eLife

Latest preprint reviews

1. A simplified and highly efficient cell-free protein synthesis system for prokaryotes

   This article has 5 authors:

   1. Xianshengjie Lang
   2. Changbin Zhang
   3. Jingxuan Lin
   4. Zhe Zhang
   5. Wenfei Li

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The study presents valuable findings of an optimized E. coli cell-free protein synthesis (eCFPS) system that has been simplified by reducing the number of core components from 35 to 7; furthermore, the findings communicate a simplified 'fast lysate' preparation that eliminates the need for traditional runoff and dialysis steps. This study is an advance towards simplifying protein expression workflows, and the evidence provided is solid, starting with nanoluc, a protein that expresses readily in many systems, to applications to more challenging proteins like the functional self-assembling vimentin and the active restriction endonuclease Bsal. Data on the underlying mechanisms and efficiency of the presented system in terms of protein yield relative to other known cell-free systems would greatly enhance the findings' significance and the strength of the evidence. The paper remains of interest to scientists in microbiology, biotechnology and protein synthesis.

   Reviewed by eLife

2. A retrospective analysis of 400 publications reveals patterns of irreproducibility across an entire life sciences research field

   This article has 12 authors:

   1. Joseph Lemaitre
   2. Désirée Popelka
   3. Blandine Ribotta
   4. Hannah Westlake
   5. Sveta Chakrabarti
   6. Li Xiaoxue
   7. Mark A. Hanson
   8. Haobo Jiang
   9. Francesca Di Cara
   10. Estee Kurant
   11. Fabrice David
   12. Bruno Lemaitre

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study presents an impressive large-scale effort to assess the reproducibility of published findings in the field of Drosophila immunity. The authors analyse 400 papers published between 1959 and 2011, and assess how many of the claims in these papers have been tested in subsequent publications. In a companion article they report the results of experiments to test a subset of the claims that, according to the literature, have not been tested. The present article also explores if various factors related to authors, institutions and journals influence reproducibility in this field. The evidence supporting the claims is solid, but there is considerable scope for strengthening and extending the analysis. The limitations inherent to evaluating reproducibility based on the published literature should also be acknowledged.

   Reviewed by eLife

3. Defining the chromatin-associated protein landscapes on Trypanosoma brucei repetitive elements using synthetic TALE proteins

   This article has 8 authors:

   1. Roberta Carloni
   2. Tadhg Devlin
   3. Pin Tong
   4. Christos Spanos
   5. Tanya Auchynnikava
   6. Juri Rappsilber
   7. Keith R. Matthews
   8. Robin C. Allshire

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work significantly advances our understanding of chromatin organization within regions of repetitive sequences in the parasitic protozoan Trypanosoma brucei. Using cutting edge interdisciplinary tools, the authors provide compelling evidence for two discrete types of repetitive DNA element-associated proteins- one set involved in essential centromere function; and, the other involved in glycoprotein antigenic variation via homologous recombination. Thus, these fundamental findings have implications for this parasite's biology, and for therapeutic targeting in kinetoplastid diseases. This work will be exciting to those in the centromere/mitosis and parasite immunity fields.

   Reviewed by eLife, Review Commons

4. Microbiota/gut/neuron axis promotes Drosophila ageing via Acetobacter, Tachykinin, and TkR99D

   This article has 7 authors:

   1. Diana Marcu
   2. David R Sannino
   3. Anthony J Dornan
   4. Rita Ibrahim
   5. Atharv Kapoor
   6. Miriam Wood
   7. Adam J Dobson

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study demonstrates that in Drosophila melanogaster, tachykinin (Tk) expression is regulated by the microbiota. The authors present convincing evidence that axenic flies raised with no microbiota are longer-lived than conventionally reared animals, and that Tk expression and Tk receptors in the nervous system are required for this effect. They further test individual bacterial strains for their role in these effects and connect the effect to loss of lipid stores and suggest that FOXO may be involved in the phenotype, results that are of interest to the fields of environmental perception, host microbiome interactions, and geroscience.

     [Editors' note: this paper was reviewed by Review Commons.]

