eLife

Latest preprint reviews

1. Spontaneous fluctuations in global connectivity reflect transitions between states of high and low prediction error

   This article has 5 authors:

   1. Paul C Bogdan
   2. Shenyang Huang
   3. Lifu Deng
   4. Simon W Davis
   5. Roberto Cabeza

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study uses a valuable combination of functional magnetic resonance imaging and electroencephalography (EEG) to study brain activity related to prediction errors in relation to both sensorimotor and more complex cognitive functions. It provides incomplete evidence to suggest that prediction error minimisation drives brain activity across both types of processing and that elevated inter-regional functional coupling along a superior-inferior axis is associated with high prediction error, whereas coupling along a posterior-anterior axis is associated with low prediction error. The manuscript will be of interest to neuroscientists working on predictive coding and decision-making, but would benefit from more precise localisation of EEG sources and more rigorous statistical controls.

   Reviewed by eLife

2. Spyglass: a framework for reproducible and shareable neuroscience research

   This article has 29 authors:

   1. Kyu Hyun Lee
   2. Eric L Denovellis
   3. Ryan Ly
   4. Jeremy Magland
   5. Jeff Soules
   6. Alison E Comrie
   7. Daniel P Gramling
   8. Jennifer A Guidera
   9. Rhino Nevers
   10. Philip Adenekan
   11. Chris Brozdowski
   12. Samuel R Bray
   13. Emily Monroe
   14. Ji Hyun Bak
   15. Michael E Coulter
   16. Xulu Sun
   17. Emrey Broyles
   18. Donghoon Shin
   19. Sharon Chiang
   20. Cristofer Holobetz
   21. Andrew Tritt
   22. Oliver Rübel
   23. Thinh Nguyen
   24. Dimitri Yatsenko
   25. Joshua Chu
   26. Caleb Kemere
   27. Samuel Garcia
   28. Alessio Buccino
   29. Loren M Frank

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study presents a framework for a shareable data analysis pipeline aimed at improving reproducibility in neuroscience. The evidence for robustness and inter-laboratory operability is convincing. However, aspects such as accessibility for new users, flexibility for custom analyses, and plans for long-term maintenance remain incomplete. Overall, this work will be of interest to neuroscientists engaged in the analysis of large-scale neuronal recordings.

   Reviewed by eLife

3. MORC2 Mediates Transcriptional Regulation Through Liquid-Liquid Phase Separation and DNA Binding

   This article has 9 authors:

   1. Yanshen Zhang
   2. Weiya Xu
   3. Wenxiu Duan
   4. Yu Wei
   5. Wenli Jiang
   6. Feng Zhu
   7. Chengdong Huang
   8. Chao Wang
   9. Yihui Bi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This useful study has demonstrated that MORC2 undergoes phase separation in cells and established multiple interactions responsible for the phase separation. While the characterizations of protein-protein and protein-DNA interactions are solid, there is currently incomplete evidence supporting the claim that MORC2 phase separation contributes to the gene regulatory role of MORC2 in cells. With a stronger link between MORC2 phase separation and cellular function, and further analysis of how disease-linked mutations impact condensation propensity, this study would be of significant interest to biophysicists and molecular biologists working on the role of condensates in gene regulation.

   Reviewed by eLife

4. Quantitative computerized analysis demonstrates strongly compartmentalized tissue deformation patterns underlying mammalian heart tube formation

   This article has 4 authors:

   1. Morena Raiola
   2. Miquel Sendra
   3. Jorge Nicolás Dominguez
   4. Miguel Torres

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work substantially advances our understanding of tissue deformation and growth patterns during the earliest stages of mammalian heart development. One of the strengths of the work is the compelling quantitative approach to analyzing time-lapse imaging data using an original computational pipeline, which goes beyond the current state of the art and provides new insights into heart tube formation. Overall, this rigorous study will be of broad interest to computational and developmental biologists studying tissue dynamics.

   Reviewed by eLife

5. A GCN1-independent activator of the kinase GCN2

   This article has 18 authors:

   1. JiaYi Zhu
   2. Giulia Emanuelli
   3. Glenn R Masson
   4. Vanesa Vinciauskaite
   5. Henriette Willems
   6. Andrew Lim
   7. Christopher Alan Brown
   8. David Winpenny
   9. Murray Clarke
   10. Rebecca Gilley
   11. Fergus Preston
   12. Jordan Wilson
   13. Aldo Bader
   14. Taufiq Rahman
   15. Joseph E Chambers
   16. John Skidmore
   17. Nicholas W Morrell
   18. Stefan J Marciniak

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a screen for small-molecule activators of the kinase GCN2 that phosphorylates the eukaryotic translation initiation factor 2 alpha (eIF2α) in response to diverse stress stimuli. Among the compounds identified, one stands out as a potent activator that functions independently of GCN1, which is important for probing mechanisms of Integrated Stress Response regulation and may have translational relevance in the context of pathogenic GCN2 mutations. While some reviewers found the biochemical analyses convincing, others viewed the cellular evidence as limited, particularly with respect to time points, endogenous readouts, and broader cell-type validation, which prevents a clear assessment of the compound's potential potency in a physiological context.

