eLife

Latest preprint reviews

1. Population analyses reveal heterogenous encoding in the medial prefrontal cortex during naturalistic foraging

   This article has 2 authors:

   1. Ji Hoon Jeong
   2. June-Seek Choi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study by Jeong and Choi studied neural activity in the medial prefrontal cortex (mPFC) while rats performed a foraging paradigm in which they forage for rewards in the absence or presence of a threatening object (Lobsterbot). The authors present interesting observations suggesting that the mPFC population activity switches between distinct functional modes conveying distinct task variables- such as the distance to the reward location and types of threat-avoidance behaviors-depending on the location of the animal. Although the specific information represented by individual neurons remains to be clarified through further investigation, the reviewers thought that this study is solid, appreciated the value of studying neural coding in naturalistic settings, and felt that this work offers significant insights into how the mPFC operates during foraging behavior involving reward-threat conflict.

   Reviewed by eLife

2. Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons

   This article has 10 authors:

   1. Ricardo Raudales
   2. Gukhan Kim
   3. Sean M Kelly
   4. Joshua Hatfield
   5. Wuqiang Guan
   6. Shengli Zhao
   7. Anirban Paul
   8. Yongjun Qian
   9. Bo Li
   10. Z Josh Huang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors develop a novel genetic strategy for specific and comprehensive labeling of axo-axonic cells, also referred to as chandelier cells, in the mouse brain. The approach and analysis are rigorous such that the data convincingly support the key conclusions, including the expanded distribution of axo-axonic cells throughout the brain. This study provides important new information about the distribution of a significant neuronal cell type, as well as new tools for future studies. This work will be of broad interest to neuroscientists who work on the anatomical and functional organization of neural circuits.

   Reviewed by eLife

3. Identification and characterization of intermediate states in mammalian neural crest cell epithelial to mesenchymal transition and delamination

   This article has 9 authors:

   1. Ruonan Zhao
   2. Emma L Moore
   3. Madelaine M Gogol
   4. Jay R Unruh
   5. Zulin Yu
   6. Allison R Scott
   7. Yan Wang
   8. Naresh K Rajendran
   9. Paul A Trainor

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This fundamental study reports compelling findings that intermediate states exist in epithelial-mesenchymal transition (EMT) during natural development and differentiation of mammalian neural crest cells, similar to recent reports in cancer. The authors determined that there were at least two paths to delamination and migration - one that occurs during S-phase of cell cycle and another during G2/M phase, and that the process of delamination is not restricted to cell fate. Finally, the authors showed that expression of Dlc1 may be used to identify cells in an intermediate state of EMT as well as their spatial location in the mouse embryo. The work will be of interest to developmental biologists, neurobiologists and cancer researchers.

   Reviewed by eLife

4. Revealing intact neuronal circuitry in centimeter-sized formalin-fixed paraffin-embedded brain

   This article has 16 authors:

   1. Ya-Hui Lin
   2. Li-Wen Wang
   3. Yen-Hui Chen
   4. Yi-Chieh Chan
   5. Shang-Hsiu Hu
   6. Sheng-Yan Wu
   7. Chi-Shiun Chiang
   8. Guan-Jie Huang
   9. Shang-Da Yang
   10. Shi-Wei Chu
   11. Kuo-Chuan Wang
   12. Chin-Hsien Lin
   13. Pei-Hsin Huang
   14. Hwai-Jong Cheng
   15. Bi-Chang Chen
   16. Li-An Chu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The reprocessing and reanalysis of archived samples can yield further insights from past experiments. Here, a useful procedure to perform tissue clearing and immunolabeling on large-scale formalin-fixed paraffin-embedded brain specimens is convincingly evaluated on a set of archival pathology specimens, and its applicability to further such samples is analyzed. This method will be of interest to both neuroscientists and pathologists.

