eLife

Latest preprint reviews

1. Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer’s disease risk genes

   This article has 5 authors:

   1. François Kroll
   2. Joshua Donnelly
   3. Güliz Gürel Özcan
   4. Eirinn Mackay
   5. Jason Rihel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important manuscript sets out to identify sleep/arousal phenotypes in larval zebrafish carrying mutations in Alzheimer's disease (AD)-associated genes. The authors provide detailed phenotypic data for F0 knockouts of each of 7 AD-associated genes and then compare the resulting behavioral fingerprints to those obtained from a large-scale chemical screen to generate new hypotheses about underlying molecular mechanisms. The data presented are solid, although extensive interpretation of pharmacological screen data does not necessarily reflect the limited mechanistic data. Nonetheless, the authors address most reviewer concerns in their revised version, providing invaluable new analyses. Phenotypic characterization presented is comprehensive, and the authors develop a well-designed behavioral analysis pipeline that will provide considerable value for zebrafish neuroscientists.

   Reviewed by eLife

2. Intracellular mechanical fingerprint reveals cell type specific mechanical tuning

   This article has 3 authors:

   1. Till M. Muenker
   2. Bart E. Vos
   3. Timo Betz

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Münker and colleagues use an optical tweezer setup to apply oscillatory forces to endocytosed/phagocytosed glass beads over a wide frequency range (from ~1 to 1000 Hz) and probe cytoplasmic material properties at multiple time scales in six different cell types. Using statistical methods and principal component analysis, they find that the active and passive mechanical properties of cells can be described by 6 parameters (from power law fits) that allow characterizing the viscous and elastic nature of the cytoplasmic material as well as an effective active energy driven by cellular metabolism. Overall, this is very well done and important work, using convincing and state-of-the-art methods, albeit with some limitations related to the way the beads are internalized.

   Reviewed by eLife

3. Molecular determinants of Neu5Ac binding to a tripartite ATP independent periplasmic (TRAP) transporter

   This article has 8 authors:

   1. Parveen Goyal
   2. KanagaVijayan Dhanabalan
   3. Mariafrancesca Scalise
   4. Rosmarie Friemann
   5. Cesare Indiveri
   6. Renwick CJ Dobson
   7. Kutti R Vinothkumar
   8. Subramanian Ramaswamy

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable work provides novel insights into the substrate binding mechanism of a tripartite ATP-independent periplasmic (TRAP) transporter, which may be helpful for the development of specific inhibitors. The structural analysis is convincing, but additional work will be required to establish the transport mechanism as well as well as binding sites for all ligands. This study will be of interest to the membrane transport and bacterial biochemistry communities.

   Reviewed by eLife

4. Convolutional networks can model the functional modulation of the MEG responses associated with feed-forward processes during visual word recognition

   This article has 6 authors:

   1. Marijn van Vliet
   2. Oona Rinkinen
   3. Takao Shimizu
   4. Anni-Mari Niskanen
   5. Barry Devereux
   6. Riitta Salmelin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     van Vliet and colleagues show a useful correlation between internal states of a convolutional neural network (CNN) trained on visual word stimuli with three specific components of evoked MEG potentials during reading in humans. The findings are solid, though quantitative evidence that model can produce any of the phenomena that the human visual system is known to have (e.g., feedback connections, sensitivity to word frequency), or that it has comparable performance to human behaviour (i.e., similar task accuracy with a comparable pattern of mistakes) would make the conclusions much stronger.

   Reviewed by eLife

5. The title and authors for this article are not available from our external data provider yet:
   10.48550/arxiv.2212.01191v3

6. Downregulation of semaphorin 4A in keratinocytes reflects the features of non-lesional psoriasis

   This article has 16 authors:

   1. Miki Kume
   2. Hanako Koguchi-Yoshioka
   3. Shuichi Nakai
   4. Yutaka Matsumura
   5. Atsushi Tanemura
   6. Kazunori Yokoi
   7. Shoichi Matsuda
   8. Yuumi Nakamura
   9. Naoya Otani
   10. Mifue Taminato
   11. Koichi Tomita
   12. Tateki Kubo
   13. Mari Wataya-Kaneda
   14. Atsushi Kumanogoh
   15. Manabu Fujimoto
   16. Rei Watanabe

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This paper advances an important new concept in psoriasis pathogenesis and implicates Sema4a as a homeostatic regulator that is highly epithelial-specific. The findings are convincing and lend support for the biology described here as a mechanism with therapeutic implications.

   Reviewed by eLife

7. Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning

   This article has 17 authors:

   1. Ruihan Dong
   2. Rongrong Liu
   3. Ziyu Liu
   4. Yangang Liu
   5. Gaomei Zhao
   6. Honglei Li
   7. Shiyuan Hou
   8. Xiaohan Ma
   9. Huarui Kang
   10. Jing Liu
   11. Fei Guo
   12. Ping Zhao
   13. Junping Wang
   14. Cheng Wang
   15. Xingan Wu
   16. Sheng Ye
   17. Cheng Zhu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a useful pipeline for de novo design of antimicrobial peptides active both against bacteria and viruses. The method is based on deep learning, using a GAN generator and a regression tasked to predict antimicrobial activity. The experimental evidence supporting the conclusions is solid, with 24 validated peptides, although some additional justifications of the computational strategy would be a plus. This work will be of interest to the community working on machine learning for biomedical applications and specifically on antimicrobial peptides.

   Reviewed by eLife

8. The success of artificial selection for collective composition hinges on initial and target values

   This article has 3 authors:

   1. Juhee Lee
   2. Wenying Shou
   3. Hye Jin Park

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study of artificial selection in microbial communities shows that the possibility of selecting a desired fraction of slow and fast-growing types is impacted by their initial fractions. The evidence, which relies on mathematical analysis and simulations of a stochastic model, is compelling. It highlights the tension between selection at the strain and the community level. This study should be of interest to researchers interested in ecology, both theoretical and experimental.

   Reviewed by eLife

9. Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase

   This article has 9 authors:

   1. Yuqian Wang
   2. Guibin Wang
   3. Lishan Zhang
   4. Qilan Cai
   5. Meizhen Lin
   6. Dongping Huang
   7. Yuyue Xie
   8. Wenxiong Lin
   9. Xiangmin Lin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     In this valuable study, the authors studied a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila, which lacks homology with eukaryotic counterparts, thus underscoring its unique evolutionary trajectory within the bacterial domain. They attempt to demonstrate deacetylase activity, however, whilst the revised manuscript has been improved, significant aspects of the data are still incomplete and require further refinement. The work will be of interest to microbiologists studying metabolism and post-translational modifications.

   Reviewed by eLife

10. Stable sequential dynamics in prefrontal cortex represents subjective estimation of time

    This article has 8 authors:

    1. Yiting Li
    2. Wenqu Yin
    3. Xin Wang
    4. Jiawen Li
    5. Shanglin Zhou
    6. Chaolin Ma
    7. Peng Yuan
    8. Baoming Li

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This useful study reports how neuronal activity in the prefrontal cortex maps time intervals during which animals wait to reach a reward, with this mapping remaining consistent across days. While most claims are supported by solid evidence, the study could have benefitted from an improved experimental design to more clearly disambiguate correlations between neuronal patterns and not only time but also stereotypical behaviors and restraint from impulsive decisions. This study will be of particular interest to neuroscientists focused on decision-making and motor control.

    Reviewed by eLife