   Reviewed by eLife, Review Commons

5. THE FAM53C/DYRK1A axis regulates the G1/S transition of the cell cycle

   This article has 15 authors:

   1. Taylar Hammond
   2. Jong Bin Choi
   3. Miles W Membreño
   4. Janos Demeter
   5. Roy Ng
   6. Debadrita Bhattacharya
   7. Thuyen N Nguyen
   8. Griffin G Hartmann
   9. Caterina I Colón
   10. Carine Bossard
   11. Jan M Skotheim
   12. Peter K Jackson
   13. Anca Pasca
   14. Seth M Rubin
   15. Julien Sage

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study identifies the uncharacterised protein FAM53C as a novel, potential regulator of the G1/S cell cycle transition, linking its function to the DYRK1A kinase and the RB/p53 pathways. The work is valuable and of interest to the cell cycle field, leveraging a strong computational screen to identify a new candidate. The findings are solid, although confidence in the siRNA depletion phenotypes would have been higher with rescue experiments using an siRNA-resistant cDNA and more robust quantification of some immunoassay data.

     [Editors' note: this paper was reviewed by Review Commons.]

   Reviewed by eLife, Review Commons

6. Noncanonical amino acid incorporation enables minimally disruptive labeling of stress granule and TDP-43 proteinopathy

   This article has 7 authors:

   1. Hao Chen
   2. Haocheng Wang
   3. Yuning Lu
   4. Peng Chen
   5. Zhongfan Zheng
   6. Tao Zhang
   7. Jiou Wang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Amyotrophic lateral sclerosis (ALS) affects nerve cells in the brain and spinal cord. The authors' approach to use genetic code expansion to tag two ALS proteins associated with stress granules has value and should be useful in the ALS field. Parts of the work are well done, but there are concerns that the evidence is incomplete overall, and additional controls would strengthen the study.

   Reviewed by eLife

7. Adaptation of endothelial cells to microenvironment topographical cues through lysyl oxidase like-2-mediated basement membrane scaffolding

   This article has 17 authors:

   1. Marion F Marchand
   2. Noémie Brassard-Jollive
   3. Claire Leclech
   4. Jorge Barrasa-Fano
   5. Yoann Atlas
   6. Claudia Umana-Diaz
   7. Apeksha Shapeti
   8. Corinne Ardidie-Robouant
   9. Tristan Piolot
   10. Sabrina Martin
   11. Philippe Mailly
   12. Christophe Guilluy
   13. Abdul I Bakarat
   14. Catherine Monnot
   15. Hans Van Oosterwyck
   16. Stéphane Germain
   17. Laurent Muller

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents important findings describing the early assembly of vascular basement membrane and how vascular cells switch from responding to cues provided by the external environment to those provided by self-assembled basement membrane. The evidence supporting the claims of the authors is convincing, with state-of-the-art microscopy and several different culture conditions examined. The work will be of interest to cell biologists studying the ECM, vascular development, as well as medical scientists focused on diseases that depend on vascular growth.

   Reviewed by eLife

8. Loss of the s2U tRNA modification induces antibiotic tolerance and is linked to changes in ribosomal protein expression

   This article has 5 authors:

   1. Katherine L Cotten
   2. Abigail McShane
   3. Peter C Dedon
   4. Thomas J Begley
   5. Kimberly M Davis

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work examines how tRNA modifications influence antibiotic tolerance, providing novel insights that may have therapeutic uses. The evidence supporting the conclusions is convincing. Strengths of the manuscript include the mechanism of tRNA modification influencing antibiotic tolerance and the precise measurement techniques used throughout. Further analysis of growth rate impacts and specific identification of the proteins responsible for the effect would further strengthen the manuscript.

   Reviewed by eLife

9. The Fd4 transcription factor translates transient spatial cues in progenitors into long-term lineage identity

   This article has 2 authors:

   1. Sen-Lin Lai
   2. Chris Q Doe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study focuses on the molecular mechanisms underlying the generation of neuronal diversity. Taking advantage of a well-defined neuroblast lineage in Drosophila, the authors provide convincing evidence that two transcription factors of the conserved forkhead box (FOX) family provide a mechanistic link between transient spatial cues that initially specify neuroblast identity and terminal selector genes that define post-mitotic neuron identity. The findings will be of interest to developmental neurobiologists.

   Reviewed by eLife

10. Continuous flashing suppression of V1 responses and the perceptual consequences revealed via two-photon calcium imaging and transformer modeling

    This article has 5 authors:

    1. Cai-Xia Chen
    2. Xin Wang
    3. Dan-Qing Jiang
    4. Shi-Ming Tang
    5. Cong Yu

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This important study shows that orientation tuning of V1 neurons is suppressed during a continuous flash suppression paradigm, especially when the neurons have a binocular receptive field. However, the evidence presented is incomplete and, in particular, does not distinguish whether this suppression is due to reduced contrast or due to masking.

    Reviewed by eLife