eLife

Latest preprint reviews

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. Adult stem cells and niche cells segregate gradually from common precursors that build the adult Drosophila ovary during pupal development

   This article has 5 authors:

   1. Amy Reilein
   2. Helen V Kogan
   3. Rachel Misner
   4. Karen Sophia Park
   5. Daniel Kalderon

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript describes a very extensive set of experiments charting the origin and fate of various cell populations in the Drosophila ovary that is a powerful system to explore interactions between adult stem cells and their niches. The authors put forward a new view of how different cell types acquire their fates during development. This is a more nuanced view than extant models, involving common progenitors from which different cell fates (stem cell, progeny and niche cells) arise gradually and relying on spatiotemporal cues.

     (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

8. Gut bacterial aggregates as living gels

   This article has 2 authors:

   1. Brandon H Schlomann
   2. Raghuveer Parthasarathy

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript provides an innovative merging of biophysical models with imaging data to explain the physical structure of microbial communities in the gut of zebrafish. Using imaging data to examine cluster sizes for eight different bacterial strains in the larval zebrafish gut, the authors report a common family of size distributions and show that these distributions arise naturally from a simple biophysical model of aggregation that tends to condense the system to a single massive cluster, reminiscent of gel formation observed in non-living systems. Within-host microbial dynamics represent an area of tremendous interest, as the microbiome is increasingly recognized to play a role in host physiology. This work contributes to a new perspective by elucidating physical mechanisms driving spatial segregation of these communities, opening the door to future studies that incorporate traditional genomic and microbiological insight with the physical and mechanical dynamics of microbial communities in living hosts.

     (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 #3 agreed to share their names with the authors.)

   Reviewed by eLife

9. Schema representations in distinct brain networks support narrative memory during encoding and retrieval

   This article has 3 authors:

   1. Rolando Masís-Obando
   2. Kenneth A Norman
   3. Christopher Baldassano

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper reports a methodologically rigorous investigation into the neural mechanisms supporting encoding and retrieval of specific and general information in the context of memory schemas for events, or "scripts." Its findings will be of general interest to neuroscientists and cognitive psychologists who work both with typical young adults (as studied int he present works) and in particular populations (e.g., development and/or aging; patients with brain damage). The work is particularly comprehensive in how it links both specific and general narrative representation at both encoding and retrieval with later memory behavior, which is a notable strength.

     (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. Microglia and CD206+ border-associated mouse macrophages maintain their embryonic origin during Alzheimer’s disease

    This article has 5 authors:

    1. Xiaoting Wu
    2. Takashi Saito
    3. Takaomi C Saido
    4. Anna M Barron
    5. Christiane Ruedl

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This study by Wu et al., examined in a mouse model of Alzheimer how the lifespan and kinetics of both border-associated myeloid cells and microglia are affected. Taken together, these data provide evidence on the replenishment of CNS-associated myeloid cells under both steady-state and pathology.

      (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