On 2024-12-01 12:54:07, user xPeer wrote:

Courtesy review from xPeerd.com

Summary<br /> The preprint titled "Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids" describes a novel method utilizing integrases for high-efficiency integration of gene libraries onto the yeast OrthoRep plasmid. This method facilitates continuous in vivo gene diversification and evolution, improving transformation efficiency and enabling the generation of large, diverse gene libraries. The study demonstrates this approach with mock nanobody libraries and shows promising potential for broader applications in protein engineering and yeast genetics.

Major Revisions<br /> 1. Claim Confidence and Validation:<br /> - Doubts arise around the degree to which the claimed efficiency improvements can be generalized beyond the specific experimental parameters used. While TP901 integrase is shown to be highly effective, the generalizability to other integrases and diverse organism contexts needs further empirical validation. Citations within the document should more thoroughly delineate the extent and limitations observed in different experimental setups, ensuring that readers understand both the strengths and potential constraints of the approach.<br /> - The manuscript briefly mentions (in the introduction and results sections) comparative transformation efficiencies but lacks detailed statistical analysis and discussion on potential variances across different yeast strains or growth conditions.

1. Methodological Transparency:
2. The preprint should provide more detailed step-by-step protocols, especially for the transformation and sorting processes, to improve reproducibility. Information such as specific buffer compositions, incubation times, and electroporation settings would greatly benefit other researchers attempting to replicate the findings.

3. The current data representation (e.g., Fig. S1, S2) should go beyond simple efficiency comparisons and instead include discussions on potential confounding factors or biases that could have influenced observed results.

4. Data Integration and Interpretation:

5. The interpretation of multiple integrations per cell should include discussions around the biological implications of such events and how they might influence long-term genome stability and gene expression profiles in yeast cells.
6. Consideration of any unintended off-target effects or genomic instabilities caused by high-frequency integrase activity should be examined more comprehensively.

Minor Revisions<br /> 1. Typos and Formatting Issues:<br /> - Correct minor typographical errors such as "chromitinization" which should be "chromatinization".<br /> - Maintain consistency in the citation format and ensure that all figures and tables are accurately referenced within the text.

1. AI Content Analysis:
2. It is estimated that approximately 10-15% of the text could have been influenced by AI-generated content, specifically in highly repetitive methodological details and generalized scientific language. These sections might benefit from further scrutiny to ensure precision and contextual specificity.

Recommendations<br /> 1. Empirical Validation: Conduct additional empirical studies across various yeast strains and potentially other model organisms to validate and extend the utility of the TP901 integrase-mediated integration strategy.<br /> 2. Protocol Detail Enhancement: Provide more comprehensive methodological details and standard operating procedures (SOPs) to assist in replication and application.<br /> 3. In-depth Statistical Analysis: Include detailed statistical analyses for transformation efficiency data and other quantitative results.<br /> 4. Extended Discussions: Broaden discussions on possible biological implications, off-target effects, and the broader impact on genomic stability to anticipate and address potential challenges in practical applications.<br /> 5. Enhanced Figures and Tables: Ensure that all supplemental figures and tables are adequately referenced and described in the main text to aid in data transparency and comprehension.

By addressing these recommendations, the manuscript can improve both its scientific robustness and practical utility, greatly enhancing its value to the research community interested in gene library integration and continuous evolution methodologies.

On 2024-12-01 12:25:06, user Belter Xin wrote:

This manuscript has been published in PNAS: https://www.pnas.org/doi/10.1073/pnas.2407096121

On 2024-11-30 22:24:18, user xPeerd wrote:

Peer review report from http://xpeerd.com

Summary<br /> The preprint presents a novel strategy termed Transient Overexpression of P-glycoprotein (P-gp) for Cardiac reprogramming (TopCare) aimed at mitigating doxorubicin (Dox)-induced cardiotoxicity in cancer chemotherapy. The approach employs lipid nanoparticles (LNPs)-based mRNA therapeutics to transiently overexpress P-gp in cardiomyocytes, reducing intracellular Dox levels and associated cytotoxic effects, both in vitro and in vivo. The study demonstrates promising results, including enhanced survival rates and improved cardiac function in treated mice and pigs. However, detailed analysis and validation in clinical settings are needed.

Major Revisions<br /> 1. Ethics and Concerns on mRNA Technology:<br /> The preprint does not provide comprehensive information on the long-term safety and potential mutagenic effects of repeated mRNA administration. Although the authors claim no potential insertion mutagenesis, a detailed toxicological assessment must be included.<br /> - Example: The long-term impact on genomic stability has been vaguely mentioned (Section: Results, Page 6) but needs further elaboration.

1. Effectiveness on Large Animal Models:<br /> While the study highlights the preliminary success in pigs, it lacks comprehensive physiological data, myocardial histopathology, and the functional impact across different heart failure stages.

2. Example: The pig model data is summarized, but detailed statistical analysis and larger sample size validation are crucial (Discussion, Page 7).

3. Broader Relevance and Risk Mitigation:<br /> The potential immunogenicity of LNPs and mRNA therapeutics should be discussed to address the broader clinical relevance and possible adverse immune responses.

4. Example: Immune response considerations are barely discussed (Page 10), which is critical for clinical translation.

Recommendations<br /> 1. Enhance Toxicology and Safety Data:<br /> Include detailed data on the longitudinal impact of mRNA administration, focusing on potential genomic stability issues and systemic safety profiles. Consider supplementary studies evaluating mutagenic and oncogenic risks.<br /> 2. Comprehensive Animal Model Studies:<br /> Expand the large animal model studies to include a broader sample size and various cardiovascular conditions, supplemented with detailed histopathological analyses.<br /> 3. Immune Response Mitigation:<br /> Address potential immunogenicity by conducting comprehensive immunological assessments on treated animals and documenting any adverse reactions. Present a risk mitigation strategy for the clinical setting.<br /> 4. Expanded Clinical Relevance Exploration:<br /> Provide a more robust discussion on how to adapt the TopCare strategy to different cancer treatments, varying dosages, and combined therapies to ensure broader applicability.

Minor Revisions<br /> 1. Textual and Formatting Errors:<br /> - Correct minor typographical errors and ensure consistent formatting across sections. Specific errors to address:<br /> - Page 2, Title capitalization inconsistency ("Cardiac Reprogramm...").<br /> - Figure labels and axis titles should follow uniform font size and style (Section: Results).<br /> 2. AI Content Analysis:<br /> - Estimated AI Content: Approximately 10-15%.<br /> - Highlighted AI-Detected Sections: Repetitive and templated language indicating likely AI aid in introduction and discussion.<br /> - Epistemic Impact Assessment: The AI-generated segments maintain consistency but could benefit from nuanced, domain-specific language refinements to underline originality and expertise..

Overall, the preprint provides an innovative and promising approach to tackling cardiotoxicity in chemotherapy but requires crucial improvements and detailed validations before realistic clinical applications.

On 2024-11-30 19:30:43, user avtrader wrote:

BioRxiv Violation

The author claims no competing interests, yet he and others have said he is the Science Director for Mission Ivorybill. Mission Ivorybill's stated goal--is to save the Ivory-billed Woodpecker. Mission Ivorybill or the related, The Louisiana Wilds do not seem to be federal non-profits via a 501-c3 data base search.

Mission Ivorybill raises money via various channels and seems to be a commercial entity; this violates BioRxiv's publication rules for authors in addition to being a non-disclosed conflict by the author. Mission Ivorybill also has Go Fund Me efforts, publications, etc. and the organization is IBWO-centric. The author participates vigorously in marketing Mission Ivorybill. He controls and/or participates in Mission Ivorybill's media and marketing efforts such as their Facebook page and Zoom public presentations. The author reviews evidence gathered by Mission Ivorybill yet fails to disclose the relationship tainting this prepaper's Abstract and Conclusions.

Mission Ivorybill is mentioned in the subject paper. The author is well known to exaggerate claims of Ivory-bills recently proselytizing a video of a Tufted Titmouse was an Ivory-billed Woodpecker is association with a Mission Ivorybill presentation and on social media. The founder of Mission Ivorybill quickly distanced himself from the false Ivory-billed claims by the author.

The author receives organizational support, professional and informal introductions, recognition, publicity and public face-time from Mission Ivorybill/The Louisiana Wilds perhaps in return for his often aggressive marketing efforts for Mission Ivorybill. His efforts have even included researching and contacting employers, to disparge and econimically damage people who disagree with him on the Ivory-bill's status.

The author may have purposely not disclosed this unambiguous conflict and his association with a possible commercial entity whose only product is the Ivory-billed Woodpecker. Related the subject BioRxiv prepaper has some hyperbolic, marketing-like claims that are not based in science.

On 2024-10-31 14:41:16, user CT wrote:

It’s been known for decades that Blue Jay kents and IBWO kents differ spectrographically… duhhh. And a LOT of other sounds may mimic IBWO kents to the human ear as well (though the paper explores but one single avian species)… all being spectrographically different. This paper adds little to the known literature, except to try to reach further conclusions (actually redundant, re-stated conclusions in previous work) from unsubstantiated assumptions. <br /> I’d be amazed if one can find 2 or 3 (or even one) PhD. level scientists in the entire country who will defend the methods and exaggerated conclusions put forth here.

On 2024-11-30 10:38:30, user Balázs Vedelek wrote:

We recently read with great interest your paper titled “Adaptive protein coevolution preserves telomere integrity” and found your findings on the evolution of Drosophila telomere capping to be quite engaging. The topic of the current manuscript is essentially the same that we addressed earlier by biochemical and informatical means ( https://doi.org/10.1371/journal.pone.0142771 , https://doi.org/10.1098/rsob.210261) . Upon reading your work, we noticed that our earlier research in this area appears to have not been acknowledged. <br /> Given that, while the experimental approaches differ, both of our studies address essentially the same phenomena and build on the same underlying principles, we believe that proper acknowledgment of our studies would be a beneficial addition to your manuscript. <br /> We truly appreciate your contributions to the field and look forward to seeing how your research continues to evolve.<br /> Thank you for your attention to this matter.

On 2024-11-29 09:51:01, user Simon Gascoin wrote:

Dear authors<br /> I also revisited Roland et al. results in the light of our recent study on biases in Landsat greening trends by Bayle et al. (2024) https://www.cesbio.cnrs.fr/multitemp/is-antarctica-greening/

Bayle, A., Gascoin, S., Berner, L. T., & Choler, P. (2024). Landsat-based greening trends in alpine ecosystems are inflated by multidecadal increases in summer observations. In Ecography. https://doi.org/10.1111/ecog.07394

On 2024-11-28 11:08:54, user Marco Barreca wrote:

Dear all, the peer-reviewed version was out on 24 October, you can find it at this link: https://www.nature.com/articles/s41698-024-00730-7 <br /> The DOI is: https://doi.org/10.1038/s41698-024-00730-7

On 2024-11-28 10:07:05, user Sholto David wrote:

Abstract: "Since 2009, successful hoaxes usually appeared at a year of one or more a year" - perhaps this should say "at a rate of one or more a year"? Current phrasing doesn't quite make sense.

On 2024-11-27 23:21:01, user Monica Berger wrote:

Great preprint and I agree about the two basic types of hoaxes.

I keenly followed the Conceptual Penis hoax (Boghossian and Lindsay) as it unfolded in real time as I was writing my book on predatory publishing. Although it initially correctly stated that the Conceptual Penis hoax as exposing gender studies, he later says they published in a predatory journal. This is incorrect. There were peer review problems but no predatory publishing.

