eLife

Latest preprint reviews

1. RNF25 is activated as a response to amino acid starvation-induced ribosome collisions in competition with GCN2

   This article has 3 authors:

   1. Ivan Kisly
   2. Ivo Zemp
   3. Ulrike Kutay

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides conditionally useful evidence that amino acid starvation and other stresses induce RNF25-dependent ubiquitination of RPS27A/eS31, extending this pathway beyond A-site-trapping conditions and implicating GCN1. However, incomplete and largely indirect evidence was provided to support key mechanistic claims-notably competition between RNF25 and GCN2 for GCN1 and a role in resolving ribosome collisions. Additional direct and orthogonal evidence is required to substantiate these conclusions.

   Reviewed by eLife

2. Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer

   This article has 6 authors:

   1. Ningjun Duan
   2. Yijia Hua
   3. Zhengxing Zhou
   4. Nan Jin
   5. Wei Li
   6. Yongmei Yin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding that coordinated changes in epigenetic modifications and three-dimensional chromatin architecture may drive primary trastuzumab resistance in HER2+ breast cancer. Moreover, this manuscript identifies SGK1 as a potential therapeutic target. The evidence supporting the claims of the authors is solid, although the inclusion of a more direct validation of the key findings using tumor samples from patients with clinical trastuzumab resistance would have strengthened the study. The work will be of interest to scientists or clinicians working in the field of BCs.

   Reviewed by eLife

3. Opposing BOLD signals and oxygen metabolism largely arise from statistical uncertainty in metabolic estimates

   This article has 3 authors:

   1. Ole Goltermann
   2. Alexander Huth
   3. Christian Büchel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This manuscript provides a timely and important statistical re-evaluation of a paper by Epp et al., on the discordance of BOLD and CMRO2 measures. The authors present a convincing case based on rigorous re-analysis of the data that these previous results arise predominantly from uncertainty in measurement, rather than physiological features. These findings have implications that are of importance to all studies of brain function using BOLD FMRI.

   Reviewed by eLife

4. How local antibiotic use, carriage duration, resistance costs and international travel shape resistance frequency in E. coli in France

   This article has 10 authors:

   1. Olivier Cotto
   2. André Birgy
   3. Mélanie Magnan
   4. Stéphane Béchet
   5. Stéphane Bonacorsi
   6. Robert Cohen
   7. Corinne Levy
   8. Forough L. Nowrouzian
   9. Olivier Tenaillon
   10. François Blanquart

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable paper uses a mathematical model applied to a dataset of E coli / ESBL carriage and transmission to infer drivers of drug resistance in France. The strength of support for the study findings is incomplete. While the research question is of importance, and the mathematical model has structural and methodological integrity, numerous issues are noted: insufficient description of the data, lack of included equations and code, definitions of antibiotic use that are not complete, low sensitivity of assays for carriage, technical issues with statistical prior selection and parameter identification, and application of non-regional ECDC surveillance data to France.

   Reviewed by eLife

5. De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response

   This article has 10 authors:

   1. Rui Yang
   2. Kaiyuan Zheng
   3. McGuire Metts
   4. Yiluo Wang
   5. Danyan Yin
   6. Kevin P. Li
   7. Agnieszka A. Prazmowska
   8. David F. Kashatus
   9. Brian Kuhlman
   10. Jie Yang

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This potentially valuable study describes the development of protein binders targeting DELE1, a protein involved in activating the integrated stress response when mitochondria are perturbed (the mitoISR pathway. The strategy appears to be successful, as several designed proteins were shown to bind DELE1, disrupt DELE1 oligomerization, and attenuate ISR activation. However, the demonstration of the utility of these inhibitory binders is incomplete, particularly given the limited biological outcomes examined in the current study, thus limiting the significance of the paper in its current form.