   Reviewed by eLife

5. Mono-methylated histones control PARP-1 in chromatin and transcription

   This article has 4 authors:

   1. Gbolahan Bamgbose
   2. Guillaume Bordet
   3. Niraj Lodhi
   4. Alexei Tulin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study presents convincing evidence for an association between PARP-1 and H4K20me1 in transcriptional regulation, supported by biochemical and ChIP-seq analyses. The work contributes significantly to our understanding of how Parp1 associates with target genes to regulate their expression.

   Reviewed by eLife

6. Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level

   This article has 6 authors:

   1. Hina Khan
   2. Partha Paul
   3. Harsh Goar
   4. Bhanwar Bamniya
   5. Navin Baid
   6. Dibyendu Sarkar

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study describes how PhoP regulates cyclic-AMP production in the human pathogen Mycobacterium tuberculosis. The authors provide convincing evidence that PhoP acts as a repressor of the cyclic-AMP-specific phosphodiesterase, Rv0805, which can degrade cyclic-AMP. The revised manuscript has addressed all outstanding comments and the work will be of interest to bacteriologists.

   Reviewed by eLife

7. Genome-scale annotation of protein binding sites via language model and geometric deep learning

   This article has 3 authors:

   1. Qianmu Yuan
   2. Chong Tian
   3. Yuedong Yang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors introduce a valuable machine-learning model for predicting binding sites of diverse ligands, including DNA, RNA, peptides, proteins, ATP, HEM, and metal ions, on proteins. The method is freely accessible and user-friendly. The authors have conducted thorough benchmarking and ablation studies, providing convincing evidence of the model's overall performance, despite some imperfections of the comparisons to other methods that arise from intrinsic differences between training methods and data.

   Reviewed by eLife

8. A syngeneic spontaneous zebrafish model of tp53-deficient, EGFRvIII, and PI3KCAH1047R-driven glioblastoma reveals inhibitory roles for inflammation during tumor initiation and relapse in vivo

   This article has 4 authors:

   1. Alex Weiss
   2. Cassandra D'Amata
   3. Bret J Pearson
   4. Madeline N Hayes

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a valuable syngeneic zebrafish model for studying glioblastoma and will be of interest to neuro-oncologists and cancer biologists. Using a feasible in vivo model to study the tumour microenvironment, cell/cell interaction, and immunity, the data are compelling, and opens up new lines of inquiries for future investigation on the impact of efferocytosis on tumor progression and cell of origin in this model as well as assessments of drug resistance mechanisms, using inhibitors to MAPK , Akt and/or mTOR pathway.

   Reviewed by eLife

9. When abstract becomes concrete, naturalistic encoding of concepts in the brain

   This article has 3 authors:

   1. Viktor Nikolaus Kewenig
   2. Gabriella Vigliocco
   3. Jeremy I Skipper

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Kewenig et al. present a timely and valuable study that extends prior research investigating the neural basis of abstract and concrete concepts by examining how these concepts are processed in a naturalistic stimulus: during movie watching. The authors provide convincing evidence that the varying strength of the relationship between a word and a particular visual scene is associated with a change in the similarity between the brain regions active for concrete and abstract words. This work makes a contribution that will be of general interest within any field that faces the inherent challenge of quantifying context in a multimodal stimulus.

   Reviewed by eLife

10. A previously undescribed scene-selective site is the key to encoding ego-motion in naturalistic environments

    This article has 4 authors:

    1. Bryan Kennedy
    2. Sarala N Malladi
    3. Roger BH Tootell
    4. Shahin Nasr

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      In this manuscript, the authors present a wealth of fMRI data at both 3T and 7T to identify a scene-selective region of the intraparietal gyrus ("PIGS") that appears to have some responsivity to characteristics of ego-motion. In a series of experiments, they delineate the anatomical location of PIGS and functionally differentiate it from nearby V6 and OPA. Evidence for these important findings is solid, but further investigations as to the role of this region in processing ego-motion will be needed to confirm this conclusion.

    Reviewed by eLife