They submitted the article to a prestigious gender studies journal, NORMA: International Journal for Masculinity Studies, from Taylor and Francis. The journal rejected the article and transferred the article down to another T & F lower-tier open access journal, Cogent Social Sciences. This editorial process is called “cascading.” The less prestigious journal peer-reviewed it and, when it was accepted, requested an APC. After publication, the authors revealed the hoax, and the article was retracted; the journal explained that the peer reviewers for the lower tier publication lacked experience. See: https://www.skeptic.com/reading_room/conceptual-penis-social-contruct-sokal-style-hoax-on-gender-studies/

On 2024-11-27 10:42:17, user S. Bachellier-Bassi wrote:

Why is Candida albicans grown in a medium designed for bacteria ? Does it influence the efficiency of hyphal development ?

On 2024-11-27 03:40:20, user rdshrestha wrote:

Interesting work, but the assertion that 'CNTN2 known to plays a role in murine retina development but not in human' is not accurate. In recent study, utilizing human telencephalon-eye organoids, we demonstrated the expression of CNTN2 in human retinal development. We highlighted its differential expression in early RGCs of human fetal retinas, suggesting its potential as a marker for RGC isolation and underscoring a conserved role in retinal development across species. Reference: https://doi.org/10.7554/elife.87306

On 2024-11-26 19:42:30, user Shelley wrote:

Well cocaine and heroin isn't the same thing at all one is more targeted than the other...

On 2024-11-26 15:54:10, user Prof. T. K. Wood wrote:

Congratulations on your discovery of a novel hibernation factor.<br /> 1. p. 11 middle paragraph has some unintended text.<br /> 2. p. 3: why not include the mechanism of ppGpp to 100S via RMF/Hpf for persister cell formation and 100S undimerized with HflX to resuscitation (low ppGpp) since it is related and mechanistic for the physiological relevance of hibernating ribosomes ( https://doi.org/10.1016/j.bioflm.2019.100018 )?

On 2024-11-25 14:04:59, user Chie Kodera wrote:

Hello,<br /> This article is already published here.<br /> https://www.degruyter.com/document/doi/10.1515/mim-2024-0002/html <br /> Can I ask you to put the link?<br /> Thank you.

On 2024-11-25 14:02:29, user Chie Kodera wrote:

Hello,<br /> This article is already published here.<br /> https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07503-7 <br /> Can I ask you to put the link?<br /> Thank you.

On 2024-11-25 11:52:43, user Ronan O'Cualain wrote:

Please consider referencing the work done by Herrera et al ( https://pubmed.ncbi.nlm.nih.gov/32565759/ ) which includes AFA ultrasonication, S-trap sample processing, and DDA of FFPE micro-dissected sections.

On 2024-11-25 11:32:41, user Sebastien Leclercq wrote:

That is a nice study, well done, although not bringing breakthrough ideas : it is not a great surprise that conjugative plasmids PTUs are more prone to spread AMR genes than non mobile ones, and are also more prone to recombine because they meet more unrelated DNA. At least it is now demonstrated.

I however have some doubt about the host range analysis, because the methods applied are not very clear. It is written that the host range was assigned with COPLA (l.159). But I guess that the host range inferred by COPLA includes all plasmids in their database for each PTU, including some containing AMR genes. So in the last (and most important) section of the manuscript, removing the ARG-carrying plasmids from the AMR+ PTUs will not change the host range classification given by COPLA. <br /> This bring an inconsistency between the given host range and the actual plasmids in the 118 ARG-free PTUs investigated.<br /> My feeling is that the rare grade V+VI PTUs are actually caused by ARG carriage, bringing a great fitness advantage in very distant bacterial hosts in which plasmids should otherwise struggle to maintain because of maladaptation.<br /> It will be necessary I think to calculate the host range only with the data investigated in the study, simply by looking at the plasmid's host taxonomy and not rely on COPLA results. Like this it can be calculated independently for the various sets of PTUs (with/without pAMR).

Other samll comment : in figure 2 355 PTUs containing 13,048 plasmids are given in top panl but less than 8000 plasmids and 50 PTUs are given in bottom panel, and it is not indicated what was the display threshold in bottom panel. Please provide the threshold.

On 2024-11-24 20:45:05, user Forrest Weghorst wrote:

Interesting work. I recommend reading my recent paper prior to final publication. I would love to know whether your conclusions about mammalian MALAT1 and NEAT1 translate to their non-mammalian orthologs.

https://doi.org/10.1007/s00239-023-10151-y

On 2024-10-28 15:02:24, user nuala oleary wrote:

Hi,

I wanted to point out a small issue with the references to NCBI Datasets. The author names are misformatted. It should read as follows:

O’Leary NA, Cox E, Holmes JB, Anderson WR, Falk R, Hem V, Tsuchiya MTN, Schuler GD, Zhang X, Torcivia J, Ketter A, Breen L, Cothran J, Bajwa H, Tinne J, Meric PA, Hlavina W, Schneider VA. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Sci Data. 2024 Jul 5;11(1):732. doi: 10.1038/s41597-024-03571-y.

Thanks!

On 2024-11-23 17:12:00, user Leila wrote:

This paper has now been published in Ecology and Evolution: <br /> Fouda, L., Negus, S. R. B., Lockley, E. C., Fairweather, K., Lopes, A., Lopes, A., Correia, S. M., Taxonera, A., Schofield, G., & Eizaguirre, C. (2024). Productive foraging grounds enhance maternal condition and offspring quality in a capital breeding species. Ecology and Evolution, 14, e70137. https://doi.org/10.1002/ece3.70137

On 2024-11-23 12:41:45, user Caroline Fernandes Dos Santos wrote:

Published version: https://doi.org/10.1002/ansa.202000111

On 2024-11-23 12:36:19, user Caroline Fernandes Dos Santos wrote:

Published version: https://doi.org/10.33696/diabetes.1.015

On 2024-11-23 00:09:48, user Lee Bardwell wrote:

Nice work! Are the supplementary tables available?

On 2024-11-22 19:56:01, user Giovanni Bussi wrote:

Authors of the review

Giovanni Bussi, Ivan Gilardoni

This report was written after a journal club given by GB in the bussilab group meeting. All the members of the group, including external guests, are acknowledged for participating in the discussion and providing feedback that was useful to prepare this report. The corresponding author of the original manuscript was consulted before posting this report.

Summary

The authors introduce a method to perform maximum entropy reweighting of molecular dynamics (MD) trajectories, specifically addressing the choice of regularization parameters. Interestingly, an automatic procedure to determine the relative strength of the regularization terms acting on different experimental datapoints is proposed. The method is then applied to extensive MD simulations of 5 intrinsically disordered proteins (IDPs) using 3 different force fields. For 3 of the tested IDPs, different simulations converge to the similar ensembles after reweighting. For the other 2, the ensemble overlap is too limited, and the reweighted ensemble is significantly force-field dependent.

We are mostly interested in the methodological part of the paper. Technical innovations are:

* The idea of including the statistical error of the MD, as computed with block analysis, in the regularization term.<br /> * The idea of performing preliminary regularization scans for individual sets of experiments to tune the relative uncertainty, and ultimately end up with a single parameter (prefactor) to be tuned.<br /> * The idea of tuning the parameters monitoring the Kish sample size.

To our knowledge, the comparative results for the 5 IDPs and 3 force fields are also new and very relevant.

Comments

* Could there be some speculation by the authors on the relative role of the water model and of the protein force field? The way results are presented, it is not clear if the reason for the discrepancies is in the protein force field or in the water model. Maybe it is not possible to disentangle them.<br /> * The authors evaluate the errors of the employed forward models by applying the Flyvbjerg block analysis method, which only estimates statistical errors, without keeping into account possible systematic errors in the forward models themselves. We would suggest to clarify it in the text.<br /> * In many sentences of the main text, the authors use the word "weight" to refer both to the statistical weight of each frame in the trajectory and to the strength of the experimental restraints. To avoid undesired misunderstandings, we suggest to use words like "strength" or "confidence" of the experimental data/restraints etc.<br /> * Figure 2B is unexpected. The authors used the derivation from Cesari et al JCTC (2016) to introduce uncertainty in the experimental observation. This is formally equivalent to BioEn (Koefinger and Hummer, 2015) if the theta hyperparameter is set to 1. If we understood correctly how the global scaling was applied, its scan would correspond to a scan over theta in the BioEn formalism. When doing so, it can be proven analytically that the chi^2 should be a monotonic function of the regularization hyperparameter. Hence, when the authors decrease sigma_global, the average RMSE should decrease monotonically. However, in the figure all the reported RMSEs seem to be increasing for sigma → 0, so their average will increase. This seems inconsistent. Is this related to some issues with the minimization process (e.g., minimizations with a very low sigma are not converging)? Or is there something we misunderstood in the explanation?<br /> * The perfect match of the SAXS data for PaaA2 for the AMBER force field (before reweighting) is striking. Was perhaps the force field optimized using this system as a reference? If so, we would suggest to mention this in the text.<br /> * “An IDP ensemble containing ten consecutive residues [...] neighboring residues”. This is super interesting. Could the author explicitly compute this and show it? We believe it is a very interesting example of what can be observed in an MD simulation and not in a bulk experiment, and so it would be relevant to know if the answer is force field dependent or not. For instance, one could plot a 2D map with DDG associated to the helical content.<br /> * The authors quantify the similarity of two ensembles by computing the normalized overlap integral of the kernel densities in the ELViM latent space. This quantity is, by construction, sensitive to this particular choice of the ensemble representation, based on the C\alpha carbon atoms, which is in effect a dimensionality reduction. We agree that it is in practice unfeasible to evaluate the similarity between ensembles sampled in different MD simulations using quantities that do not rely on dimensionality reduction. However, when comparing reweighted with unbiased ensembles, we expect the Kish sample size to be relatively low (around 0.1), whereas the shown density overlap S is high (>0.66 for all the examined IDPs - values along the diagonal in Fig. 8B). Does this happen because the employed dimensionality reduction (based on C\alpha carbon atoms) focuses more on some robust part of the structural ensembles, preserved by the reweighting? Or is it because two different (possibly uncomparable) metrics are used?<br /> * The authors comment that leave-one-out cross validation should not be used with correlated data, and claim that this is the reason for the unexpected good performance of cross validation in Figure 2C. This is very interesting as, to our knowledge, has not been seen before. Adding more points in the low-Kish-size region might be interesting.<br /> * At some point the authors write "We note a conceptual similarity of the reweighting procedure proposed here with the concept of gentle ensemble refinement in the recently published work of Kofinger and Hummer.32 " We believe the authors meant to cite Ref. 33 rather than Ref. 32.

On 2024-11-22 17:35:04, user Jonas wrote:

Now published PLoS Biol. 2024 Nov 18;22(11):e3002879. doi: 10.1371/journal.pbio.3002879. PMID: 39556620

On 2024-11-22 00:31:35, user 柏本理緒 wrote:

Now published in Molecules doi: https://doi.org/10.3390/molecules29235490

On 2024-11-21 18:56:40, user Ding Quan Ng wrote:

Peer-review version published in Neurotherapeutics: https://doi.org/10.1016/j.neurot.2024.e00480

On 2024-11-21 18:12:02, user Diane Codding wrote:

Please update to the published article: https://doi.org/10.3998/tia.5109

On 2024-11-21 16:07:10, user Phillip Gienapp wrote:

This manuscript has now been published as:

JJC Ramakers, TE Reed, MP Harris & P Gienapp (2023) Probing variation in reaction norms in wild populations: the importance of reliable environmental proxies. Oikos e09592 doi: 10.1111/oik.09592

On 2024-11-21 14:17:04, user Anna Esteve-Codina wrote:

This preprint is already published: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-11015-5

On 2024-11-21 06:52:29, user Eva wrote:

Dear authors,<br /> Thx for sharing the study.

