Latest preprint reviews

1. Passive shaping of intra- and intercellular m6A dynamics via mRNA metabolism

   This article has 13 authors:

   1. David Dierks
   2. Ran Shachar
   3. Ronit Nir
   4. Miguel Angel Garcia-Campos
   5. Anna Uzonyi
   6. Ursula Toth
   7. Walter Rossmanith
   8. Lior Lasman
   9. Boris Slobodin
   10. Jacob H Hanna
   11. Yaron Antebi
   12. Ruth Scherz-Shouval
   13. Schraga Schwartz

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study presents a fundamental finding on how levels of m6A levels are controlled, invoking a consolidated model where degradation of modified RNAs in the cytoplasm plays a primary role in shaping m6A patterns and dynamics, rather than needing active regulation by m6A erasers and other related processes. The evidence is compelling and uses transcriptome-wide data and mechanistic modeling. However, it is possible that m6A-erasers will have roles in specific developmental contexts or conditions, so this model may not apply universally.

   Reviewed by eLife

2. CausalXtract: a flexible pipeline to extract causal effects from live-cell time-lapse imaging data

   This article has 10 authors:

   1. Franck Simon
   2. Maria Colomba Comes
   3. Tiziana Tocci
   4. Louise Dupuis
   5. Vincent Cabeli
   6. Nikita Lagrange
   7. Arianna Mencattini
   8. Maria Carla Parrini
   9. Eugenio Martinelli
   10. Hervé Isambert

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     In this fundamental study, the authors describe a new data processing pipeline that can be used to discover causal interactions from time-lapse imaging data. The utility of this pipeline was convincingly illustrated using tumor-on-chip ecosystem data. The newly developed pipeline could be used to better understand cell-cell interactions and could also be applied to perform temporal causal discovery in other areas of science, meaning this work could potentially have a wide range of applications.

   Reviewed by eLife

3. Regulation of lung cancer initiation and progression by the stem cell determinant Musashi

   This article has 10 authors:

   1. Alison G Barber
   2. Cynthia M Quintero
   3. Michael Hamilton
   4. Nirakar Rajbhandari
   5. Roman Sasik
   6. Yan Zhang
   7. Carla F Kim
   8. Hatim Husain
   9. Xin Sun
   10. Tannishtha Reya

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study shows a significant role for Mushashi-2 (Msi2) in lung adenocarcinoma. The authors provided solid data that support the requirement for Msi2 in tumor growth and progression, although the study would have been strengthened by including more patient samples and additional evidence regarding Msi2+ cells being more responsive to transformation. These findings are of interest to both the lung cancer and the RNA binding protein fields.

   Reviewed by eLife

4. Robust variability of grid cell properties within individual grid modules enhances encoding of local space

   This article has 4 authors:

   1. William T Redman
   2. Santiago Acosta-Mendoza
   3. Xue-Xin Wei
   4. Michael J Goard

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study characterizes the variability in spacing and direction of entorhinal grid cells and shows how this variability can be used to disambiguate locations within an environment. These claims are supported by solid evidence, yet some aspects of the methodology should be clarified. This study will be of interest to neuroscientists working on spatial navigation and, more generally, on neural coding.

   Reviewed by eLife

5. A General Mechanism for the General Stress Response in Bacteria

   This article has 9 authors:

   1. Rishika Baral
   2. Kristin Ho
   3. Ramasamy P Kumar
   4. Jesse B Hopkins
   5. Maxwell B Watkins
   6. Salvatore LaRussa
   7. Suhaily Caban-Penix
   8. Logan A Calderone
   9. Niels Bradshaw

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study combines genetic analysis, biochemistry, and structural modeling to reveal new insights into how changes in protein-protein structure activate signal transduction as part of the bacterial general stress response. The data, collected using validated and standard methods, and the interpretations are solid, although additional experimental structural evidence would strengthen the proposed model and its potential application to other systems. This manuscript, which provides multiple avenues for follow-up studies, will be of broad interest to microbiologists, structural biologists, and cell biologists.

