss that these changes are a consequence of the disruptions of the BBB but also that these changes induce changes in the BBB. To address this and confirm that the changes in immune genes and fatty acids is a consequence of the altered BBB, they should include experiment expressing SWS in the surface glia and measure if that normalizes these changes. Another major aspect that should be addressed is the effect of aging. As the authors point out, loss of SWS causes age-dependent phenotypes (shown by the author and others) and with the exception of figure 3F, the age isn't even mentioned in any of the other figures. Furthermore, at least some of the experiments should be done at different ages to determine whether the phenotype is progressive; this includes the permeability assays and the measurements of immune genes (the latter could also support whether changes in the immune genes affect the BBB or vice versa the BBB changes cause the upregulation of immune genes).

As the reviewer suggested, in order to establish a connection between age-dependent correlation between neurodegeneration and inflammation, we analyzed the mRNA expression levels of antimicrobial peptides in the heads of both 15- and 30-day-old sws loss-of-function mutants, as well as in flies with sws downregulation specifically in SPG cells (moody>swsRNAi). We found that the expression levels of the antimicrobial peptides are increased in the age-dependent manner in the tested mutants (Figure 5D, red and orange bars). Following the reviewer’s recommendation, we also performed an experiment where we expressed NTE/SWS in the surface glia in a sws mutant background (sws1; moody>sws, rescue). We measured mRNA levels of Attacin A, Cecropin A, and Diptericin in the heads of 15- and 30-day-old flies (Figure 5D, blue bars). The results showed that the levels of all three AMPs were not significantly different or slightly upregulated in the heads of “rescue” animals compared to Oregon R controls (Figure 5D, compare green and blue bars, and see Supplementary Table 1). Importantly, the levels of all AMPs were significantly lower in the heads of 30-day-old rescue animals than in the heads of the same age sws1mutants (Figure 5D, compare red and blue bars, green stars, see also Supplementary Table 1). These findings further support our hypothesis that sws deficit in the surface glia induces an immune response in age-dependent manner.

We did not conduct the Dextran permeability assay in older flies because approximately 90% of the 15-day-old flies with swsderegulation already exhibited impaired permeability of the BBB. This suggests that the phenotype is quite severe and may not show significant age-dependent progression. Moreover, older mutant flies were extremely weal, and it is likely that they would not have survived the peritoneal injection procedure.

Lastly, the authors claim that septate junctions are defective in sws mutants. However, this should be confirmed by EM studies (which the authors have already done) besides immunohistochemistry which doesn't provide enough resolution.

As the reviewer suggested, for a more detailed detection of septate junctions, we conducted additional electron microscopy experiments. The images included in Figure 6D-F show irregular aggregates and disruptions in the structures of septate junctions and membranes in sws mutants compared to controls. Additionally, we display the appearance of tight junctions in moody mutants (Supplementary Figure 5E-F), which look dramatically different compared to sws junctions and, as previously described, appear overgrown.

Reviewer #2 (Significance (Required)):

A role of SWS in maintaining the BBB and what consequences this has provides another insight how this protein (and its homolog NTE) affects brain health. Although a function of SWS in glia (as well as in neurons) has previously been described, changes in the surface glia and the BBB is a novel aspect. However, the causative role of SWS on some of the described consequences (see above) should be confirmed. Although the manuscript can add to a better understanding of the connection between disruptions of the BBB and neurodegenerative diseases, which is of interest for a broader field of researchers, the discussion of the results is quite speculative.

We appreciate the recognition of the novelty of this work and its potential contribution of our manuscript to a better understanding of the connection between disruptions of the BBB and neurodegenerative diseases. We thank the reviewer for the constructive feedback and hope that introduced changes, along with additional experimental data that address the concerns raised, strengthen the proposed role of sws in the formation of tight junctions in the BBB and its age-dependent maintenance.

Reviewer #3 (Evidence, reproducibility and clarity (Required)):

Summary: The study of the formation and maintenance of the blood-brain barrier (BBB) is a growing field of study, partly due to its strong link with neurological disorders. The BBB depends on the role of multiple cell types and mechanisms. Mutations in the conserved phospholipase NTE/SWS can lead to neurodegeneration, and previous work from the authors shows that SWS loss leads to abnormal glial morphology. In this work, authors use Drosophila to further study this phenotype, showing that SWS is mostly expressed in the BBB-related glia and that its loss leads to abnormal BBB permeability, increased inflammatory response and neural cell death. Interestingly, authors observed a dependence for the BBB-defective phenotype on aging, with important implications for SWS/NTE and neurodegeneration. Overall, the work represents a clear advance in the poorly explored role of NTE/SWS in neurodegeneration, with a broad impact on the understanding of BBB maintenance. This work shows a combination of multiple and appropriate experimental approaches, including confocal microscopy, EM, RT-qPCR, or gas chromatography-mass spectrometry among others.

Major comments:

The use of sws1 and sws1/sws4 transheterozygous animals, together with the use of sws RNAi is a solid approach to validate that the reported phenotypes are due to SWS loss. Using these models, the authors performed a convincing structural analysis of the subperineurial glia phenotype, and showed that it is accompanied by a defective BBB, inflammation and neuronal cell death. The key conclusions are properly supported by the data. However, there are some claims in the text that are not supported by any data in the Figures, but only qualifications. This needs to be fixed:

-Page 6, third paragraph:

"...we specifically downregulated sws in the nervous system using the double driver line that allows downregulation of sws in glia and neurons (repo, nSyb-Gal4, Suppl. Fig. 2C-Cʹ). Since these animals had the same disorganized structure of brain surface as the loss-of-function mutant..." Supp. Fig. 2C-C' only shows expression of CD8:GFP and nlacZ reporters by repo and nSyb-Gal4, but there is no data showing sws RNAi expression by these drivers.

We thank the reviewer for noticing these referencing mistakes. We have corrected the references to the expression patterns of the glial and/or neuronal Gal4 drivers (Supplementary Figure 1D, E and F). Bar graph in Supplementary Figure 1C shows RT-qPCR analysis of sws mRNA levels from flies with glial and/or neuronal sws downregulation (repo>swsRNAi, nSyb>swsRNAiand repo, nSyb>swsRNAi), and the images of mutant brains in Supplementary Figure 2 and Figure 2A-C show the surface glia phenotypes in these mutants.

"...Moreover, downregulation of sws in all glial cells (repo>swsRNAi) resulted in the same phenotype. At the same time, upon sws downregulation in neurons,... (Suppl. Fig. 4)..." Suppl. Fig. 4 only shows nsyb>swsRNAi data but not repo>swsRNAi

We show now both repo>swsRNAi and nSyb>swsRNAi (Supplementary Figure 2C and 2E, respectively).

-Page 6, fourth paragraph:

"Importantly, expression of Drosophila or human NTE in these glia cells rescued this phenotype (Fig. 2H)"

In addition to the indicated quantifications, it is essential to show some representative data showing the phenotype when Drosophila or human NTE are expressed in glial cells of sws mutant animals. We agree with the reviewer that it is important to show the rescue phenotypes. We have included images of the brain surface of sws mutants that have Drosophila or human NTE expressed in glial cells (Figure 2D and Supplementary Figure 2F).

-Page 9, last paragraph: "We found that in moody mutants, the surface glia phenotype analyzed using CoraC as a marker could also be suppressed by NSAID and rapamycin (Fig. 5A)." In addition to the indicated quantifications, it is essential to show some representative data showing the phenotype with and without treatments.

We appreciate the reviewer's suggestion, and as recommended, we have included representative data showing the phenotype with and without treatments in Supplementary Figure 4C-D.

A more detailed analysis of two aspects of the data would clearly improve the manuscript, whose findings are a bit superficial in the current state:

• The exact mechanism by which BBB permeability leads to brain inflammation remains unknown. Authors show that accumulation of polyunsaturated fatty acids (known to regulate inflammation) occurs in sws-depleted animals. However, they only observed a correlation between this phenotype and the inflammatory response, while is not clear whether the accumulation of polyunsaturated fatty acids causes inflammation in this model or is a consequence of it. An attempt to rescue the accumulation of polyunsaturated fatty acids (i.e., knocking down a required enzyme for their production) in sws mutants might help to understand this. Also, the fact that the defective BBB phenotype observed in either sws KO and glia-specific KD can only be partially rescued by the use of inflammation inhibitors, suggests that other pathways are involved.

We agree with reviewer that since the use of inflammation inhibitors only partially rescue the defective BBB phenotype in swsmutants, it implies the involvement of additional pathways. While our data reveal a correlation between the accumulation of polyunsaturated fatty acids and the inflammatory response, whether this accumulation causes inflammation in our system remains to be studied. We have revised the text to ensure that this explanation is clearly stated without overemphasis.

• While the differences between the phenotypes caused by sws or moody loss are well characterized, it would be key for this work to further study the mechanisms by which sws controls septate junctions. The authors propose the organization of lipid rafts, but some experiments in that direction to check this hypothesis. For example, can authors reproduce the septate junction phenotype of sws mutant (Fig. 6C) by using a different approach to induce defective lysosomes in subperineurial glia?

We appreciate the reviewer's suggestion for such an insightful experiment. To investigate whether the septate junction phenotype observed in sws mutants can be replicated in mutants with defective lysosomes in subperineurial glia, we downregulated several key lysosomal genes in SPG cells: moody>DysbRNAi, moody>Npc1aRNAi, moody>PldnRNAi, andmoody>spinRNAi (Supplementary Figure 6A-E). We were happy to see that downregulation of any of these genes resulted in abnormal formation of SJs and membrane organization in SPG cells. These additional experiments strongly support our hypothesis that lysosomal control of membrane homeostasis significantly impacts the appearance of SJs. Thank you for this excellent idea.

The attempt of the proposed approaches above should require about 3-6 months of investment, with limited economic effort, given the availability and diversity of lines found in the existing stock centres such as Bloomington or Vienna.

The data is presented very clearly, and the methods are adequately detailed, and the experiments and statistical analysis are adequate.

Minor comments:

Prior studies are referenced appropriately, but there is a case that should be addressed. On Page 3, first paragraph, regarding the sentence: "However, the molecular mechanisms underlying inflammaging remain unclear". I recommend specifying what is known and what is unknown in the field. Ideally describing (briefly) the knowledge about lipids, inflammaging and neurodegeneration, which are the specific topics of the research. Otherwise, the current sentence is too vague, while there is a lot of work published about it.

As the reviewer suggested we have extended the first part of our introduction to briefly describe how inflammaging is connected with the BBB, fatty acid metabolism and lysosomal functions.

The text and figures are clear and accurate. The logic of the experiments and the results are exposed very clearly (for example, the Suppl. Tables are very helpful). There are a few minor issues, however, that should be addressed:

• Page 4, first paragraph: regarding the sentence: "For various obvious reasons, humans are not ideal subjects for age-related research.", I recommend specifying the main reasons (i.e. life cycle, ethical issues, etc.?).

Thank you, the main reasons are specified now.

• I would recommend moving the text "For various obvious reasons...disrupted upon ageing." From its current position to just before "Drosophila melanogaster is an excellent...". This would keep a better logic in the text by explaining NTE first and later introducing the models to study its function. Presenting then Drosophila.

Thank you, done.

• To support the sentence "Together, Drosophila satisfies...neurodegeneration during aging", instead of citing so many papers, I recommend citing just one current review about it, since the amount of literature supporting the claim is huge and should not be limited to a few "random" articles. An alternative might be indicating that the lab has used Drosophila for this aim before, and then citing the examples from the literature.

Thank you for this suggestion, now we referenced few recent reviews and referred to our previous work on the topic.

• Page 4, second paragraph: if NTE/SWS is going to be used as a synonym for NTE/SWS loss of function (or other type) model, it needs to be specified. Otherwise, refers to the proteins and sentences like "NTE/SWS has been shown to result in lipid droplet accumulation..." are misleading. Thank you for the suggestion; we have now specified that NTE/SWS is used as a synonym for the SWS protein in Drosophila and corrected this throughout the manuscript.

• Page 4, last paragraph: the first time that "BBB" is used, its meaning should be specified. And three lines below use "BBB" instead of blood-brain barrier.

Thank you, corrected.

**Referees cross-commenting**

I agree with the comments provided by the other reviewers. They are well reasoned and cover some aspects of the work that I did not see. Regarding the main issue, the three revisions point at the same direction, that is the limited analysis about the mechanism underlying the phenotypes.

Reviewer #3 (Significance (Required)):

• Describe the nature and significance of the advance (e.g. conceptual, technical, clinical) for the field. This work represents a substantial advance in the understanding of NTE/SWS function in the context of neurodegeneration, and opens potential approaches to treat related disorders (they successfully use anti-inflammatory compounds to ameliorate some of the key phenotypes). However, the findings are a bit superficial in terms of mechanisms, and further analysis (see major comments) would notably improve the significance of the manuscript. This should be realistic and suitable, given the advantages of the Drosophila model and the availability of tools.

• Place the work in the context of the existing literature.

The role of SWS in regulating lysosomal function is potentially supported by NTE-deficient mice data (Akassoglou et al., 2004; Read et al., 2009), where different types of neurons show similar dense bodies containing concentrically laminated and multilayered membranes than those observed in this work in Drosophila sws mutant. Potentially, the rest of the work has a translation to mammals, which is supported by the fact that ectopic expression of NTE rescues some of the key phenotypes described in the manuscript.

• State what audience might be interested in and influenced by the reported findings. Neuroscience in general, since the study of BBB and neurodegeneration has a clear general interest in the whole field.

• Define your field of expertise with a few keywords to help the authors contextualize your point of view. Indicate if there are any parts of the paper that you do not have sufficient expertise to evaluate. Drosophila; Neurodegeneration; Hereditary Spastic Paraplegia; Alzheimer's disease; Motor neurons; Microglia; Endoplasmic reticulum; Mitochondria.

Lipid metabolism is the part of the manuscript where I have less expertise to evaluate, only having general knowledge about it.

We appreciate the positive evaluation of our work, the careful reading, and the valuable suggestions provided by the reviewer, including recommendations for additional experiments and changes in the text. We believe that the implemented changes, combined with the new experimental data, have improved the manuscript, making it ready for publication.

References

Artiushin G, Zhang SL, Tricoire H, Sehgal A (2018) Endocytosis at the Drosophila blood-brain barrier as a function for sleep. Elife 7

Cao Y, Chtarbanova S, Petersen AJ, Ganetzky B (2013) Dnr1 mutations cause neurodegeneration in Drosophila by activating the innate immune response in the brain. Proc Natl Acad Sci U S A 110: E1752-1760

Kretzschmar D, Hasan G, Sharma S, Heisenberg M, Benzer S (1997) The swiss cheese mutant causes glial hyperwrapping and brain degeneration in Drosophila. J Neurosci 17: 7425-7432

Muhlig-Versen M, da Cruz AB, Tschape JA, Moser M, Buttner R, Athenstaedt K, Glynn P, Kretzschmar D (2005) Loss of Swiss cheese/neuropathy target esterase activity causes disruption of phosphatidylcholine homeostasis and neuronal and glial death in adult Drosophila. J Neurosci 25: 2865-2873

eLife assessment

This important study by Lee and colleagues examined how neural representations are transformed between the olfactory tubercle (OT) and the ventral pallidum (VP) using single neuron calcium imaging in head-fixed animals trained in classical conditioning. They show that the dimensionality of neural responses is lower in the VP than in the OT and suggest that VP responses represent values in a more abstract form while OT contains more odor information, potentially enhancing odor contrast. The reviewers found the results overall convincing although the nature of OT responses needs to be investigated further.

Dang, she really grieved for him this time.

He died almost instantaneously

Resolved the problem I had where I mistakenly deleted this [local tracking branch]?

ls .git/refs/remotes/origin/HEAD ls: cannot access '.git/refs/remotes/origin/HEAD': No such file or directory

Author Response

The following is the authors’ response to the original reviews.

Public Reviews:

Reviewer #1 (Public Review):

Summary:

The OSCA/TMEM63 channels have recently been identified as mechanosensitive channels. In a previous study, the authors found that OSCA subtypes (1, 2, and 3) respond differently to stretch and poke stimuli. For example, OSCA1.2 is activated by both poke and stretch, while OSCA3.1, responds strongly to stretch but poorly to poke stimuli. In this study, the authors use cryo-EM, mutagenesis, and electrophysiology to dissect the mechanistic determinants that underlie the channels' ability to respond to poke and stretch stimuli.

The starting hypothesis of the study is that the mechanical activation of OSCA channels relies on the interactions between the protein and the lipid bilayer and that the differential responses to poke and stretch might stem from variations in the lipid-interacting regions of OSCA proteins. The authors specifically identify the amphipathic helix (AH), the fenestration, and the Beam Like Domain (BLD) as elements that might play a role in mechanosensing.

The strength of this paper lies in the technically sound data - the structural work and electrophysiology are both very well done. For example, the authors produce a high-resolution OSCA3.1 structure which will be a useful tool for many future studies. Also, the study identifies several interesting mutants that seemingly uncouple the OSCA1.2 poke and stretch responses. These might be valuable in future studies of OSCA mechanosensation.

However, the experimental approach employed by the authors to dissect the molecular mechanisms of poke and stretch falls short of enabling meaningful mechanistic conclusions. For example, we are left with several unanswered questions surrounding the role of AH and the fenestration lipids in mechanosensation: Is the AH really important for the poke response if mutating residues conserved between OSCA1.2 and OSCA3.1 disrupts the OSCA1.2 ability to respond to poke but mutating the OSCA1.2 AH to resemble that of OSCA3.1 results in no change to its "pokability"? Similar questions arise in response to the study of the fenestrationlining residues.

We thank the reviewer for their feedback. We believe that the different OSCA1.2 mutants on their own suggest an involvement of the AH and fenestration-lining residues in its mechanosensitive response. We attribute the inability to restore the poke response of OSCA3.1 with similar mutations to its inherent high threshold to this particular stimulus and perhaps other structural differences, or a combination of them, that we did not probe in this study. We agree more work is required in the field to address these remaining questions and further dissect the difference between poke and stretch responses.

Reviewer #2 (Public Review):

Summary:

Jojoa-Cruz et al. determined a high-resolution cryo-EM structure in the Arabidopsis thaliana (At) OSCA3.1 channel. Based on a structural comparison between OSCA3.1 and OSCA1.2 and the difference between these two paralogs in their mechanosensitivity to poking and membrane stretch, the authors performed structural-guided mutagenesis and tested the roles of three structural domains, including an amphipathic helix, a beam-like domain, and a lipid fenestration site at the pore domain, for mechanosensation of OSCA channels.

Strengths:

The authors successfully determined a structure of the AtOSCA3.1 channel reconstituted in lipid nanodiscs by cryo-EM to a high resolution of 2.6 Å. The high-resolution EM map enabled the authors to observe putative lipid EM densities at various sites where lipid molecules are associated with the channel. Overall, the structural data provides the information for comparison with other OSCA paralogs.

In addition, the authors identified OSCA1.2 mutants that exhibit differential responses to mechanical stimulation by poking and membrane stretch (i.e., impaired response to poke assay but intact response to membrane stretch). This interesting behavior will be useful for further study on differentiating the mechanisms of OSCA activation by distinct mechanical stimuli.

Major weakness:

The major weaknesses of this study are the mutagenesis design and the functional characterization of the three structural domains - an amphipathic helix (AH), a beam-like domain (BLD), and the fenestration site at the pore, in OSCA mechanosensation.

(1) First of all, it is confusing to the reviewer, whether the authors set out to test these structural domains as a direct sensor(s) of mechanical stimuli or as a coupling domain(s) for downstream channel opening and closing (gating). The data interpretations are vague in this regard as the authors tend to interpret the effects of mutations on the channel 'sensitivity' to different mechanical stimuli (poking or membrane stretch). The authors ought to dissect the molecular bases of sensing mechanical force and opening/closing (gating) the channel pore domain for the structural elements that they want to study.

We agree with the reviewer that our data are unable to distinguish the transduction of a mechanical stimulus and channel gating. We set up to determine whether these features were involved in the mechanosensitive response. However, as the reviewer points out, evaluating whether they work as direct sensors or coupling domains would require a more involved experimental design that lies beyond the scope of this work. Thus, we do not claim in our study whether these features act as direct sensors of mechanosensitive stimuli or as coupling domains, only their involvement.

Furthermore, the authors relied on the functional discrepancies between OSCA1.2 (sensitive to both membrane poking and stretch) and OSCA3.1 (little or weak sensitivity to poking but sensitive to membrane stretch). But the experimental data presented in the study are not clear to address the mechanisms of channel activation by poking vs. by stretch, and why the channels behave differently.

We had hoped that when we switched regions of the OSCA1.2 and OSCA3.1 channels we would abolish poke-induced responses in OSCA1.2 and confer poke-induced sensitivity to OSCA3.1. We agree with the reviewer that we were not able to pinpoint the reason or multiple reasons, as it could be a compounded effect of several differences, that caused OSCA3.1 higher threshold and thus we could not confer to it an OSCA1.2-like phenotype. Yet, we shed some light on some of the structural differences that appear to contribute to OSCA3.1 behavior, as mutagenesis of OSCA1.2 to resemble this channel led to OSCA3.1-like phenotype.

(2) The reviewer questions if the "apparent threshold" of poke-induced membrane displacement and the threshold of membrane stretch are good measures of the change in the channel sensitivity to the different mechanical stimuli.

The best way to determine an accurate measure of sensitivity to mechanical stimuli is stretch applied to a patch of membrane. There are more complicating factors that influence the determination of "apparent threshold" in the whole cell poking assay, including visualizing when the probe first hits the cell (very difficult to see). With that said, the stretch assay has its own issues such as the creep of the membrane into the pipette glass which we try to minimize with positive pressure between tests.

(3) Overall, the mutagenesis design in the various structural domains lacks logical coherence and the interpretation of the functional data is not sufficient to support the authors' hypothesis. Essentially the authors mutated several residues on the hotspot domains, observed some effects on the channel response to poking and membrane stretch, then interpreted the mutated residues/regions are critical for OSCA mechanosensation. Examples are as follows.

In the section "Mutation of key residues in the amphipathic helix", the authors mutated W75 and L80, which are located on the N- and C-terminal of the AH in OSCA1.2, and mutated Pro in the OSCA1.2 AH to Arg at the equivalent position in OSCA3.1 AH. W75 and L80 are conserved between OSCA 1.2 and OSCA3.1. Mutations of W75 and/or L80 impaired OSCA1.2 activation by poking, but not by membrane stretch. In comparison, the wildtype OSCA3.1 which contains W and L at the equivalent position of its AH exhibits little or weak response to poking. The loss of response to poking in the OSCA1.2 W/L mutants does not indicate their roles in pokinginduced activation.