We have two doubts about the results:<br /> 1. During the RNA/Chimera annealing step, you applied “The samples were incubated at 95℃ for 1 minute and transferred to ice immediately.” However, the original study of Nm-VAQ and other similar experiments usually use gradient and slow cooling to ensure that the RNA and chimera have sufficient time to specifically bind rather than preferentially form secondary structures on their own, thereby affecting the subsequent cleavage of RNase H. This may be the reason for the ‘background’ described in this study and the much higher level of Nm modification seen in Fig 3C than the results in the original article.

1. In page 7, “PLXNB2, RPL10, and TOP1 were identified as potential candidates for mRNAs with Nm modifications based on various mapping techniques. G498 for PLXNB2, G150 for RPL10, and U877 for TOP1 were the potential sites of 2’-O-methylation”, which only cited reference 29. However, we found ref 29 only reported PLXNB2 as a potential Nm site. Could the authors please point out the provenance of the other two test loci?

Appreciate your attention.

On 2024-11-20 19:25:41, user Monir Modaresinejad wrote:

I am pleased to announce that our preprint has been published in the American Journal of Pathology. You can access the published version here: https://www.sciencedirect.com/science/article/pii/S0002944024003547

On 2024-11-20 15:57:30, user Miriam Zagers wrote:

We recommend that you read our follow-up study as well. In this study, we developed and tested a human embryo culture medium based on these in vivo results, on human preimplantation embryos. The blastocyst formation rate in the culture medium mimicking the uterine environment was similar to that of the control medium. DOI: https://doi.org/10.1101/2024.11.19.623474

On 2024-11-20 15:06:42, user Nicolas Locatelli wrote:

This manuscript has been published in BMC Genomics w/ open access on 11/20/2024 with the title: "Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora". The "now published in..." link at the top of this preprint will be coming soon.

On 2024-11-20 14:47:46, user MD Devignes wrote:

This is a preliminary version of our study on HLA epitope recognition. A more advanced and peer-reviewed version is about to get published in Bioinformatics Advances (DOI: 10.1093/bioadv/vbae186).

On 2024-11-20 06:54:52, user Olivier Espeli wrote:

Nice work Emily and Kirsten. Congratulations!

On 2024-11-20 00:14:41, user Eric Gorgens wrote:

THe manuscript was already published but it was not yet linked to the final version: https://onlinelibrary.wiley.com/doi/full/10.1111/btp.13226

On 2024-11-19 17:15:17, user Robert Becker wrote:

Have you tried using embeddings (like ProBERT) as input? I've found a lot of success with this for B-Factor and strongly recommend experimenting with this.

On 2024-11-19 16:24:35, user Jesus Valencia wrote:

An exhaustive analysis of viral diversity in blackflies collected from Onchocerciasis-endemic areas is presented. While it provides valuable data, the study has limitations that affect the coherence between its main objective and results. The title and introduction suggest a focus on neurotropic viruses associated with epilepsy linked to Onchocerca volvulus (OAE), but the results primarily describe viral diversity without providing evidence of these viruses. Possible explanations for the absence of neurotropic viruses are not discussed, nor are methodological alternatives proposed to address this issue. To improve the narrative, it is recommended to reframe the title and present the work as an exploratory study on viral diversity in blackflies.

Methodologically, the sample size (10 blackflies per pool) and the lack of information about the genus of the collected blackflies compromise the representativeness of the data. Additionally, the criteria for excluding incomplete sequences are inconsistent, as incomplete Riboviria sequences were retained, potentially biasing abundance results.

Regarding the figures, Figure 2 lacks a clear description of its columns, hindering interpretation. Figure 3 presents phylogenetic trees with barely distinguishable details, complicating analysis. In Figure 4, the point corresponding to Blackfly flavivirus does not clearly cluster with invertebrate hosts, weakening conclusions about its specificity. Analyses based on PCA and dinucleotide composition are interesting but insufficient to infer viral tropism without experimental validation. The supplementary files, although relevant, lack proper descriptions, and the main text does not specify which supplementary figure to consult, limiting their utility.

Although the study does not successfully address its main objective, it provides an important starting point for future research on the viral diversity of blackflies and highlights the need for further investigation into their relationship with human diseases in endemic areas.

On 2024-11-19 16:05:20, user Jose Morales Perez wrote:

Dear authors,<br /> I am a biology student with an interest in the evolution of animal communication systems, and out of curiosity, I came across your research titled “Prediction of the Next Elements in Chimpanzee Gesture Sequences.” I would like to congratulate you on your innovative approach and the richness of the information you present. The study is very interesting and makes a significant contribution to the field of animal communication, especially by providing a quantitative approach to chimpanzee behavior. However, I have identified a few aspects that could be improved to make the report clearer and more accessible.

First, the text refers to a "Table 2," but this table does not appear in the report, which could cause confusion for readers. This might be an issue of incorrect enumeration or an omission, so I would recommend reviewing and correcting this to ensure consistency in data presentation.

Regarding the figures, while the information is clear and understandable, some of them could benefit from adjustments in formatting to improve their visual presentation. For instance, in Figure 4, the axes are generically labeled as “X” and “Y”; it would be helpful if these were more specifically defined to aid in interpretation. Additionally, the axis titles are in lowercase, which could be standardized for consistency. In Figure 6, the title is not centered, and some axis subtitles and the legend do not follow the proper formatting, which may make them harder to read. In Figure 8, the abbreviation “NB” is used without an explanation, which could cause ambiguity for readers unfamiliar with the term.

Lastly, I believe it would be useful to include a section for keywords, as they are crucial for indexing and searching for the article, thus improving its accessibility and understanding.

The work is of high quality, and with these small adjustments, it could further enhance its presentation and clarity. Once again, congratulations on your effort and contribution to the field.

On 2024-11-19 11:21:21, user Daniel Rodríguez wrote:

This preprint has been published as:<br /> Rodríguez-León, D.S., Uzunov, A., Costa, C. et al. Deciphering the variation in cuticular hydrocarbon profiles of six European honey bee subspecies. BMC Ecol Evo 24, 131 (2024). https://doi.org/10.1186/s12862-024-02325-z

On 2024-11-19 06:59:56, user Em wrote:

Will do, thanks for the suggestions!

On 2024-10-05 08:38:14, user Martin GIURFA wrote:

Great work, congratulations! <br /> You may be interested in having a look at the following works, which relate to your findings:

° Pheromones modulate reward responsiveness and non-associative learning in honey bees. Baracchi D, Devaud JM, d'Ettorre P, Giurfa M. Sci Rep. 2017 Aug 29;7(1):9875. doi: 10.1038/s41598-017-10113-7

° Pheromone components affect motivation and induce persistent modulation of associative learning and memory in honey bees. Baracchi D, Cabirol A, Devaud JM, Haase A, d'Ettorre P, Giurfa M. Commun Biol. 2020 Aug 17;3(1):447. doi: 10.1038/s42003-020-01183-x.

Good luck with the next steps!

On 2024-11-18 19:32:52, user Jeffrey Bryan wrote:

This has now been published in peer-reviewed form in Communications Biology. Hoang MH, Skidmore ZL, Rindt H, Chu S, Fisk B, Foltz JA, Fronick C, Fulton R, Zhou M, Bivens NJ, Reinero CN, Fehniger TA, Griffith M, Bryan JN, Griffith OL. Single-cell T-cell receptor repertoire profiling in dogs. Commun Biol. 2024 Apr 22;7(1):484. doi: 10.1038/s42003-024-06174-w. PubMed PMID: 38649520; PubMed Central PMCID: PMC11035579.

https://pmc.ncbi.nlm.nih.gov/articles/PMC11035579/

On 2024-11-18 17:31:52, user Prof. T. K. Wood wrote:

Cyclic-di-GMP is not a quorum sensing compound.

On 2024-11-18 13:41:59, user Min-Ho Nam wrote:

This manuscript has been published in the Crispr Journal.<br /> DOI: 10.1089/crispr.2021.0025

On 2024-11-18 06:20:24, user Diana Duarte wrote:

Thanks for the interest in this manuscript. The peer reviewed article can be found on Plant Molecular Biology https://link.springer.com/article/10.1007/s11103-024-01523-z?utm_source=rct_congratemailt&utm_medium=email&utm_campaign=oa_20241101&utm_content=10.1007%2Fs11103-024-01523-z

On 2024-11-17 07:22:07, user Velyudhan Mohan Kumar wrote:

This study, identifying orthologs of human sleep-related genes in the Lokiarchaeota will certainly help in understanding human sleep physiology. The study supports the concept that sleep is a conserved biological function and evolutionarily distinct new features have developed later. The findings that the genes associated with energy metabolism and cellular repair, which play a primordial role of sleep in cellular maintenance in the Lokiarchaeota, suggest the origin and evolutionary purpose of sleep. The results are in line with the previous assumptions regarding the restorative and protective functions of sleep, including cellular maintenance and gene protection. Moreover, such researches can provide valuable information for drug development as conservation and evolutionary background of genes linked to disease could lead to the discovery of novel therapeutic targets.

This work has used both phylogenomics and bioinformatics to solve a biological problem. This research illustrates the scope of such studies in finding solutions to many biological problems. Why sleep is necessary and is maintained by evolution is not fully answered. From an evolutionary standpoint, phylogenetic approaches would help to unravel some of the unresolved mysteries of nature. The phylogenomics approach to sleep science is rather new, but combining phylogenomics and bioinformatics research on a range of species may help in understanding facts which are still unknown.

On 2024-11-05 08:41:43, user Seithikurippu R Pandi-Perumal wrote:

We greatly appreciate your constructive feedback and the recognition of Professor Imachi's significant contributions, which we have acknowledged in our manuscript. We fully agree that, ideally, certain wet lab experiments might have strengthened our findings to provide additional insights. However, there was no funding for our ongoing effort. If adequate funding were to be available, we would have pursued a certain set of experiments that we thought would add value to our work. This limitation is transparently discussed in our manuscript, and we consider our current data a valuable "stepping stone" for additional work in this exciting area of research.

Looking ahead, we are well-positioned to undertake follow-up experiments, contingent upon the availability of appropriate funding and other resources such as access to the strains. However, we do recognize the challenges involved in maintaining and rearing such specialized organisms in the laboratory setting. For example, replicating their native hydrothermal vent conditions and performing wet lab operations under those constraints condition pose additional significant technical and logistical hurdles. These unique challenges underscore the complexity and significance of our research. With support, we would eagerly and carefully advance this aspect of our research in the future.

Regarding your comment on sleep and circadian cycles in this organism, the identified sleep orthologs underscore that their functional characteristics diverge from those in human sleep processes. From the circadian clock perspectives, organisms whose circadian clocks have periodicities that correspond with those of their cyclic surroundings have survival advantage than those whose periodicities do not. If the development of circadian clocks was driven by circadian resonance, then animals with ~24h periodicity should be more fit in a 24-hour environment than in any other periodic or aperiodic time scale. Alternatively, the persistence of functional clocks and photoentrainment mechanisms implies that circadian clocks provide some "intrinsic adaptive advantage" to organisms in the absence of cyclical environments, where there is no apparent need to synchronize behavioral and metabolic processes with the geophysical cycles ( https://doi.org/10.1186/1740-3391-3-7) . The inherent benefit of clock mechanisms, there, is most likely derived from their ability to help coordinate the organisms' numerous internal metabolic functions.

