eLife

Latest preprint reviews

1. Both prey and predator features predict the individual predation risk and survival of schooling prey

   This article has 7 authors:

   1. Jolle Wolter Jolles
   2. Matthew MG Sosna
   3. Geoffrey PF Mazué
   4. Colin R Twomey
   5. Joseph Bak-Coleman
   6. Daniel I Rubenstein
   7. Iain D Couzin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study, which will be of interest to behavioral ecologists, uses highly quantitative video tracking approaches to understand the predictors of predators' success in attacking schooling fish and will be of interest to behavioral, evolutionary, and movement ecologists. While some of the results seem unsurprising (e.g., that predators tend to successfully capture prey that are closer to them), the manuscript as a whole highlights the importance of tracking the perspective of the predator as well as of the prey, and shows that animals that are central to a group may sometimes be the most vulnerable. Although the experiments and data analyses are commendable, the manuscript would benefit from more careful discussion of its overall implications for the evolution of collective behavior, including potential limits of the experimental design.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

2. Mapping the single-cell landscape of acral melanoma and analysis of the molecular regulatory network of the tumor microenvironments

   This article has 13 authors:

   1. Zan He
   2. Zijuan Xin
   3. Qiong Yang
   4. Chen Wang
   5. Meng Li
   6. Wei Rao
   7. Zhimin Du
   8. Jia Bai
   9. Zixuan Guo
   10. Xiuyan Ruan
   11. Zhaojun Zhang
   12. Xiangdong Fang
   13. Hua Zhao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     He and collaborators analyse eight samples from six patients with acral melanoma through single-cell RNA sequencing. They describe the tumour microenvironment in these tumours, including descriptions of interactions among distinct cell types and potential biomarkers. The study is thoroughly done. In its final form, this study will help to inform our knowledge of the immune infiltration on the poorly studied acral melanoma subtype, the most common type of the disease in several countries in Africa, Asia and Latin America.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

3. COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

   This article has 2 authors:

   1. Wan Yang
   2. Jeffrey L Shaman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents a modeling framework that can be used to track the complex behavioral and immunological landscape of the COVID-19 pandemic over multiple surges and variants in South Africa, which has been validated previously for other regions and time periods. This work may be useful for infectious disease modelers, epidemiologists, and public health officials as they navigate the next phase of the pandemic or seek to understand the history of the epidemic in South Africa.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife, ScreenIT

4. Neuroinflammation in neuronopathic Gaucher disease: Role of microglia and NK cells, biomarkers, and response to substrate reduction therapy

   This article has 17 authors:

   1. Chandra Sekhar Boddupalli
   2. Shiny Nair
   3. Glenn Belinsky
   4. Joseph Gans
   5. Erin Teeple
   6. Tri-Hung Nguyen
   7. Sameet Mehta
   8. Lilu Guo
   9. Martin L Kramer
   10. Jiapeng Ruan
   11. Honggge Wang
   12. Matthew Davison
   13. Dinesh Kumar
   14. DJ Vidyadhara
   15. Bailin Zhang
   16. Katherine Klinger
   17. Pramod K Mistry

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Patients with Gaucher disease can have significant and crippling neurological manifestations. The study uses novel mouse models of neurodegeneration associated with glucocerebrosidase 1 (GBA1) deficiency. It provides a detailed analysis of the alterations caused by targeted deletion of GBA1, including cellular, genetic and metabolic alterations in neurons, microglia, and infiltrating immune cells. The work defines novel mechanisms driving neuroinflammation in neuronopathic Gaucher disease.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

5. 3D optogenetic control of arteriole diameter in vivo

   This article has 5 authors:

   1. Philip J O'Herron
   2. David A Hartmann
   3. Kun Xie
   4. Prakash Kara
   5. Andy Y Shih

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript by O'Herron et al. describes an all-optical method combining optogenetic stimulation and 2-photon microscopy imaging to simultaneously manipulate and monitor brain microvasculature contractility in three dimensions. The method employs a spatial light modulator to create three-dimensional activation patterns in the brains of cranial window-model transgenic mice expressing the excitatory opsin, ReaChR, in mural cells (smooth muscle cells and pericytes). This provides a powerful new in vivo technique to control blood flow into the brain and to understand its actions on brain function.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