   Reviewed by eLife

6. CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function

   This article has 6 authors:

   1. Longxin Xie
   2. Jessica Merjane
   3. Cristian A Bergmann
   4. Jiazhen Xu
   5. Bryan Hurtle
   6. Christopher J Donnelly

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Recent studies have demonstrated that depletion of nuclear TDP-43 leads to loss of its nuclear function resulting in changes in gene expression and splicing of target mRNAs. This study developed a sensitive and robust sensor for TDP-43 activity that should impact the field's ability to monitor whether TDP-43 is functional or not. Though limited to cell culture, the evidence presented is convincing and is the first demonstration that a GFP on/off system can be used to assess TDP-43 mutants as well as loss of soluble TDP-43. The findings are valuable and may represent a novel tool to investigate TDP-43-associated disease mechanisms.

   Reviewed by eLife

7. Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

   This article has 18 authors:

   1. Hong Yang
   2. Cheng Zhang
   3. Woonghee Kim
   4. Mengnan Shi
   5. Metin Kiliclioglu
   6. Cemil Bayram
   7. Ismail Bolat
   8. Özlem Özdemir Tozlu
   9. Cem Baba
   10. Nursena Yuksel
   11. Serkan Yildirim
   12. Shazia Iqbal
   13. Jihad Sebhaoui
   14. Ahmet Hacımuftuoglu
   15. Mathias Uhlen
   16. Jan Boren
   17. Hasan Turkez
   18. Adil Mardinoglu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors present a valuable study exploring the interaction between JNK signaling and high sucrose feeding. The strength of evidence supporting these observations is solid, including multi-tissue transcriptomic and metabolic analyses, followed by network modeling approaches to define the organs and pathways involved. Reviewers provided several suggestions to improve the manuscript including clarifications of model and analyses, as well as explanations for within-group variations and confirming RNA-seq results at the level of metabolite processes highlighted.

   Reviewed by eLife

8. Isobaric crosslinking mass spectrometry technology for studying conformational and structural changes in proteins and complexes

   This article has 2 authors:

   1. Jie Luo
   2. Jeff Ranish

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript presents a valuable new quantitative crosslinking mass spectrometry approach using novel isobaric crosslinkers. The data are solid and the method has potential for a broad application in structural biology if more isobaric crosslinking channels are available and the quantitative information of the approach is exploited in more depth.

   Reviewed by eLife

9. Aberrant FGF signaling promotes granule neuron precursor expansion in SHH subgroup infantile medulloblastoma

   This article has 6 authors:

   1. Odessa R. Yabut
   2. Hector Gomez
   3. Jessica Arela
   4. Jesse Garcia Castillo
   5. Thomas Ngo
   6. Samuel J. Pleasure

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides potentially highly valuable new insight into the role of Fgf signalling in SUFU mutation-linked cerebellar tumors and indicates novel therapeutic interventions via inhibition of Fgf signalling. The evidence supporting the major claims, however, is at this point currently incomplete. A more robust analysis of gene expression patterns and deeper mechanistic insight would significantly enhance this study, which could have wide-ranging implications for the treatment of specific cerebellar tumors.

   Reviewed by eLife

10. Unveiling the Crucial Role of Pro-inflammatory Macrophages in the Immune Network Imbalance of the maternal-fetal interface with Preeclampsia

    This article has 13 authors:

    1. Haiyi Fei
    2. Xiaowen Lu
    3. Zhan Shi
    4. Xiu Liu
    5. Cuiyu Yang
    6. Xiaohong Zhu
    7. Yuhan Lin
    8. Ziqun Jiang
    9. Jianmin Wang
    10. Dong Huang
    11. Liu Liu
    12. Songying Zhang
    13. Lingling Jiang

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      This valuable study investigates the immune system's role in pre-eclampsia. The authors map the immune cell landscape of the human placenta and find an increase in macrophages and Th17 cells in patients with pre-eclampsia. Following mouse studies, the authors suggest that the IGF1-IGF1R pathway might play a role in how macrophages influence T cells, potentially driving the pathology of pre-eclampsia. There is solid evidence in this study that will be of interest to immunologists and developmental biologists, however, some of the conclusions require additional detail and/or more appropriate statistical tests.

    Reviewed by eLife