In extreme habitats like hydrothermal vents, in the absence of photic cues, organisms likely rely on alternative timing mechanisms, such as temperature or chemical gradients, adapted to their unique environmental niche. In organisms such as Lokiarchaeota, the absence of circadian regulation due to the extreme hydrothermal environment may have driven the evolution of alternative timing mechanisms. Without light cycles, these organisms likely rely on other environmental cues, such as temperature fluctuations or chemical gradients, to regulate physiological processes. This adaptation might provide them with flexible metabolic and behavioural responses suited to their habitat. This suggests that evolutionary forces and selective environmental pressures unique to hydrothermal vents shaped a different evolutionary pathway for metabolic, and chemosynthetic mechanisms for survival than light-regulated, temporal mechanisms seen in surface-dwelling and terrestrial species. It's possible that daily and seasonal variations during evolution further honed the organisms for survival.

On 2024-11-04 12:05:23, user S. Krishnaswamy wrote:

Sleep in bacteria and archae is usually associated with a state of dormancy or persistency. But that is different from the circadian cycle of sleep. It is therefore surprising to see orthologs of human sleep genes in the deep sea vent dweller like this archae. Unless they had a different function there. It would be interesting to mutate some of the identified genes and see the effect in the cultures grown in the lab of Hiroyuki Imachi

On 2024-11-17 04:42:42, user De Novo Enzyme Enjoyer wrote:

Fantastic paper, breathtaking results. Just one minor suggestion—when I searched for RFam on GitHub, I found a repo with an almost identical name (Rfam) already exists, for an RNA bioinformatics tool. So to avoid confusion/difficulty locating the Rosetta Flow Atomic Matching codebase (and paper, whenever Ahern et al comes out), it might be a good idea to change the shorthand nickname for the model before publishing the repo (and the papers). RFlam, RoFAM and RoFlam all appear to have more unique namespace than RFam, while still being just two syllables to pronounce. Just a thought!

On 2024-11-17 03:09:55, user Diane Codding wrote:

This article has been published in The ADVANCE Journal: https://www.advancejournal.org/article/122098-the-clash-of-academic-hierarchy-and-inclusive-leadership-evolution-of-leadership-in-a-nationwide-diversity-equity-and-inclusion-initiative

On 2024-11-16 17:11:50, user Jishizhan Chen wrote:

Dear all, please read and cite the formal publication of this preprint here: https://doi.org/10.1016/j.ijbiomac.2024.137253

On 2024-11-16 16:34:07, user Yi Liang wrote:

This preprint has just been published in Science Advances as follows: Li-Qiang Wang#, Yeyang Ma#, Mu-Ya Zhang#, Han-Ye Yuan, Xiang-Ning Li, Wencheng Xia, Kun Zhao, Xi Huang, Jie Chen, Dan Li, Liangyu Zou, Zhengzhi Wang, Weidong Le, Cong Liu*, Yi Liang*. Amyloid fibril structures and ferroptosis activation induced by ALS-causing SOD1 mutations. Science Advances 2024 Nov 1, 10(44), eado8499.

On 2024-11-15 21:56:15, user Mikaela Follmer wrote:

this paper is now published in nature communications --> https://doi.org/10.1038/s41467-024-53642-2

On 2024-11-15 07:55:21, user Giovanni Bussi wrote:

Authors of the review

Olivier Languin-Cattoën, Giovanni Bussi

Summary

The authors use Molecular Dynamics with enhanced sampling techniques to gain insight in the directional catch-bond mechanism of Vinculin tail (Vt) interaction with F-actin. They construct two models of the Vt-actin complex that are hypothesized to represent a weak state and a strong state in a force-activated allostery model of the catch bond. They use enhanced sampling techniques to estimate the free-energy landscape of the unbinding process in each state, as well as the unbinding kinetics, in absence and presence of pulling forces of variable intensities and directions along the actin filament axis. Their results demonstrate higher kinetic stability for the strong state with respect to the hypothesized weak one, with unbinding kinetics in range of experimental expectations, confirming the viability of a “3-state” (2 bound states, 4 unbinding pathways) kinetic model of the bidirectional catch bond observed in single-molecule experiments. They additionally observe an increase in bond lifetimes for moderate constant pulling force (10-20 pN) in both directions, indicating an intrinsic catch-bond behavior within each “allosteric” state that may superimpose to the overall allosteric one. They show how an external pulling force affects the positioning of the H1 α-helix believed to act as a regulatory motif of the weak-to-strong transition, providing a compelling structural hypothesis for a force-induced allosteric mechanism. Finally, they provide molecular insight on the difference in stability between both states, highlighting the role of a C-terminal extension (CTE) and the redistribution of Vt-actin contacts under force.

Comments

* We wonder if the nomenclature “Holo” can be confusing at first glance for the reader, given the historical usage of the holo- and apo- prefixes to designate protein constructs with and without their constitutive prosthetic groups (usually non-proteic cofactors)

* We suggest that the authors make clearer the composition of the Holo and Aligned protein sequences given the different numbering in 6UPW and 1QKR (that we guess is due to the presence of Metavinculin instead of Vinculin), that in our understanding are identical except for the absence of the leading H1 helix.

* In FES calculations, since the constant force (that is, a linear bias) is applied on the same coordinate Q_‖, we expect that the resulting FES could be entirely predicted from the FES at zero force by simple addition of the linear slope, given sufficient exploration of the Q_‖ direction during the OPES-MetaD sampling. This fact could be used by the authors to assess the consistency between the FES computed at different forces. Alternatively, one may want to first aggregate the OPES-MetaD simulations at all forces using appropriate reweighting, and then estimate minimum free-energy paths and free-energy barriers at arbitrary force using the aggregated FES. This approach might lead to a better statistical use of the vast amount of simulations and a smoother estimate of the FES at all forces within the studied range. Finally, the multiple trajectories (20 replicates x 9 force values) could be used in a single bootstrap to assess the statistical uncertainty of the results (see below).

* Given the coarse nature of the set of chosen CVs (Q_‖ and Q_⊥) it is unclear whether the Vt is able to regain its canonical binding site during OPES-MetaD, notably because of free rotation with respect to the actin filament. <br /> - The authors acknowledge the difficulty in the methods (sec. 5.5) without explicitly stating whether such rebinding events happen at all in their simulations. We believe this is an important piece of information for proper understanding of the FES presented. We would suggest showing time series to clarify how many binding/unbinding events are observed.<br /> - One might expect that the absence of recrossing lead to a poor estimate of the free energy difference between the bound and unbound states as well as the height of the binding free energy barrier. On the bright side, the estimate of the unbinding barrier – which is the one they are the most interested in – can still be expected to be reliable.<br /> - The authors suggest to run multiple (20) separate OPES-MetaD simulations to compensate for this limitation. It should be acknowledged that independent runs starting from the bound state will not correct for the systematic bias caused by the absence of rebinding events. A bootstrap on these replicas would anyway estimate their statistical error.<br /> - We wonder if the use of the more specific CV Q_contact might allow for such recrossing to happen within OPES-MetaD, without the need of aggregating a high number of independent trajectories. In our understanding the authors only used Q_contact to assess the robustness of the free-energy barrier height to the precise choice of the projection space, but did not try to perform OPES-MetaD directly on this CV space, which could be instructive.

* The authors analyze the FES by determining a minimum free-energy path using the “String method” as a post-processing method. <br /> - The Methods section might benefit from some information about the use of the method, in particular that it is directly applied on the 2D CV-space projected FES (as opposed to a search of a minimum energy path on the full potential energy surface as originally proposed in [50]), and provide details about initialization (choice of end points for the string, number of nodes, initial interpolation) and robustness to these parameters in the converged paths and corresponding barrier estimates.<br /> - Since the FES are aggregated from 20 independent OPES-MetaD runs, it might be relatively straightforward to estimate errors (for example using bootstrapping) and provide error bars on Fig 2c. We believe this would strengthen the significance of the observed barrier difference.

* One may be concerned about the significance and reliability of the constructed “Aligned” state, since this state was constructed by aligning Vt to another conformation (in what we could refer to as “docking-by-homology”) with little experimental confirmation that such a state is stable in vitro. We understand that the model constitutes the core hypothesis of the whole computational approach, and that the consistency of the computational outcomes with single-molecule experiments themselves validates its plausibility. Nevertheless, it could be argued that lower binding affinity and lifetime are to be expected from a suboptimal binding partner in a suboptimal binding pose. This raises the question of whether the proposed model corresponds to a specific binding mode in reality, or if the results could be reproduced with a different alignment. Is this ruled out by the stability observed in the 500 ns simulations shown in Fig S1?

* In Sec 3.2 §4, the authors say “these results [...] do not quantitatively explain the observed experimental results, since the experimental changes in lifetime shown in Fig. 1D reflect a net 1.4 kcal/mol change in barrier in the negative direction, and 0.6 kcal/mol in the positive direction (if one assumes a constant prefactor the kinetic rate constant)”. It was somewhat unclear to us where these values come from (Are they computed from the fitted 3-state model in SI S1? At a specific value of the pulling force?) and how exactly they are compared to the computed barriers for Holo and Aligned to conclude to a discrepancy (Overestimated?)

* In Sec 3.4 §3, the authors convincingly remark that in two out of five simulations of Holo+H1 state pulled towards the barbed end, the conformation of H2–H5 becomes more similar to the Aligned (unbound Vt) structure, suggesting a first step in the strong → weak allosteric transition. We wonder if (i) the specific contacts made with actin and (ii) the specific intra-domain contacts of H1 with the H2–H5 bundle are also indicative of a displacement toward the Aligned state, since this would be an even stronger argument validating the proposed model.

* Given the relative simplicity of the supposed allosteric motif and the suggestive results of the Holo+H1 simulations, we cannot help but wonder whether the authors also tried to "unfold" the H1 helix in the Aligned model with a N-terminal pulling force since this seems a very natural test to look for equally suggestive indications of a weak → strong allosteric transition under force.

* Typos or writing remarks:<br /> - Fig 1B: The caption is inconsistent with the figure. In the caption, p₁ denotes the COM of Vt helices H2–H5, p₂ the COM of actin A1/A2 and p₃ the COM of actin A4/A5. On the figure instead (p₁, p₂, p₃) → (p₃, p₁, p₂).<br /> - Some repetitions that might be elegantly avoided<br /> x “capture the difficult-to-capture” (abstract)<br /> x “protein of interest [...] on our molecule of interest” (introduction §1)<br /> x “takes into account a Boltzmann weighted average over all possible configurations [...] a Boltzmann weighted average over all possible configurations” (introduction §4)<br /> - Typos<br /> x “FimH-manose” → “FimH-mannose” (introduction §8)<br /> x “which is the the direction” (3.1 §1)<br /> x “These approximate one-dimensional free energy pathways also give us a way to define when the system has crossed into the unfolded state” → Maybe the authors meant “unbound state” (3.1 §1)<br /> x “not all of the catch bond need come from” → “need to come from” (3.2 §3)<br /> x “we note that these results are suggestive, they do not quantitatively” → We wonder if the authors intended a formulation along the lines of: “we note that despite being suggestive, these results do not quantitatively” (3.2 §4)<br /> x “a constant prefactor the kinetic rate constant” → “a constant prefactor for the kinetic rate constant” (3.2 §4)<br /> x “grafted to our Holo structure random orientation” → “grafted to our Holo structure with a random orientation” (3.4 §2)<br /> x “TIP3 water” → “TIP3P water” (5.1 §2)

Acknowledgements

This report was written after a journal club given by OLC in the bussilab group meeting. All the members of the group, including external guests, are acknowledged for participating in the discussion and providing feedback that was useful to prepare this report. The corresponding authors of the original manuscript were consulted before posting this report.

On 2024-11-15 05:26:52, user Shigeaki Saitoh wrote:

The final version of this article is published in https://doi.org/10.1083/jcb.202404085 .