   Reviewed by eLife

6. In situ X-ray-assisted electron microscopy staining for large biological samples

   This article has 5 authors:

   1. Sebastian Ströh
   2. Eric W Hammerschmith
   3. David W Tank
   4. H Sebastian Seung
   5. Adrian Andreas Wanner

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study explores the kinetics of heavy metal staining of tissue using time-lapse imaging with X-ray micro computed tomography (CT). It will be of interest to the wide community of scientists preparing biological samples for electron microscopy (EM), in particular large-volume EM. While at present the relation between CT imaging and EM contrast remains to be quantified, this study has the potential to become a reference for the field in establishing a quantitative tool for assessing and developing staining protocols.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

7. Polysome-CAGE of TCL1-driven chronic lymphocytic leukemia revealed multiple N-terminally altered epigenetic regulators and a translation stress signature

   This article has 6 authors:

   1. Ariel Ogran
   2. Tal Havkin-Solomon
   3. Shirly Becker-Herman
   4. Keren David
   5. Idit Shachar
   6. Rivka Dikstein

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, Ogran and colleagues provide evidence suggesting that T-Cell Leukemia/Lymphoma 1 (TCL1) protein may promote alternative transcription site selection and promoter usage in chronic lymphoid leukemia. It is further proposed that these TCL1-dependent alterations lead to the production of N-terminally truncated versions of proteins including chromatin regulators while bolstering expression of transcription factors including MYC. Collectively, it was found that these results are of broad interest inasmuch as they suggest previously unappreciated rewiring of epigenetic, transcriptional, and translational programs in leukemic cells. To this end, this article should be of significant interest across a variety of fields of biomedical research ranging from regulation of gene expression to cancer research. The paper would be strengthened by mechanistic data linking TCL1 to alterations in transcription site selection and/or alternative promoter usage and by stronger validation of the expression of N-truncated proteins and their functional consequences.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

8. Green fluorescent protein-like pigments optimise the internal light environment in symbiotic reef-building corals

   This article has 6 authors:

   1. Elena Bollati
   2. Niclas H Lyndby
   3. Cecilia D'Angelo
   4. Michael Kühl
   5. Jörg Wiedenmann
   6. Daniel Wangpraseurt

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to marine biologists, and has particular relevance to those studying symbiotic corals. The use of compelling experimental optical measurements performed in situ allows testing of previous predictions on protein-based pigments that are found in many coral species. Specifically, the study analyzes the role of two classes of pigments, the Red Fluorescent Proteins (RFPs) and the Chromo proteins. It provides direct measurement data that suggest that RFPs can indeed provide additional light to the symbionts by converting the prevalent blue-green light at depth in orange-red light that penetrates more in the tissues of the polyps, thus increasing the number of photons available for photosynthesis. The authors also provide evidence based on light measurement for a possible photoprotective role of Chromoproteins, although the study does not yet provide any direct evidence for an ecological benefit of such light conversion/light protective functions.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

9. Histone H3 clipping is a novel signature of human neutrophil extracellular traps

   This article has 9 authors:

   1. Dorothea Ogmore Tilley
   2. Ulrike Abuabed
   3. Ursula Zimny Arndt
   4. Monika Schmid
   5. Stefan Florian
   6. Peter R Jungblut
   7. Volker Brinkmann
   8. Alf Herzig
   9. Arturo Zychlinsky

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study describes a new antibody to identify human neutrophil extracellular traps (NETs) also in tissue samples. The paper might not only introduce an important novel tool for many areas of biomedical research, but it also touches cell biological questions of importance. The usefulness of the NET-specific antibody is impressively developed in the paper, while the mechanistic concepts are not yet fully established.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

10. Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxation mechanism

    This article has 2 authors:

    1. Amy Osterman
    2. Alfonso Mondragón

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Osterman and Modragon report the first crystal structure of topoisomerase V in complex with DNA. Topoisomerase V is an unusual protein in that homologs have only been found in the archaeal Methanopyrus genus. The paper is likely of interest to those studying topoisomerase biology and biochemistry, and the wider audience interested in DNA replication and repair transactions.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife