eLife

Latest preprint reviews

1. Inhibition of SARS-CoV-2 polymerase by nucleotide analogs: a single molecule perspective

   This article has 20 authors:

   1. Mona Seifert
   2. Subhas Chandra Bera
   3. Pauline van Nies
   4. Robert N. Kirchdoerfer
   5. Ashleigh Shannon
   6. Thi-Tuyet-Nhung Le
   7. Xiangzhi Meng
   8. Hongjie Xia
   9. James M. Wood
   10. Lawrence D. Harris
   11. Flávia S. Papini
   12. Jamie J. Arnold
   13. Steven C. Almo
   14. Tyler L. Grove
   15. Pei-Yong Shi
   16. Yan Xiang
   17. Bruno Canard
   18. Martin Depken
   19. Craig E. Cameron
   20. David Dulin

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work presented in this manuscript paper may advance our understanding of an important class of anti-viral drugs (nucleoside analogs) that target polymerase enzymes by being directly incorporated into the product strand. This class of drugs is known to be quite diverse in their precise mechanisms of action, yet many of the particular details have remained elusive, often due to experimental limitations. The current study employs a single-molecule magnetic-tweezers platform to provide a new paradigm for the mechanism of drug remdesivir against the SARS-CoV-2 polymerase target. The authors propose that remdesivir does not prevent the complete viral RNA synthesis but causes an increase of polymerase pausing and back tracking. This paper is of broad interest to readers and scientists working on SARS-CoV-2 and general nucleotide inhibitors. The work includes the single molecule characterization of other NAs.

     (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, ScreenIT

2. Neuropsychological evidence of multi-domain network hubs in the human thalamus

   This article has 5 authors:

   1. Kai Hwang
   2. James M Shine
   3. Joel Bruss
   4. Daniel Tranel
   5. Aaron Boes

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Hwang et al. address the important question about whether specific thalamic sub-regions serve as essential "hubs" for interconnecting diverse cognitive processes. Using a group of patients with isolated thalamic lesions (n=20), and a group of size-matched lesions outside the thalamus (n=42), they report that lesions to the anterior-medio-dorsal thalamus are most likely to cause widespread cognitive deficit. Evidence from existing task-based and resting-state fMRI data sets, as well as data sets on gene expression further provide evidence the importance of these regions as a network hub for domain general cognitive 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

3. Members of the ELMOD protein family specify formation of distinct aperture domains on the Arabidopsis pollen surface

   This article has 6 authors:

   1. Yuan Zhou
   2. Prativa Amom
   3. Sarah H Reeder
   4. Byung Ha Lee
   5. Adam Helton
   6. Anna A Dobritsa

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     How pollen apertures are formed is not well understood. By studying Arabidopsis mutants producing pollen with aberrant aperture numbers, the authors identify proteins from the ELMOD protein family as important regulators for aperture formation. They use genetics, transgenic constructs, and site-directed mutagenesis to pinpoint important residues for protein function in this process, and show that changes in expression levels of one protein can have dramatic effects on patterning. This paper will interest scientists interested in cell polarity, patterning, and evolution of diverse morphologies. This is also the first study of the ELMOD protein family, whose potential GTPase activating activities have not yet been investigated in plants.

     (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 and Reviewer #2 agreed to share their names with the authors.)

   Reviewed by eLife

4. Profiling sensory neuron microenvironment after peripheral and central axon injury reveals key pathways for neural repair

   This article has 6 authors:

   1. Oshri Avraham
   2. Rui Feng
   3. Eric Edward Ewan
   4. Justin Rustenhoven
   5. Guoyan Zhao
   6. Valeria Cavalli

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Using single cell RNA seq, the authors characterize the sensory neuron microenvironment in dorsal root ganglia after sciatic nerve crush, dorsal root crush and dorsal column transection spinal cord injury 3 days after injury. The data revealed differentially expressed genes and pathways with sciatic nerve and dorsal root crushes co-clustering, whereas spinal cord injury largely co-clusters with uninjured. The results reveal influences of the tissue microenvironment and neuron extrinsic factors on axonal regeneration and also provide new insights into the role of PPARa signaling in regeneration after dorsal root crush. This is an impressive data collection effort across multiple cell types that will be of importance for generating new hypotheses in the field. The impact could be further broadened by increased attention to functional validation of the findings.

     (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. External signals regulate continuous transcriptional states in hematopoietic stem cells

   This article has 12 authors:

   1. Eva M Fast
   2. Audrey Sporrij
   3. Margot Manning
   4. Edroaldo Lummertz Rocha
   5. Song Yang
   6. Yi Zhou
   7. Jimin Guo
   8. Ninib Baryawno
   9. Nikolaos Barkas
   10. David Scadden
   11. Fernando Camargo
   12. Leonard I Zon

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an interesting resource paper, describing the response of hematopoietic stem and progenitor cells to a few drugs commonly used to stress hematopoiesis. Transcriptomic analyses reveal interesting patterns, and the authors use ATAC-seq to investigate whether stem and progenitor subpopulations may be primed to respond in specific ways based on their chromatin accessibility. This turns out not to be the case when directly responsive genes are analyzed, and rather differences can be found in the promoter accessibility of genes further downstream.