On 2024-11-14 20:30:07, user Patrick Neale wrote:

This prepint is now published, citation:<br /> PLoS ONE 19(10): e0305505. https://doi.org/10.1371/journal.pone.0305505

On 2024-11-14 15:48:57, user Mikel Garcia-Marcos wrote:

Based on information brought up to the attention of the authors, the passage below will be modified in the final published version. More specifically, it has been clarified that the isoformof Rap1GAP used in the EMTA does not affect nucleotide exchange and that additional evidence supports that the this system detects active Galpha(i/o). These conclusions are partially supported by evidence presented in paper that has been published (doi: 10.1126/scisignal.adi4747).

"For example, EMTA biosensors for G proteins of the Gi/o family are based on using Rap1GAP as a detector module, for which it is unclear whether it affects nucleotide exchange on different Gα subunits of this family or its preference for binding to Gα-GTP or Gα-GDP dissociated from Gβγ (35, 36), thereby raising questions about what is exactly represented by the BRET changes detected by this sensor."

On 2024-11-14 11:34:17, user John wrote:

Watch our PowerPoint presentation at the MMEE2024 conference:<br /> https://youtu.be/dwZRbpUDZq0

On 2024-11-14 08:45:38, user BioPioneer wrote:

Another paper had solved this problem and was published about two years ago:

Najafi, A., Jolly, M. K., & George, J. T. (2023). Population dynamics of EMT elucidates the timing and distribution of phenotypic intra-tumoral heterogeneity. Iscience, 26(7).

On 2024-11-13 14:57:57, user Jozef Nissimov wrote:

Very cool study Debbie and team. We recently did some work on the nblA protein as well that perhaps may be of interest: https://academic.oup.com/ve/article/10/1/veae082/7775594

On 2024-11-13 01:32:45, user mo wrote:

How can I get the data for the supplemental document, please?

On 2024-11-12 22:52:53, user Francesco Iorio wrote:

now published in Nature Communications<br /> https://www.nature.com/articles/s41467-024-53163-y

On 2024-11-12 14:14:42, user Velyudhan Mohan Kumar wrote:

In this report, human sleep-related gene orthologs have been studied in the unicellular green alga Chlamydomonas reinhardtii, which had been earlier considered as a model organism for the study of photosynthesis and flagella/cilia. Comparative genomics, which is an essential tool in biological research, is a very potent method that yields biological insights that are not possible with any other approach. It could also help us understand the human genome study, which has the potential to help us comprehend human sleep and sleep disorders. Phylogenomics gives a more profound comprehension of the discoveries made possible by comparative genomics.<br /> The results of this study indicate that the calcium signaling and synaptic transmission involved in sleep regulation are conserved across phyla, and a simple model organisms like Chlamydomonas may be useful in elucidating higher-order, complex behaviors such as sleep.

Chlamydomonas do not possess the complexity of the sleep seen in vertebrates. However, knowing their genetic makeup can help researchers to understand general molecular processes that may be used to understand sleep in more complex organisms. Comparative phylogenomic studies are also important in understanding human sleep disorders, and they may open new avenues for developing new therapeutic approaches.

On 2024-11-10 23:56:25, user Yi Shen wrote:

Dear bioRxiv team,

this preprint has been published in PNAS now.<br /> https://www.pnas.org/doi/abs/10.1073/pnas.2301366120

It will be great to link this preprint to the final publication. Thanks.

Yi Shen (First and corresponding author)

On 2024-11-10 18:38:49, user Michele Bonus wrote:

Hi! DataSAIL seems to be working well for me -- at least on protein structures using the built-in FoldSeek-based clustering.<br /> Regarding the paper: I believe there is something amiss with the coloring in Figure 2. In the lower sub-panel for the identity-based 1D cold split, shouldn't the rows be colored instead of the columns? Right now you are showing the same protein-identity-based split as in the upper sub-panel, and I believe you meant to show sub-optimal partitioning w.r.t. the "ligands" / chemical scaffolds.

On 2024-11-06 13:37:11, user Dieter Steinhilber wrote:

I recommend to read the paper by Alnouri et al. https://pubmed.ncbi.nlm.nih.gov/39365815/ and this one: https://pubmed.ncbi.nlm.nih.gov/35125345/ . From the experimental data, it is rather unlikely that there is a functional high affinity binding site for LXA4 and RvD1 at FPR2 and that the SPM ligands are functional at the mentioned GPCRs

On 2024-11-06 08:57:18, user himanshukhandelia wrote:

Very interesting work. I was curious about the surface tension being applied. For semi-isotropic pressure coupling, the tension is automatically set to zero, and does not need to be set explicitly. Why is this being done?

We previously demonstrated that even ATP could bind to lipid membranes. 10.1021/acs.langmuir.9b01240. So does UMP (shown by both scattering, fluorescence and simulations (https://doi.org/10.1039/C9S....

One caveat is that the charge on these nucleotide phosphates are most likely overestimated (see for example https://doi.org/10.1021/acs.jpcb.2c06077 and https://doi.org/10.1016/j.xcrp.2021.100343 . One way to address this is the rescale charges on the P and O atoms, as well as ions. However, a more systematic force field approach may be needed in the future. Pavel Jungwirth is working on this. https://www.developmentaid.org/organizations/awards/view/470320/doing-charges-right-modelling-ioncontrolled-biological-processes-with-the-correct-toolbox-q-scaling

On 2024-11-06 01:23:49, user sun zhen wrote:

The results of this paper are not credible.

Based on the gel result, we can see that only introns are removed by oligo dT purification, lots of precursor and nicked RNA still in the products. Obviously, there will be a decrease in dsRNA compared with RNA kit purification which removed nothing from the crude circRNA products.

When it comes to in vitro expression test, I am surprised to see even the expression of RNA kit circRNA is better than HPLC purified circRNA.We have also tested and compared RP-HPLC purified circRNA (circEGFP and circFLuc from GenScript) before, they got much higher expression than RNA kit purified circRNA or RNase R treatment crude circRNA.

As the purity of circRNAs is very important for their expression (which can reduce their immunogenicity) based on previous reports, the in vitro or in vivo data in this paper are not convincing.

On 2024-11-05 13:53:35, user Damien Garcia wrote:

The article has been published please link the archive to the published manuscript.<br /> https://doi.org/10.1093/plphys/kiab529

On 2024-11-05 13:49:01, user Damien Garcia wrote:

The article has been published could you link it to the publication:<br /> https://doi.org/10.1093/plcell/koae175

On 2024-11-05 11:17:02, user Guei-Sheung Liu wrote:

The paper has been published as below<br /> Proc Natl Acad Sci U S A. 2024 Nov 5;121(45):e2408345121. doi: 10.1073/pnas.2408345121. Epub 2024 Oct 30.<br /> Characterization of RNA editing and gene therapy with a compact CRISPR-Cas13 in the retina

On 2024-11-04 22:41:00, user Michael wrote:

typo in Sequence section? "pester and mortal" Did you mean pestle and mortar?

On 2024-10-29 04:24:41, user Dan MacNulty wrote:

The age estimates are impressive. To help readers appreciate the significance of these estimates, consider adding more background about what’s currently known about the age of aspen clones in general. Do estimates exist for other clones? If so, how do they compare to your estimates? How does your aging method compare to previous methods?

On 2024-11-04 22:27:12, user Brian Meckes wrote:

Link to published manuscript

https://www.cell.com/iscience/fulltext/S2589-0042(24)02240-5

On 2024-11-04 15:18:52, user Kasper van Gelderen wrote:

With my group we have been using this to 3D segment confocal timeseries, it works great! Recently, it has been updated and also works again via a Google colab form, so very low user threshold.

On 2024-11-04 15:12:37, user Jorge Hernández wrote:

Dear authors, is there a way to access the supplementary data? I am looking for all the Marchantia TFs tried to express as HALO fusions.<br /> Thanks in advance!

On 2024-11-04 12:14:36, user Chris Hunter wrote:

This paper was published in GigaScience in July 2023. https://doi.org/10.1093/gigascience/giad044

On 2024-11-04 10:28:20, user MRR wrote:

There are open reviews of this preprint Qeios:

https://www.qeios.com/read/WPW9WN

https://www.qeios.com/read/EHRP24

https://www.qeios.com/read/MGCKD5

On 2024-11-03 15:04:26, user B. Hendrich wrote:

I think you mean "potency". "Pluripotency" refers to the ability to make all cell types in the embryo. Trophectoderm stem cells cannot do that.

On 2024-11-01 16:14:55, user Haider, Saqlain wrote:

Dear Authors,<br /> Thank you for sharing this exciting work on the role of ABA and GI in recruiting CO at FT promoter to activate its transcription (and flowering). I appreciate the detailed analysis and valuable insights you've provided. I have a few questions and observations that may help clarify some aspects of the study:<br /> 1. Higher CO in aba1-6 mutants at ZT12<br /> In figure 2A, a slight increase in CO expression could be observed in aba1-6 mutants compared to WT plants though this expression declines at ZT16. Further, a higher CO expression is detected at ZT12 and ZT16 in SUC2::CO:CIT-aba1-6 compared with SUC2::CO:CIT (in WT background). It remains somewhat unclear as to why the lack of ABA is leading to a slight (yet) increase in CO transcription. It is noted that in 9 days old seedlings at ZT16 (figure 2B), there is a decline in CO expression yet aba1-6 mutants transformed with SUC2:CO:CIT in figure 2A have a higher CO at ZT16 than WT transformed with SUC2:CO:CIT. What could be the reason behind that. Finally, it will be valuable if authors could measure the CO-FT expression at ZT12 in 9 days old seedlings (like they did for 13 days old). <br /> 2. Higher Pol-II occupancy at CORE in WT<br /> In figure 4B, a higher enrichment/occupancy of RNA Pol II could be detected at TSS of FT in WT compared with SUC2::HA:CO aba1-6 and SUC2::HA:CO gi100. Yet, these lines flower much earlier than WT (figure 5B). How do authors explain this discrepancy as low Pol II occupancy would lead to a lower FT (and delayed flowering). Moreover, it will be interesting if authors could quantify and compare the FT expression in WT (Col-0), WT (with either SUC2::CO:CIT or SUC2::HA:CO), aba1-6 (with either SUC2::CO:CIT or SUC2::HA:CO), and gi-100 (with either SUC2::CO:CIT or SUC2::HA:CO). For example, do authors expect FT levels to be same in aba1-6, gi-100 (transformed with SUC2::HA:CO) as they flower nearly at the same time (Figure 5B). Moreover, as SUC2::HA:CO aba1-6 gi-100 show a slight delay in flowering compared with either SUC2::HA:CO aba1-6 or SUC2::HA:CO gi-100, it will be interesting to analyse FT transcript accumulation between genotypes. Taken together, addressing these points will increase the readers understanding and make the paper more concise.<br /> 3. ChIP and RNA Pol II occupancy assayed at ZT12 (not ZT16)<br /> In figure 3,4, and 5 the ChIP assays and RNA Pol II occupancy was quantified at ZT12. CO transcript peaks around that time point in long day (LD) conditions but the FT peak is observed at ZT16. Previously, it has been shown that reduced FT peak at ZT16 leads to delay in flowering ( https://doi.org/10.1111/pce.13557) . Authors mention CO binding is observed at ZT12 at CORE (line 329-331) but the delayed flowering phenotype is justified by FT levels so it will be interesting to check CO binding together with RNA Pol II enrichment at ZT16 and then compare both these assays (ZT 12 and ZT16). <br /> 4. RNA Pol II Occupancy at TSS in WT vs. SUC2::HA:CO abi1-6 and SUC2::HA:CO gi-100 with Delayed Flowering in WT <br /> SUC2::HA:CO: gi-100 and SUC2::HA:CO: abi1-6 lines show a drastic decline in Pol II occupancy at TSS of FT, yet these lines flower significantly earlier than WT. Would you consider discussing possible mechanisms by which this delay occurs, despite higher Pol II occupancy, to help clarify this interesting finding? Finally, the SUC2::CO:CIT gi-100 lines flower nearly at same time as SUC2::CO:CIT (figure 5B). Although in supplementary figure 9, an increase in bolting time (flowering in terms of number of days) in SUC2::CO:CIT gi-100 lines could be seen. A few additional details or a discussion of possible mechanisms might help contextualize this observation.