Besides, the P2R mutation on OSCA1.2 AH showed no effect on the channel activation by poking, suggesting Arg in OSCA3.1 AH is not responsible for its weak response to poking. Together the mutagenesis of W75, L80, and P2R on OSCA1.2 AH does not support the hypothesis of the role of AH involved in OSCA mechanosensation.

Mutagenesis of OSCA1.2 in the amphipathic helix for residues W75 and L80 suggests a role of the helix in the poke response in OSCA1.2, regardless of OSCA3.1 having the same residues. Furthermore, the lack of alteration in the response for mutant P77R suggests that specific residues of the helix are involved in this response and is not a case where any mutation in the helix will lead to a loss of function.

OSCA3.1 WT exhibits a high-threshold response (near membrane rupture) in the poke assay without any mutations, and this could be due to other features, for example, the residues lining the membrane fenestration, as well as features not identified/probed in this study. We agree with the reviewer that the differences in the AH do not explain the different response to poke in OSCA1.2 and OSCA3.1, and we have added this statement explicitly in the discussion for clarification (line #251-252).

In the section "Replacing the OSCA3.1 BLD in OSCA1.2", the authors replaced the BLD in OSCA 1.2 with that from OSCA3.1, and only observed slightly stronger displacement by poking stimuli. The authors still suggest that BLD "appears to play a role" in the channel sensitivity to poke despite the evidence not being strong.

We agree with the reviewer that the experiments carried out show little difference between the response of OSCA1.2 WT and OSCA1.2 with OSCA3.1 BLD, and we have stated so (line #259: “Substituting the BLD of OSCA1.2 for that of OSCA3.1 had little effect on poke- or stretchactivated responses. Although these results suggest that the BLD may not be involved in modulating the MA response of OSCA1.2…”). However, the section of the discussion that the reviewer points out also considers evidence provided by recent reports from Zheng, et al. (Neuron, 2023) and Jojoa-Cruz, et al. (Structure, 2024) and we suggest an hypothesis to reconcile our findings with these new evidence.

OSCA1.2 has four Lys residues in TM4 and TM6b at the pore fenestration site, which were shown to interact with the lipid phosphate head group, whereas two of the equivalent residues in OSCA3.1 are Ile. In the section "Substitution of potential lipid-interacting lysine residues", the authors made K435I/K536I double mutant for OSCA1.2 to mimic OSCA3.1 and observed poor response to poking but an intact response to stretch. Did the authors mutate the Ile residues in OSCA3.1 to Lys, and did the mutation confer channel sensitivity to poking stimuli resembling OSCA1.2? The reviewer thinks it is necessary to perform such an experiment, to thoroughly suggest the importance of the four Lys residues in lipid interaction for channel mechanoactivation.

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are no longer able to perform such experiments.

Reviewer #3 (Public Review):

Summary:

Jojoa-Cruz et al provide a new structure of At-OSCA3.1. The structure of OSCA 3.1 is similar to previous OSCA cryo-em structures of both OSCA3.1 and other homologues validating the new structure. Using the novel structure of OSCA3.1 as a guide they created several point mutations to investigate two different mechanosensitive modalities: poking and stretching. To investigate the ability of OSCA channels to gate in response to poking they created point mutations in OSCA1.2 to reduce sensitivity to poking based on the differences between the OSCA1.2 and 3.1 structures. Their results suggest that two separate regions are responsible for gating in response to poking and stretching.

Strengths:

Through a detailed structure-based analysis, the authors identified structural differences between OSCA3.1 and OSCA1.2. These subtle structural changes identify regions in the amphipathic helix and near the pore that are essential for the gating of OSCA1.2 in response to poking and stretching. The use of point mutations to understand how these regions are involved in mechanosensation clearly shows the role of these residues in mechanosensation.

Weaknesses:

In general, the point mutations selected all show significant alterations to the inherent mechanosensitive regions. This often suggests that any mutation would disrupt the function of the region, additional mutations that are similar in function to the WT channel would support the claims in the manuscript. Mutations in the amphipathic helix at W75 and L80 show reduced gating in response to poking stimuli. The gating observed occurs at poking depths similar to cellular rupture, the similarity in depths suggests that these mutations could be a complete loss of function. For example, a mutation to L80I or L80Q would show that the addition of the negative charge is responsible for this disruption not just a change in the steric space of the residue in an essential region.

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

Recommendations for the authors:

Reviewer #1 (Recommendations For The Authors):

I have several questions regarding some of the aspects of your study:

Mutation of the hydrophobic W75 and L80 in OSCA1.2 to charged residues significantly decreases the poke response in OSCA1.2 without affecting the stretch response. However, W75 and L80 are also present in OSCA3.1, which does not respond efficiently to poke. You conclude that these two residues are important for the poke response, but do not delve into why, if these residues are important, OSCA3.1 is not poke-sensitive.

In addition, mutation of the OSCA1.2 AH to resemble that of OSCA3.1 does not produce channels that are less poke-sensitive. Given the data presented, if AH were a universal "poke sensor", one could also expect WT OSCA3.1 to exhibit a robust poke response, like OSCA1.2. Here I think it would be important to explain in more detail how this data might fit together.

We thank the reviewer for bringing up this issue. We decided to test the importance of the AH due to the presence of similar structures in other mechanosensitive channels. Our data showed that single and double mutants of the AH of OSCA1.2 affected its poke response but not stretch. This supports the idea of the AH involvement in the poke response. Yet, we agree that the differences in the AH between OSCA1.2 and OSCA3.1 (P77R mutation) do not explain the higher threshold of OSCA3.1, we have explicitly added this in line #255. The particular OSCA3.1 phenotype may be due to other differences in the structure, for example, differences in the membrane fenestration area, or a combined effect of several differences, which we believe is more likely.

I also have some questions about the protein-lipid interactions in the fenestration. A lipid has been observed in this location in both OSCA1.2 and OSCA3.1 structures. Mutation of the two OSCA1.2 lysines to isoleucines results in channels that are resistant to poke which leads to the conclusion that the interactions between the fenestration lysines and lipids are important for the poke response.

Here, there are several questions that arise but are not answered:

It is not shown what happens when OSCA3.1 isoleucines are mutated to lysines - do these mutants result in poke-able channels? Is the OSCA3.1 mechanosensing altered?

We performed a preliminary test on OSCA3.1 I423K/I525K double mutant (n = 3). However, we did not see an increase in poke sensitivity. We attributed this to other unexplored differences in OSCA3.1 having an effect in channel mechanosensitivity.

It is implied that the poke response is predicated on the lysine-lipid interaction. However, lipid densities are present in both OSCA1.2 and OSCA3.1 structures, indicating that both fenestrations interact with lipids. How can we be certain that the mutation of lysine to isoleucine does not disrupt an inter-protein interaction rather than a protein-lipid one? For example, the K435I mutation might disrupt interactions with D523 or the backbone of G527?

The reviewer brings up a good point. We believe the phenotype seen is due to a different strength in the interaction between lipids and proteins, however, disrupted interaction with other residues is a valid alternative explanation. We agree that the suggested experiments will further clarify the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

Similarly, the effects of single lysine-to-isoleucine (K435I or K536I) mutations are not explored.

The observed effect might be caused by only one of these substitutions.

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

I also wanted to take this opportunity to ask a couple of philosophical (?) questions about using a mammalian system to study ion channels that have evolved to function in plants. Your study highlights the intimate relationship between the lipid bilayer and protein function/mechanosensitivity. Plant cells contain high levels of sterols and cerebrosides that would significantly affect both cell stiffness and the specific interactions that can be formed between the protein and the lipid bilayer. I wonder if the properties of the lipid bilayer might shift the thresholds for poke and/or stretch stimuli and if structural elements that do not appear to have a major role in mechanosensation in a mammalian cell (e.g., BLD) might be very influential in a lipid environment that more closely resembles that of a plant?

Conversely, is it possible that OSCA channels are not poke-sensitive in plant cells? These questions are beyond the scope of your study, but they might be a nice addition to your discussion.

The reviewer poses a great question. Electrophysiological approaches for studying plant mechanosensitive channels suffer the limitation of not being able to fully reconstitute the environment of a plant cell. To be able to patch the cell, the cell wall needs to be disposed of, which eliminates the tension generated from this structure onto the membrane. In that sense, performing these assays in plant cells or another system would not give us a fully accurate picture of the physiological thresholds of these channels. Given this limitation, we performed our study with mammalian cells given our expertise with them. Like the reviewer, we are also intrigued by the effect of different membrane compositions on the behavior of OSCA channels and how these channels will behave under physiological conditions, but we agree with the reviewer that these questions are out of the scope of our work. To address this point, in line #294 we have added: “It is also important to note that the membrane of a plant cell contains a different lipid composition than that of HEK293 cells used in our assays, and thus these lipids, or the plant cell wall, may alter how these channels respond to physiological stimuli.”

Line 313 For structural studies, human codon-optimized OSCA3.1. Could you please clarify what this means?

We have changed the phrase to “For structural studies, the OSCA3.1 (UniProt ID: Q9C8G5) coding sequence was synthesized using optimized codons for expression in human cells and subsequently cloned into the pcDNA3.1 vector” in line #327 to clarify this sentence.

As a final comment, in the methods you use references to previously published work. I would strongly encourage you to replace these with experimental details.

We understand the reviewer’s argument. However, this article falls under eLIFE’s Research Advances and will be linked to the original published work to which we reference the method. As suggested in the guidelines for this type of article, we only described the methods that were different from the original paper.

Reviewer #2 (Recommendations For The Authors):

(1) In line 85, provide C-alpha r.m.s.d. values for the structural alignment among OSCA3.1, OSCA1.1, and OSCA1.2 protomers.

As requested, we have added the C-alpha RMSD in line #86.

(2) In line 90, should the figure reference to Fig. 1d be Fig. 1e?

We thank the reviewer for catching this error. We have corrected it in the manuscript.

(3) In lines 89-94, what putative lipid is it resolved in the OSCA3.1 pore? Can the authors assign the lipid identity? Is this the same or different from the lipids resolved in OSCA1.2, OSCA1.1, and TMEM63?

In the model, we have built the lipid as palmitic acid to represent a lipid tail, but the resolution in this area makes it difficult to ascertain the identity of said lipid, hence we cannot compare to lipids in other orthologs.

(4) In lines 115-121, the authors describe the presence of AHs and their functional roles in MscL and TMEM16. It will be more informative if the authors can add figures to show the structure of MscL and highlight the analogous AH. In addition, the current Supplementary Fig. 6 is not informative so it should be improved. It is not clear to the reviewer why that stretch of helix in TMEM16 is equivalent or analogous to the AH in OSCAs, either sequence alignment or a detailed structural alignment is helpful to address this point. Also, in lines 120-121, it says this helix in TMEM16 "does not present amphipathic properties", please show the sequence or amphipathicity of the helix.

We thank the reviewer for the feedback on this figure. Supplementary Fig. 6 has been thoroughly modified to address the reviewer’s concerns. We now include a panel showing the structure of MscL and its amphipathic helix. We have modified the alignment of OSCA3.1 to a TMEM16 homolog to make clearer the homologous positioning of the helices in question and zoom in to show their sequences.

(5) In discussion, lines 249-257, the authors referred to a recent study that suggested three evolutionarily coupled residue pairs located on BLD and TM6b. The authors speculate that the reason they did not observe a significant effect of channel response to poke/stretch stimuli in the BLD swapping between OSCA1.2 and 3.1 is due to the 2 of 3 salt bridges remaining for the residue pairs. To test the importance of these residue pairs and their coupling for channel gating, instead of swapping the entire BLD, can the authors systematically mutate the residue pairs, disrupt the salt-bridge interactions, and analyze the effect on channel response to mechanical force?

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

(6) The reviewer suggests the authors tone down the elaboration of polymodal activation of OSCA by membrane poking and stretch.

We believe the idea of polymodal activation is sufficiently toned down as we only postulate it as a possibility and following we give an alternative explanation based on methodological limitations: “Nonetheless, the discrepancy could be due to inherent methodological differences between these two assays, as whole-cell recordings during poking involve channels in inaccessible membranes (at the cell-substrate interface) and channel interactions with extracellular and intracellular components, while the stretch assay is limited to recording channels inside the patch.”

(7) In lines 81-83, the authors described the BLD as showing increased flexibility, and the EM map at this region is less well resolved for registry assignment. In the method for cryo-EM image processing and Supplementary Fig. 1, the authors only carried out 3D refinement and classification at the full channel level. Have the authors attempted to do focus refinement or classification at the BLD domain in order to improve the local resolution or to sort out conformational heterogeneity? The reviewer suggests doing so because the BLD domain is a hot spot that the authors have proposed to play an important role in OSCA mechanosensation. Conformational changes identified in this region might provide insights into its role in the channel function.

We thank the reviewer for this suggestion. We have performed focused classification on the BLD with and without surrounding regions and, in our hands, it did not improve the resolution or provide further insights.

Reviewer #3 (Recommendations For The Authors):

Here are a few specific minor corrections that should be addressed

(1) In lines 117-135, in the discussion of Figure 2, the data shows an apparent increase in the poking threshold to gate W75K/L80E. The substantial increase in the depth required to gate the channel suggests that these channels are less sensitive to poking. Would it be possible to compare the depth at which these two patches show activity and the depth at which the other 22 cells ruptured? Line 161 mentions that the rupture threshold of HEK cells is close to the gating of OSCA3.1 at 13.8 µm.

The distance just before the cell ruptured in 22 cells with no response was 12.5 +/- 2.5 um. The distance at which the cells ruptured was 0.5 um more (13 +/- 2.5 n=22). We have added this last value in line #137.

(2) Would it be possible in Figures 2 panels b and c, 3, and figure 4 to label the WT as WT OSCA1.2?

We thank the reviewer for pointing this out. We agree this modification will improve the clarity of the figures and have changed the figures to follow the reviewer’s suggestion.

(3) Can you provide a western blot of the mutations described in Figure 2? This would provide insight into the amount of protein at the cell surface and available to respond to poking, the stretch data shows that these channels are in the membrane but does not show if they are in the membrane in similar quantities.

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

(4) The functional differences between the two channels are projected to be tied to several distinct point mutations, however, the data could be strengthened by additional point mutations at all sites to show that the phenotypes are due to the mutations specifically not just any mutation in the region.

We thank the reviewer for this suggestion. We agree that the suggested experiments will further improve the quality of the results, but we are unable to perform such experiments due to the authors having moved on from the respective labs.

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Author Response

The following is the authors’ response to the original reviews.

Reviewer #1 (Public Review):

However, there are several concerns to be explained more in this study. In addition, some results should be revised and updated.

Thank you for your comments. The concerns were addressed by the description and experiment.

Some results were revised and updated accordingly.

Reviewer #2 (Public Review):

The minor weakness of the study is inconsistent use of terminology throughout the manuscript, occasional logic-jump in their flow, and missing detailed description in methodologies used either in the text or Materials and Methods section, which can be easily rectified.

Thank you for your review. We have revised the manuscript and corrected errors according to your comments.

Reviewer #3 (Public Review):

Importantly, besides the Miwi ubiquitination experiment which is performed in a heterologous and therefore may not be ideal for extracting conclusions, the possible involvement of ubiquitination was not shown for any other proteins that the authors found that interact with FBXO24. Could histones and transition proteins be targets of the proposed ubiquitin ligase activity of FBXO24, and in its absence, histone replacement is abrogated?

Thank you for your comments. The histones and transition proteins were not found in the immunoprecipitates of FBXO24, suggesting they are not the direct targets of FBXO24, shown in Figure S3G.

Miwi should be immunoprecipitated and Miwi ubiquitination should be detected (with WB or mass spec) in WT testis.

We agree with this suggestion. In the revision, the expression and ubiquitination of MIWI were detected in WT testis by the immunoprecipitation and ubiquitination assay, as shown in Figure 8H.

Therefore, the claim that FBXO24 is essential for piRNA biogenesis/production (lines 308, 314) is not appropriately supported.

We appreciate the comment. We have revised the description and modified the claim on page 11.

Reviewing Editor's note for revision

(1) As noted by all three reviewers, as currently written the rationale to focus on MIWI is not entirely clear. A transitional narrative to focus on MIWI needs to be provided as well as an explanation for how the absence of FBXO24 as an E3 ubiquitin ligase is responsible for the observed mRNA and protein differential expression.

We appreciate your comments. We have supplemented the transitional narrative by focusing on MIWI and explained mRNA and protein differential expression upon FBXO24 deletion, shown on Page 7 and Page 13, respectively.

(2) As it can be indirect, mass spec detection of MIWI in testis co-IP and MIWI ubiquitination should be detected (with WB or mass spec) in WT testis.

In the revision, the expression and ubiquitination of MIWI were detected in WT testis by the immunoprecipitation and ubiquitination assay, as shown in Figure 8H.

(3) Please tone down the claim that FBXO24 is essential for piRNA biogenesis/production as it requires further evidence.

We have revised the description and modified the claim on page 11.

(4) Ontology analysis of the genes with abnormally spliced mRNAs to provide an explanation for developmental defects.

In the revision, we have performed the ontology analysis and provided new data regarding the abnormally spliced genes, as shown in Figure S4D.

Reviewer #1 (Recommendations For The Authors):

Major comments

(1) The authors performed mainly with the WT (or knock-in) and Fbxo24-knockout mouse model. Do the heterozygous males and their sperm have any physiological defects like FBXO24-deficient mice?

This is a good question. We did the phenotype analysis and found that heterozygous males are all fertile, and their sperm do not have any physiological defects.

(2) Fbxo24-KO sperm carries swollen mitochondria. How do the mitochondria affect sperm function?

Thank you for raising this interesting question. Based on our data and published literature, the defective mitochondria were associated with energetic disturbances and reduced sperm motility, as shown on Page 12.

(3) TEM images show that Fbxo24-KO spermatids carry swollen mitochondria and enlarged chromatoid bodies. How the swollen mitochondria and enlarged chromatid are defective for sperm motility and flagellar development, requires more explanation. In addition, it is unclear how the enlarged diameter of the chromatoid body is critical for normal sperm development.

Thank you for your comments. The chromatoid bodies are considered to be engaged in mitochondrial sheath morphogenesis. Analysis of the chromatoid bodies' RNA content reveals enrichment of PIWI-interacting RNAs (piRNAs), further emphasizing the role of the chromatoid bodies in post-transcriptional regulation of spermatogenetic genes. We added this explanation on Page 12-13.

(4) The authors only show band images to compare the protein amounts between WT and KO sperm and round spermatids. As the blots for loading controls are not clear, the authors should quantify the protein levels and perform a statistical comparison.

We quantified the protein levels and performed a statistical comparison, as shown in Figure S3B.

(5) The authors show the defective sperm head structure from Fbxo24-KO sperm in Figure 5. However, the Fbxo24-KO sperm heads seem quite normal in Figure 3. How many sperm show defective sperm head structure? In addition, the authors observed altered histone-to-protamine conversion in sperm, but it is unclear whether the altered nuclear protein conversion causes morphological defects in the sperm head.

We appreciate the comments. In our study, we found over 80% of Fbxo24 KO sperm showed defective structure in the sperm head. Altered histone-to-protamine conversion caused the decondensed nucleus of Fbxo24 KO sperm. Notably, in many knockout mice studies, impaired chromatin condensation is frequently associated with abnormal sperm head morphology, as shown in reference 15 of Page 8.

(6) The authors compare the protein levels of RNF8, PHF7, TSSK6, which participate in nuclear protein replacement in sperm. However, considering the sperm is the endpoint for the nuclear protein conversion, it is unclear to compare the protein levels in mature sperm. The authors might want to compare the protein levels in developing germ cells.

Thank you for your comment. Yes, we actually detected the protein levels of RNF8, PHF7, and TSSK6 in the testes, not in sperm. We have corrected it in the Figure 5E. We apologize for our carelessness.

(7)This reviewer suggests describing more rationales for how the authors focus on the MIWI protein. Also, it is wondered whether MIWI is also detected from testis co-IP mass spectrometry.

We agree with this suggestion. Since MIWI was a core component of CB and also identified as an FBOX24 interacting partner from our immunoprecipitation-mass spectrometry (IP-MS) (Table S1), we focused on the examination of MIWI expression between WT and Fbxo24 KO testes. We have added this description in the revision (see lines 191-193 on page 7).

(8) The authors need to provide a more detailed explanation for how the altered piRNA production affects physiological defects in germ cell development. In addition, it will be good to describe more how the piRNAs affect a broad range of mRNA levels.

Thank you for your comments. The previously published studies have demonstrated that piRNAs could act as siRNAs to degrade specific mRNAs during male germ cell development and maturation. We have cited these studies on lines 369-372 of Page 13.

(9) The authors observed an altered splicing process in the absence of FBXO24. However, it is a little bit confusing how the altered splicing events affect developmental defects. Therefore, the authors should state which mRNAs have undergone abnormal splicing processes and provide ontology analysis for the genes.

We have performed the ontology analysis and showed the new data in Figure S4D.

Minor comments

(1) Figure 1A-C - Statistical comparison is missed. Numbers for biological replication should be described in corresponding legends.

Thank you for your careful review. We have provided the statistical comparison and the numbers for biological replication in the legends of Figure 1A-C.

(2) Figure 1E, F - Current images can't clearly resolve the nuclear localization of the FBXO24 testicular germ cells. To clarify the intracellular localization, the authors should provide images with higher resolution.

The resolution of Figure 1E, F was improved, as suggested. Thank you!

(3) Figure 1E, F - Scale bar information is missing.

The scale bars of Figure 1E, F were provided.

(4) It will be much better to show the predicted frameshift and early termination of the protein translation in Fbxo24-knockout mice.

The predicted frameshift of Fbxo24-knockout mice was added and shown in Figure S1B.

(5) It is required to provide primer information for qPCR.

The primer information for qPCR was provided, as shown in Table S7.

(6) The authors describe that Fbxo24-KO sperm show abrupt bending of the tail. However, the description is unclear and the sperm shown in Figure 3C seems quite normal. The authors should clarify the abnormal bending pattern of the tail and show quantified results.

Thank you for pointing out this issue. In Fbxo24 KO sperm, abnormal bending of the sperm tails mainly included neck bending and midpiece bending. We have shown them in Figure S3A.

(7) The authors mention that Fbxo24-KO sperm have swollen mitochondria at the midpiece, but this is also unclear. How many mitochondria are swollen in Fbxo24-KO sperm?

This is a good question. However, since it is very difficult to observe all of the mitochondria in each sperm using the electronic microscope, we could not quantify the swollen mitochondria in Fbxo24 KO sperm.