     (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

6. RNA splicing programs define tissue compartments and cell types at single-cell resolution

   This article has 12 authors:

   1. Julia Eve Olivieri
   2. Roozbeh Dehghannasiri
   3. Peter L Wang
   4. SoRi Jang
   5. Antoine de Morree
   6. Serena Y Tan
   7. Jingsi Ming
   8. Angela Ruohao Wu
   9. Tabula Sapiens Consortium
   10. Stephen R Quake
   11. Mark A Krasnow
   12. Julia Salzman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes an analysis of cell type-specific alternative splicing using 10x scRNA-seq data. This work shows that in spite of the challenges associated with the analysis of such datasets, it is possible to identify alternative exons with differential splicing between tissue compartments and to some extent reveal cell types by splicing profiles of single cells. This work is informative regarding what can be done to analyse alternative splicing using 10X data and fills in a gap in the field.

     (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. Quantitative theory for the diffusive dynamics of liquid condensates

   This article has 8 authors:

   1. Lars Hubatsch
   2. Louise M Jawerth
   3. Celina Love
   4. Jonathan Bauermann
   5. TY Dora Tang
   6. Stefano Bo
   7. Anthony A Hyman
   8. Christoph A Weber

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of broad interest to chemists and biologists studying complex coacervate systems, including biomolecular condensates. Its model provides a new way of obtaining diffusion properties inside and outside the condensates without the necessity of nontrivial assumptions. The model's capability is well presented by applying to experimental data and through further investigating the model through simulations.

     (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. The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas

   This article has 15 authors:

   1. Peter Neofotis
   2. Joshua Temple
   3. Oliver L Tessmer
   4. Jacob Bibik
   5. Nicole Norris
   6. Eric Pollner
   7. Ben Lucker
   8. Sarathi M Weraduwage
   9. Alecia Withrow
   10. Barbara Sears
   11. Greg Mogos
   12. Melinda Frame
   13. David Hall
   14. Joseph Weissman
   15. David M Kramer

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Many algae, such as Chlamydomonas, form a pyrenoid under certain conditions to enable high photosynthetic rates during inorganic carbon limitation. The data presented here support that hydrogen peroxide, a common by-product of hyperoxia and CO2 limitation, induces pyrenoid formation in Chlamydomonas, even when CO2 levels are high. Although the underlying genetic mechanisms remain unresolved, these observations offer an exciting starting point to dissect the molecular components that drive pyrenoid formation. Therefore, this paper is of interest to a broad audience of scientists working in the areas of photosynthesis, synthetic biology of agriculture, and algal biotechnology.

     (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

9. Simultaneous brain, brainstem, and spinal cord pharmacological-fMRI reveals involvement of an endogenous opioid network in attentional analgesia

   This article has 5 authors:

   1. Valeria Oliva
   2. Ron Hartley-Davies
   3. Rosalyn Moran
   4. Anthony E Pickering
   5. Jonathan CW Brooks

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of great interest to researchers interested in cognitive modulations of sensory processing as well as in the brain mechanisms of pain. It shows that attentional modulations of pain are associated with changes in neural communication between cortical areas, brainstem and spinal cord which are sensitive to opioidergic but not to noradrenergic modulations. These findings are conclusively supported by state-of-the-art simultaneous pharmacological fMRI of the brain and the spinal cord.

     (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

10. A novel bivalent chromatin associates with rapid induction of camalexin biosynthesis genes in response to a pathogen signal in Arabidopsis

    This article has 5 authors:

    1. Kangmei Zhao
    2. Deze Kong
    3. Benjamin Jin
    4. Christina D Smolke
    5. Seung Yon Rhee

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study proposes the identification of "bivalent chromatin" in genes associated with the biosynthesis of secondary metabolites in Arabidopsis and describes an investigation into the role of chromatin states in the regulation of the major Arabidopsis phytoalexin. Perturbation of either H3K27me3 or H3K18ac levels using mutants were used to show that there were effects on the expression of these metabolic genes. It has previously been shown that H3K27me3 and H3K18ac colocalize in the Arabidopsis genome and that genes targeted by PRC2/H3K27me3 in Arabidopsis are enriched for genes that respond to the environment and/or developmental cues. Therefore, the reported changes to the regulation of these genes in defective mutants are as expected, although the finding of this study will still be of interest to those working on pathogen-induced changes to plant metabolism.

      (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