Thank you again for sharing this preprint. I hope these comments are helpful and supportive of your ongoing work. Please feel free to reach out if you'd like further clarification on any of my points.<br /> Thanks<br /> Saqlain

On 2024-11-01 14:02:04, user Cameron Thrash wrote:

Hello. May I respectfully recommend a few relevant references for the discussion of SAR11 recombination and speciation?

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data<br /> https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-2-27

High intraspecific recombination rate in a native population of Candidatus Pelagibacter ubique (SAR11)<br /> https://enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1462-2920.2007.01361.x

The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective<br /> https://journals.asm.org/do...

A comparison of homologous recombination rates in bacteria and archaea<br /> https://academic.oup.com/ismej/article/3/2/199/7588207?login=false

On 2024-11-01 13:06:13, user Maxim Greenberg wrote:

Hello, this paper has now been published in Nat Struct Mol Bio. https://doi.org/10.1038/s41594-024-01405-4 Thank you!

On 2024-11-01 13:04:11, user Maxim Greenberg wrote:

Hello, This paper has now been published in Nucleic Acids Research: https://doi.org/10.1093/nar/gkae724 Thank you!

On 2024-11-01 09:15:08, user David Žihala wrote:

Dear Authors,

Thank you for sharing your impressive work in the form of a preprint. I have a question regarding one aspect of the study that I found a bit confusing. Could you clarify why it was necessary to decontaminate the samples from mouse cells? If two samples were excluded from downstream analysis due to high mouse cell content (over 65%), could you please provide information on the mouse cell content in the remaining samples? Additionally, I am curious about how this type of contamination could have occurred.

Best regards,<br /> David Zihala

On 2024-11-01 04:07:38, user Christoph Hagen wrote:

peer-reviewed and published: https://dx.doi.org/10.1038/s41564-024-01716-8

On 2024-10-31 23:46:29, user Derek Narendra wrote:

This has now been published here:

Lin HP, Petersen JD, Gilsrud AJ, Madruga A, D'Silva TM, Huang X, Shammas MK, Randolph NP, Johnson KR, Li Y, Jones DR, Pacold ME, Narendra DP. DELE1 maintains muscle proteostasis to promote growth and survival in mitochondrial myopathy. EMBO J. 2024 Oct 8. doi: 10.1038/s44318-024-00242-x. Epub ahead of print. PMID: 39379554.

On 2024-10-31 18:13:20, user Avi Flamholz wrote:

See detailed comments here https://prereview.org/reviews/14019384

On 2024-10-31 15:54:51, user Josh Mitteldorf wrote:

The comparison you have made supports the conclusion "that aging is not governed by a conserved universal program" but not the specific alternative you propose, "adaptations to damage and environmental conditions." I suggest that it may be that the ecological need for managing length of life is universal, but that it is implemented differently in different species. Salmon destroy their bodies with glucocorticoids; elephants fail to grow a 7th set of teeth and can't chew their food; mice get cancer; rats get heart disease -- but the underlying adaptive motivations might be universal. The best evidence for this is the role of insulin signaling, which accelerates aging across the animal kingdom.

On 2024-10-31 15:40:16, user James Amos-Landgraf wrote:

In your methods you state that you purchased C57BL/J mice from the four vendors. These mice are only available from Jackson Lab. The other mice you purchased are C57BL/6N substrains that specific to the vendor. NTac, NCrl, and NHsd. The biggest factor you need to address is the B6J have a mutation in the Nnt (nicotinamide nucleotide transhydrogenase) gene that dramatically influences metabolism. You should address this in your interpretation of bacterial community shifts. There is a good review of these differences that Jax has published on their web site and in various publications. https://www.genengnews.com/sponsored/heres-what-you-need-to-know-about-the-c57bl-6-substrains/

On 2024-10-31 14:51:48, user YC Han wrote:

This study holds considerable promise, but its findings are significantly undermined by the notable delay in developmental stages observed in embryos injected with CRISPRi/a + sgRNAs, as evident in Figures 1-3. For instance, the embryo injected with CRISPRi + tyr sgRNAs marked with 48 hpf in Figure 1B, appears to be developmentally equivalent to a 30 hpf wild-type embryo, which exhibits substantially fewer pigment cells than embryos at 48 hpf. This discrepancy raises concerns about the direct impact of the CRISPRi/a + sgRNAs injection, whether or not the delay development was caused by an unintended consequence.<br /> I strongly recommend that the authors reexamine their results and conduct a comparative analysis of CRISPRi/a + sgRNAs-injected and control embryos at equivalent conventional developmental stages, as described by Kimmel et al (1995, PMID: 8589427). This crucial consideration will not only enhance the study's rigor but also provide valuable insights to the zebrafish research community.

On 2024-10-30 21:32:37, user Vanesa Amarelle wrote:

The paper is now available at<br /> https://link.springer.com/article/10.1007/s42770-024-01512-w

On 2024-10-30 18:03:54, user Verónica Kovacec wrote:

This article has now been published in Microbial Genomics, under doi: https://doi.org/10.1099/mgen.0.001297

On 2024-10-30 14:15:51, user Anonymous wrote:

Dear authors,

as part of a group activity in our lab we discussed your very interesting paper with the goal to review it. The below review is the result of this exercise and therefor reflects the thoughts and concerns of several people. We hope this helps you with your way forward to publish the paper in a good journal.

Review:

The manuscript by De Tito et al. reports a hitherto unknown role for ATG9 in recruitment of PI4K2A to damaged lysosomes to control the levels of PI(4)P, lysosomal membrane contact site formation with the ER, and lipid transfer from ER to damaged lysosomes. They report that this mechanism is controlled by ARFIP2, which shuttles between the Golgi where it anchors ATG9 and lysosomes, and by the AP-3 complex, which mediates retrieval of ATG9 from lysosomes. Finally, the authors show a role for their proposed mechanism in lysosome damage induced by Salmonella infection. The manuscript deals with the timely topic of lysosomal damage repair and PI4K2A was recently emerging as a key player in this process. Mechanisms for PI4K2A recruitment to the sites of damaged lysosomes were so far elusive. Although the manuscript is certainly of interest for the field, the presented evidence on which the claims and the proposed model are based on seem not always substantial enough and further work is required.

Major concerns<br /> • Novelty and generalization: Although the findings suggest new functions for ATG9A and ARFIP2, they overlap significantly with previous work on autophagic and lysosomal repair pathways. The novelty of these findings, in comparison to earlier research, could be emphasized more clearly.<br /> • The claim that ARFIP2 "modulates lipid transfer for lysosomal repair" could benefit from additional direct evidence linking lipid transfer to lysosomal recovery and ARFIP2's specific role in this process. There is only one in vitro experiment directly showing lipid transfer modulation by ARFIP2 (Fig. 5K). The authors should use the ARFIP2 W99A mutant in this experiment to test whether lipid transfer modulation is specific and according to their model.<br /> • A central claim of the manuscript is a role for ARFIP2 in the repair of damaged lysosomes. The gold standard assay in the field is recovery of lysotracker fluorescence after LLOME-induced damage as shown in Fig. 2G. The way the experiment is presented does not instill confidence. The effects are relatively modest, it is unclear how the statistics were done, the representative images in the supplement only remotely resemble lysotracker stainings, how a reliable lysosome number from these images could be extracted is unclear, it is not shown whether and how much the cells express GFP-ARFIP2, the time points of the images do not match the relevant time points in the quantification, and the lysosome number in the different samples before LLOME treatment is not factored in. <br /> • The major lysosome repair assay in the manuscript is Galectin staining. This is a rather indirect assay as compared to the lysotracker recovery assay as it shows the damage rather than the repair. Could there be repaired lysosomes that still are positive for Galectin? Is the total Galectin expression level the same in the cell lines and conditions used? Furthermore, spot quantification for lysosomal damage markers like LGALS3 (Figure 2f) does not account for cell size or density, potentially leading to misinterpretation of the data. The authors further need to show lysotracker recovery in ATG9 loss of function to substantiate their claims.<br /> • The authors show that ARFIP2 and ATG9 affect PI4K2A localization in cells. The “delivery” of PI4K2A to lysosomes, however, which is a central claim in this manuscript, is insufficiently demonstrated. Same is true for the “retrieval” of ATG9: The authors claim that AP-3 and ARFIP2 are important for the retrieval of ATG9A vesicles. Even though they show effects of these proteins on ATG9A presence at the lysosomes, they never manage to show that retrieval really is impaired. I am not fully sure if it is possible to make videos that convincingly show this. Either they should try that, or they should not hammer so hard on the word retrieval when they never show it specifically. <br /> • The dynamic interactions of the relevant components need to be better demonstrated and characterized. E.g. interactions ATG9-PI4K2A interaction needs to be proven and characterized better (e.g. by co-IP, immunogold or similar techniques). Otherwise the role of ATG9 is much secondary, and should be a ARFIP2-mainly focused paper. The experiments in figure 4H and 4G seem ideally suited for this purpose but the authors fail to show the relevant components in the same blot.<br /> • The increased formation of membrane contact sites is insufficiently demonstrated. The authors need to use electron microscopy, super resolution microscopy, SPLICS or other appropriate techniques to make this claim<br /> • The way of quantifying protein localization to lysosomes (intensity lysosomes/total) seems heavily dependent on the lysosome coverage of the cells. In conditions where to my impression the overall number of lysosomes also changes, I would like to see a negative control that demonstrates that the enhanced lysosome localization is not just by chance, since there are more lysosomes. This applies for instance to Figure 4E+F and 5A+B.<br /> • I am not satisfied with the data analysis they presented. The authors should indicate the statistical test for each piece of data they analysed including an explanation, why did they chose particular test. For instance, in fig. 2g they compare the amount of puncta or lysosomes (it is not clear as well) in the cell in a pairwise manner. It would be more appropriate to implement a statistical test that can compare the curves fitted with the data points or a test which can compare each time point individually, i.e. Kaplan-Meier plot.

Minor comments<br /> • The zooms generally miss scalebars<br /> • Which part of the picture the zoom is from is often not indicated<br /> • Many of the images are hard to interpret because of low contrast, I would recommend to put their individual channels in grey<br /> • Fig3f. requires a better representative image and although there is a line indicated there is no line plot<br /> • Fig. 1c: show quantification for pS6K<br /> • Fig. 2b: data points are the same as figure 1b<br /> • Fig. 3: Live-imaging of ATG9A with AP-3D1 is needed

On 2024-10-30 08:51:15, user Thomas Munro wrote:

Given LM189's structural similarity to salmeterol and higher efficacy, I suspect there would be wide interest in whether it shares salmeterol's peculiar time course: activation that persists for hours after washout, but can be reversed by antagonists, and “reasserts” after antagonist washout. The cited patents claim “a particularly long duration of action”, which suggests LM189 may be even more extreme than salmeterol, but don't appear to give any results.<br /> It might be possible to get this data without the dreaded reviewer experiments. Glaxo (now GSK) offers to share clinical trial data. Presumably they would also be willing to share in vitro data for an off-patent compound like this, which has no privacy or IP concerns.

On 2024-10-29 14:01:42, user Amandine Véber wrote:

In this bioRxiv preprint, the authors question part of the methodology that we have used in Jay et al. (2022) , as well as the conclusions we have drawn from our study. In order to clarify the different points of misunderstanding that have led to these criticisms, in the document available at this link we provide a response which, we hope, will demonstrate the validity of our approach.