(8) Scale bar information is missed - Fig 3C insets, Fig 3D, Fig 3F insets, 4A insets, Figure 4C insets.

All the scale bars have been added.

(9) How many sperm have annulus defects? In Figure 3F, WT sperm does not have an annulus, which could be damaged during sample preparation. Is the annulus defects in Fbxo24-KO sperm consistent?

Thank you for asking these questions. Based on our results, about 30% of Fbxo24 KO sperm showed defective annulus structure. Since both TEM (Figure 3F) and SEM (Figure 3G) results clearly showed the defective annulus structure of Fbxo24 KO sperm, we believe the annulus defects are consistent and highly unlikely caused by sample preparation.

(10) A Cross-section image for the endpiece of Fbxo24-KO sperm is not suitable. There is a longitudinal column structure of the principal piece.

Thank you for your comments. It is difficult to observe a completely longitudinal structure of sperm tail under TEM. The cross-section of the endpiece and principal piece allowed us know the structure of the axoneme, ODFs and fibrous sheath (FS).

(11) The endpiece of Fbxo24-KO sperm seems to have a normal axoneme. Do all endpieces of Fbxo24KO sperm have normal axoneme? Also, the authors need to describe whether an axonemal structure is damaged and disrupted in all Fbxo24-KO sperm.

Our TEM data showed the axonemal structure was impaired in the endpiece of Fbxo24 KO sperm (See right panels of Figure 3H). Moreover, based on the ultrastructure analysis of TEM, we found over 90% of Fbxo24 sperm had a damaged axonemal structure.

(12) Reference blots in Fig 3I, 3J, 4E (left), 5C and 5E are quite faint. The authors should replace the blot images.

Thank you for pointing out this. We have rerun Western blot multiple times but could not obtain better images due to antibody sensitivity. However, we quantified the protein levels and performed a statistical comparison, as shown in Figure S3B, to establish a good readout from these images for the readers.

(13) Loading controls are required - 7D-H.

Done as suggested. Thanks!

(14) How do the authors measure the midpiece length? From where to where? This should be clarified.

Good question. We measured the midpiece length from the sperm neck to the sperm annulus by MitoTracker staining. We have clarified this on Page 16.

(15) How are the bands for Fbxo24 shifted during IP in Fig 7A?

The protein modification in the interaction may cause the band shift.

(16) There are several typos throughout the manuscript. Please check carefully and fix them.

Thank you for your careful review. We have corrected and fixed all the typos as far as we can.

Reviewer #2 (Recommendations For The Authors):

Major comments

(1) Please provide a schematic of HA-Fbxo24 knock-in construct and strategy together with knockout (Figure S2) or even separately early in Figure S1. The description of using the transgenic mouse is mentioned even earlier than the knockout but there are no citations or methods provided in the text other than that listed in Materials and Methods.

Thank you for your suggestion. As suggested, the schematic of the HA-Fbxo24 knock-in strategy has been supplemented in Figure S2A. The description of using the transgenic mouse has been added to the results, as shown on page 4 of lines 102-103.

Also, it is not clear to what extent the phenotypic and molecular characterization of HA-transgenic mice is performed. For example, Lines 134-139: The use of Fbxo24-HA labeled transgenic mice results in the rescue of spermatogenesis and fertility as shown in Figure 2F by measuring the litter size. It is not clear how this observation leads the author to state that this rescues defects in spermiogenesis. Please clarify how and what other measures are taken to support this conclusion. Is the observed infertility due to defects in spermatogenesis or spermiogenesis?

Thank you for your question. We crossed FBXO24-HATag males with FBXO24−/− females to obtain FBXO24−/−; FBXO24-HATag males. We examined the testes volume and histological morphology of FBXO24−/−; FBXO24-HATag males and found that they were similar to FBXO24+/−; FBXO24-HATag littermates, indicating that spermatogenesis was restored, as shown in Figure S2H.

(2) Line 107 vs Line 114: Please use the terminology spermatogenesis and spermiogenesis consistently throughout the text. Earlier in the introduction, the authors clearly defined that spermatogenesis involves three phases, with the third phase referred to as spermiogenesis. However, the author concludes in the first line that "FBXO24 plays a role during spermatogenesis" while summarizing at the end of the paragraph that this protein is "expressed in haploid spermatids specifically during spermiogenesis". Therefore, it is not clear whether the authors conclude that FBXO24 is important for all of spermatogenesis (line 107) or only for part of spermiogenesis (line 114). Another example is line 219 vs. 238: At this point in the manuscript, it is again unclear whether the authors want to study molecular changes during spermatogenesis or spermiogenesis upon FBXO24 depletion. Many examples of such cases throughout the text, and it is recommended to be consistent in using more restrictive terminology whenever applicable for a clear interpretation.

We thank you for your careful review. We have double-checked the terminology of spermatogenesis and spermiogenesis and made it consistent throughout the text of the revised manuscript.

(3) It is not clear how rampant/frequent the Fbxo24-knockout sperm show defects in head morphology based on Figures 3C, 3F, and 5A since it seems that there are some sperm showing relatively normallooking sperm heads. Please provide quantification.

We have performed the quantification and found that over 80% of Fbxo24 KO sperm showed defective structures in the sperm head.

(4) Figure 3B: The authors describe in the figure legend that 3 mice were analyzed in each group. The standard deviation for the WT analysis is missing, or if the author wanted to set the WT value to 100%, the bar and scale shown on the y-axis do not fit. The value for WT looks more like 95%.

We have indeed analyzed sperm motility based on the WT value set at 100% and have revised Figure 3B in the revision. We apologize for this oversight.

(5) Figure 3 B and C: It is not clear how the motility is measured. Is CASA used (not described in Methods). The conclusion about abnormal flagellar bending in KO spermatozoa cannot be drawn from the static microscopic images alone. Please provide more details of motility analysis together with videos of live cell imaging.

The sperm motility was measured manually using a hemocytometer, according to the reference.

We provided the details of sperm motility analysis in the Materials and Methods section on Page 16.

(6) Figure 3 I and J: These are one of a few figures that are not supported by statistical analysis. In particular, for 3I, GAPDH controls of WT and KO protein do not show equal loading, which could explain the lower expression of the KO protein. Please show normalized bar graphs with multiple biological replicates or at least show a representee technical replicat that shows equal loading of GAPDH to better support the conclusion.

Thank you for your suggestion. Statistical comparison of relative protein expression was supplemented, as shown in new Figure S3B.

(7) Line 184: It is not clear how the authors define a swollen mitochondrion? Are there any size criteria (roundness) that can be measured to distinguish between a swollen and a non-swollen mitochondrion? It is recommended to use another terminology as often 'swollen' implies there is a difference in osmolarity but there is no experiment to support this implication.

Thank you for your comment. We have changed the “swollen” to “vacuolar” in the revision, as shown on Page 7.

(8) Figure S4, without a bright field image, it is hard to see the purity and morphology of the isolated prep. Please provide the bright field images together or as overlaid images.

We agree with your comment. We have provided the overlaid images in new Figure S4A.

(9) There is a big logic jump in what prompts the authors to look MIWI protein level and link the observation to MIWI/piRNA pathway in both Introduction and Results while it is one of the main findings. It is recommended to provide a better rationale and logical flow in the text.

Thank you for your suggestion. We have added a sentence explaining why we wanted to focus on studying MIWI expression (see lines 190-193 on page 7).

Minor comments

(1) Please keep all the conventions of gene vs. protein nomenclature. For example, write the genes mentioned in the figures in italics with the first letter in Capital, as it is done in the main part. Proteins should be in ALL CAPITAL like FBXO24.

The names of gene and protein have been revised in the revision, as suggested.

(2) In the MM section, the name of the manufacturer and the location of the materials used are missing in several sections. Please go back through the MM section and add this information in the appropriate places.

Done as suggested. Thank you!

(3) On page 4, the authors mentioned that "Further qPCR analysis of developmental testes and purified testicular cells showed that FBXO24 mRNA was highly expressed in the round spermatids and elongating spermatids (Fig 1B-C)". Please include statistical analyses for Fig 1B-C as well as for Fig 1A to support the written statements.

Statistical comparison was supplemented, as shown in Figure 1. P-values are denoted in figures by *p < 0.05.

(4) Figure 3E: Please describe in more detail how the length of the midpiece was measured. Was it based on TEM images or based on fluorescent images using MitoTracker?

As we responded to Reviewer #1, we measured the midpiece length from the sperm neck to the sperm annulus by MitoTracker staining. We have clarified this in the Method and Material section on Page 16.

(5) Line 431: In the "Electron Microscopy" section of the MM part, the author should indicate the ascending ethanol series (%) used.

Done as suggested. Thank you!

(6) Line 432: The thickness of the sections prepared is missing, as well as an indication of the microtome used.

We have added thickness and the microtome in the Method and Material section on Page 16.

(7) Line 433: If the generated tiff files have been processed with Adobe Photoshop, this information is missing.

We have provided information on the usage of Adobe Photoshop for the generation of tiff files on Page 17.

(8) Lines 445, 452, 467: In some places in the paper, the temperature is written with a space between the number and {degree sign}C, and sometimes it is not. Please go through the paper and make it consistent. The usual spelling is 4{degree sign}C.

We have gone through the manuscript and checked all the spelling of temperature writing to make them consistent. Thank you for careful review.

(9) Line 469: The gel documentation system used is not mentioned.

Done as suggested. Thank you!

(10) Line 469: The 'TM' should be superscripted.

Done as suggested.

(11) Line 489: A space is missing between the changes and the parenthesis.

Done as suggested.

(12) Line 495-496: The authors write that the fractions enriched with round spermatids after sedimentation were collected manually. Was a determination of cell concentration - e.g., 2 x106 cells/ml -performed after collection of the cells? How were the cells stored until use? Please add the sedimentation time and used temperature.

Store the cell in the 1´ Krebs buffer on ice. The cell sediment was through a BSA density gradient for 1.5 h at 4°C. The cell concentration was determined after collection, as shown on Page 18.

(13) Line 505: spelling error. Instead of " manufacturer's procedure" it is written manufactures' instructions.

The spelling error was corrected.

(14) Line 520: Please write a short sentence on how the purification of the 16-40 nt long RNA was performed.

The length of 16–40 nt RNA was enriched by polyacrylamide gel electrophoresis. We added this information on Page 19 of line 531.

(15) Line 528: The version of the used GraphPad software is missing.

The version of GraphPad software was supplemented, as shown on Page 19.

(16) Line 677: For qPCR analyses, the number of mice analyzed (N) and a statistical evaluation are missing.

The statistical comparison and the numbers for biological replication were added, as shown on Page 26.

(17) Figure 3D: Please add a scale bar.

Done as suggested. Thanks!

(18) Line 371 and Line 377: Two times "in summary" is written. Please make one summary for the whole paper.

This sentence was revised, as shown in Page 13.

(19) Line 382: To be consistent in the whole paper, please write Figure 10 in bold letters.

Done as suggested.

(20) Please make the size and font of the references consistent with the main text.

Done as suggested. Thanks again for your careful review.

Reviewer #3 (Recommendations For The Authors):

I would like to see the description of the FBXO24 immunoprecipitation experiment performed in HEK293T cells. This somatic cell line does not normally express Miwi, so how Miwi was detected in FBXO24 mCherry IP beads? It is not mentioned if Miwi is expressed from a recombinant vector in this experiment. Similarly, I would like to see a better description of the experiment described in the same paragraph towards the end of it with the ubiquitin peptides, it is not clear.

Thank you for your comments. FBXO24-mCherry was expressed in HEK293T cells and the immunoprecipitates was incubated with the protein lysate of the testes (see lines 268-272 on Page 10). The description of the ubiquitin experiment was added as well, as shown in lines 283-286 on Page 10.

Line 263: I think the term ectopic here is not appropriate, a correction is needed.

We have changed “ectopic” to “increased” in the revision (see line 268 on Page 10).

I would like the authors to provide a tentative explanation or evidence of why FBXO24 KO males are completely sterile, even though there are still mature sperm produced with some motility. Since there are defects in nuclear condensation it will be very relevant to check DNA damage/fragmentation, which could contribute to the sterility phenotype.

This is a good suggestion. We reanalyzed the sperm DNA damage by TUNEL staining and shown the new data in Figure S3E-F.

Line 213: There have been some conflicting reports about the role of RNF8 in spermiogenesis, but a recent report has shown that RNF8 is not involved in histone PTMs that mediate histone to protamine transition (Abe et al Biol Reprod 2021 https://doi.org/10.1093%2Fbiolre%2Fioab132).

Thank you for your comment. We have cited this critical reference and discussed it in Discussion section on Page 12.

Figure 7: I would like to see zoomed-out views of the affected exons, so that flanking unaffected exons can be used as a reference for unaffected splicing. Most of the genome browser views in this image only show affected exons and it is impossible to see if these alone are affected or if the reduced RNAseq coverage in those exons is a result of overall reduced mapped reads in these genes. Also, a fixed Y axis with the same max value should be shown for these genome browser snapshots so that the expression level is comparable between the two genotypes.

Thank you for your comments. Loading control of RT-PCR and scale range of Y axis were added in new Figure 7.

Minor corrections:

Line 70: correct "..functions as protein-protein interaction..".

Thank you for your careful review. We have corrected this sentence (see line 69 on Page 3).

Line 101: correct "..qPCR analysis of developmental testis..".

We have corrected this sentence (see line 100 on Page 4). Thanks again.

Line 116: correct "..results in detective..".

Corrected.

Line 186: correct ".. explored..".

Corrected.

Line 218: correct ".. gene expressions.

Corrected.

Line 221: correct "..genes significantly differentiated expressed".

Corrected.

Line 241: FBXO24 was shown earlier in both cytoplasm and nucleus.

We have changed “FBXO24 is mainly confined to the nucleus” to “FBXO24 expressed in the nucleus”, as shown in line 247 on Page 9.

Line 501-502: correct "..reverse transcriptional".

“reverse transcriptional” was changed into “reverse transcription”, showing in Page 18.

Line 686: correct ".. deficiency male..".

Corrected.

Line 769: correct "..Western blots were adopted..".

Corrected.

Line 784: correct "..WT tesis..".

Corrected.

I cannot understand exactly what is shown in Figure 9B. Some elements marked on the X-axis are single base locations (-2K, TSS, +2K) and others are stretches of sequences so they cannot be equivalent. Why there is only an intron shown? There should be a measure of normalized expression on the Y-axis.

Thank you for your questions. The X-axis means that genome segments were scaled to the same size and were calculated the signal abundance, which was analyzed by computeMatrix. Aim to know the piRNA source, piRNA was mapped to the gene body, including introns, CDS and UTRs. The value of the Y-axis is the normalized count.

Figure 6F is not needed.

Figure 6F was used to illustrate the number of different types of mRNA splicing upon FBXO24 deletion in the round spermatids. To better understand the splicing for the reader, we decided to keep it.

The last two paragraphs of the discussion seem to be redundant.

Thank you for pointing out this. We have revised the last two paragraphs of the discussion.

Reviewer #1 (Public Review):

In this study, Li et al., report that FBXO24 contributes to sperm development by modulating alternative mRNA splicing and MIWI degradation during spermiogenesis. The authors demonstrated that FBXO24 deficiency impairs sperm head formation, midpiece compartmentalization, and axonemal/peri-axonemal organization in mature sperm, which causes sperm motility defects and male infertility. In addition, FBXO24 interacts with various mRNA splicing factors, which causes altered splicing events in Fbxo24-null round spermatids. Interestingly, FBXO24 also modulates MIWI levels via its polyubiquitination in round spermatids. Thus, the authors address that FBXO24 modulates global mRNA levels by regulating piRNA-mediated MIWI function and splicing events in testicular haploid germ cells.

This study is performed with various experimental approaches to explore and elucidate underlying molecular mechanisms for the FBXO24-mediated sperm defects during germ cell development. Overall, the experiments were designed properly and performed well to support the authors' observation in each part. In addition, the findings in this study are useful for understanding the physiological and developmental significance of FBXO24 in the male germ line, which can provide insight into impaired sperm development and male infertility.

In the revised manuscript, the authors address most of the concerns raised in the previous review. The following are representative remaining points.

• Quantification of the defective, vacuolar mitochondria (80%) and missing annulus (30%) was not shown in the figures or described in the results as well as in a few other figures.

No matter how much I try ad wrap my head around this- I can’t seem to grasp why a spiral would be preferred over a line, especially since it seems the dots must be colour coded regardless, and to me the colours of the dots in these examples is what I’ve used to interpret the timelines in the examples. Can’t find anything else about it online either!

Author Response

Reviewer #1 (Public Review):

Summary:

Heer and Sheffield used 2 photon imaging to dissect the functional contributions of convergent dopamine and noradrenaline inputs to the dorsal hippocampus CA1 in head-restrained mice running down a virtual linear path. Mice were trained to collect water rewards at the end of the track and on test days, calcium activity was recorded from dopamine (DA) axons originating in the ventral tegmental area (VTA, n=7) and noradrenaline axons from the locus coeruleus (LC, n=87) under several conditions. When mice ran laps in a familiar environment, VTA DA axons exhibited ramping activity along the track that correlated with distance to reward and velocity to some extent, while LC input activity remained constant across the track, but correlated invariantly with velocity and time to motion onset. A subset of recordings taken when the reward was removed showed diminished ramping activity in VTA DA axons, but no changes in the LC axons, confirming that DA axon activity is locked to reward availability. When mice were subsequently introduced to a new environment, the ramping to reward activity in the DA axons disappeared, while LC axons showed a dramatic increase in activity lasting 90 s (6 laps) following the environment switch. In the final analysis, the authors sought to disentangle LC axon activity induced by novelty vs. behavioral changes induced by novelty by removing periods in which animals were immobile and established that the activity observed in the first 2 laps reflected novelty-induced signal in LC axons.

Strengths:

The results presented in this manuscript provide insights into the specific contributions of catecholaminergic input to the dorsal hippocampus CA1 during spatial navigation in a rewarded virtual environment, offering a detailed analysis of the resolution of single axons. The data analysis is thorough and possible confounding variables and data interpretation are carefully considered.

Weaknesses:

Aspects of the methodology, data analysis, and interpretation diminish the overall significance of the findings, as detailed below.

The LC axonal recordings are well-powered, but the DA axonal recordings are severely underpowered, with recordings taken from a mere 7 axons (compared to 87 LC axons). Additionally, 2 different calcium indicators with differential kinetics and sensitivity to calcium changes (GCaMP6S and GCaMP7b) were used (n=3, n=4 respectively) and the data pooled. This makes it very challenging to draw any valid conclusions from the data, particularly in the novelty experiment. The surprising lack of novelty-induced DA axon activity may be a false negative. Indeed, at least 1 axon (axon 2) appears to be showing a novelty-induced rise in activity in Figure 3C. Changes in activity in 4/7 axons are also referred to as a 'majority' occurrence in the manuscript, which again is not an accurate representation of the observed data.

The reviewer points out a weakness in the analysis of VTA axons in our dataset. The relatively low n (currently 7) comes from the fact that VTA axons in the CA1 region of the hippocampus are very sparse and very difficult to record from (due to their sparsity and the low level of baseline fluorescence inherent in long range axon segments). This is the reason they have not been recorded from in any other lab outside of our lab. LC axons, on the other hand, are more abundant in CA1. In the paper when comparing VTA versus LC axons we deal with the mismatch in n by downsampling the LC axons to match the VTA axons and repeated this 1000 times to create a distribution. However, because the VTA axon n is relatively low, it is possible that we have not sampled the VTA axon population sufficiently and therefore have a biased population in our dataset. The issue is that it takes months for the baseline expression of GCaMP to reach sufficient levels to be able to record from VTA axons, and it is typical to find only a single axon in a FOV per animal. There are additional reasons why mice and/or axon recordings do not reach criteria and cannot be included in the dataset (these exclusion criteria are reported in the Methods section). For instance, out of the 54 DAT-Cre mice injected, images were never conducted in 36 for lack of expression or because mice failed to reach behavioral criteria. Another 11 mice were excluded for heat bubbles that developed during imaging, z-drift of the FOV, or bleaching of the GCaMP signal.

However, we do have n=2 additional VTA axon recordings that we will add to the dataset to bring the n up from 7 to 9. We plan on re-analyzing the data with n=9 VTA axons and making comparisons to down-sampled LC axons as described above. This boost in n will increase the power of our VTA axon analysis. To more formally test whether this is sufficient for statistical tests, we plan to utilize the G*power power-analysis tool to compute statistical power for each of the different tests we use. We will report this in the next version of the paper. However, the n=2 additional axons were nor recorded in the novel environment, so the next version will remain at n=7 for the novel environment analysis. We agree with the reviewer that the lack of the novelty induced DA axon activity may be a false negative, and so we will adjust the description of our results and discussion accordingly.

During the data collection of VTA axon activity we tried two variants of GCaMP: 6s and 7b, to see if one would increase the success rate of finding and recording from VTA axons. Given the long time-course of these experiments and the low yield in success, we pooled the GCaMP variants together to increase statistical power. Because the 2 additional VTA DA axons that were recorded from expressed GCaMP6s, the next version of the paper will have n=5 GCaMP6s, and n=4 GCaMP7b VTA DA axons, which will allow us to compare the activity of the two sensors in the familiar environment. The reviewer correctly pointed out that the sensors themselves could confound our results, and so they should not be pooled unless we can show they do not produce different signals in the axons. We will make this comparison and report the findings in the next version of the paper. If we find no significant differences, we will pool the data. If differences are detected, we will keep these axons separate for subsequent analysis and comparisons to LC axons.

The authors conducted analysis on recording data exclusively from periods of running in the novelty experiment to isolate the effects of novelty from novelty-induced changes in behavior. However, if the goal is to distinguish between changes in locus coeruleus (LC) axon activity induced by novelty and those induced by motion, analyzing LC axon activity during periods of immobility would enhance the robustness of the results.

This is indeed true, and this suggested analysis could further support our conclusions regarding the LC novelty signal. For the next version of the paper, we will use the periods of immobility to analyze and isolate any novelty induced activity in LC axons. However, following exposure to the novel environment, mice spend much less time immobile, therefore there may not be sufficient periods of immobility close in time to the exposure to the novel environment (which is when the novelty signal occurs). We plan to analyze mouse behavior during the early exposure to the novel environment for immobility and check whether we have enough of this behavior to perform the suggested analysis.

The authors attribute the ramping activity of the DA axons to the encoding of the animals' position relative to reward. However, given the extensive data implicating the dorsal CA1 in timing, and the remarkable periodicity of the behavior, the fact that DA axons could be signalling temporal information should be considered.

