eLife

Latest preprint reviews

1. GTPase activating protein DLC1 spatio-temporally regulates Rho signaling

   This article has 5 authors:

   1. Max Heydasch
   2. Lucien Hinderling
   3. Jakobus van Unen
   4. Maciej Dobrzynski
   5. Olivier Pertz

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable finding on how the GAP DLC1, a deactivator of the small GTPase RhoA, regulates RhoA activity globally as well as at Focal Adhesions. Using a new acute optogenetic system coupled to a RhoA activity biosensor, the authors present solid evidence that DLC1 amplifies local Rho activity at Focal Adhesions. Nevertheless, the proposed mechanism could be further supported by a deeper analysis of the data.

   Reviewed by eLife

2. Microglia facilitate and stabilize the response to general anesthesia via modulating the neuronal network in a brain region-specific manner

   This article has 15 authors:

   1. Yang He
   2. Taohui Liu
   3. Quansheng He
   4. Wei Ke
   5. Xiaoyu Li
   6. Jinjin Du
   7. Suixin Deng
   8. Zhenfeng Shu
   9. Jialin Wu
   10. Baozhi Yang
   11. Yuqing Wang
   12. Ying Mao
   13. Yanxia Rao
   14. Yousheng Shu
   15. Bo Peng

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable finding on the mechanisms underlying general anesthesia, with a focus on microglial regulation. The evidence supporting the claims of the authors is solid, although some of the novelty of these findings may be reduced based on the recent publication of a similar study. The work will be of interest to medical biologists working on mechanisms of anesthesia, microglia, and neuron-microglia interaction.

   Reviewed by eLife

3. Protein language model-embedded geometric graphs power inter-protein contact prediction

   This article has 2 authors:

   1. Yunda Si
   2. Chengfei Yan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a useful deep learning-based inter-protein contact prediction method named PLMGraph-Inter which combines protein language models and geometric graphs. The evidence supporting the claims of the authors is solid. The authors show that their approach may be used in cases where AlphaFold-Multimer performs poorly. This work will be of interest to researchers working on protein complex structure prediction, particularly when accurate experimental structures are available for one or both of the monomers in isolation.

   Reviewed by eLife

4. Genome-wide Functional Characterization of Escherichia coli Promoters and Sequence Elements Encoding Their Regulation

   This article has 9 authors:

   1. Guillaume Urtecho
   2. Kimberly D. Insigne
   3. Arielle D. Tripp
   4. Marcia S. Brinck
   5. Nathan B. Lubock
   6. Christopher Acree
   7. Hwangbeom Kim
   8. Tracey Chan
   9. Sriram Kosuri

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Urtecho et al. use genome-integrated massively parallel reporter assays to catalog and characterize promoters throughout the Escherichia coli genome. The result is a state-of-the-art atlas of promoters, coupled with information on their regulation, that is readily accessible through the website http://ecolipromoterdb.com. This compelling work provides an important resource for researchers studying bacterial transcriptional regulation.

   Reviewed by eLife

5. Sensorimotor mechanisms selective to numerosity derived from individual differences

   This article has 5 authors:

   1. Giovanni Anobile
   2. Irene Petrizzo
   3. Daisy Paiardini
   4. David Burr
   5. Guido Marco Cicchini

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This potentially important paper addresses the question of how numerical information is represented in the human brain. Experimental findings are interpreted as providing evidence for a sensorimotor mechanism that involves channels, each tuned to a particular numerical range. While this is an interesting application of methodologies used to identify the presence of channels, the evidence supporting the claim that these have a sensorimotor basis is incomplete.

   Reviewed by eLife

6. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2112.05098

7. The reuniens nucleus of the thalamus facilitates hippocampo-cortical dialogue during sleep

   This article has 6 authors:

   1. Diellor Basha
   2. Amirmohammad Azarmehri
   3. Elian Proulx
   4. Sylvain Chauvette
   5. Maryam Ghorbani
   6. Igor Timofeev

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The important manuscript presents convincing evidence of temporal correlations during specific oscillatory activity between the prefrontal cortex, thalamic nucleus reuniens, and the hippocampus, in naturally sleeping animals. Such correlations represent solid evidence to support the notion that the thalamic nucleus reuniens participates in the hippocampal and prefrontal cortex dialogue subserving memory processes.

   Reviewed by eLife

8. Sex differences in discrimination behavior and orbitofrontal engagement during context-gated reward prediction

   This article has 5 authors:

   1. Sophie Peterson
   2. Amanda Maheras
   3. Brenda Wu
   4. Jose Chavira
   5. Ronald Keiflin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable manuscript reveals sex differences in bi-conditional Pavlovian learning and conditional behavior. Males learn hierarchical context-cue-outcome associations more quickly, but females show more stable and robust task performance. These sex differences are related to cellular activation in the orbitofrontal cortex. Although the evidence supporting these claims is convincing, some assertions of sex differences in context-dependent discrimination behaviour may be slightly overstated yet have strong potential to guide future research to clarify the nature of these differences. The results will be of interest to many behavioural neuroscientists, particularly those who investigate sex-specific behaviours.

   Reviewed by eLife

9. A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

   This article has 4 authors:

   1. Arkadiy K Golov
   2. Alexey A Gavrilov
   3. Noam Kaplan
   4. Sergey V Razin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Identifying chromatin interactions with high sensitivity and resolution at the genome-wide scale continues to be technically challenging. This study introduces findings based on the improved MNase-based proximity ligation method, MChIP-C, which enables genome-wide measurement of chromatin interactions at single-nucleosome resolution. The evidence presented in this manuscript is convincing, and the technological advancements will be valuable for the study of 3D genome architecture.

   Reviewed by eLife

10. Biobank-wide association scan identifies risk factors for late-onset Alzheimer’s disease and endophenotypes

    This article has 19 authors:

    1. Donghui Yan
    2. Bowen Hu
    3. Burcu F Darst
    4. Shubhabrata Mukherjee
    5. Brian W Kunkle
    6. Yuetiva Deming
    7. Logan Dumitrescu
    8. Yunling Wang
    9. Adam Naj
    10. Amanda Kuzma
    11. Yi Zhao
    12. Hyunseung Kang
    13. Sterling C Johnson
    14. Cruchaga Carlos
    15. Timothy J Hohman
    16. Paul K Crane
    17. Corinne D Engelman
    18. Alzheimer’s Disease Genetics Consortium (ADGC)
    19. Qiongshi Lu

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      In the last 15 years, large-scale association studies (GWAS) have served to estimate the association between genome-wide common variants and a large number of disparate traits and diseases in humans. This valuable method provides a new way to find correlations between the genetic component of a phenotype of interest, and all this wealth of genetic information. This software adds as a new tool to investigate genetic correlation between traits, and to generate new mechanistic hypotheses and dissect the role of the observed associations in disease heterogeneity. The results of the application of their method are solid and generally agree with what others have seen using similar AD and UKB data.

    Reviewed by eLife