   Reviewed by eLife

6. D-serine suppresses one-carbon metabolism by competing with mitochondrial L-serine transport

   This article has 18 authors:

   1. Masataka Suzuki
   2. Kenichiro Adachi
   3. Pattama Wiriyasermukul
   4. Mariko Fukumura
   5. Ryota Tamura
   6. Yoshinori Hirano
   7. Yumi Aizawa
   8. Tetsuya Miyamoto
   9. Sakiko Taniguchi
   10. Masahiro Toda
   11. Hiroshi Homma
   12. Kohsuke Kanekura
   13. Kenji Yasuoka
   14. Takanori Kanai
   15. Masahiro Sugimoto
   16. Shushi Nagamori
   17. Masato Yasui
   18. Jumpei Sasabe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This work presents valuable new data on the role of D-Serine and how it competes with its stereoisomer L-Serine to influence metabolism. The work presents a variety of solid experimental data combined with simulated results to investigate the mechanisms focused on one-carbon metabolism, which is relevant for several research fields. However, some claims are only partially supported by data, and critical areas comparing L- vs D-Serine and further mechanistic studies are incomplete. Furthermore, while the work has potential for various fields, the work has only been studied in a limited cell type and context.

   Reviewed by eLife

7. Identification of nuclear pore proteins at plasmodesmata: potential role in intercellular transport?

   This article has 19 authors:

   1. T Moritz Schladt
   2. Manuel Miras
   3. Jona Obinna Ejike
   4. Mathieu Pottier
   5. Lin Xi
   6. Andrea Restrepo-Escobar
   7. Masayoshi Nakamura
   8. Niklas Pütz
   9. Sebastian Hänsch
   10. Chen Gao
   11. Julia Engelhorn
   12. Marcel Dickmanns
   13. Gwendolyn V Davis
   14. Ahan Dalal
   15. Sven Gombos
   16. Ronja Lange
   17. Rüdiger Simon
   18. Waltraud X Schulze
   19. Wolf B Frommer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Plasmodesmata are channels that allow cell-cell communication in plants; based on the functional similarities between facilitated transport within plasmodesmata and into the nucleus, the authors speculate that nuclear pore complex proteins might be involved in plasmodesmata function. If supported, this would transform our understanding of cell-to-cell communication in plants. The authors localize nuclear pore complex proteins to plasmodesmata using proteomics and heterologous overexpression; however, the data are incomplete since key controls for localization, functionality, and expression level of fluorescent protein fusions are absent.

   Reviewed by eLife

8. The fate of pyruvate dictates cell growth by modulating cellular redox potential

   This article has 9 authors:

   1. Ashish G Toshniwal
   2. Geanette Lam
   3. Alex J Bott
   4. Ahmad A Cluntun
   5. Rachel Skabelund
   6. Hyuck-Jin Nam
   7. Dona R Wisidagama
   8. Carl S Thummel
   9. Jared Rutter

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work demonstrates that compartmentalized cellular metabolism is a dominant input into cell size control in a variety of mammalian cell types and in Drosophila. The authors show that increased pyruvate import into the mitochondria in liver-like cells and in primary hepatocytes drives gluconeogenesis but reduces cellular amino acid production, suppressing protein synthesis. The evidence supporting the conclusions is compelling, with a variety of genetic and pharmacologic assays rigorously testing each step of the proposed mechanism. This work will be of interest to cell biologists, physiologists, and researchers interested in cell metabolism, and is significant because stem cells and many cancers exhibit metabolic rewiring of pyruvate metabolism.

   Reviewed by eLife

9. Lipid packing contributes to the confinement of caveolae to the plasma membrane

   This article has 10 authors:

   1. Elin Larsson
   2. Aleksei Kabedev
   3. Hudson Pace
   4. Jakob Lindwall
   5. Fouzia Bano
   6. Robert G Parton
   7. Christel AS Bergström
   8. Ingela Parmryd
   9. Marta Bally
   10. Richard Lundmark

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports the important finding that the dynamin inhibitor Dyngo-4a broadly affects lipid packing and plasma membrane dynamics, independently of its action on dynamin. While solid computational, biophysical, and cell-based evidence supports this conclusion, there is incomplete support for the authors' main claim on the role of lipid packing in caveolae internalization, as the causal relationship remains unclear and direct analyses are lacking. With stronger evidence, this work would be of significant interest to cell biologists, biophysicists, and chemists interested in membrane remodeling and drug-membrane interactions.

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

   Reviewed by eLife, Review Commons

10. Stall force measurement of the kinesin-3 motor KIF1A using a programmable DNA origami nanospring

    This article has 5 authors:

    1. Nobumichi Takamatsu
    2. Hiroko Furumoto
    3. Takayuki Ariga
    4. Mitsuhiro Iwaki
    5. Kumiko Hayashi

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      Optical tweezers have been instrumental to the determination of mechanical parameters of molecular motors. This study by Takamatsu et al. reports key mechanical parameters of kinesin KIF1A using fluorescence microscopy, wherein the motor is tethered to a DNA nanospring, without the use of an optical trapping apparatus, which represents an exciting development. The approach and the findings reported change current thinking about KIF1A‑mediated transport, with potential implications for understanding human disease. The findings are important and the strength of the evidence is compelling.

    Reviewed by eLife