This is a very good point. We agree that the VTA DA axons could be signaling temporal information, as we have previously shown that these axons also exhibit ramping activity when you average their activity by time to reward (Krishnan et. al., 2022). We will conduct this analysis on this dataset. We have not, however, conducted any experiments designed to separate out time from distance, such as the experiments conducted in Kim et. al., 2020. Therefore, we cannot determine whether this is due to proximity in space to reward or time to reward. We will clarify in our text that by proximity, we mean either place or time, and cannot conclude which feature of the experience drives the VTA axon signal.

Krishnan, L.S., Heer, C., Cherian, C., Sheffield, M.E. Reward expectation extinction restructures and degrades CA1 spatial maps through loss of a dopaminergic reward proximity signal. Nat Commun 13, 6662 (2022).

Kim, HyungGoo R., Athar N. Malik, John G. Mikhael, Pol Bech, Iku Tsutsui-Kimura, Fangmiao Sun, Yajun Zhang, et al. A Unified Framework for Dopamine Signals across Timescales. Cell 183, no. 6 (2020).

The authors should explain and justify the use of a longer linear track (3m, as opposed to 2m in the DAT-cre mice) in the LC axon recording experiments.

LC axon activity was recorded on a 3m track to match the track length from an experiment we recently published (Dong et al., 2021) in which mice were exposed to a novel 3m track while populations of CA1 pyramidal cells were recorded. In that paper we described the time course of place field formation on the novel track. We wanted to test if LC axons signaled novelty (as we hypothesized) and whether the time course of LC axon activity matched the time course of place field formation. We briefly discuss this in the Discussion section of this paper and hypothesize that LC axons in CA1 could open a window of plasticity in which new place fields can form.

VTA axons were recorded on a 2m track (same VR tracks as LC axons were recorded on) to match another recent paper from our lab in which reward expectation was manipulated (Krishnan et al, 2022). In that study CA1 populations of pyramidal cells were recorded during the reward expectation experiment. To match the experience during recordings of VTA axons in CA1 to test how reward expectation may influence axon signaling along the track, we also used a 2m track. The idea was to check how VTA dopaminergic inputs to CA1 may influence CA1 population dynamics along the track.

Although the tracks were identical for LC and VTA recordings for both the familiar and novel tracks in terms of visual cues and design, the track lengths are different (simply modulated by gain control of the rotary encoder). To account for this we normalized the lengths for our comparison analysis. This normalization allows for a direct comparison of the patterns of activity across the two types of axons, controlling for the potential confound introduced by the different track lengths. By adjusting the data to a common scale, we could assess the relative changes in activity levels at matched spatial bins, ensuring that any observed differences or similarities are due to the intrinsic properties of the axons rather than differences in track lengths. However, the different lengths do make the animal’s experience slightly different. This is somewhat offset by the observations in our study that none of the LC or VTA axon signals would be expected to be majorly influenced by variations in track length. For instance, LC axons are associated with velocity and a pre-motion initiation signal, neither of which would be influenced by track length. VTA axons are also associated with velocity, which would not influence a direct comparison to LC axon velocity signals as mice reach maximal velocity very rapidly along the track. VTA axons do ramp up in activity as they approach the reward zone, and this signal could be modulated by track length (or maybe not if the signal is encoding time to reward rather than distance). However, LC axons show no ramping to reward signals, so a comparison across axons recorded on different track lengths for this analysis is justified.

However, to add rigor to comparisons of axon dynamics recorded along 2m and 3m tracks, we plan to plot axon activity of both sets of axons by time to reward, and actual (un-normalized) distance from reward.

Krishnan, L.S., Heer, C., Cherian, C., Sheffield, M.E. Reward expectation extinction restructures and degrades CA1 spatial maps through loss of a dopaminergic reward proximity signal. Nat Commun 13, 6662 (2022).

Dong, C., Madar, A. D. & Sheffield, M.E. Distinct place cell dynamics in CA1 and CA3 encode experience in new environments. Nat Commun 12, 2977 (2021).

Reviewer #2 (Public Review):

Summary:

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

The main findings were as follows:

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

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

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

Strengths:

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

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

Weaknesses:

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

(2) Some aspects of the methodology would benefit from clarification.<br /> First, to help others to better scrutinize, evaluate, and potentially to reproduce the research, the authors may wish to check if their reporting follows the ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines for the full and transparent reporting of research involving animals (https://arriveguidelines.org/). For example, I think it would be important to include a sample size justification (e.g., based on previous studies, considerations of statistical power, practical considerations, or a combination of these factors). The authors should also include the provenance of the mice. Moreover, although I am not an expert in 2-photon imaging, I think it would be useful to provide a clearer description of exclusion criteria for imaging data.

We thank the reviewer for helping us formalize the scientific rigor of our study. There are ten ARRIVE Guidelines and we have addressed most of them in our study already. However, there is an opportunity to add detail. We have listed below all ten points and how we have or will address each one.

(1) Experimental design - we go into great depth explaining the experimental set-up, how we used the autofluorescent blebs as imaging controls, how we controlled for different sample sizes between the two populations, and the statistical tests used for comparisons. We also carefully accounted for animal behavior when quantifying and describing axon dynamics both in the familiar and novel environments.

(2)Sample size - We state both the number of ROIs and mice for each analysis. Wherever we state how many axons had a certain kind of activity, we will also state the number of mice we saw this activity in. For the next version of the paper, we plan to conduct a power analysis using G*power to assess the power of our sample sizes for statistical analysis.

(3) Inclusion/exclusion criteria - Out of the 36 NET-Cre mice injected, 15 were never recorded for either failing to reach behavioral criteria, or a lack of visible expression in axons. Out of the 54 DAT-Cre mice injected, images were never conducted in 36 for lack of expression or failing to reach behavioral criteria. Out of the remaining 21 NET-CRE, 5 were excluded for heat bubbles, z-drift, or bleaching, while 11 DAT-Cre were excluded for the same reasons. This was determined by visually assessing imaging sessions, followed by using the registration metrics output by suite2p. This registration metric conducted a PCA on the motion-corrected ROIs and plotted the first PC. If the PC drifted largely, to the point where no activity was apparent, the video was excluded from analysis.

(4) Randomization - Already included in the paper is a description of random down sampling of LC axons to make statistical comparisons with VTA axons. LC axons were selected pseudo-randomly (only one axon per imaging session) to match VTA sampling statistics. This randomization was repeated 1000 times and comparisons were made against this random distribution.

(5) Blinding-masking - no blinding/masking was conducted as no treatments were given that would require this. We will include this statement in the next version.

(6) Outcomes - We defined all outcomes measured, such as those related to animal behavior and related axon signaling.

(7) Statistical methods - None of the reviewers had any issues regarding our description of statistical methods, which we described in detail in this version of the paper.

(8) Experimental animals - We described that DAT- Cre mice were obtained through JAX labs, and NET-Cre mice were obtained from the Tonegawa lab (Wagatsuma et al. 2017)

(9) Experimental procedure - Already listed in detail in Methods section.

(10) Results - Rigorously described in detail for behaviors and related axon dynamics.

Wagatsuma, Akiko, Teruhiro Okuyama, Chen Sun, Lillian M. Smith, Kuniya Abe, and Susumu Tonegawa. “Locus Coeruleus Input to Hippocampal CA3 Drives Single-Trial Learning of a Novel Context.” Proceedings of the National Academy of Sciences 115, no. 2 (January 9, 2018): E310–16. https://doi.org/10.1073/pnas.1714082115.

Second, why were different linear tracks used for studies of VTA and LC axon activity (from line 362)? Could this potentially contribute to the partly distinct activity correlates that were found for VTA and LC axons?

A detailed response to this is written above for a similar comment from reviewer 1.

Third, the authors seem to have used two different criteria for defining immobility. Immobility was defined as moving at <5 cm/s for the behavioral analysis in Figure 3a, but as <0.2 cm/s for the imaging data analysis in Figure 4 (see legends to these figures and also see Methods, from line 447, line 469, line 498)? I do not understand why, and it would be good if the authors explained this.

This is an error leftover from before we converted velocity from rotational units of the treadmill to cm/s. This will be corrected in the next version of the paper.

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

This is a great point. The decreased velocity in the novel environment could lead to a diminished novelty response in LC axons. We will add a discussion point on this in the next version. This could also be the case for VTA axons, so will add a discussion point that the lack of novelty signaling seen in VTA axons could be due to reduced velocity masking this signal.

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

Mice receive their water reward through a waterspout that is immobile and positioned directly in front of their mouth (which is also immobile as they are head fixed) and water delivery is triggered by a solenoid when the mice reach the end of the virtual track. Therefore, because the waterspout remains in the same place relative to the mouse, and the water reward is not delivered until they reach the end of the virtual track, there is nothing for the mice to detect. We will update the paper to make this clearer.

Additionally, on the initial laps with no reward, the ramping activity is still present (Krishnan et al, 2022) indicating this activity is not directly related to the presence/absence of water but is instead caused by reward expectation.

Reviewer #3 (Public Review):

Summary:

Heer and Sheffield provide a well-written manuscript that clearly articulates the theoretical motivation to investigate specific catecholaminergic projections to dorsal CA1 of the hippocampus during a reward-based behavior. Using 2-photon calcium imaging in two groups of cre transgenic mice, the authors examine the activity of VTA-CA1 dopamine and LC-CA1 noradrenergic axons during reward seeking in a linear track virtual reality (VR) task. The authors provide a descriptive account of VTA and LC activities during walking, approach to reward, and environment change. Their results demonstrate LC-CA1 axons are activated by walking onset, modulated by walking velocity, and heighten their activity during environment change. In contrast, VTA-CA1 axons were most activated during the approach to reward locations. Together the authors provide a functional dissociation between these catecholamine projections to CA1. A major strength of their approach is the methodological rigor of 2-photon recording, data processing, and analysis approaches. These important systems neuroscience studies provide solid evidence that will contribute to the broader field of learning and memory. The conclusions of this manuscript are mostly well supported by the data, but some additional analysis and/or experiments may be required to fully support the author's conclusions.

Weaknesses:

(1) During teleportation between familiar to novel environments the authors report a decrease in the freezing ratio when combining the mice in the two experimental groups (Figure 3aiii). A major conclusion from the manuscript is the difference in VTA and LC activity following environment change, given VTA and LC activity were recorded in separate groups of mice, did the authors observe a similar significant reduction in freezing ratio when analyzing the behavior in LC and VTA groups separately?

In response to this comment, we will analyze the freezing ratios in DAT-Cre and NET-Cre mice separately. However, other members of the lab have seen the same result in other mouse strains (See Dong et al. 2021), so we do not expect to see a difference (but it is certainly worth checking).

(2) The authors satisfactorily apply control analyses to account for the unequal axon numbers recorded in the LC and VTA groups (e.g. Figure 1). However, given the heterogeneity of responses observed in Figures 3c, 4b and the relatively low number of VTA axons recorded (compared to LC), there are some possible limitations to the author's conclusions. A conclusion that LC-CA1 axons, as a general principle, heighten their activity during novel environment presentation, would require this activity profile to be observed in some of the axons recorded in most all LC-CA1 mice.

We agree with the reviewer’s point here. To help avoid this problem, when downsampling LC axons to compare to VTA axons, we matched the sampling statistics of the VTA axons/mice (i.e. only one LC axon was taken from each mouse to match the VTA dataset).

However, in the next version of the paper we will also report the number of mice that we see a significant novel response in. We will also add the number of mice with significant activity for each of the measures in the familiar environment (e.g. how many mice had axons positively correlated with velocity).

Additionally, if the general conclusion is that VTA-CA1 axons ramp activity during the approach to reward, it would be expected that this activity profile was recorded in the axons of most all VTA-CA1 mice. Can the authors include an analysis to demonstrate that each LC-CA1 mouse contained axons that were activated during novel environments and that each VTA-CA1 mouse contained axons that ramped during the approach to reward?

As stated above, we will add the number of mice that had each activity type we reported here.

(3) A primary claim is that LC axons projecting to CA1 become activated during novel VR environment presentation. However, the experimental design did not control for the presentation of a familiar environment. As I understand, the presentation order of environments was always familiar, then novel. For this reason, it is unknown whether LC axons are responding to novel environments or environmental change. Did the authors re-present the familiar environment after the novel environment while recording LC-CA1 activity?

This is an important point to address. While we never varied the presentation order of the familiar vs novel environments, we did record the activity of LC axons in some of the mice in a dark environment (no VR cues) prior to exposure to the familiar environment. We will look at these axons to address whether they respond to initial exposure to the familiar environment. This will allow us to check whether they are responding to environmental change or novelty. We will add this analysis to the next version of the paper.

eLife assessment

This study presents important findings on the differential activity of noradrenergic and dopaminergic input to dorsal hippocampus CA1 in head-fixed mice traversing a runway in a virtual environment that is familiar or novel. While the data appear to be rigorously analysed, and the observed divergence in the dynamics of activity in the dopaminergic and noradrenergic axons is solid, there are some methodological concerns that mean the strength of evidence is currently incomplete.

Reviewer #1 (Public Review):

Summary:

Heer and Sheffield used 2 photon imaging to dissect the functional contributions of convergent dopamine and noradrenaline inputs to the dorsal hippocampus CA1 in head-restrained mice running down a virtual linear path. Mice were trained to collect water rewards at the end of the track and on test days, calcium activity was recorded from dopamine (DA) axons originating in the ventral tegmental area (VTA, n=7) and noradrenaline axons from the locus coeruleus (LC, n=87) under several conditions. When mice ran laps in a familiar environment, VTA DA axons exhibited ramping activity along the track that correlated with distance to reward and velocity to some extent, while LC input activity remained constant across the track, but correlated invariantly with velocity and time to motion onset. A subset of recordings taken when the reward was removed showed diminished ramping activity in VTA DA axons, but no changes in the LC axons, confirming that DA axon activity is locked to reward availability. When mice were subsequently introduced to a new environment, the ramping to reward activity in the DA axons disappeared, while LC axons showed a dramatic increase in activity lasting 90 s (6 laps) following the environment switch. In the final analysis, the authors sought to disentangle LC axon activity induced by novelty vs. behavioral changes induced by novelty by removing periods in which animals were immobile and established that the activity observed in the first 2 laps reflected novelty-induced signal in LC axons.

Strengths:

The results presented in this manuscript provide insights into the specific contributions of catecholaminergic input to the dorsal hippocampus CA1 during spatial navigation in a rewarded virtual environment, offering a detailed analysis of the resolution of single axons. The data analysis is thorough and possible confounding variables and data interpretation are carefully considered.

Weaknesses:

Aspects of the methodology, data analysis, and interpretation diminish the overall significance of the findings, as detailed below.

The LC axonal recordings are well-powered, but the DA axonal recordings are severely underpowered, with recordings taken from a mere 7 axons (compared to 87 LC axons). Additionally, 2 different calcium indicators with differential kinetics and sensitivity to calcium changes (GCaMP6S and GCaMP7b) were used (n=3, n=4 respectively) and the data pooled. This makes it very challenging to draw any valid conclusions from the data, particularly in the novelty experiment. The surprising lack of novelty-induced DA axon activity may be a false negative. Indeed, at least 1 axon (axon 2) appears to be showing a novelty-induced rise in activity in Figure 3C. Changes in activity in 4/7 axons are also referred to as a 'majority' occurrence in the manuscript, which again is not an accurate representation of the observed data.

The authors conducted analysis on recording data exclusively from periods of running in the novelty experiment to isolate the effects of novelty from novelty-induced changes in behavior. However, if the goal is to distinguish between changes in locus coeruleus (LC) axon activity induced by novelty and those induced by motion, analyzing LC axon activity during periods of immobility would enhance the robustness of the results.

The authors attribute the ramping activity of the DA axons to the encoding of the animals' position relative to reward. However, given the extensive data implicating the dorsal CA1 in timing, and the remarkable periodicity of the behavior, the fact that DA axons could be signalling temporal information should be considered.

The authors should explain and justify the use of a longer linear track (3m, as opposed to 2m in the DAT-cre mice) in the LC axon recording experiments.

Reviewer #2 (Public Review):

Summary:

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

The main findings were as follows:

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

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

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

Strengths:

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

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

Weaknesses:

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

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

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

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

sad, because these men are broken, need therapy and do whats expected, resents them and run away, keeping someone else miserable in their traumas and issues.

Driving until exhaustion mirrors the mental fatigue caused by unceasing voices.

The main character gets scared because of the sermon while Rio wants to head out to adventure, they get into an argument

He came to a realization that these voices in his head are the stories of people who are like himself. His story is only a fraction of the man but are all one braid. he says that these faces have been witnessing his story because its all the same.

it kinda reminds me of how pen was drowned so her father to live

I read this line and I automatically thought of the fact that everyone has walked into a room and has probably said this in their head. The insecurity's just pouring out.

wow! as a member of the LGBTQ community I really enjoyed reading this. It was super cool as the whole article is about to see firsthand accounts because it really shows a different picture in your head. It is super cool seeing this page of a transgender women who's page is something I would have enjoyed interacting with being on the internet before I was even born !

Reviewer #1 (Public Review):

Neurons are not static-their activity patterns change as the result of learning, aging, and disease. Reliable tracking of activity from individual neurons across long time periods would enable studies of these important dynamics. For this reason, the authors' efforts to track electrophysiological activity across days without relying on matching neural receptive fields (which can change due to learning, aging, and disease) is very important.

By utilizing the tightly-spaced electrodes on Neuropixels probes, they are able to measure the physical distance and the waveform shape 'distance' between sorted units recorded on different days. To tune the matching algorithm and to validate the results, they used the visual receptive fields of neurons in the mouse visual cortex (which tend to change little over time) as ground truth. Their approach performs quite well, with a high proportion of neurons accurately matched across multiple weeks.

This suggests that the method may be useable in other cases where the receptive fields can't be used as ground truth to validate the tracking. This potential extendibility to tougher applications is where this approach holds the most promise. However, the study only looks at one brain area (visual cortex), in one species (mouse), using one type of spike sorter (Kilosort), and one type of behavioral prep (head-fixed). While the authors suggest methods to generalize their technique to other experimental conditions, no validation of those generalizations was done using data from different experimental conditions. Anyone using this method under different conditions would therefore need to perform such validation themselves.

decaptitate(v): to cut off the head of person

is the princess being compared to artemis??

taking a vacation and then getting pissed right as you come back home is kinda real

ok so they do look alike, imagine how hard it is for penelope...

In this passage, the Son rises with the sun — on the dawning of the third morning of battle, the Son of god goes forth on a great chariot, inspired by the vision of Ezekiel, flaming, rife with precious stones, and moving on pure spirit, ‘wheel[s] within wheel[s]’ [6.750-9]. So great is his divine power that he restores the heavenly battlefield to its former beauty, but the rebel forces refuse to give in and rally once more. The narrator questions how such spirits, former denizens of heaven, could be so foolish as to not quail before the might of the Divine. In the next line [791] the narrator offers an explanation: the rebel angels recognize the sight as awe-inspiring and of great power, but rather than being cowed, they covet it, and draw strength from their envy and their wish to be in that position. Spurned by this decidedly impious motivation, they face their foes again, as the Son speaks to his own forces.

The passage highlights once more how the discontent among Satan’s forces rallies them and spurs them onward, just as Satan himself believed his ‘merit’ to be offended when he was fell. It’s also a passage, however, that uses pagan and mythological elements to enhance the godliness of the Son, rather than the perverseness of the devil. Milton uses the goddess Victory, or Nike, as a consort of the Son [762-3], and he carries a bow and quiver of thunderbolts [763-4], which evoke images of Jupiter or Zeus.

n lines 547-557, the speaker is describing how Zophiel just finished warning the other angels of Satan’s return to battle. Hearing the news of Satan’s return, the angels “took alarm / And onward move Embattl’d” (6.549-550). In the distance, the angels are able to see the enemy advancing towards them “with shadowing Squadrons Deep / To hide the fraud” (6.554-555). After a moment, the angels are able to see Satan and the lines end with him commanding.

Raphael continues to talk about the conflict between Satan and God. Michael and Satan had been arguing, they then stop talking and begin to fight. They are described as “two planets” (6.13): each leading their own constellation, or army. When these two powerful forces meet, Michael chops Satan's sword in half and then slashes his right side. Satan bleeds a “nectarous”(6.32) substance, but his wound quickly heals. Raphael notes that this is the first time Satan has felt pain. His minions quickly transport him back to his chariot, but he is very upset, as he realizes that he may not be as matchless a fighter as he had previously believed. Meanwhile, the battle rages on. Gabriel is fighting Moloch while Uriel, Raphael, and Abdiel all defeat various rebel angels. As the battle continues to turn south for Satan’s crew, they begin to flee. This battle is the first time that these angels have felt pain or fear, which is rather unsettling to them. Night falls, and both armies set up camp, with Satan calling for a meeting of his council.

The speaker is describing these events throughout the passage.

Here Satan enters the battle in Heaven. Abdiel strikes Satan with incredible swiftness, shocking and enraging the rebel angel (6.189-200). This may bear out Abdiel's claim that his greater moral fortitude and reason will guide him even in physical combat.

The battle nearly makes Hell out of Heaven, with clashing swords, flames, and booming trumpets filling the air (6.206-225). This draws to mind Satan's cohorts extolling the virtues of hell as despite its horrific qualities, it was free and essentially at peace. It seems the behaviour of a place's inhabitants have more influence on its quality than the place itself. This idea of violence and sin entering Heaven is mirrored by the fall of man, with Raphael previously claiming that had Earth existed during the war, it would have felt its effects then.

The perfection of the angels is not diminished however, as even in combat they are graceful. Each angelic warrior is his own leader, yet they all work in unison. There are no acts of cowardice or self-service as in a human conflict (6.226-245)

Finally, Michael and Satan meet in battle. This is the dramatic height of the passage, as the two oldest and strongest arch-angels begin to fight (6.250-261).

(#18) H1b. Lastly I was wondering if we could go over this statement in the conclusion, as it seemed pretty important to me (but I could be very wrong), “It allows us to estimate the effect of level 2 variables while providing effect estimates of level 1 variables that are unbiased by a possible correlation with the level 2 error.” (Osamudia)

Response: The within estimates (for example of age) will be free of bias due to u_i, because they are the FE estimates.

(Anna) They threw a lot of equations at us in this reading, and I really am not an equation minded person (the variables get all mixed up in my head and they are hard for me to decipher) can you say which ones are most important for this week and maybe briefly explain the math?

Response: I think of the math here as the way of demonstrating the connections between the different models. You can put that in a mental footnote and try to focus on working on an intuitive understanding of the key things: Within variation : Changes (over time) within level 2 units (mothers in this case). I.e., changes across pregnancies for the same person. Between variation: differences across mothers, where the variables are the average of the mother’s variables. For something like mother’s age or smoking behavior, this is the average at level 2. Then focus on why this is exciting: we can see, in the same model, whether within variation has the same effect as between variation. Circle back to why this is really important (it is telling us something about what is going on with fixed unobserved characteristics).

Somewhat reflects on Carla and Sylvia, as Carla 'butts' Sylvia by siding with Clark in the end

Author Response

The following is the authors’ response to the original reviews.

Reviewer #1 (Public Review):

(1.1) This work introduces a new method of imaging the reaction forces generated by small crawling organisms and applies this method to understanding locomotion of Drosophila larva, an important model organism. The force and displacement data generated by this method are a qualitative improvement on what was previously available for studying the larva, improving simultaneously the spatial, temporal, and force resolution, in many cases by an order of magnitude. The resulting images and movies are quite impressive.

We thank the reviewer for their recognition of the achievements our work presents and for their feedback with regard to what they consider our most important findings and the points raised in their review. We will address these points individually below.

(1.2) As it shows the novel application of recent technological innovations, the work would benefit from more detail in the explanation of the new technologies, of the rationales underlying the choice of technology and certain idiosyncratic experimental details, and of the limitations of the various techniques. In the methods, the authors need to be sure to provide sufficient detail that the work can be understood and replicated. The description of the results and the theory of motion developed here focus only on forces generated when the larva pushes against the substrate and ignores the equally strong adhesive forces pulling the larva onto the substrate.

As the reviewer correctly points out, our present work adapts a recently developed set of methods (namely, ERISM and WARP) for use with small soft-bodied animals. The foundational methods have been described in detail in previous publications (refs, 23 and 26). However, upon reflection, we agree that more information can be provided to ensure our work is more accessible and reproducible. We also agree that some additional clarifying information on our approach could be helpful. We have addressed this in the following ways:

(1) We have included a detailed Key Resources table in the methods section to allow for maximum transparency on equipment and reagent sourcing. This can now be found on Pages 16-19.

(2) We have modified the ‘Freely behaving animals force imaging’ section of the Materials and Methods section to include more detailed information on practical aspects of conducting experiments. These changes can be found on page 23-24 (lines 566–567, 571-577).

(3) We have re-ordered the Materials and Methods section, such that microcavity fabrication and microcavity characterisation occur prior to the description of ERISM and WARP experiments - this change should hopefully aid replication. Details regarding the application of a silicone well to the surface of microcavities have also been added (lines 472-474).

(4) We have added additional text in the Introduction and Results (Pages 3-4 and 7, lines 56-86, and 152-153) to explain our rationale for using ERISM/WARP and additional text in the discussion that discusses the potential role(s) of adhesive forces in larval locomotion (Page 12, lines 301307).

(1.3) The substrate applies upward, downward, and horizontal forces on the larva, but only upward and downward forces are measured, and only upward forces are considered in the discussions of "Ground Reactive Forces." An apparent weakness of the WARP technique for the study of locomotion is that it only measures forces perpendicular to the substrate surface ("vertical forces" in Meek et al.), while locomotion requires the generation of forces parallel to the substrate ("horizontal forces"). It should be clarified that only vertical forces are studied and that no direct information is provided about the forces that actually move the larva forward (or about the forces which impede this motion and are also generated by the substrate). Along with this clarification, it would be helpful to include a discussion of other techniques, especially micropillar arrays and traction force microscopy, that directly measure horizontal forces and of why these techniques are inappropriate for the motions studied here.

We attempted to provide a streamlined Introduction in our initial submission and then compared ERISM/WARP to other methods in our discussion. We are happy to provide a brief overview of substrate force measurement methods in the introduction to help set the stage for readers. The Introduction section of our revised manuscript now contains the following comparison of different mechanobiological imaging techniques on pages 3-4 lines 56-86:

‘However, in the field of cellular mechanobiology, many new force measuring techniques have been developed which allow measurement of comparatively small forces from soft structures exhibiting low inertia (15–17) often with relatively high spatial-resolution. Early methods such as atomic force microscopy required the use of laser-entrained silicon probes to make contact with a cell of interest (15). This approach is problematic for studying animal behaviour due to the risk of the laser and probe influencing behaviour. Subsequently, techniques have been developed which allow indirect measurement of substrate interactions. One such approach is Traction Force Microscopy (TFM) in which the displacement of fluorescent markers suspended in a material with known mechanical properties relative to a zero-force reference allows for indirect measurement of horizontally aligned traction forces (17–19). This technique allows for probe-free measurement of forces, but the need to obtain a precise zero-force reference would make time-lapse measurements on behaving animals challenging; further, depending on the version used, it has insufficient temporal resolution for the measurement of forces produced by many behaving animals, despite recent improvements (20). A second approach revolves around the use of micropillar arrays; in this technique, horizontally-aligned traction forces are measured by observing the deflection of pillars made of an elastic material with known mechanical properties. This approach can be limited in spatial resolution and introduces a non-physiological substrate that may influence animal behavior (21,22).

Recently we have introduced a technique named Elastic Resonator Interference Stress Microscopy (ERISM) which allows for the optical mapping of vertically aligned GRFs in the pico and nanonewton ranges with micrometre spatial resolution by monitoring local changes in optical resonances of soft and deformable microcavities. This technique allows reference-free mapping of substrate deformations and calculation of vertically directed GRFs; it has been used to study a range of questions related to exertion of cellular forces (23–25). Until recently, this technique was limited by its low temporal resolution (~10s), making it unsuitable for recording substrate interaction during fast animal movements, but a further development of ERISM known as wavelength alternating resonance pressure microscopy (WARP), has been demonstrated to achieve down to 10 ms temporal resolution (26). Given ERISM/WARP allows for probe-free measurement of vertical ground reaction forces with high spatial and temporal resolution, it becomes an attractive method for animal-scale mechanobiology.’

(1.4) The larvae studied are about 1 mm long and 0.1 mm in cross-section. Their volumes are therefore on order 0.01 microliter, their masses about 0.01 mg, and their weights in the range of 0.1 micronewton. This contrasts with the force reported for a single protpodium of 1 - 7 micronewtons. This is not to say that the force measurements are incorrect. Larvae crawl easily on an inverted surface, showing gravitational forces are smaller than other forces binding the larva to the substrate. The forces measured in this work are also of the same magnitude as the horizontal forces reported by Khare et al. (ref 32) using micropillar arrays.

I suspect that the forces adhering the larva to the substrate are due to the surface tension of a water layer. This would be consistent with the ring of upward stress around the perimeter of the larva visible in S4D, E and in video SV3. The authors remark that upward deflection of the substrate may be due to the Poisson's ratio of the elastomer, but the calibration figure S5 shows that these upward deflections and forces are much smaller than the applied downward force. In any case, there must be a downward force on the larva to balance the measured upward forces and this force must be due to interaction with the substrate. It should be verified that the sum of downward minus upward forces on the gel equals the larva's weight (given the weight is neglible compared to the forces involved, this implies that the upward and downward forces should sum to 0).

We have carefully calculated the forces exerted by protopodia and are confident in the accuracy of our measurements as reported. We further agree with the reviewer’s suggestion that gravitational forces can be largely neglected.

As the reviewer points out, one would expect forces due to upward and downward deflections to cancel when considering the entire system. However, we see indications that the counteracting / balancing force often acts over a much larger area than the acting force, e.g. a sharp indentation by a protopodium might be counteracted by an upward deflection over a 10-20 fold larger radius and hence 100 to 400-fold larger area, thereby reducing the absolute value of the upward deflection at any given pixel surrounding the indentation. This in turn increases error in determining the integrated upward deformation, making it difficult to perform an absolute comparison of acting and counteracting force. Further, recording the entire counteracting force induced deformation would require acquiring data with a prohibitively large field of view.

We agree that in some situations, water surface tension may be adhering animals to the substrate. Importantly, this is a challenge that the animal faces outside the lab in its natural environment of moist rotting fruit and yeast. The intricate force patterns seen in our study in the presence of water surface tension are therefore ecologically relevant. In other situations (e.g. preparing for pupation), larvae are able to stick to dry surfaces, suggesting that other adhesive forces such as mucoid adhesion can also come into play in certain behavioural contexts. A full characterization of the effects of water tension and mucoid adhesion are beyond the scope of this study. However, we have now added a sentence on pages 8 and 12 commenting on these other biomechanical forces at play:

‘We also observed that the animals travel surrounded by a relatively large water droplet (lines 189-190).’

‘We observed that larvae travel surrounded by moisture from a water droplet, which produces a relatively large upwardly directed force in a ring around the animal. The surface tension produced by such a water droplet likely serves a role in adhering the animal to the substrate. However, during forward waves, we found that protopodia detached completely during SwP, suggesting this surface tensionrelated adhesion force can be easily overcome by the behaving animal. (lines 301-307) .’

(1.5) Much of the discussion and the model imply that the sites where the larva exerts downward force on the gel are the sites where horizontal propulsion is generated. This assumption should be justified. Can the authors rule out that the larva 'pulls' itself forward using surface tension instead of 'pushing' itself forward using protopodia?

Determining the exact ‘sites’ where horizontal propulsion is generated is challenging. In our conceptual model, movement is not initiated by protopodia per se, but rather by a constellation of muscle contractions, which act upon the hydrostatic skeleton, which in turn causes visceral pistoning that heaves larvae forward. This is based on previous findings in Ref 31. While there are indeed downward protopodial ‘vaulting’ forces prior to initiation of swing, we propose that the main function of protopodia is not to push the larvae forward, but rather to provide anchoring to counteract opposing forces generated by muscles. We agree that water surface tension could also be sculpting biomechanical interactions; however, a full characterization of how water surface tension shapes larval locomotion is beyond the scope of this study.

Since we have observed larvae move over dry terrain (e.g. glass) without an encasing water bubble, we do not believe that an encasing water bubble is strictly required for locomotion. We have also seen no obvious locomotion related modulations in the pulling forces created by water bubbles encasing larva, which would be expected if animals were somehow using water tension to pull themselves forward. Overall, the most likely explanation is that larvae use a mixture of biomechanical tactics to suit the moment in a given environment. This represents a challenge but also an opportunity for future research.

We have now added additional text in the ‘Functional subdivisions within protopodia’ subsection to discuss these nuances (page 14, lines 382-387):

‘This increased force transmitted into the substrate is unexpected as the forces generated for the initiation of movement should arise from the contraction of the somatic muscles. We propose that the contraction of the musculature responsible for sequestration acts to move haemolymph into the protopodia thus exerting an increased pressure onto the substrate while the contact area decreases as a consequence of the initiation of sequestration.’

and (page 15, lines 398-399):

‘Water surface films appear to facilitate larval locomotion in general but the biomechanical mechanisms by which they do this remain unclear.’

(1.6) More detail should be provided about the methods, their limitations, and the rationale behind certain experimental choices.

We thank the reviewer for this comment. As this significantly overlaps with a point raised earlier, we kindly direct them to our answer to comment #1.2 above.

(1.7) Three techniques are introduced here to study how a crawling larva interacts with the substrate: standard brightfield microscopy of a larva crawling in an agarose capillary, ERISM imaging of an immobilized larva, and WARP imaging of a crawling larva. The authors should make clear why each technique was chosen for a particular study - e.g. could the measurements using brightfield microscopy also be accomplished using WARP? They should also clarify how these techniques relate to and possibly improve on existing techniques for measuring forces organisms exert on a substrate, particularly micropillar arrays and Traction Force Microscopy.

Indeed, each of the three methods used has a specific merit. The brightfield microscopy was selected to track features on the animal’s body and to provide a basic control for the later measurements. However, this technique cannot directly measure the substrate interaction, it only allows inferences to be made from tracked features at the substrate interface. ERISM provides high resolution maps of the indentation induced by the larva; it is also extensively validated for mapping cell forces and the data analysis is robust against defects on the substrate (refs 23, 24 and 25). However, as we explain in the manuscript, ERISM lacks the temporal resolution needed to monitor mechanical activity of behaving larva. Its use was therefore limited to the study of anaesthetised animals. For mapping forces exerted by behaving larva, we used WARP which is a further development of ERISM that offers higher frame rates but at the cost of requiring more extensive calibration (Supplementary Figure S4). The streamlined introduction of the different methods in our original manuscript originates from our attempt to be as concise as possible. However, as state in response to comment #1.2, we agree that additional explanation and discussion will be helpful for readers and that it will helpful to briefly refer to other methods for force mapping. We have now added references to a variety of techniques in the Introduction (Page 3-4, lines 56-86) as stated in a prior response.

(1.8) As written, "(ERISM) (19) and a variant, Wavelength Alternating Resonance Pressure microscopy (WARP) (20) enable optical mapping of GRFs in the nanonewton range with micrometre and millisecond precision..." (lines 53-55) may generate confusion. ERISM as described in this work has a much lower temporal resolution (requires the animal to be still for 5 seconds - lines 474-5); In this work, WARP does not appear to have nanonewton precision (judging by noise on calibration figures) and it is not clear that it has millisecond precision (the camera used and its frame rate should be specified in the methods).

Previous studies have demonstrated the capabilities and limitations of ERISM and WARP. Upon reflection, we agree that our wording here could be more precise. To clarify our claim, we now separate the statements on ERISM and WARP in the introduction as follows (page 4, lines 78-83):

“Until recently, this technique was limited by its low temporal resolution (~10s) making it unsuitable for use in recording substrate interaction during fast animal movements, but a further development of ERISM known as wavelength alternating resonance pressure microscopy (WARP), has been demonstrated to achieve down to 10 ms temporal resolution (26)”

While WARP can achieve comparable force resolution as ERISM when used in a cellular context (c.f. Ref 26), we agree that for the present study, the resolution was in the 10s of nanonewton range, due to the need to use stiffer substrates and larger fields of view.

The camera used in our work was specified in the appropriate subsection of the Materials and Methods (“All WARP and ERISM images were acquired using an Andor Zyla 4.2 sCMOS camera (Andor Technology, Belfast, UK)”). We apologise that the exact frame rate used in our current work was not mentioned in our original manuscript; this has now been added to the ‘Freely behaving animals force imaging’ section of the Materials and Methods (page 23, lines 574-577).

(1.9) It would be helpful to have a discussion of the limits of the techniques presented and tradeoffs that might be involved in overcoming them. For instance, what is the field of view of the WARP microscope, and could it be increased by choosing a lower power objective? What would be required to allow WARP microscopy to measure horizontal forces? Can a crawling larva be imaged over many strides by recentering it in the field of view, or are there only particular regions of the elastomer where a measurement may be made?

We agree with the reviewer that some discussion of the limitations of our technique will allow readers to have a more informed appreciation of what we are capable of measuring using WARP. However, as this is the first work to ever demonstrate such measurements, the limitations and tradeoffs cannot all be known with certainty at the present stage.

To answer your individual questions:

(1) There is a trade-off between numerical aperture and the ability to resolve individual interference fringes. Since our approach to calculate displacement from reflection maps relies upon counting of individual fringe transitions, going to a lower powered objective risks having these fringes blend and thus the identification of the individual transitions becoming impossible. The minimum numerical aperture of the objective will therefore generally depend on the steepness of indentations produced by the animals; the steeper an indentation, the closer the neighbouring fringes and thus the higher the required magnification to resolve them.

(2) From WARP and ERISM data, one can make inferences about horizontal forces, as is described in detail in our earlier publications about ERISM (ref, 23). However, quantitation of horizontal forces at sufficient temporal resolution to allow the investigation of behaving Drosophila larva is currently not possible.

(3) Many strides can indeed be imaged using our technique, however, this comes with additional technical challenges. Whether or not the animal itself can be recentred is an ongoing challenge. We have found that the animals are amenable to recentring themselves within the field of view if chasing an attractive odorant. However, manual recentering using a paintbrush risks destroying the top surface of the soft elastic resonator and recentering the microscope stage would require real-time object tracking which has been outside the scope of this original work, given the other challenging requirements on hardware and optics for obtaining high quality force maps.

To provide more information on limitations of our technique, we have added the following text into the discussion (pages 13-14, lines 356-370).

‘Despite the substantial advances they have provided, the use of WARP and ERISM also brings challenges and has several technical limitations. For example, fabrication of resonators is much more challenging than preparation of the agarose substrates conventionally used for studying locomotion of Drosophila. This problem is compounded by the fragility of the devices owing to the fragility of the thin gold top mirror. This becomes problematic when placing animals onto the microcavities, as often the area local to the initial placement of the animal is damaged by the paintbrush used to move the animals. Further, as a result of the combining of the two wavelengths, the effective framerate of the resultant displacement and stress maps is equal to half of the recorded framerate of the interference maps. To be able to monitor fast movements, recording at very high framerates is therefore necessary which, depending on hardware, might require imaging at reduced image size, but this in turn reduces the number of peristaltic waves that can be recorded before the animal escapes the field of view. A further limitation is that WARP and ERISM are sensitive mainly to forces in the vertical direction; this is complementary to TFM, which is sensitive to forces in horizontal directions. Using WARP in conjunction with high speed TFM (possibly using the tuneable elastomers presented here) could provide a fully integrated picture of underlying vertical and horizontal traction forces during larval locomotion.’ And further on page 13, lines 337-341:

‘More detailed characterisation of this behaviour remains a challenge owing to the changing position of the mouth hooks. Due to their rigid structure and the relatively large forces produced in planting, mouth hooks produce substrate interaction patterns which our technique struggles to map accurately due to overlapping interference fringes ambiguating the fringe transitions.’

We trust that the above discussion and our modifications to our manuscript resulting from these will address the reviewer’s concerns.

Reviewer #2 (Public Review):

(2.1) With a much higher spatiotemporal resolution of ground dynamics than any previous study, the authors uncover new "rules" of locomotory motor sequences during peristalsis and turning behaviors. These new motor sequences will interest the broad neuroscience community that is interested in the mechanisms of locomotion in this highly tractable model. The authors uncover new and intricate patterns of denticle movements and planting that seem to solve the problem of net motion under conditions of force-balance. Simply put, the denticulated "feet" or tail of the Drosophila larva are able to form transient and dynamic anchors that allow other movements to occur.

We thank the reviewer for their feedback and the information regarding which of our results is likely to resonate most impactfully with readers from a biological background.

The biology and dynamics are well-described. The physics is elementary and becomes distracting when occasionally overblown. For example, one doesn't need to invoke Newton's third law, per se, to understand why anchors are needed so that peristalsis can generate forward displacements. This is intuitively obvious.

We are sorry to hear that the reviewer found some of the physics details distracting. To address this concern, we have simplified some of the language while still attempting to keep the core arguments intact. For context and analogy, we still believe that including a brief reference to the laws of motion is helpful for some readers to explain some of our results and highlight their general implications, especially with regard to anchoring against reaction forces.

One of our objectives is to make this article accessible and interesting for biologists and physicists at all levels. We feel it is important to reach out to both communities and try to be inclusive as possible in our writing. Newton’s 3rd law is clearly relevant for our study and it is a common point of reference for anyone with a highschool education, and so we feel it is appropriate to mention it as a way to help readers across disciplines understand the biophysical challenges faced by the animals we study.

(2.2) Another distracting allusion to "physics" is correlating deformation areas with displaced volume, finding that "volume is a consequence of mass in a 2nd order polynomial relationship". I have no idea what this "physics" means or what relevance this relationship has to the biology of locomotion.

Upon reflection, we agree that this language may be overly complex and distracts from what is, at its core, a simple, but important principle governing how Drosophila larvae interact with their substrates. The point we are trying to make is that our data show that forces exerted by an animal are proportional in a non-linear way to contact area. This suggests that to increase force exerted on the substrate, an animal must increase contact area. We do not observe contact area remaining constant while force increases, or vice versa. To make this result more clear, we have made several changes in our revised manuscript. Figure 5B no longer shows the relationship between the protopodial contact area and the displaced volume of the elastic resonator, but instead now shows the protopodial contact area and recorded force transmitted into the substrate. This then shows that in order to increase force transmitted into the substrate, these animals must increase their contact area. We have made changes to the figure legend of Figure 5 and the statements in the Results section accordingly (Page 9, lines 220-222).

2.3 The ERISM and WARP methods are state-of-the-art, but aside from generally estimating force magnitudes, the detailed force maps are not used. The most important new information is the highly accurate and detailed maps of displacement itself, not their estimates of applied force using finite element calculations. In fact, comparing displacements to stress maps, they are pretty similar (e.g., Fig 4), suggesting that all experiments are performed in a largely linear regime. It should also be noted that the stress maps are assumed to be normal stresses (perpendicular to the plane), not the horizontal stresses that are the ones that actually balance forces in the plane of animal locomotion.

We largely agree with the statement made by the reviewer here. However, we have found that in many contexts, audiences appreciate having the absolute number of the forces and stresses involved reported. Therefore, where possible, we have used stress maps, rather than displacement maps. We also observe that while stress and displacement maps show similar patterns, features sometimes appear sharper in the stress map, which is a result of the finite element algorithm being able to attribute a broad indentation to a somewhat more localised downward force. We have thus opted to keep to original stress maps. We have been more explicit about WARP and ERISM being more tuned to recording vertically directed forces throughout the revised manuscript (lines 75, 78, 86, 162, 301, 305, 336).

We have also modified our Discussion section to encourage further investigation of our proposed model using a technique more tuned to horizontal stresses (pages 12-13, lines 324-328):

‘However, WARP microscopy is best suited to measurements of forces in the vertical direction, and though we can make inferences such as this as they are a consequence of fundamental laws of physics, we present this conclusion as a testable prediction which could be confirmed using a force measurement technique more tuned to horizontally directed forces relative to the substrate.’

(2.4) But none of this matters. The real achievements are the new locomotory dynamics uncovered with these amazing displacement measurements. I'm only asking the authors to be precise and down-to-earth about the nature of their measurements.

We thank the reviewer for their perceptiveness in finding that though the forces are interesting, the interactions themselves are the most noteworthy result here. We trust that with the changes made in our revised manuscript, the description is now more “down-to-earth”, more concise where appropriate, and accurate as to which results are particularly important and novel.

(2.5) It would be good to highlight the strength of the paper -- the discovery of new locomotion dynamics with high-resolution microscopy -- by describing it in simple qualitative language. One key discovery is the broad but shallow anchoring of the posterior body when the anterior body undertakes a "head sweep". Another discovery is the tripod indentation at the tail at the beginning of peristalsis cycles.