In this document, we first address the main questions raised by our colleagues and then carefully go through our paper to emphasize its main contributions. The format of this response makes it not eligible for publication in standard open archives, hence our non-standard way of making it available online. A link to it can also be found there .

The current debate which was generated by Jay et al. (2022) is grounded on the very interesting question of which control scenario is appropriate to assess the efficiency of the "sheltering effect" that we investigate there, and we hope to contribute to this discussion with sound logical arguments and relevant biological concepts.

Amandine Véber, Paul Jay and Tatiana Giraud

On 2024-10-29 10:08:15, user Jiayu Wang wrote:

Our database is available at https://datasync.ed.ac.uk/index.php/s/qlIgUlTTzW8KjXM

On 2024-10-29 09:45:14, user Stew Late wrote:

For Figures 4B and 4C, I suggest placing the "D. melanogaster" label in the same style as in Figures 4D and 4E.

On 2024-10-28 20:29:55, user Pedro H. Oliveira wrote:

Another recent large-scale screening of the bacterial defensome has been performed: https://www.nature.com/articles/s41467-024-46489-0

On 2024-10-28 09:39:36, user Isabella Capellini wrote:

A revised version of this manuscript is now available in Proceedings B:<br /> Mortlock E, Silovský V, Güldenpfennig J, Faltusová M, Olejarz A, Börger L, Ježek M, Jennings DJ, Capellini I. 2024 Sleep in the wild: the importance of individual effects and environmental conditions<br /> on sleep behaviour in wild boar. Proc. R. Soc. B 291: 20232115.<br /> https://doi.org/10.1098/rspb.2023.2115

On 2024-10-25 17:03:55, user Thomas Nicol wrote:

This article is now published in cardiovascular research https://doi.org/10.1093/cvr/cvad101

On 2024-10-25 12:37:11, user Yuta Takada wrote:

There was a mistake in line 80. The correct reference is figure S1A, not figure S2A.

On 2024-10-24 17:27:06, user Kyle Barrie wrote:

Published: https://www.nature.com/articles/s41594-024-01412-5

On 2024-10-24 16:51:29, user Allisandra Rha wrote:

Interesting work. The multimodal approach definitely enhanced the integration outcomes and is well-designed. While it is of benefit that AAV efficiently reaches the nucleus, moving forward would you consider evaluating other delivery methods for nuclear translocation to account for patients that are seropositive for AAV antibodies?

Also, the paper is under-referenced. I would encourage you to look at the text and provide more citations to support your claims.

On 2024-10-23 00:20:34, user CDSL JHSPH wrote:

I really enjoyed reading your preprint "Universal rules govern plasmid copy number." Your analysis of plasmid copy number across diverse bacterial genera is impressive and the discovery of a scaling law linking plasmid size and PCN is a huge contribution to the understanding of plasmid biology. I was wondering, based on your discussion on the intrinsic variability of PCN in high-copy number plasmids versus low-copy number plasmids, how these variations impact the fitness of bacterial populations, especially under different selective pressures. Additionally, given plasmids' role in gene transfer, how might the scaling law and PCN-size trade-off influence the evolution of plasmid-encoded traits, such as antibiotic resistance genes or virulence factors? <br /> I look forward to seeing how this research progresses! Thank you!

On 2024-10-19 00:01:15, user CDSL JHSPH wrote:

Thank you for sharing your research! I found your paper on PCN very insightful, especially the discovery of "universal rules" governing PCN. The large-scale analysis of plasmids provides valuable insights into plasmid number variability and regulation, with potential applications in both research and biotechnology. I do have a few questions. Could replicon dominance bring evolutionary advantage, particularly under natural conditions where plasmids may compete for replication resource? Additionally, under external constraints, is there a threshold where dominance shifts between replicons? <br /> I very much enjoyed the article, and look forward to how these findings evolve in future studies.

On 2024-10-23 00:19:08, user CDSL JHSPH wrote:

I really enjoyed learning about this new Bento Lab because it opens the doors for so many new positive things. I think the paper is written in a way that people will understand the differences between BL and TL and agree that there are so many advantages to the BL. I think your strongest part is how you explain your data from the figures since you talk about the how and identify how to understand the figures and tables. I would say for figure one; I was wondering if maybe also using bar graphs since it shows a clearer way of differentiation like Figure 2. I also think instead of tables, more figures will help the public understand their pros and cons better visually. I also think that the sludge's low read count should be addressed more. While it is mentioned that the Flongle's limitations might have affected the detection of less abundant entities, why do you think happened to that sample, and how could you express that to the audience? I think you could strengthen their argument by referencing specific species, ARGs, or plasmid types they suspect might have been missed due to the lower read count. To end this, I think the authors did a great job explaining the differences, and my only concerns were adding figures and explaining the sludge sample.

On 2024-10-19 18:05:46, user CDSL wrote:

This article is a good demonstration of the potential of portable DNA sequencing technology for rapid detection of pathogens and antimicrobial resistance in the field, especially for public health emergencies in low-resource or remote areas, and the results section, in particular, is very detailed. However, I feel that there are some deficiencies in the discussion part. It is mentioned in both the introduction and the results that the differences are evaluated from five aspects, but I do not seem to see obvious discussion about DNA yield and purity in the discussion part. Also, have you considered separating the restrictions into a separate section? That may help the reader to read in a more organized way.

On 2024-10-22 20:43:09, user Thomas Sorger wrote:

Erratum: The tree in Panel A of Figure 9 is incorrect. <br /> It will be corrected in a forthcoming revision.

On 2024-10-22 19:27:34, user Andy Flies wrote:

This chapter is now published.<br /> Slyp, B., Darby, J.M., Flies, A.S. (2024). Conversion of Mouse-Derived Hybridomas to Tasmanian Devil Recombinant IgG Antibodies. In: Good-Jacobson, K.L. (eds) Memory B-Cells. Methods in Molecular Biology, vol 2826. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3950-4_17

On 2024-10-22 19:01:27, user CDSL JHSPH wrote:

I believe this is an excellent study and paper, with valuable contributions to the field. It was very well-written, and the methodology very clearly described and reproducible. Given the global clinical significance of malaria, the biological implications of this study can be used as a basis for further studies into the biology of circadian rhythms in malaria transmission, as well as clinical translation for efficient prevention and control strategies and more effective treatments.

Similar to what previous reviewers have noted, I noticed some inconsistencies between some of the figures and the apparently corresponding results in the text, especially as it relates to the percentages of the transcriptome displaying cyclic expression profiles, for both the mosquito salivary glands and sporozoites. The figures and/or results should therefore be corrected accordingly.

A possible limitation to the study, which I don't believe was addressed in the paper, was that different mosquito (Anopheles stephensi vs Anopheles gambiae) and parasite (Plasmodium berghei versus Plasmodium falciparum, vivax, ovale, malariae, or knowlesi) species from the ones which are primarily known to cause malaria in humans, were used for analysis in this study. This may limit direct clinical translation of these results for malaria in humans. There should be a statement addressing this in the discussion. Furthermore, the amount of gene homology between the species used in the study and the species causing disease in humans should be stated for reference. If there were any reasons it was not possible or necessary to use the species known to be most associated with disease in humans, this should be stated.

On 2024-10-22 01:49:09, user CDSL JHSPH wrote:

I thoroughly enjoyed reading your paper, and I believe this study brings valuable new insights into how circadian rhythms influence malaria transmission. This information will undoubtedly impact future strategies for combating malaria, but also other vector-borne diseases. However, I noticed some inconsistencies between the results and the corresponding figures. I might be wrong and misread it but I wanted to bring it to your attention and clarify it on my side as well. In certain sections, figures were cited but did not seem to align with the content discussed. I can mention for example:<br /> - “We found that 27-49% of salivary gland genes displayed a cyclic expression profile, (Fig. 1B-E) representing 5-10x more than what has been previously reported for the mosquito’s head or body”. For C-E, I don’t see how this is actually depicted. Could you please explain; even the next sentence as well I don’t understand how C-E are supposed to back the arguments you are trying to make <br /> - Some figures like 1G and 1H are mentioned in the legend of your figures and in the text as well but are not shown in the figures, why?<br /> Those are not the only inconsistencies I noticed, but before proceeding on citing them, I want to make sure that I am not misreading and not understanding.

If my assumptions are true, clarifying them would greatly improve the paper’s clarity and presentation of your significant findings. I am looking forward to reading your answer.

Best regards,<br /> Critical Dissection Class 2024/2025

On 2024-10-19 02:11:16, user Yak Nak wrote:

The manuscript provides an exciting and valuable look into how circadian rhythms influence malaria transmission by aligning mosquito feeding behavior and parasite activity. The use of RNA-sequencing to uncover rhythmic gene expression in mosquito salivary glands is a significant strength and offers important new insights into the mechanisms behind malaria transmission. The figures are clear and effectively illustrate how these rhythms correlate with mosquito feeding efficiency and parasite infection capabilities, though the figure legends could benefit from more detailed explanations, especially for readers unfamiliar with gene expression data. The introduction is solid but could be improved by providing a more detailed discussion of previous research on circadian rhythms in malaria parasites to better frame the novelty of this study. The discussion section does a good job connecting the findings to broader vector-borne diseases like Zika and dengue, but it would be even stronger with specific examples of how these results could inform practical malaria control strategies, such as optimizing the timing of interventions based on mosquito feeding times. Overall, this is a well-conducted study with important findings, and a few revisions could further enhance its clarity and impact. Two follow-up questions:

1. Could the authors clarify why specific time intervals (every 4 hours) were chosen for RNA-sequencing, and would more frequent sampling provide additional insights?
2. Also, how might environmental factors such as temperature or humidity influence these circadian rhythms, and could this affect transmission in different regions?

On 2024-10-18 18:57:00, user CDSL JHSPH wrote:

I really like this article. Thank you for sharing your article. Malaria remains a major global health challenge, and understanding the biological rhythms of mosquito vectors and malarial parasites is crucial for improving control strategies. However, previous studies have only revealed that mosquitoes have daily rhythmic behaviors. You provided new insights. First, about half of the genes in the mosquito salivary gland transcriptome show 24-hour rhythmic expression, and second, the gene expression of sporozoites in the salivary glands also shows circadian rhythms (parasite movement and infection ability). In addition, you mentioned in the discussion that the parasites and mosquitoes have evolved in coordination with the circadian rhythms, and jointly affect host infection by regulating parasite movement and mosquito blood feeding time. This is very interesting, and your findings provide a new perspective for understanding the temporal regulation mechanism of malaria transmission. At the same time, you mentioned optimizing the insecticide spraying time strategy according to the peak period of mosquito activity. In addition, your findings may also have reference effects on other diseases.

But I have some questions. First, it is good that you use 12h dark and 12h light to simulate day and night. But in the wild, the temperature and humidity vary between day and night. Perhaps the natural day-night cycle could be better simulated by changing temperature and humidity. Secondly, you mentioned that some observations may apply to uninfected mosquitoes, but you did not specifically discuss the potential differences in rhythms and behaviors between uninfected and infected mosquitoes.

Finally, thank you again for your contribution and new ideas.

On 2024-10-21 14:16:12, user MJ Muzzatti wrote:

This article is now published in the Journal of Economic Entomology http://dx.doi.org/10.1093/jee/toae208

On 2024-10-21 14:15:22, user Julian C wrote:

Accepted for publication in Journal of Proteome Research (comment added by the corresponding author).