   Reviewed by eLife

6. Temporal Dynamics of Cortical State Plasticity Following Adult Vision Loss

   This article has 3 authors:

   1. Ismaël Djerourou
   2. Maurice Ptito
   3. Matthieu P. Vanni

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study employs longitudinal widefield cortical imaging to investigate how bilateral vision loss reshapes spontaneous activity across the mouse cortex over time, revealing a state-dependent alteration in the locomotion-related modulation of visual cortical activity. The work provides solid support for its main findings and offers a thorough characterization of the large-scale reorganization of cortical dynamics following adult vision loss. However, the mechanistic interpretation remains limited, as the conclusions are based on a single abrupt and irreversible manipulation without sham controls and on a recording approach that cannot resolve the cell-type-specific mechanisms invoked in the discussion.

   Reviewed by eLife

7. Training neural networks from scratch in a videogame leads to brittle brain encoding

   This article has 5 authors:

   1. François Paugam
   2. Basile Pinsard
   3. Marie St-Laurent
   4. Guillaume Lajoie
   5. Lune Bellec

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a valuable paper that compares various deep learning models, trained with different objective functions, on their ability to predict fMRI data collected during naturalistic video gameplay. The data and analysis provide solid within-distribution evidence that models trained with PPO and imitation learning outperform untrained models and standard convolutional networks. However, the evidence for brittleness in out-of-distribution encoding remains incomplete, as the claim that this stems from the networks' training rather than from alternative causes-like overfitting of ridge regression parameters-is not yet fully supported.

   Reviewed by eLife

8. Intracellular growth of Chlamydia trachomatis leads to global histone hypermethylation by impairing demethylation

   This article has 20 authors:

   1. Chloé I. Charendoff
   2. Félix V. Louchez
   3. Yongzheng Wu
   4. Lee Dolat
   5. Guillaume Velasco
   6. Stéphanie Perrinet
   7. Adrian Gabriel Torres
   8. Laure Blanchet
   9. Magalie Duchateau
   10. Quentin Giai Gianetto
   11. Mariette Matondo
   12. Laurence Del Maestro
   13. Slimane Ait-Si-Ali
   14. Frédéric Bonhomme
   15. Gaël A. Millot
   16. Vannary Meas-Yedid
   17. Lluís Ribas de Pouplana
   18. Elisabeth D. Martinez
   19. Raphael H. Valdivia
   20. Agathe Subtil

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a valuable study of changes in host genome histone methylation and transcription changes associated with Chlamydia infection. The data presented are solid but further analysis would strengthen the authors overall conclusions.

   Reviewed by eLife

9. Acyl Carrier Protein is Essential for Apicoplast Biogenesis in Malaria Parasites Independent of Fatty Acid Synthesis

   This article has 9 authors:

   1. Sage W. R. Geher
   2. Seyi Falekun
   3. Jessica N. Pita-Aquino
   4. Russell P. Swift
   5. Megan Okada
   6. Yasaman Jami-Alahmadi
   7. James A. Wohlschlegel
   8. Sean T. Prigge
   9. Paul A. Sigala

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study identifies a non-canonical essential role for acyl carrier protein in maintaining apicoplast metabolism and blood-stage survival in Plasmodium falciparum. The main conclusions are largely supported by strong genetic and biochemical evidence, although some claims regarding the dispensability of fatty acid synthesis pathways remain incomplete. The work provides novel mechanistic insight into ACP-mediated stabilization of pyruvate kinase II and will be of broad interest to the malaria and apicoplast biology communities.

   Reviewed by eLife

10. Optical single-channel recording of CRAC channels with HaloTag and a Ca ²⁺ -sensitive ligand

    This article has 2 authors:

    1. Harsharan Dhillon
    2. Richard S. Lewis

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This study presents a fundamental methodological advance that enables measurements of single-channel gating behavior of CRAC channels whose unitary currents are too small to be resolved electrically. By combining a channel-tethered calcium-sensitive dye (JF646-BAPTA) with voltage-clamp TIRF imaging, the authors discovered new kinetic behaviors of CRAC channels and further identified a dye-blinking artifact with implications that are of importance for optical single-channel studies. Although the work is convincing and the findings have biological relevance, some quantitative aspects of the study can be strengthened by additional analysis.

    Reviewed by eLife