We thank the reviewer for this recommendation. We agree that including a more explicit statement of some of our findings, especially with regards to these new posterior tripod structures and the whole-abdomen preparatory anchoring prior to head sweeps, would make the paper more impactful. As a result, we have modified the discussion section to include a statement for each new result and have also amended our abstract as a result (lines 407-416):

“Here we have provided new insights into the behaviour of Drosophila larval locomotion. We have provided new quantitative details regarding the GRFs produced by locomoting larvae with high spatiotemporal resolution. This mapping allowed the first detailed observations of how these animals mitigate friction at the substrate interface and thus provide new rules by which locomotion is achieved. Further, we have ascribed new locomotor function to appendages not previously implicated in locomotion in the form of tripod papillae, providing a new working hypothesis of how these animals initiate movement. These new principles underlying the locomotion outlined here may serve as useful biomechanical constraints as called for by the wider modelling community (39).”

(2.6) As far as I know, these anchoring behaviors are new. It is intuitively obvious that anchoring has to occur, but this paper describes the detailed dynamics of anchoring for the first time. Anchoring behavior now has to be included in the motor sequence for Drosophila larva locomotion in any comprehensive biomechanical or neural model.

We agree with the reviewer on this. We think it is best to let our colleagues reflect on our findings and then decide how best to include them in future models.

Recommendations for the authors:

Reviewer #1 (Recommendations For The Authors):

Please be sure to describe in a figure caption or in the methods the details of the optical setup, especially the focal lengths of all the lenses, including the objective, and part numbers of the LEDs and filters. It would be helpful to have a figure in the main paper explaining the principles of ERISM/WARP microscopy along with the calibration measurements and computational pipeline (this would mainly combine elements already in the supplement). Such a figure should also include details of the setup that are alluded to in the methods but not fully explained (for instance, a "silicone well" is referred to in the methods but never described). The calibration of elastomer stiffness that now appears in the main text could be made a supplementary figure, unless there is some new art in the fabrication of the elastomers that should be highlighted as an advance in the main text.

We appreciate the importance of explaining our methods to readers.

In response to the public comments, we have added further details in our methods section to clarify practical aspects and ensure that readers will be able to reproduce our work.

In Supplemental Figure 2, we show the full optical light path for ERISM and WARP along with named components. In addition, the principles of ERISM and WARP microscopy have already been extensively described in previous publications (See Refs 23-26). In light of this, we feel that the best approach in this paper is to direct readers to those publications.

We feel that it is appropriate to present the calibration of elastomer stiffness in the main text because this is indeed a new innovation that is not just about making the elastomers but making force sensors based on these different materials. This is really important because it shows how researchers can tune the stiffness of an ERISM/WARP elastomer to match the type of tissue or organism under study. This is really the key technical advance that enables whole animal biomechanics across a range of animal sizes, so we think it is appropriate to keep it in the main text.

We want to make sure that we do not oversell this point, and we feel that we make it sufficiently clear in the main text of our manuscript that making elastomer based force sensors of appropriate stiffness is important, when we state

“First, we developed optical microcavities with mechanical stiffnesses in the range found in hydrogel substrates commonly used for studying Drosophila larval behaviour, i.e. Young’s modulus (E) of 10-30kPa (36–38).” (p. 5, ll. 124) and later

“Here we used Drosophila larvae as a test case, but our methods now allow elastic optical resonators to be tuned to a wide range of animal sizes and thus create new possibilities for studying principles of neuro-biomechanics across an array of animals.” (p. 12, ll. 337)

I would appreciate a description of the "why" behind some experimental choices, as understanding the motivation would be helpful for other researchers looking to adopt these techniques.

We have now added additional text in the introduction and discussion that explains the rationale behind our experimental choices. in more detail. Please see our response to Reviewer 1’s public comments on the same point.

(1) The WARP and ERISM experiments were conducted on a collagen coated gold surface rather than agarose. Why? EG does agarose not adhere to the gold, or would its thickness interfere with the measurement?

The gold layer is applied above the elastomer and the collagen on top of the gold layer makes the gold a more natural biological surface for the animals. Agarose is unsuitable as an elastomer because it would dry during the vacuum based deposition of the gold. It is also unsuitable as a surface coating on top of the gold as the coating on the gold needs to very thin to preserve the spatial and mechanical resolution of our sensors. Further, processing of agarose generally requires temperatures of 60°C and higher which we find can damage the elastomer / gold films.

(2) The ERISM measurements are made on a cold anesthetized animal right as it starts to wake up (visible mouth-hooks movement), which presents some difficulty. Why not start imaging while the animal is still completely immobile? Or why not use a dead larva?

This approach allowed us to get measurements of forces exerted by denticles that are physiologically and biomechanically accurate. In dead or fully anesthetized animals, one cannot be sure that the forces exerted by denticles and denticle bands are representative of the forces exerted by an animal with active hydrostatic control.

(3) In the ERISM setup the monochromator is spatially filtered by focusing through pinhole, while in the WARP setup, the LEDs are not.

Yes that’s correct. The LED light sources used in WARP have better spatial homogeneity than the tungsten filament used in ERISM and so a pinhole is not required in WARP.

(4) SV4 shows the interference image of a turning larva (presumably from one illumination wavelength) rather than a reconstruction of the displacement or stresses. Why?

We felt that in this particular case the interference images provided a clearer representation of the behavioural sequence, showing both the small indentations generated by individual denticles and the larger indentations of the animal overall.

Lines 49-50 "a lack of methods with sufficient spatiotemporal resolution for measuring GRFs in freely behaving animals has limited progress." This needs a discussion of what sufficient spatial and temporal resolutions would be and how existing methods fall short of these goals.

We have now rewritten the introduction to include an overview of other alternative approaches and of what we see as the requirements here. See our response to the public comments.

Figure caption 1B (line 789) refers to "concave areas of naked cuticle (black line) which generally do not interact with the substrate" While I think this might be supported by later WARP images, it's not clear how the technique of figure 1 measures interaction, which could e.g. be mediated by surface tension of a transparent fluid.

The technique of Figure 1 provides qualitative information which as the reviewer points out is validated by WARP measurements later.

Lines 184-189 "However, unexpectedly, we observed an additional force on the substrate when protopodia leave the substrate (SI) and when they are replanted (ST). To investigate whether this force was due to an active behaviour or due to shifting body mass, we plotted integrated displacement (i.e. displaced volume) against the contact area for each protopodium, combining data from multiple forwards waves (Figure 5B). Area is correlated with displaced volume for most time points, indicating that volume is a consequence of mass in a 2nd order polynomial relationship." I couldn't follow this argument at all.

We have now reworded this section and explained our rationale. Also see our response to a similar critique in Reviewer 2’s public comments.

Generally the authors might reconsider their use of acronyms. e.g. (244-246) "SI latencies were much more strongly correlated with wave duration across most segments than ST latencies. SIs scale with SwP and this could be mediated by proprioceptor activity in the periphery" is made more difficult to parse by the abbreviations.

As we need to refer to these terms multiple times throughout the manuscript, we feel the use of acronyms is appropriate here.

The video captions are inadequate. Please expand on them to explain clearly what is shown, and also describe in the methods how the data were acquired and processed. For instance, it seems that in SV3 a motion correction algorithm is applied so that the larva appears stationary even as it crawls forward. I think "fourier filtered" means that the images were processed with a spatial high pass filter - this should be explained and the parameters noted.

We have revisited the video captions provided in the supplementary information document and conclude that these contain the important information. The mode of acquisition are described in the methods, e.g. Video 1 and 2 see section in Methods on “Denticle band kinematic imaging” and Videos 3 and 4 see section in Methods on WARP. Supplementary Video 3 does not make use of motion correction; indeed, one can see the larvae moving upwards/forwards in the field of view. We apologize for not explaining the Fourier filtering process for Video 3. We have now modified the video caption to read as follows:

Video SV3. WARP imaging during forwards peristalses.

Video showing high frame rate displacement maps produced by a freely behaving Drosophila larva. Displacement maps were Fourier filtered to make denticulated cuticle more readily visible and projected in 3D to show the effects of substrate interaction. Details of the Fourier filtering procedure were described elsewhere [Kronenberg et al, Nat Cell Biol 19, 864–872 (2017)].

What were the reflectances of the bottom (10 nm Au/Cr) and top (15nm Au) metal layers at the wavelengths used? I imagine the bottom layer should be less than 38%, the top layer higher, and the product of the square of the bottom transmission and the top reflectance coefficients equal to the bottom reflectance (to make the two paths of the interferometer contribute equal intensity), but none of this is stated.

The reflectance of the gold mirrors was studied in detail in prior work on ERISM. See Kronenberg et al, Nat Cell Biol 19, 864–872 (2017). We therefore refrained from adding a complete optical characterization of the ERISM sensors again here. In brief, we found that a reflectance >13% at each Au mirror is required for reliable ERISM measurements.

The description of the gold coated elastomer as a microcavity is confusing to me. Does the light really make multiple round trips between the plates before returning to the detector? The loss of light on each round trip would depend on the reflectance and parallelism of the top and bottom mirrors. From the WARP calculation it's appears that there is only one round trip - a pi/2 phase shift results from the calculation for one round trip: 2pi*2nL 5nm/(630nm)^2, with n = 1.4 and L = 8 microns - if there were two round trips, the phase shift would be pi etc. Would this better be described as a mostly common path interferometer?

The physics of our devices is best described within the framework of thin film interference and (weak) microcavity optics. Indeed, light can make multiple roundtrips, though it gets attenuated with each reflection. The complete calculation of the multiple roundtrips is only required to obtain quantitative information on the amount of light that is reflected. The spectral position of minima in reflectance can also be obtained from assuming one roundtrip which is what is done in the description of the WARP calculations.

Figure 2 e,f: the line fits appear to be dominated by the data points at 2 s. If these are removed, do the fits change? To support the argument that 2e shows a correlation and 2f does not, some kind of statistical test, ideally a hierarchical bootstrap, should be conducted to compare between the two measurements.

If we remove the data points at 2 s, then R^2’s for swing initiation latencies change as follows: A2: 0.35 to 0.005; A4: 0.78 to 0.31; A6: 0.61 to 0.01. The data in 2e,f are the averages from 3 waves in each animal and so the data points at 2 s are not simply the result of single ‘rogue’ waves but rather averages of several trials. Further, if all individual waves are plotted, we can see that the overall trends are still visible.

We don’t think it is appropriate to remove the data at 2 s from our analysis, but we take the point regarding statements about presence or absence of correlation in a formal sense. We have therefore changed the wording in the description of 2e,f to refer simply to the fact that wave duration can ‘largely determine' latencies in some instances, but is less able to in other instances, as is suggested by the R^2 (coefficient of determination) data. In discussion, we have also adjusted our wording.

Figure 4 - please provide in the main figure or as a supplement the full images (i.e. not cropped to the assumed shape of the larva)

We do not feel that it is necessary or helpful to provide the full images given that the focus of the analysis is on dynamics of protopodia movements.

Figure 5e top: single data points around wave duration 0.6s appear to dominate fit lines. Does removing these points alter the fits? To support the argument that 5e top shows a correlation and 5e bottom does not, some kind of statistical test, ideally a hierarchical bootstrap, should be conducted to compare between the two measurements.

In Figure 5e, we are showing all waves analysed across animals. If we remove the datapoints at 0.6 s, A2 R^2 changes from 0.24 to 0.05, A4 R^2 changes from 0.48 to 0.11, A6 R^2 changes from 0.69 to 0.34; however we don’t feel it is appropriate to remove these data from our analysis. We take the point about needing to be cautious about making claims about correlation versus no correlation and have now reworded description of these results along same lines as Figure 4.

It appears from the methods (467-489) that animals were kept wet for warp imaging but not for ERISM imaging. Please confirm or explain further the presence or absence of a water layer in these two sets of measurements, as this could affect the adhesion forces.

In each case, the animals were transferred onto experimental substrates with a moistened paintbrush. We have added text explicitly stating this in the methods section.

Kim et al. Nature Methods 2017 (10.1038/nmeth.4429) describes recording two images separated by less than 60 microseconds using a scientific CMOS camera with a frame rate of 200 Hz. This is accomplished by triggering a pulsed LED once at the end of one frame's capture window and then a second time at the beginning of the next frame's window (see Supplementary Figure 10). I'm not sure if this trick is widely known, but it's worth considering if the authors are running into a problem with movement between the two wavelength exposures in their WARP setup.

Thank you for this tip. We will take this under consideration for future work.

Is the setup compatible with optogenetics? (EG is the red light dim enough that it wouldn't activate CsChrimson, or could a longer wavelength led be used for interferometry?) If so, activation of mooncrawler descending neuron (MDN) could be used to study backward crawling (or thermogenetic activation of MDN), e.g. to contrast the sites and order of "anchoring" between the two directions of crawling.

The set-up is potentially compatible with optogenetics. We are in the process of exploring this in current ongoing work.

Reviewer #2 (Recommendations For The Authors):

Simplify/reduce the commentary about force measurements, and highlight the clear, qualitative descriptions of the novel locomotion patterns that they have observed. The microscopy and movements seem to matter more than the ground force estimations.

We have addressed these issues in our responses to Reviewer 2’s public comments.

Reviewer #2 (Public Review):

The biology and dynamics is well-described. The ERISM and WARP methods are state-of-the-art. The most important new information is the highly accurate and detailed maps of displacement. The real achievements are the new locomotory dynamics uncovered with amazing displacement measurements. One key discovery is the broad but shallow anchoring of the posterior body when the anterior body undertakes a "head sweep". Another discovery is the tripod indentation at the tail at the beginning of peristalsis cycles. This paper describes the detailed dynamics of anchoring for the first time. Anchoring behavior now has to be included in the motor sequence for Drosophila larva locomotion in any comprehensive biomechanical or neural model.

Problematic if you're going to go to war in a couple years - need to be able to receive your commands

Visual in my head of some prepubescent kid making fart noises into his radio set, and a Navy operator on the other end losing his mind

n this passage the angel Abdiel is speaking. He rejects Satan's cause, claiming "I see thy fall / determin'd" (5.878-9), correctly prophesising the failure of the rebel angels. Furthermore, he warns Satan of Godís wrath, claiming that "[the] Golden Sceptre which thou didst reject / is now an Iron Rod to bruise and break / thy disobedience" (5.886-8).

The inclusion of Abdiel acts as a tool for Milton to undermine the cause of Satan. By creating an angel who is able to realize Satan's goals are a "perfidious fraud" (5.880), God's righteousness is confirmed. After the initial schism in Heaven, none of the angels which sided with God defect to Satan's army. In contrast the sole defector of Satan's followers, Abdiel, creates doubt within the fall angels' argument. Including dissent within Satan's legions completely undermines his legitimacy as a rebel with a just cause. Therefore, one can assume that the rebellious angels are inherently evil and that God's cause is righteous.

Superior Glenohumeral ligament: 0 abduction, resisits anterior and inferior translation The middle glenohumeral ligament: 45 degrees abduction limits anterior translation Inferior Glenohumeral ligament: 90 abduction, resisits inferior translation of the humeral head. anterior band stops 90/90 ER Posterior band stops 90/90 IR

unknown word 1: a bump, blow, or jolt to the head that does not cause symptoms

you can feel his hurt and rage. He had had enough. The details helped me to feel what he was feeling.

seems as though Richard was an aggressive player and penalties were deserved

it takes a lot of strength to carry a 200 pound man across your shoulders/ back. Shows a lot of strength and commitment to the sport

If they knew he had a problem with anger and violence, why didn't they address it more aggressively and make him get help before all hell broke loose.

This represents the spread of long-distance communication and the initial invention that led to the creation of many other operations involving the telephone. This did not take as long as I thought especially when technology was at its infancy.

UGHGHGHHIFKKKKKKR408JX,.KLPSFIOEW8 US,C;FLZDODJNZKC,SN ./XID.HZFJZMX SFYUKD

UGHGH THIS IS SO IN CHARACTER THOO

oh he's WINNING

WOAH

yas overthinking

girl he's head over heels for you

oh he is BEGGING for more

he's real too sometimes

NOOOO stop the presentation is probably about her

nooo her mask shatters

oof

OH THEYRE SO USELESS

Reviewer #1 (Public Review):

Strengths:

- The paper is clearly written, and all the conclusions stem from a set of 3 principles: circular topology, rotational symmetry, and noise minimization. The derivations are sound and such rigor by itself is commendable.

- The authors provide a compelling argument on why evolution might have picked an eight-column circuit for path-integration, which is a great example of how theory can inform our thinking about the organization of neural systems for a specific purpose.

- The authors provide a self-consistency argument on how cosine-like activity supports cosine-like connectivity with a simple Hebbian rule. However, their framework doesn't answer the question of how this system integrates angular velocity with the correct gain in the absence of allothetic cues to produce a heading estimate (more on that on point 3 below).

Weaknesses:

- The authors make simplifying assumptions to arrive at the cosine activity/cosine connectivity circuit. Among those are the linear activation function, and cosine driving activity u. The authors provide justification for the linearization in methods 3.1, however, this ignores the well-established fact that bump amplitude is modulated by angular velocity in the fly head direction system (Turner-Evans et al 2017). In such a case, nonlinearities in the activation function cannot be ignored and would introduce harmonics in the activity. Furthermore, even though activity has been reported to be cosine-like, in fact in the fruit fly it takes the form of a somewhat concentrated activity bump (~80-100 degrees, Seelig & Jayaraman 2015; Turner-Evans et al 2017), and one has to take into account the smoothing effect of calcium dynamics too which might make the bump appear more cosine-like. So in general, it would be nice to see how the conclusions extend if the driving activity is more square-like, which would also introduce further harmonics. Overall, it would be interesting to see whether, despite the harmonics introduced by these two factors interacting in the learning rule, Oja's rule can still pick up the "base" frequency and produce sinusoidal weights (as mentioned in methods 3.8). At this point, the examples shown in Figure 5 (tabula rasa and slightly perturbed weights) are quite simple. Such a demonstration would greatly enhance the generality of the results.

- The match of the theoretical prediction of cosine-like connectivity profiles with the connectivity data is somewhat lacking. In the locust the fit is almost perfect, however, the low net path count combined with the lack of knowledge about synaptic strengths makes this a motivating example in my opinion. In the fruit fly, the fit is not as good, and the function-fitting comparison (Methods Figure 6) is not as convincing. First, some function choices clearly are not a good fit (f1+2, f2). Second, the profile seems to be better fit by a Gaussian or other localized function, however the extra parameter of the Gaussian results in the worst AIC and AICc. To better get at the question of whether the shape of the connectivity profile matches a cosine or a Gaussian, the authors could try for example to fix the width of the Gaussian (e.g. to the variance of the best-fit cosine, which seems to match the data very well even though it wasn't itself fit), and then fit the two other parameters to the data. In that case, no AIC or AICc is needed. And then do the same for a circular distribution, e.g. von Mises. In addition, the theoretical prediction of cosine-like connectivity is not clearly stated in the abstract, introduction, or discussion. As a prediction, I believe it should be center forward, as it might be revisited again in the future in lieu of e.g. new experimental data.

- I find the authors' claim that Oja's rule suffices to learn the insect head direction circuit (l. 273-5) somewhat misleading/vague. The authors seem to not be learning angular integration here at all. First, it is unclear to me what is the form of u(t). Is it the desired activity in the network at time t given angular velocity? This is different than modelling a population of PEN neurons jointly tuned to head direction and angular velocity, and learning weights so as to integrate angular velocity with the correct gain (Vafidis et al 2022). The learning rule here establishes a self-consistency between sinusoidal weights and activity, however, it does not learn the weights from PEN to EPG neurons so as to perform angular integration. Similar simple Hebbian rules have been used before to learn angular integration (Stringer et al 2002), however, they failed to learn the correct gain. Therefore, the authors should limit the statement that their simpler learning rule is enough to learn the circuit (l. 273-5), making sure to outline differences with the current literature (Vafidis et al 2022).

Author Response

Reviewer #1 (Public Review):

Strengths:

• The paper is clearly written, and all the conclusions stem from a set of 3 principles: circular topology, rotational symmetry, and noise minimization. The derivations are sound and such rigor by itself is commendable.

• The authors provide a compelling argument on why evolution might have picked an eight-column circuit for path-integration, which is a great example of how theory can inform our thinking about the organization of neural systems for a specific purpose.

• The authors provide a self-consistency argument on how cosine-like activity supports cosine-like connectivity with a simple Hebbian rule. However, their framework doesn't answer the question of how this system integrates angular velocity with the correct gain in the absence of allothetic cues to produce a heading estimate (more on that on point 3 below).

Weaknesses:

• The authors make simplifying assumptions to arrive at the cosine activity/cosine connectivity circuit. Among those are the linear activation function, and cosine driving activity u. The authors provide justification for the linearization in methods 3.1, however, this ignores the well-established fact that bump amplitude is modulated by angular velocity in the fly head direction system (Turner-Evans et al 2017). In such a case, nonlinearities in the activation function cannot be ignored and would introduce harmonics in the activity.

We thank the reviewer for pointing out this omission. We added a paragraph at the end of section 4.1 clarifying that transient non-linearity, for instance when the circuit is actively receiving external input, is compatible with our work because we only need linearity in the line attractor, but not outside (lines 407-419).

“In more intuitive terms, the neurons have a saturating nonlinear activation function where they modulate their gain based on the total activity in the network. If the activity in the network is above the desired level, r, the gain is reduced and the activity decreases, and when the activity of the network is less than desired level, both the gain and the activity increase. Note that in this scenario transient deviations from the line attractor, which would induce nonlinear behaviour in the circuit dynamics, are tolerable. External inputs, u(t), could transiently modify the shape of the activity, producing activity shapes deviating from what the linear model can accommodate. For example, the shape of the bump attractor could be modified through nonlinearities while the insect attains high angular velocity (Turner-Evans et al., 2017).

Such nonlinear dynamics do not conflict with the theory developed here, which only requires linearity when the activity is projected onto the circular line attractor. In our framework, the linearity of integration at the circular line attractor is not a computational assumption, but rather it emerges from the principle of symmetry.”

Furthermore, even though activity has been reported to be cosine-like, in fact in the fruit fly it takes the form of a somewhat concentrated activity bump (~80-100 degrees, Seelig & Jayaraman 2015; Turner-Evans et al 2017), and one has to take into account the smoothing effect of calcium dynamics too which might make the bump appear more cosine-like. So in general, it would be nice to see how the conclusions extend if the driving activity is more square-like, which would also introduce further harmonics.

We added a cautionary comment on the sinusoidal activity (lines 222-226).

“We note, however, that data from the fruit fly shows a more concentrated activity bump than what would be expected from a perfect sinusoidal profile (Seelig and Jayaraman, 2015; Turner-Evans et al., 2017), and that calcium imaging (which was used to measure the activity) can introduce biases in the activity measurements (Siegle et al., 2021; Huang et al., 2021). Thus the sinusoidal activity we model is an approximation of the true biological process rather than a perfect description.”

