eLife

Latest preprint reviews

1. Spatially resolved transcriptomics reveals pro-inflammatory fibroblast involved in lymphocyte recruitment through CXCL8 and CXCL10

   This article has 11 authors:

   1. Ana J Caetano
   2. Yushi Redhead
   3. Farah Karim
   4. Pawan Dhami
   5. Shichina Kannambath
   6. Rosamond Nuamah
   7. Ana A Volponi
   8. Luigi Nibali
   9. Veronica Booth
   10. Eleanor M D'Agostino
   11. Paul T Sharpe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The findings of this article provide valuable information on the spatial dynamics of the human oral mucosa in chronic inflammatory disease. The strength of evidence presented is solid and should yield a better understanding of common mucosal diseases in humans.

   Reviewed by eLife

2. Toward a more informative representation of the fetal–neonatal brain connectome using variational autoencoder

   This article has 4 authors:

   1. Jung-Hoon Kim
   2. Josepheen De Asis-Cruz
   3. Dhineshvikram Krishnamurthy
   4. Catherine Limperopoulos

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents an application of a deep learning approach (adult-trained variational autoencoder) to describe the development of the functional brain connectome in human fetuses and neonates. The results suggest that this may lead to a better characterization of the complex patterns of brain maturation during this period. The evidence is convincing but the impact of other confounding factors in addition to maturation on the results could be explored and further analysis should be considered to highlight how this method can account for non-linear patterns of development, as well as the biological plausibility of the observed brain states. This work is of potential methodological interest to researchers exploring functional brain networks and brain development notably with deep learning.

   Reviewed by eLife

3. The SARS-CoV-2 accessory protein Orf3a is not an ion channel, but does interact with trafficking proteins

   This article has 14 authors:

   1. Alexandria N Miller
   2. Patrick R Houlihan
   3. Ella Matamala
   4. Deny Cabezas-Bratesco
   5. Gi Young Lee
   6. Ben Cristofori-Armstrong
   7. Tanya L Dilan
   8. Silvia Sanchez-Martinez
   9. Doreen Matthies
   10. Rui Yan
   11. Zhiheng Yu
   12. Dejian Ren
   13. Sebastian E Brauchi
   14. David E Clapham

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The function of specific proteins made by SARS-CoV-1 and SARS-CoV-2 is under debate, with diverging claims previously published regarding the ability of Orf3a proteins from either virus to form ion channels. The authors undertook a thorough characterization of Orf3a from CoV-1 and CoV-2 by combining data from a range of different structural and functional experiments, arguably providing the most compelling evidence to date that Orf3a from viruses is not an ion channel. Instead, the orthologue-specific interaction with a component of a larger protein complex suggests a role of one of the two membrane proteins in the endo-lysosomal pathway. The work is significant from a fundamental science perspective, for its implications for COVID antiviral development strategies, and also for establishing guidelines for future identification of true viral ion channels.

   Reviewed by eLife

4. Flexible coding of time or distance in hippocampal cells

   This article has 6 authors:

   1. Shai Abramson
   2. Benjamin J Kraus
   3. John A White
   4. Michael E Hasselmo
   5. Dori Derdikman
   6. Genela Morris

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript by Abramson and colleagues is a new analysis of previously published data from experiments in which rats ran on a treadmill in either fixed-time or fixed-distance trials. The valuable results provide solid evidence to demonstrate that time and distance cells are more common in fixed-time and fixed-distance trials, respectively. These findings suggest that the hippocampus flexibly shifts between representing variables depending on their relevance.

   Reviewed by eLife

5. Growth cone advance requires EB1 as revealed by genomic replacement with a light-sensitive variant

   This article has 5 authors:

   1. Alessandro Dema
   2. Rabab Charafeddine
   3. Shima Rahgozar
   4. Jeffrey van Haren
   5. Torsten Wittmann

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In their manuscript, Dema et al. showcase an important tool to study the role of the microtubule end-binding protein, EB1. This important study is the first to locally inactivate EB1 in human neurons, and while the authors have previously published the effects of replacing endogenous EB1 with a light-sensitive variant, the novelty in this current study is that they use a one-step gene editing replacement method in addition to using human neurons derived from iPSCs. The data is of high quality and the evidence supporting the conclusions is solid, although including more controls are needed to strengthen the study. The findings of this work will be of interest to cell biologists and neurobiologists, while the methods utilized will have an even broader general interest.

   Reviewed by eLife

6. A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma

   This article has 9 authors:

   1. Haley R Noonan
   2. Alexandra M Thornock
   3. Julia Barbano
   4. Michael E Xifaras
   5. Chloe S Baron
   6. Song Yang
   7. Katherine Koczirka
   8. Alicia M McConnell
   9. Leonard I Zon

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable enhancer reporter of TGFb signaling in melanoma that has a conserved function in both human cell lines and zebrafish. The reporter data is solid and provides interesting insights into TGFb targets in melanoma. However, the model that macrophages preferentially phagocytose certain subsets of melanoma cells is still incomplete, and more data will be needed before this process is clearly understood.

   Reviewed by eLife

7. The dark kinase STK32A regulates hair cell planar polarity opposite of EMX2 in the developing mouse inner ear

   This article has 7 authors:

   1. Shihai Jia
   2. Evan M Ratzan
   3. Ellison J Goodrich
   4. Raisa Abrar
   5. Luke Heiland
   6. Basile Tarchini
   7. Michael R Deans

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study advances our understanding of the molecular players downstream of the transcription factor Emx2 that establish planar cell polarity in hair cells of the mammalian inner ear. The conclusions, which are supported by compelling evidence, will be of interest to those studying the development and function of the vestibular system and mechanisms of planar cell polarity.

   Reviewed by eLife

8. High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter

   This article has 7 authors:

   1. Shamayeeta Ray
   2. Samuel P Berry
   3. Eric A Wilson
   4. Casey H Zhang
   5. Mrinal Shekhar
   6. Abhishek Singharoy
   7. Rachelle Gaudet

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript provides fundamental new insight into protein conformational transitions underlying the transport mechanism of Nramps, an important and widespread transporter family that facilitates the uptake and movement of essential transition metals. Eight new crystallographic structures of the prokaryotic homolog draNRMP in a variety of ligand-bound and conformational states, along with companion molecular dynamics simulations and metal binding and transport assays, provide compelling evidence supporting most of the conclusions. These findings will be of broad interest to scientists studying transport mechanisms and ligand recognition.

   Reviewed by eLife

9. Inferential eye movement control while following dynamic gaze

   This article has 2 authors:

   1. Nicole Xiao Han
   2. Miguel Patricio Eckstein

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important work substantially advances our understanding of how human eye movements are shaped by social cues. Using clever experimental manipulations and innovative artificial intelligence analysis tools, the paper identifies distinctive patterns of saccadic eye movements tracking another person's gaze during dynamic video-scene viewing. This work will be of broad interest to psychologists, biologists, and neuroscientists interested in human social behavior.

   Reviewed by eLife

10. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence

    This article has 3 authors:

    1. Zachary Baker
    2. Molly Przeworski
    3. Guy Sella

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This study reports an important theoretical model with simulations of meiotic recombination hotspots and Prdm9 evolution. By integrating recently identified biological properties of Prdm9, the model provides compelling evidence for novel features of hotspots and Prdm9 evolution. Yet, the model, the different steps in implementing parameters, and the predictions are difficult to follow and would benefit from clarification.

    Reviewed by eLife