On 2024-10-20 08:57:36, user Alireza Mani wrote:

This paper is now published at https://doi.org/10.1016/j.bbrc.2024.150854

On 2024-10-20 07:36:15, user XKM wrote:

This study has now been published in PLoS Biology.<br /> https://doi.org/10.1371/journal.pbio.3002615

On 2024-10-19 19:13:36, user sam wrote:

It would be good to see how altered the phosphoproteome is after FACS. Thats a long time for the cells and a lot can change in phosphopatterns in a matter of seconds .

On 2024-10-19 18:51:50, user Alessio Ciulli wrote:

This comment is to advise readers that our preprint has been published in Sci. Adv. 10, eado6492 (2024). https://doi.org/10.1126/sciadv.ado6492

On 2024-10-19 18:49:33, user Alessio Ciulli wrote:

This comment is to advise readers that our preprint has been published in Nat Commun 15, 8885 (2024). https://doi.org/10.1038/s41467-024-52871-9

On 2024-10-19 00:19:59, user CDSL JHSPH wrote:

This article is rigorous. I like the comparison between phages in gut and that in the sea water. And the analysis of phages in hCom2 mice is well designed. Yet I think the equations and the explanations in the result and the method part are not very readable. I’m confused about the meaning of lysogen-host ratio and relative coverage, the role of dilution rate and so on. Plus, figure 2B is not very informative and by just looking at it, I cannot have a clue of what you were doing to get the range of induction rate. But overall your results support your conclusions firmly and clearly.

On 2024-10-18 13:39:11, user Oscar wrote:

Dear James and co-authors,

I trust you are already working on submitting this manuscript to a reputable journal. As one of the researchers with the most publications on CAV1 in Ewing Sarcoma (Oscar M. Tirado), I would like to offer some comments and suggestions for your consideration:

It might be beneficial to mention that CAV1 is a demonstrated direct target of EWS::FLI1, as this could add further context to your findings.

Regarding the presence of caveolae in Ewing Sarcoma cells, I assume you've reviewed the manuscript (DOI: 10.1016/j.canlet.2016.11.020). In most of the cells studied, including TC71, the levels of Cavin-1, as well as caveolae, are extremely low. As such, the majority of CAV1’s functions in EwS are likely independent of caveolae, which aligns with the results you’ve presented.

I noticed the focus on the AKT pathway in your work. Have you considered discussing the MAPK pathway as well? It is also affected and likely plays a significant role in the processes you're describing.

In Figure 4, CAV1 emerges as a potential driver, along with EphA2. I’m sure you are familiar with this study as well (DOI: 10.1002/ijc.31405), which may provide further insights.

I agree with your assessment that CAV1 plays a key role in the progression of EwS, and your findings align with many of the conclusions we've drawn in our own research. I would be happy to assist further, either through this platform or via personal contact, as we've known each other for many years from various EwS meetings.

Best regards,<br /> Oscar M. Tirado

On 2024-10-18 01:51:53, user Tushar R. wrote:

Summary

Here, the authors sought to apply cryo-EM guided metainterference-based MD simulations to find modeling inaccuracies of flexible helical regions linked to their artificial representation by a single-structure model. They first applied their approach to the group II intron ribozyme from Thermosynechococcus elongatus, one of a few cryo-EM structures available in the PDB that featured mostly RNA and was obtained using a single-structure refinement procedure. They confirmed that remodeling with their approach mostly affected flexible regions at the solvent-exposed stem loops that were not phylogenetically conserved. They found that functional domains that were well-ordered, phylogenetically conserved, and were clearly represented by the cryo-EM density required no remodeling. Extending this analysis through other PDB structures revealed that poor modeling at flexible helical regions was broadly applicable to all RNA-containing cryo-EM-derived structures in the 2.5 - 4 Å resolution range.

Major Points:

It is difficult to keep track of the different parameters applied for each simulation. These are scattered in the text. It would be very helpful for the reader to understand these if the authors could make a table of all the MD simulations with specifications on helices restrained, approach, simulation time, force fields present, equilibration time etc.

Clarification regarding the helical restraints and the simulation time for the initial production run would be helpful—i.e. Why was a simulation time of 2.5 ns chosen, and would this be long enough for your purposes considering the relatively high complexity of the system?

Were restraints applied to the 3 helices (b,d,i) that unfolded in subsequent simulations or were they only applied to the other 6 helices?

In the section “Base Pairing Analysis of the Protein Data Bank,” it is mentioned that the analysis likely over-estimates the problematic modeling of helices in cryo-EM derived RNA structures. Given that 15 Å is larger than the expected 8-11 Å (Pietal, M. J., 2012) distance for N1/N9 distance, would this not underestimate the number of problematic helices?

A detailed analysis of H-bonding within the 6 helices would be useful to get a mechanistic understanding of why the 3 helices (b,d,i) unfold and the other 6 don't—for example, it might be helpful to provide a comparison with the model generated from a single structure approach to know if the same H-bonds exist in it or not as the model forwarded by this paper.

ERMSD approach: we know relatively less about non-Watson Crick base pairing apart from Hoogsteen and G-U wobble base pairs since so much depends on the context (specific region of the structure, ion concentration, pH etc.) (we’re still thinking about how to phrase this point).<br /> Balance between experimental measurements and MD sampled conformational states: lack of experimental validation when remodeling mismodeled regions for RNA - how do we know when specific interactions are too ideal?

How is variability between forcefield parameters for divalent metal ions or other ions addressed, especially considering that these are required for proper folding of RNA?

Dispersive interactions play a huge role in RNA integrity: how confident can we be about these parameters when comparing various nucleic acid specific force fields? Can these differences lead to unfolding of the 3 properly base paired helices?

With reference to the line on page 4: “The trajectories obtained with metainference simulations were then analyzed by back-calculating the corresponding averaged density map and comparing it to the experimental one”, was the solvent density included in the back-calculated density?

What proportion of the CC_mask arises just due to fitting of rigid part of the structure and how much of it arises due to the improved fitting of the flexible regions from the 9 loops? Would it be possible to separate these contributions?

Minor Points:

Would it be possible to show Fig 2C as a violin or box plot rather than a bar plot? This would allow visualization of the distribution of CC_mask for different conditions with clusters representing conformational states that may agree with the experimental data.

Is local resolution considered while plotting the RMSF? For this purpose, it would be useful to have a local resolution estimation for the map to help the reader understand whether the unfolding of helices occurs simply because the specific regions were not well defined or if these regions are inherently flexible.

How effective is DeepFoldRNA in filling gaps in structure as it is normally known for sequence based structure prediction—specifically regarding the modeling of the 38-nucleotide gap?

For benchmarking purposes, applying this approach to other RNA structures or providing additional validation against independent experimental data (e.g., SAXS or chemical shifts from short RNA motifs) could further strengthen the conclusions.

Aside from the pre-1r (6ME0) and pre-2r (6MEC) states, Haack et al. (2019) found additional 3D classes that indicated disordered density in conserved regions, which they did not investigate further. They also suggested that the post-2r complex may be captured in one of the 3D classes that yielded a low-resolution 3D reconstruction. Is it possible that one of the structures found by the metainference method could have sampled one of the structures that were not investigated further or the post-2r complex?

Why is there a sudden fall in the number of helices formed in 32 replicas (Fig 2E)?

Sentence on page 4: “As a result, 32 replicas appeared to be the best compromise between agreement with experiment and computational cost.” Has it been ensured that this is not a result of overfitting? One of the ways to do this can be to use half-map cross validation i.e. to check if the refined ensemble fits both the half maps equally.

Have the authors tried to change the weight for 1 μs reference simulation to improve the CC_mask?

Grammar/spelling mistakes <br /> Results, Test System and Preparation, 1st Paragraph: Change “run” to “ran” to retain past test throughout the paragraph in the sentence beginning “We then run 2.5 ns-long molecular dynamics (MD) simulations in explicit solvent…”<br /> Results, Ensemble Refinement, 1st Paragraph: “Within” is misspelled as “whitin” in the sentence beginning “Conversely, when restraining their helicity, whitin this single-replica refinement approach…”<br /> Results, Ensemble Refinement, 1st Paragraph: “Specifically, all the simulations attempted with a lower number of replicas were crashing reporting missing convergence in enforcing bond constraints, which indicates that the experimental and helical restraints were mutually incompatible.”

• Tushar Raskar, Sonya Lee, James Fraser

On 2024-10-17 18:28:16, user Christine Pye wrote:

This article has now been published in the Journal of Small Animal Practice https://doi.org/10.1111/jsap.13688

On 2024-10-17 14:50:43, user Elena Grassi wrote:

The revised version is now out:<br /> https://www.nature.com/articles/s41467-024-51909-2 <br /> https://doi.org/10.1038/s41467-024-51909-2

On 2024-10-17 14:12:50, user Sahil Sahni wrote:

Article published: https://www.nature.com/articles/s41467-024-52555-4

On 2024-10-17 14:05:57, user Christina Warinner wrote:

It is very nice to see the authors statistically confirm on a large number of samples that oral bacteria contribute to the thanatomicrobiome of archaeological teeth. They may want to note that this pattern has been previously observed and reported twice before: <br /> Mann AE, Sabin S, Ziesemer KA, Vågene Å, Schroeder H, Ozga A, Sankaranarayanan K, Hofman CA, Fellows-Yates J, Salazar Garcia D, Frohlich B, Aldenderfer M, Hoogland M, Read C, Krause J, Hofman C, Bos K, Warinner C. (2018) Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports 8:9822. DOI: 10.1038/s41598-018-28091-9<br /> Vågene AJ, Campana MG, Robles García N, Warinner C, Spyrou MA, Andrades Valtueña A, Huson D, Tuross N, Herbig A, Bos KI, Krause J. (2018) Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico. Nature Ecology and Evolution 1-9. DOI:10.1038/s41559-017-0446-6.

On 2024-10-16 00:18:50, user Hamidreza Karbalaeiheidari wrote:

Hello,<br /> My preprint has now been published in ACS Synthetic Biology Journal.<br /> https://doi.org/10.1021/acssynbio.4c00437

Thanks,<br /> Hamid Reza Karbalaei-Heidari

On 2024-10-15 20:51:50, user Alexa Jennings wrote:

Overall, this paper is significant to developmental biology. Thank you for your contribution and dedication to the field. As I read through your paper, I have a few comments I would like to offer.

Fig1: While I was intrigued by the several stainings and experiments carried out by your team, it would be helpful to understand your rationale for choosing the gestational ages of interest. Additionally, since this is a comparative review, it would be useful to visualize the corresponding gestational ages in mice. I also noticed you cited these phases in mice, but it would be much more memorable if there was a clear schematic comparing the two species' gestational ages to go along with the rest of the figure as well.

Fig2: I noticed a one-way ANOVA was carried out for several of the corresponding data. However, ANOVA's are designed to compare means of groups with samples >3. In the supplemental figures, several groups were either missing data, or had samples <3. Asterisks marking significance would also be useful to visualize significance on the graphs.

Fig3&4: Quantification of fluorescence would be useful to make statistical comparisons. As is, the evidence is too correlative to make any conclusions.

Fig5: For clarity, place comparative groups in alphabetical order (ex: 5a and 5c should be 5a and 5b). Additionally, 5k-q show dim fluorescence, and should be quantified to make accurate statistical comparisons. 5f should be compared via a multivariate-ANOVA.

Final remarks: Further manipulative, molecular experiments are required to make conclusions on similarity. A stronger argument could be made if additional evidence were included. Additionally, sex and cultural differences likely will cause variation among your data. Stating the sex of the samples can help make more accurate comparisons between data. Comparative experiments between sexes and across ethnicities in humans may also be useful.

On 2024-10-15 19:33:41, user Abdul Muntakim Rafi wrote:

the paper is now published at Nature Biotechnology<br /> https://www.nature.com/articles/s41587-024-02414-w