Overall, it would be interesting to see whether, despite the harmonics introduced by these two factors interacting in the learning rule, Oja's rule can still pick up the "base" frequency and produce sinusoidal weights (as mentioned in methods 3.8). At this point, the examples shown in Figure 5 (tabula rasa and slightly perturbed weights) are quite simple. Such a demonstration would greatly enhance the generality of the results.

We also extended the self-consistency framework from Oja’s rule to the non-linear case, and found that while Oja’s rule with non-linear neurons would not give pure harmonics, the secondary harmonics will remain small. We added a sentence explaining this in the main text (section 2.4, lines 309-312) and a methods section to develop the self-consistency framework for the case of non-linear activations (section 4.7.2).

“For neurons with a nonlinear activation function, secondary harmonics would emerge, but would remain small under mild assumptions, as shown in Section 4.7.2. Oja’s rule will still cause the weights to converge to approximately sinusoidal connectivity.”

• The match of the theoretical prediction of cosine-like connectivity profiles with the connectivity data is somewhat lacking. In the locust the fit is almost perfect, however, the low net path count combined with the lack of knowledge about synaptic strengths makes this a motivating example in my opinion. In the fruit fly, the fit is not as good, and the function-fitting comparison (Methods Figure 6) is not as convincing. First, some function choices clearly are not a good fit (f1+2, f2). Second, the profile seems to be better fit by a Gaussian or other localized function, however the extra parameter of the Gaussian results in the worst AIC and AICc. To better get at the question of whether the shape of the connectivity profile matches a cosine or a Gaussian, the authors could try for example to fix the width of the Gaussian (e.g. to the variance of the best-fit cosine, which seems to match the data very well even though it wasn't itself fit), and then fit the two other parameters to the data. In that case, no AIC or AICc is needed. And then do the same for a circular distribution, e.g. von Mises.

We also included the fit with von Mises and Gaussian with the width parameters fixed to match the cosine as the reviewer suggested. We found that even though these two distributions fit the data better, the difference is very small (2%), probably due to the high variability of the fruit fly connectome data. We also changed the wording and state that the theory is compatible with experimental data.

In the Methods 4.6 (lines 568-585), we wrote

“As a complementary approach to evaluate the shape of the distribution, we first fit the Gaussian and von Mises distributions to the best fit f = 1 curve. We then freeze the width parameters of the distributions (σ_g for the Gaussian and κ_v for the von Mises) and only optimise the amplitude and vertical offset parameters (β and γ) to fit the data. This approach limits the number of free parameters for the Gaussian and von Mises distributions to two, to match the sinusoid. The results are shown in Methods Fig. 6 and Table 5. Both the fixed-width Gaussian and von Mises distributions are a slightly better fit to the data than the sinusoid, but the differences between the three curves are very small.

In simplifying the fruit fly connectome data, we assumed all synapses of different types were of equal weight, as no data to the contrary were available. Different synapse types having different strengths could introduce nonlinear distortions between our net synaptic path count and the true synaptic strength, which could in turn make the data a better or worse fit for a sinusoidal compared to a Gaussian profile. As such, we don’t consider the only 2% relative differences between the f = 1 sinusoid and fixed-width Gaussian and von Mises distributions to be conclusive.

Overall, we find that the cosine weights that emerge from our derivations are a very close match for the locust, but less precise for the fly, where other functions fit slightly better. Given the limitations in using the currently available data to provide an exact estimate of synaptic strength (for the locust), and due to the high variability of the synaptic count (for the fruit fly), we consider that our theory is compatible with the observed data.”

In addition, the theoretical prediction of cosine-like connectivity is not clearly stated in the abstract, introduction, or discussion. As a prediction, I believe it should be center forward, as it might be revisited again in the future in lieu of e.g. new experimental data.

We added the explicit prediction in the abstract and the introduction (lines 52-53).

• I find the authors' claim that Oja's rule suffices to learn the insect head direction circuit (l. 273-5) somewhat misleading/vague. The authors seem to not be learning angular integration here at all. First, it is unclear to me what is the form of u(t). Is it the desired activity in the network at time t given angular velocity? This is different than modelling a population of PEN neurons jointly tuned to head direction and angular velocity, and learning weights so as to integrate angular velocity with the correct gain (Vafidis et al 2022). The learning rule here establishes a self-consistency between sinusoidal weights and activity, however, it does not learn the weights from PEN to EPG neurons so as to perform angular integration. Similar simple Hebbian rules have been used before to learn angular integration (Stringer et al 2002), however, they failed to learn the correct gain. Therefore, the authors should limit the statement that their simpler learning rule is enough to learn the circuit (l. 273-5), making sure to outline differences with the current literature (Vafidis et al 2022).

We agree and we clarified that we focus only on the self-sustained activity condition. We appended the following text to the first and last paragraphs of section 2.4.

For the first (lines 279-284): “Our approach follows from previous research which has shown that simple Hebbian learning rules can lead to the emergence of circular line attractors in large neural populations (Stringer et al., 2002), and that a head direction circuit can emerge from a predictive rule (Vafidis et al., 2022). In contrast to this work, we focus only on the self-sustaining nature of the heading integration circuit in insects and show that our proposed sinusoidal connectivity profile can emerge naturally.”

For the last (lines 317-321): “However, this learning rule only applies to the weights that ensure stable, self-sustaining activity in the network. The network connectivity responsible for correctly integrating angular velocity inputs (given by the PEN to EPG connections in the fly) might require more elements than a purely Hebbian rule (Stringer et al., 2002), such as the addition of a predictive component (Vafidis et al., 2022).”

eLife assessment

This important work suggests that the observed cosine-like activity in the head direction circuit of insects not only subserves vector addition but also minimizes noise in the representation. The authors provide solid evidence using the locust and fruit fly connectomes. The work raises important theoretical questions about the organization of the navigation system and will be of interest to theoretical and experimental researchers studying navigation.

People can judge it all they want, but positive visualization has been studied. Rather than focusing on, "oh, God, this is scary," you focus on the task itself and doing the best you can. We as people tend to get stuck in our head. We get wrapped up in, "what if." Don't focus on what if. Envision yourself in a positive light, and your results will be more positive because the stress has faded.

This makes a lot of sense. I know before I do my speech, I'm going to practice it in front of my family. I know that practice makes perfect, and the more I go through it, both in my head, and out loud it will help tremendously. My fear is that I will forget the things in my speech that aren't written down. I think this communication class is going to help me work on my public speaking, and my confidence as well.

Hockey is crazy violent all of the time. I couldn't imagine seeing this degree of violence in any other sport.

He has let himself act too human. He needs to tell Ran that he can never be human. He's gotten Ran too used to it.

Again, the persona shows how difficult it is to abandon this relationship that she cherishes, because of all the fond memories that she remembers with her partner, and she remembers each memory so clearly that she still "see it in all in my head". When someone cherishes the memories of someone else, it is definitely almost not possible to completely forget about it and pretend like nothing has happened before. This shows how precious the persona's lover was to her, such that when they broke up, she still feels a sense of reluctance for giving up on him and a sense of great difficulty to attempt to forget about him. I feel a sense of sympathy for the persona as it is understandable to experience a deep struggle to forget a loved one; she constantly tries to forget him to prevent herself from getting more depressed, but it is just not easy to forget him due to how much she has loved him. I can reflect on the theme of love, showing how strong of a negative and painful impact love can leave on someone forever.

In the end, the persona still cannot forget about her lover, showing simply how much of an importance the persona places him in her heart. Her lover and their relationship will continue to be left reminded in her mind, leaving a permanent scar on her as shown by "Comes back to me, burning red". The rhyme of "head" and "red" also emphasises on the overwhelming negative emotions throughout their relationship which will in turn impact her even in the present after they broke up, showing how this relationship leaves a long-lasting impact on her. This negative memory to her seems like a harsh reminder of how much she has once loved someone but eventually broke up due to conflicts. And since this memory is thought actively throughout in her mind, the persona will only just feel a sense of regret and grief that she has lost her partner. This leads me to reflect on the theme of regret, as we should not do things in the present that would hurt others, especially our loved ones, which would in turn lead us to an irreparable emotional damage for a lifetime as it is not easy to forget about such things easily.

“Not the same without your head on my shoulders” reveals that the writer is unable to sleep due to him missing someone dearly and being unable to rest and relax without his or her touch. The phrase “Not the same” shows how everything has seemingly changed since she has left and shows the contrast between the happiness of being with her and the sadness now of being alone.

The phrase “growing pains” and “don’t wanna get older” shows that as he grows older things seem to be more difficult, and thus he feels that he wants ‘stop growing’ as a way to put an end to all the new problems and challenges he faces as he grows up.

The persona is using another simile which is identified by the word "like". The literal meaning refers to Elsa's (The character played by the persona) thoughts form as suddenly in her head as snowflakes do in the cold wind.

ROM

Setting

ROM

PRE: suggests the head chopping contest that will follow

At my school, there are chromebooks in most classrooms, so every student has access to a laptop during the school day. But when students head home, that's where the divide starts to show itself. I know of students who don't have computer access at home. As teachers, we need to keep in mind the challenges some students are facing in regard to the way we assign work.

• A "headstart" suggests that the listener provides the speaker with an advantage or initial momentum in pursuing their goals. “Rugged heart” implies that they have strong and resilient values, which serves as a source for the strength and inspiration for the speaker. These metaphors serve as an admiration for the listener. As “head start” signifies the listeners contribution to the speakers success, while “rugged heart” underscores the resilience shown towards challenges faced in life. This line showcases the theme of inspiration and support.

The line “Revolutionaries wait for my head on a sliver plate.” This is a metaphor and this tells me that the revolutionaries hated him and wanted to behead and kill him .

I have had a similar experience to hers, and I believe many students share a similar feeling at some point during their academic careers. In my case, I was excited to raise my hand in a class even though I rarely spoke because the content was difficult. However, a boy shouted out the answer, and the teacher moved on without acknowledging my attempt. I felt disheartened at that moment, and afterward, I lost my focus until the end of the class.

Metaphor: Keeping your head held high in the face of adversity represents confidence and resilience.

Personification: The voice is presented as a separate entity, capable of speaking, despite being a metaphor for one's inner thoughts or conscience.

Note: This response was posted by the corresponding author to Review Commons. The content has not been altered except for formatting.

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Reply to the reviewers

We would like to sincerely thank both reviewers for taking the time to examine our work, for the cogent points they have raised, and their constructive attitude aimed at improving our manuscript.

Reviewer #1

• Single-cell RNAseq (Fig. 1B) and in situ (Fig. 3D) results both indicate that SNHG7 is broadly expressed in multiple epidermal layers but more enriched in the spinous layer. Although most assays, such as colony formation and Ki67 staining, did not specifically examine the role of SNHG7 in the spinous layer, the raft culture experiment seemed to indicate specific reduction of the spinous layer (Fig. 3H), which was more prominent than basal defects. The authors should examine the defects more carefully in the raft culture system by using basal, spinous and granular markers. It is possible that SNHG7 functions to maintain limited cell proliferation while restrict premature differentiation. In addition, they should perform serial passage experiments to distinguish whether overexpression of SNGH7 can indeed confer self-renewal in long-term experiments.*

We have included staining of a range of epidermal markers in the raft cultures (ITGB1, K14, K10 and IVL) in the revised manuscript (Fig. S6B). We do not observe major changes in the distribution of any of the differentiation markers.

In terms of serial passage, we have cultured SNHG7-overexpressing or control cells for multiple passages until their growth capacity was exhausted. The SNHG7-overexpressing cells grew for approximately seven more passages than the control cells. We have added this information to the revised manuscript (Fig. S6L).

• The main proposed mechanism is the sequestration of miR34 by SNHG7. While miR34 is well known for its function in inhibiting cell proliferation, the ability of coding or noncoding RNA to sequestrate miRNAs is highly dependent on the stability and copy number of these RNAs. Since they have single-cell data with UMI information, they should estimate the copy number of SNHG7 in epithelial cell populations, and this could provide a range for the "buffering" capacity of SNHG7. They should also examine, ideally by in situ hybridization, the expression patterns of miR34 in human vs mouse skin. While miR34 expression can be induced by p53 activation, it is possible that its expression varies in different species. It'll be interesting to determine whether the lack of miR34 expression in mouse keratinocyte or mouse skin could explain the insensitivity of mouse keratinocytes to SNHG7. Finally, to further demonstrate the competition between SNHG7 and miR34 targets, they can use a heterologous luciferase reporter system with a canonical miR34 targeting site in the 3'UTR and quantify luciferase activities with or without SNHG7 (or SNHG7 mut34 variant). This assay could quantify the impact of SNHG7 on individual miR34 targets.*

We will include the analysis of the scRNAseq data to estimate the copy number of SNHG7 in the epidermal populations.

We will also perform in situ hybridization staining for miR-34 in human and mouse epidermis as well as mouse keratinocytes.

Finally, we will carry out the luciferase reporter experiments.

Reviewer #2

Major comments:

1) The premise of the study relies on the observation that SNHGs have low levels of sequence conservation. Indeed the authors aim to prove that biological functions can be identified even in the absence of evolutionary conservation. However, the extent of evolutionary conservation strongly depends on the phylogenetic scale at which it is analyzed. Here, the authors evaluate sequence conservation using PhastCons and PhyloP scores determined using alignments of human and 99 other vertebrate species. These scores reflect the extent of long-term sequence conservation. At this scale, only a small percentage of the human genome can be considered to be "conserved". It is thus not surprising that SNHG and other lncRNAs are not conserved at this scale, even if they carry some biological functions in the human genome. Here, it would be useful to redo the sequence conservation analyses using PhastCons and PhyloP scores computed on less distant species. Pre-computed scores exist for alignments containing human and other mammalian species, mainly primates (UCSC genome browser). It would also be good to provide comparisons of sequence conservation levels on the snoRNA genes and on the non-snoRNA parts of SNHGs. In addition to protein-coding genes, pseudogenes and lncRNAs, it would be good to add a perfectly neutral control for the sequence conservation in Figure 1C - for example, flanking intergenic regions for SNHGs. It might also be a good idea to analyze the GC content of SNHGs compared to other lncRNAs, since GC content can be correlated with sequence conservation levels, in particular in noncoding regions.

Importantly, the SNHG selected for detailed investigation (SNHG7) appears to be more conserved than the bulk of human lncRNAs, given that it is found in another primate and in mouse. It would be interesting to analyze in details what sequence features of this lncRNAs are conserved among species - for example, are the SNHG7 splice sites and promoter regions conserved? Are the snoRNA genes always located in the introns?

The reviewer raises very good points. We have added the conservation data of snoRNA genes (all or SNHG-resident, both significantly more conserved than SNHGs or lncRNA), and a “true neutral” control (we used the introns of 10,000 randomly sampled genes) to our PhastCons analysis (Fig.1C). We also added a conservation analysis of the promoters (defined as the 500 bp upstream of the transcription start site) of coding genes, pseudogenes, lncRNA and SNHGs (Fig, S1B). We have now performed all our conservation analyses using both PhastCons scores generated from the 100-vertebrate alignment and PhastCons scores generated from the 30-mammals (28 primate) alignment (Fig. S1E-G). We do not detect any marked difference between the two alignment sets. We have also added a comparison of the GC content in lncRNA, SNHGs, coding genes and introns (Fig.S1C).

Due to the nature of the PhyloP scores, the 30-mammal PhyloP track (phyloP30) would be unsuitable to detect additional conservation in the primate lineage using the thresholding analysis we employed in Fig. 1E. The PhyloP track gives base-wise p-values for conservation (positive values) or accelerated evolution (negative values). Using alignments of genomes that are overall more similar to each other (as in the 30-mammal alignment set) makes it more difficult to distinguish between conserved and neutrally evolving regions, because even segments that are not under constraint will look relatively similar due to the evolutionary proximity of the species in the set. For the same reason this alignment set is quite sensitive to accelerated evolution, as it contains many relatively similar genomes it the alignment.

This causes the PhyloP30 scores to be very asymmetrical around zero: the conservation (positive) scores never reach 2 (p-value of 0.01) in the whole track (not even coding regions of very well-conserved genes), while acceleration scores can reach very significant values, down to -20. Conversely, the PhyloP100 track (used in Fig.1E) is quite symmetrical around 0 and is thus better suited for the purposes of the analysis in Fig.1E, which are to detect both conserved and accelerated portions of SNHGs. We have however also inspected the PhyloP30 track manually and do not observe any clear evidence of presence of additional conserved elements in SNHG7. We have added all conservation tracks for SNHG7 to Fig. 3A.

While lncRNA orthologs can be identified by using a combination of sequence conservation, conserved synteny with surrounding genes and in some cases conserved gene structure, SNHG orthologs can additionally be identified by the embedded (conserved) intronic snoRNA sequence, which makes them easier to find even when the transcript sequence bears no similarity across species. The mouse SNHG7 sequence, for example, does not match with human SNHG7 even using the least stringent BLAST parameters. The monkey sequence is similar enough to match with the human in the 3’ of the gene, but the intron-exon structure of the 5’ is completely different. We agree with the reviewer’s assessment, however, when it comes to identification of SNHG orthologs in more evolutionary distant species, closer to the root of the vertebrate clade.

Regarding splice sites, they are often conserved among lncRNA in general (gene structure conservation occurs more frequently than sequence conservation, see Ulitsky, Nat Rev Genet, 2016). In the case of SNHG7 the structure of the gene appears conserved in the mouse (though this annotation has likely not been fully confirmed experimentally), and in the monkey based on genome alignments. However, our RACE experiments show that the 5’ end of SNHG7 in the monkey has a radically different splicing pattern when compared to human, so it is difficult to assess splicing conservation in the absence of full isoform characterization.

2) I am not perfectly convinced by the enrichment of miRNA target genes among the genes that are downregulated upon SNHG knockdown. The methods do not clearly explain how this enrichment is calculated. What is the background used for this enrichment analysis? In Figure 5C, we see that the genes predicted to be targeted by the top 10 microRNAs tend to have negative fold changes in the differential expression analysis (downregulation following knockdown). However, from Figure 5A it seems that the great majority of significantly differentially expressed (DE) genes have negative fold changes. How do the miRNA target genes differ from all other DE genes? What proportions of all predicted miRNA target genes (expressed in keratinocytes) are DE following knockdown, and how does this compare with the target genes of other miRNAs?

We have added a description of the statistical test used by MIENTURNET for the enrichment analysis to the methods section. More details can be found in the original publication. The significance of the enrichment is calculated by performing a hypergeometric test using as background the total number of miRNA-target interactions in the database and the total interactions the individual miRNA being tested engages in.

Figure 5C only includes the genes we used in our enrichment analysis (i.e. the significantly downregulated genes, not all DE genes) and it’s meant to show the extent of downregulation exhibited by the targets of the most significantly enriched miRNAs within this group of genes.

The reviewer is correct in pointing out that the imbalance between downregulated and upregulated genes (which we now further highlight in the plots in Fig. 5A-B) will tend to skew any group of genes towards having a relatively large number of downregulated genes. However, we found this bias to be particularly strong in the case of our candidate miRNAs. We now show this in volcano plots for validated targets of the candidate miRNAs and a control miRNA (Fig. S8E). In a similar way, when looking at the cumulative distributions of the fold changes of all predicted targets for a certain miRNA and comparing it to the fold change cumulative distribution of all other genes, our candidate miRNAs displayed a more pronounced shift towards downregulation than the control miR-21-5p (which we now added in Fig. S8F).

3) If keratinocyte RNA-seq data is available for other species (for example mouse), it would be interesting to test whether the high expression levels of SNHG7 and the other analyzed SNHGs are also conserved in the other species.

We will include the RNA-seq data, if available.

Minor comments:

1) The AD (atopic dermatitis) abbreviation should be explained the first time it is mentioned in the text.

We thank the reviewer for pointing out the missing abbreviation, we have now added it.

2) More details are needed regarding the MIENTURNET analyses in the methods and in the main text

We have added more details about the statistics involved to the methods (see above).

*3) Figure 5C, it is not clear how to interpret the color code for the boxplot. Does this represent the median or mean FDR of the target genes? Are only genes with FDRThe genes included in the enrichment analysis are all downregulated genes with an adjusted p-value (or FDR adjustment after the Wald test) adj”. The color scale in Fig 5C reports the significance of the enrichment for targets of the single miRNAs within the significantly downregulated genes list (FDR adjustment after the hypergeometric test), not the significance of the downregulation itself. FDR values are also used for all other enrichment analyses (GO terms, REACTOME Pathways). We apologise to the reviewer for the confusion, we have now modified the text and figures to make this clearer.

4) Figure 6D, I am not sure how to the D panel. Do the gray rectangles represent the exonic length of the SNHGs? Do the dots correspond to the positions of the miRNA target sites? Here, a more quantitative comparison with the extent of sequence conservation of miRNA binding sites in SNHGs, other lncRNAs and in protein-coding genes would be perhaps better suited.

The grey rectangles in Fig. 6D represent the total exonic length of the SNHGs (basically all exons are “stitched together” head to tail irrespective of the actual isoforms) and the dots represent the positions of the miRNA binding sites within this “maximum exonic coverage”. Since not all individual isoforms are analysed it is possible that some additional miRNA sites can be created at alternatively spliced junctions, however we would estimate the number of such sites to be small. We have added this caveat to the methods section.

The degree of conservation that is estimated by TargetScan to underlie a functional MRE in coding genes is taken into account in this analysis, as sites within SNHGs that pass this threshold are highlighted with yellow borders in the figure. We have now added a plot of the distribution of Branch length scores for MREs in SNHGs and the distribution of Branch length scores for MREs in a random sample of 250 Coding genes UTRs (Fig. S9E). A similar comparison for lncRNA is more challenging as the data is not readily available and is likely to be confounded by the nuclear localisation of a majority of lncRNA species.

I can hear myself breathing louder and louder

• The repetition of “louder” reveals how Bocchi can only hear herself in her life, strongly emphasise on how alone she feels. This is further supported by how she “can’t hear the sounds of the world”. Bocchi wrote this with the intent of implying that she can hear her breathing or rather the sounds that she make louder than the sounds the world make. This once again conveys how disconnected and isolated Bocchi feels from the rest of society. The use of diction in “strange” also strongly conveys this idea. Bocchi wrote previously that she tends to compare herself to society and its expectations or more specifically her perspective of society and its expectations. Thus it should be reasonable to conclude that Bocchi wrote the word “strange” to clear show the differences between herself and the world.

• Bocchi’s “breathing” can also be a metaphor for her thoughts and emotions, how they seem to spiral and get more and more overwhelming. In fact, if her “breathing” are her thoughts than it could also emphasise Bocchi’s desire to let it out, which could explain why they are getting louder and louder as she bottles her “breathing” or thoughts up.

I can’t hear the sounds of the world

• The “sound” symbolises how much Bocchi feels connected to society and so if she cannot hear the sounds of the world, it emphasises how outcasted she feels and how lonely she feels. This quote can also be treated as an auditory imagery, giving listeners the sense of complete quietness. This conveys how empty Bocchi feels because of her lack of connection to society.

Main message in Pre-Chorus

• I think the main message of this pre-chorus is to emphasise how Bocchi feels like her life is a mess and this is more obvious in the anime where Bocchi can be seen with a lot of interesting daydreams, such as her being chained to a wooden pole as thousands of people chant and walk around her with bright burning torches (pls watch the anime). Her head is constantly filled with potential scenarios and “what ifs”, revealing her overthinking nature. It also conveys how Bocchi feels lost and have no idea what to do with this mountain of information.

• The diction and tactile imagery of “pressure” emphasises the discomfort Bocchi feels as a result of the “information”. It conveys how Bocchi doesn’t want this “pressure” which based on the previous quotes could be society’s expectations or in later verses her social anxiety. This also emphasises how Bocchi feels that her mind is a mess. It gives listeners the idea that there is so much information in her head and that it is negatively affecting her.

• The high word intensity of the word “suffocating” then goes on the emphasise Bocchi’s suffering and pain as she processes whatever the “information” is. It convey’s how the pressure of this information is almost killing Bocchi emotionally, how she is unable to breathe and take a break. It gives listeners the idea that Bocchi is exhausted, that she is tired of having to withstand the pressure of this information. “Suffocating” can also be a metaphor for how Bocchi is unable to breathe or that she has to bottle up these emotions. This act of isolation from others will then be further elaborated and developed later on in the song.

Author Response

The following is the authors’ response to the original reviews.

eLife assessment

The manuscript from Richter et al. is a very thorough anatomical description of the external sensory organs in Drosophila larvae. It represents an important tool for investigating the relationship between the structure and function of sensory organs. Using improved electron microscopy analysis and digital modeling, the authors provide compelling evidence offering the basis for molecular and functional studies to decipher the sensory strategies of larvae to navigate through their environment.

Public Reviews:

Summary

This is a very meticulous and precise anatomical description of the external sensory organs (sensillia) in Drosophila larvae. Extending on their previous study (Rist and Thum 2017) that analyzed the anatomy of the terminal organ, a major external taste organ of fruit fly larva, the authors examined the anatomy of the remaining head sensory organs - the dorsal organ, the ventral organ, and the labial organ-also described the sensory organs of the thoracic and abdominal segments. Improved serial electron microscopy and digital modeling are used to the fullest to provide a definitive and clear picture of the sensory organs, the sensillia, and adjacent ganglia, providing an integral and accurate map, which is dearly needed in the field. The authors revise all the data for the abdominal and thoracic segments and describe in detail, for the first time, the head and tail segments and construct a complete structural and neuronal map of the external larval sensilla.

Strengths

It is a very thorough anatomical description of the external sensory organs of the genetically amenable fruitfly. This study represents a very useful tool for the research community that will definitely use it as a reference paper. In addition to the classification and nomenclature of the different types of sensilla throughout the larval body, the wealth of data presented here will be valuable to the scientific community. It will allow for investigating sensory processing in depth. Serial electron microscopy and digital modeling are used to the fullest to provide a comprehensive, definitive, and clear picture of the sensory organs. The discussion places the anatomical data into a functional and developmental frame. The study offers fundamental anatomical insights, which will be helpful for future functional studies and to understand the sensory strategies of Drosophila larvae in response to the external environment. By analyzing different larval stages (L1 and L3), this work offers some insights into the developmental aspects of the larval sense organs and their corresponding sensory cells.

Weaknesses

There are no apparent weaknesses, although it is not a complete novel anatomical study. It revisits many data that already existed, adding new information. However, the repetitiveness of some data and prior studies may be avoided for easy readability.

We would like to thank the reviewers for their respective reviews. The detailed comments and efforts have helped us to improve our manuscript. In the following, we have listed the comments one by one and provide the respective information on how we addressed the concerns.

Recommendations for the authors:

We have tried to address every single comment as far as possible. In order to structure our response a little better, we have listed the relevant page number and the original comments once again. Directly following this you will find our response and a description of what we have changed in the manuscript.

REVIEWER #1 (Recommendations For The Authors):

I have a few comments that will help the reader navigate this long and detailed paper.

REVIEWER 1.1. page 4

The final section of "the Structural organization of Drosophila larvae" needs some reorganization.

Specifically:

"The DO and the TO are prominently located on the tip of the head lobes" Can the authors rewrite the sentence in a way that it is clear that there is one DO and one VO on each side of the head? Check at the beginning of each section, please. There is a mention about hemi-segments but it is still confusing.

Done – replaced with “The largest sense organs of Drosophila larvae are arranged in pairs on the right and left side of the head.”

REVIEWER 1.2. page 5

"The sequence of sensilla is always similar for and different between T1, T2-T3, and A1-A7" This sentence is not clear, please break it into two sentences.

Done – replaced with: “We noticed varying arrangements for T1, T2-T3, and A1-A7, with a consistent sequence of sensilla in each configuration.”

REVIEWER 1.3. figures page 4

Double hair can't be found in Figure 1B or C (is it h3, h4?) - please clarify.

Done - changed to double hair organ in page 11, included double hair sketch in legend in figure 1B. We changed the name of the structure to double hair organ, to clarify that this is a compound sensillum consisting of two individual sensilla.

REVIEWER 1.4. page 5

The authors go back and forth in their descriptions of the different sensory organs. Knob sensilla and then papilla sensilla are discussed and then a few lines later a further description is done. Please unify the description of each separately.

Done – we restructured the whole section.

REVIEWER 1.5. figures page 6

"We found three hair sensilla on T1-T3, and "two" on A1-A7" - in the figure there seem to be "four" on A1-A7.

Done – we included the two hair sensilla of the double hair organ

REVIEWER 1.6. figures page 6

DORSAL ORGAN:

Can the authors explain the colour map meaning in Figure 2A? It is explained in 2C but the image already has colours. Add your sentence "Color code in A applies to all micrographs in this Figure".

Done – we added a sentence to explain that the color code in A applies to the whole figure.

REVIEWER 1.7. page 6

Page 10: which comprises seven olfactory sensilla "composing" three dendrites each: replace this with"with". At the end, we want to think 7 X 3= 21 ORNs.

Done – replaced.

REVIEWER 1.8. page 9

CHORDOTONAL ORGANS:

"We find these these DO associated ChO (doChO).. .". Please remove one "these"

Done – removed.

REVIEWER 1.9. page 8

Is the DO associated ChO part of the dorsal ganglion???? It does not look like it. Could you clarify?

Done – we added a sentence that clarifies that the ChO neuron is not iside the DOG.

REVIEWER 1.10. page 9 VENTRAL ORGAN: A figures page 12

Please add to the Figure 8 legend the description of 8c' and 8c'?

Done – added description in figure legend.

B page 9

8H, what are the *, arrows? Please clarify - it is hard to interpret the figure.

Done – we added parentheses in the figure legend that state which structures the asterisks and arrows indicate.

C page 9

"Three of them are innervated by a single neuron () and one by two neurons () (Figure 8F-I). Please add which are innervated by 1 (VO1, VO2-VO4) and which by 2 (VO3).

Done – we added parentheses that clarify which sensilla are innervated by 1 or 2 neurons.

REVIEWER 1.11. page 9

Can you add something (or speculate) about the difference in sensory processing of the different types of sensilla?

Done – new sentence in discussion:

‘Their different size and microtubule organization likely correlate with processing of different stimulus intesities applied to the mechanotransduction apparatus (Bechstedt et al. 2010).’

REVIEWER 1.12. figures page 16

PAPILLA AND HAIR SENSILLA:

FIGURE 10a, please add the name of each sensillum from p1, p2, px py, etc... (if not we have to go back to figure 1 when you describe specific ps.)

Thanks for the comment, it really makes it a lot easier for the reader.

REVIEWER 1.13. figures page 18 Figure 11, can you add the name of each hair, please?

Done – updated figure.

REVIEWER 1.14. figures pages 16, 18, 20

In Figures 10, 11, and 12 you clearly draw an area on the internal side that I assume is what you call the "electron-dense sheath". It is wider in papilla sensilla than in hair sensilla, most likely due to the difference in stimuli sensed that you explain in detail in the discussion. Can you say in the figure what this "internal" thing is? Can you add this difference to your list "Apart from the difference in outer appearance and structure of the tubular body"?

This is the basal septum, but it is not certain that it is wider in the papillae sensillae, at least we could not observe this in our data sets. The impression could have been created by different scales in the 3D reconstructions and a perspective view. Therefore, we do not want to list this as a difference here, as we are not sure.

However, we have now specified the socket septum in the figure legends and in Figures 10A, 11A and 12A.

REVIEWER 1.15. page 11

KNOB SENSILLA:

Page 25;" Knob sensilla have been described under "vaious" names such as": add various.

Done

REVIEWER 1.16. page 12

"reveals that the three hair and the two papilla sensilla are associated with a single dendrite." Can you write that "reveals THAT EACH OF the three hair and the two papilla sensilla" if not it seems that there is only one dendrite.

Done

REVIEWER 1.17. figures page 25 TERMINAL SENSORY CONES:

Please name the t1-t7 cones in Figure 15A.

Done – we updated the figure.

REVIEWER 1.18. page 13

The spiracle sense organ deserves a new paragraph. As does the papilla sensillum of the anal plate.

Done – we added subtitles before the prargraphs.

Discussion:

REVIEWER 1.19. page 15

Page 38: "v'entral" correct typo

PAGE 15

Done – we have updated the nomenclature  ventral 1 (v), ventral 2 (v’) and ventral 3 (v’’)

REVIEWER #2 (Recommendations For The Authors):

I have only a few comments:

REVIEWER 2.1. page 5

p.5, right column, middle: the use of trichoid, campaniform, and basiconical (sensilla) in previous works were based on even older papers and reviews that attempted to link EM architecture to function (e.g., KEIL, T. A. & STEINBRECHT, R. A. (1986). Mechanosensitive and olfactory sensilla of insects. In Insect Ultrastructure, vol. 2. (ed. R. C. King & H. Akai), pp. 477-516. New York/London: Plenum Press). Trichoid sensilla can be mechano-sensitive, olfactory, or gustatory; trichoid simply refers to the shape (hair). The same applies to basiconical sensilla. The use of "campaniform", which Ghysen et al called "papilla sensilla", was the only really problematic case, because these (Drosophila larval) sensilla did not really resemble closely the classical campaniform sensilla (e.g., adult haltere). The only reason we called them campaniform is because they were not more similar to any other type of (previously named) sensillum.

Thank you for the explanation. The nomenclature of structures is generally always a complex topic with often different approaches and principles. We are aware of this and have therefore tried to be as careful as possible. We were not sure from this comment whether you were suggesting to change the text or whether you wanted to explain how these names were assigned to the sensilla in the past. However, we hope that the current version is in line with your understanding, but could of course make changes if necessary (see also comments of reviewer 1).

REVIEWER 2.2. page 9

p.21, Labial Organ: the ventral lip is the labium; the dorsal one is the labrum.

Done – replaced labrum with labium.

REVIEWER 2.3. page 9

p.20/21, Ventral organ and labial organ: here, the projection of the axons could be mentioned as an ordering principle. In the previous literature, for larva and embryo, a labial organ (lbo) was described that most likely corresponds to the labial organ presented here. This (previously mentioned) lbo characteristically projects along the labial nerve to the labial segment (hence the name). It fasciculates with axons of another sensory complex, also generated by the labial segment, namely the ventral pharyngeal sensory organ (VPS). Does the labial organ described here share this axonal path?

Yes, it has the same axonal pathway and is the same organ as the lbo. We have tried to standardise the nomenclature for all important external head organs (DO, TO, VO, LO) and have therefore used abbreviations with two letters. However, to avoid confusion, we have now added that the LO was also called lbo in the past.

For the ventral organ, the segmental origin (to my knowledge) was never clarified. The axons of the ventral organ project along the maxillary nerve (which carries axons of the terminal=maxillary organ). This nerve, closely before entering the VNC, splits into a main branch to the maxillary segment (TO axons) and a thinner branch that appears to target the mandibular segment. This branch could contain the axons of the ventral organ (as described previously and in this paper). Could the authors confirm this axonal projection of the VO?

In this work, we did not focus on the axonal projections into the SEZ. This is also not a simple and fast process, as in the entire larval dataset, the large head nerves unfortunately exhibit a highly variable quality of representation. Therefore, the reconstruction of nerves and individual neurons within it is often challenging and very time-consuming. The research question is, of course, very intriguing, and one could also attempt to match each sensory neuron of the periphery with the existing map of the brain connectome. However, this is a project in itself, exceeding the scope of this work, and is therefore more feasible as a subsequent project.

REVIEWER #3 (Recommendations For The Authors):

Minor suggestions that the authors might consider:

REVIEWER 3.1. figures all

Recheck the scale bar in figures and figure legends. Missing in a few places.

Done – we replaced or added some (missing) scale bars in figures and figure legends (see annotated figure document).

REVIEWER 3.2. figures page 4

The color schematic in Figure 1 can be improved for readability.

Done – we changed the color schematic, especially for the head region to improve readability.

Reviewer #1 (Public Review):

Summary: This is a very meticulous and precise anatomical description of the external sensory organs in Drosophila larvae. It generates an integral and accurate map. The authors revise all the data for the abdominal and thoracic segments and describe in detail, for the first time, the head and tail segments.

Strengths: It is a very thorough anatomical description of the external sensory organs of the genetically amenable fruitfly. This study represents a very useful tool for the research community that will definitely be used it as a reference paper. It will allow us to investigate sensory processing in depth. The discussion places the anatomical data into a functional and developmental frame.

Reviewer #3 (Public Review):

Summary: Richter et al. present a comprehensive anatomical analysis of the external sensory organs of the D. melanogaster larva. Extending on their previous study (Rist and Thum 2017) that analyzed the anatomy of the terminal organ, a major external taste organ of fruit fly larva, the authors examined the anatomy of the remaining head sensory organs - the dorsal organ, the ventral organ, and the labial organ-also described the sensory organs of the thoracic and abdominal segments. Using improved electron microscopy, the authors performed a three-dimensional anatomical analysis of the sensilla and adjacent ganglia to construct a complete structural and neuronal map of the external larval sensilla.

Strengths: Though the manuscript is lengthy, it is written clearly, and the presented data supports the conclusion. In addition to the classification and nomenclature of the different types of sensilla throughout the larval body, the wealth of data presented here will be valuable to the scientific community. The study offers fundamental anatomical insights, which will be helpful for future functional studies and to understand the sensory strategies of Drosophila larvae in response to the external environment. By analyzing different larval stages (L1 and L3), this work offers some insights into the developmental aspects of the larval sense organs and their corresponding sensory cells.

Weaknesses: There are no apparent weaknesses. The repetitiveness of some data and prior studies may be avoided for easy readability.

Reviewer #1 (Public Review):

Summary:<br /> Compared with conventional SQUID-MEG, OPM-MEG offers theoretical advantages of sensor configurability (that is, sizing to suit the head size) and motion tolerance (the sensors are intrinsically in the head reference frame). This study purports to be the first to experimentally demonstrate these advantages in a developmental study from age 2 to age 34.

In short, while the theoretical advantages of OPM-MEG are attractive - both in terms of young child sensitivity and in terms of motion tolerance - neither was in fact demonstrated in this manuscript. We are left with a replication of SQUID-MEG observations, which certainly establishes OPM-MEG as "substantially equivalent" to conventional technology but misses the opportunity to empirically demonstrate the much-discussed theoretical advantages/opportunities.

Strengths:<br /> A replication of SQUID-MEG observations, which certainly establishes OPM-MEG as "substantially equivalent" to conventional technology but misses the opportunity to empirically demonstrate the much-discussed theoretical advantages/opportunities.

Weaknesses:<br /> The authors describe 64 tri-axial detectors, which they refer to as 192 channels. This is in keeping with some of the SQUID-MEG description, but possibly somewhat disingenuous. For the scientific literature, perhaps "64 tri-axial detectors" is a more parsimonious description.

A small fraction (<20%) of trials were eliminated for analysis because of "excess interference" - this warrants further elaboration.

Figure 3 shows a reduced beta ERD in the youngest children. Although the authors claim that OPM-MEG would be similarly sensitive for all ages and that SQUID-MEG would be relatively insensitive to young children, one trivial counterargument that needs to be addressed is that OPM has NOT in fact increased the sensitivity to young child ERD. This can possibly be addressed by analogous experiments using a SQUID-based system. An alternative would be to demonstrate similar sensitivity across ages using OPM to a brain measure such as evoked response amplitude. In short, how does Figure 3 demonstrate the (theoretical) sensitivity advantage of OPM MEG in small heads ?

The data do not make a compelling case for the motion tolerance of OPM-MEG. Although an apparent advantage of a wearable system, an empirical demonstration is still lacking. How was motion tracked in these participants?

Furthermore, while the introduction discusses at some length the phenomenon of PMBR, there is no demonstration of the recording of PMBR (or post-sensory beta rebound). This is a shame because there is literature suggesting an age-sensitivity to this, that the optimal sensitivity of OPM-MEG might confirm/refute. There is little evidence in Figure 3 for adult beta rebound. Is there an explanation for the lack of sensitivity to this phenomenon in children/adolescents ? Could a more robust paradigm (button-press) have shed light on this?

Data on functional connectivity are valuable but do not rely on OPM recording. They further do not add strength to the argument that OPM MEG is more sensitive to brain activity in smaller heads - in fact, the OPM recordings seem plagued by the same insensitivity observed using conventional systems.

The discussion of burst vs oscillations, while highly relevant in the field, is somewhat independent of the OPM recording approach and does not add weight to the OPM claims.

In short, while the theoretical advantages of OPM-MEG are attractive - both in terms of young child sensitivity and in terms of motion tolerance, neither was in fact demonstrated in this manuscript. We are left with a replication of SQUID-MEG observations, which certainly establishes OPM-MEG as "substantially equivalent" to conventional technology but misses the opportunity to empirically demonstrate the much-discussed theoretical advantages/opportunities.

Reviewer #3 (Public Review):

This study demonstrated the application of OPM-MEG in neurodevelopment studies of somatosensory beta oscillations and connections with children as young as 2 years old. It provides a new functional neuroimaging method that has a high spatial-temporal resolution as well wearable which makes it a new useful tool for studies in young children. They have constructed a 192-channel wearable OPM-MEG system that includes field compensation coils which allow free head movement scanning with a relatively high ratio of usable trials. Beta band oscillations during somatosensory tasks are well localized and the modulation with age is found in the amplitude, connectivity, and pan-spectral burst probability. It is demonstrated that the wearable OPM-MEG could be used in children as a quite practical and easy-to-deploy neuroimaging method with performance as good as conventional MEG. With both good spatial (several millimeters) and temporal (milliseconds) resolution, it provides a novel and powerful technology for neurodevelopment research and clinical applications not limited to somatosensory areas.

The conclusions of this paper are mostly well supported by data acquired under the proper method. However, some aspects of data analysis need to be improved and extended.

(1) The colour bars selected for the pseudo-T-static pictures of beta modulation in Figures 2 and 3, which are blue/black and red/black, are not easily distinguished from the anatomical images which are grey-scale. A colour bar without black/white would make these figures better. The peak point locations are also suggested to be marked in Figure 2 and averaged locations in Figure 3 with an error bar.

(2) The data points in plots are not constant across figures. In Figures 3 and 5, they are classified into triangles and circles for children and adults, but all are circles in Figures 4 and 6.

(3) Although MEG is much less susceptible to conductivity inhomogeneity of the head than EEG, the forward modulating may still be impacted by the small head profile. Add more information about source localization accuracy and stability across ages or head size.

This text describes a situation in which content on social media may be distributed in a way that is contrary to the intended purpose of the original content. Comments could indicate the impact that this situation may have on the author of the original content and how social media platforms should respond to this situation to protect the interests of users and preserve the original intent of the content.

In instances where content goes viral in a manner that diverges significantly from the original creator's intended purpose, it underscores the unpredictable and often uncontrollable nature of social media virality. The TikTok example provided highlights how users can utilize the platform's features, such as the Duet feature, to remix and reinterpret content in ways that may be unforeseen and unintended by the original creator.

Note that we don't have contemporary research here, just these books written well before the hellscape of late stage capitalism, where the vast majority of workers have had wages that barely keep up with inflation while CEO's wages from 1978 until now have increased by 1200% (according to the Economic Policy Institute)

I found this interesting. 90% seems a bit excessive, but I can easily believe that 65% of meaning is derived from nonverbal signals. As humans, we have such a funny balance with our communication. For example, you're in a club and your friend gives motions their head towards as door and with a flick of the eyes, hinting that they want to leave. From the perspective of evolution, it's easy to see how this can be the case. To me, I have an easier time picking up nonverbal signals from friends and family I'm close to, but I've gotten better at recognizing people's more subtle, nonverbal cues.

Poor women were unable to defend themselves

I read this poem silently first and there was no tone and i had a harder time where the author was coming from or what the purpose was, I couldn't really understand it. Once I read it out loud twice I grasped the way the poem was supposed to sound and the tone of what the author was trying to say. It questions wether or not its possible to see the world objectively rather than through the eyes of another person in emotion. Reading out loud readings rather than in my head have always helped me more than reading it silently.

show commits of git as a tree

To show the last 2 commits use this! git log --oneline --graph --decorate --all HEAD~2..HEAD

Persona here shows that she wants to confront her emotions head-on even after her past experience and try to explore her emotions actively.

I feel happy for the speaker as she faces her own emotions and confronts her inner conflict. This shows resilience making me feel happy as she doesn't want to give up

• There's a potential element of irony in the fact that someone has fallen for AI’s “words and cues.” It suggests that the person may have been influenced or charmed, possibly without a deeper understanding of the reality of the situation. The contrast between the superficial allure and the consequences of losing one's head adds depth to the lyrics. I can relate this back to the theme of idolatry, where an idol can influence someone so easily with the unique charisma and popularity of being someone worshipped by millions, even with simple words like “I love you.”

• The phrase "Made him lose his head over you" employs the metaphorical expression "lose his head," suggesting a state of infatuation or being deeply charmed by AI’s charisma. This creates a vivid image of someone being so affected by another person's words and cues that they become emotionally overwhelmed. This evokes the feeling of shock in me, as I would have never thought that an idol could so easily make someone fall in love with them, with simple yet powerful phrases or words that they perform.