eLife

Latest preprint reviews

1. Lipid discovery enabled by sequence statistics and machine learning

   This article has 8 authors:

   1. Priya M Christensen
   2. Jonathan Martin
   3. Aparna Uppuluri
   4. Luke R Joyce
   5. Yahan Wei
   6. Ziqiang Guan
   7. Faruck Morcos
   8. Kelli L Palmer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study reports important findings on identifying sequence motifs that predict substrate specificity in a class of lipid synthesis enzymes. It sheds light on a mechanism used by bacteria to modify the lipids in their membrane to develop antibiotic resistance. The evidence is compelling, with a careful application of machine learning methods, validated by mass spectrometry-based lipid analysis experiments. This interdisciplinary study will be of interest to computational biologists and to the community working on lipids and on enzymes involved in lipid synthesis or modification.

   Reviewed by eLife

2. Post-fertilization transcription initiation in an ancestral LTR retrotransposon drives lineage-specific genomic imprinting of ZDBF2

   This article has 22 authors:

   1. Hisato Kobayashi
   2. Tatsushi Igaki
   3. Soichiro Kumamoto
   4. Keisuke Tanaka
   5. Tomoya Takashima
   6. So I Nagaoka
   7. Shunsuke Suzuki
   8. Masaaki Hayashi
   9. Marilyn B Renfree
   10. Manabu Kawahara
   11. Shun Saito
   12. Toshihiro Kobayashi
   13. Hiroshi Nagashima
   14. Hitomi Matsunari
   15. Kazuaki Nakano
   16. Ayuko Uchikura
   17. Hiroshi Kiyonari
   18. Mari Kaneko
   19. Hiroo Imai
   20. Kazuhiko Nakabayashi
   21. Matthew Lorincz
   22. Kazuki Kurimoto

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     The authors analyses describe a novel mechanism by which a retrotransposon-derived LTR may be involved in genomic imprinting and demonstrate imprinting of the ZDBF2 locus in rabbits and Rhesus macaques using allele-specific expression analysis. This imprinting of the ZDBF2 locus correlates with transcription of GPR1-AS orthologs. The accompanying genomic analysis is very well executed allowing for the conclusions reached in the manuscript. The revisions made at the request of the reviewers in this important manuscript strengthen the evidence from the genomic analyses, and as a result, the evidence is now convincing and will be informative to the genomics and developmental biology communities.

   Reviewed by eLife

3. The neural correlates of novelty and variability in human decision-making under an active inference framework

   This article has 4 authors:

   1. Shuo Zhang
   2. Yan Tian
   3. Quanying Liu
   4. Haiyan Wu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study addresses a central question in systems neuroscience (validation of active inference models of exploration) using a combination of behaviour, neuroimaging, and modelling. The data provided offers solid evidence that humans do perceive, choose and learn in a manner consistent with the essential ingredients of active inference, and that quantities that correlate with relevant parameters of this active inference scheme are encoded in different regions of the brain.

   Reviewed by eLife

4. Impact of protein and small molecule interactions on kinase conformations

   This article has 14 authors:

   1. Valentina Kugler
   2. Selina Schwaighofer
   3. Andreas Feichtner
   4. Florian Enzler
   5. Jakob Fleischmann
   6. Sophie Strich
   7. Sarah Schwarz
   8. Rebecca Wilson
   9. Philipp Tschaikner
   10. Jakob Troppmair
   11. Veronika Sexl
   12. Pascal Meier
   13. Teresa Kaserer
   14. Eduard Stefan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This article reports an important bioluminescence-based reporter system to evaluate kinase conformations. This assay is applied to four different kinases that have unique, very special regulatory features, thereby indicating that the assay can be used to provide convincing evidence on the conformational state of a large number of kinases. This paper will be of interest to researchers working on kinases and their conformational states.

   Reviewed by eLife

5. Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant

   This article has 7 authors:

   1. Patsy R Tomlinson
   2. Rachel G Knox
   3. Olga Perisic
   4. Helen Su
   5. Gemma V Brierley
   6. Roger L Williams
   7. Robert K Semple

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study reports on PI3KR mutations and a paradoxical mechanism of PI3KR signaling. The strength of evidence for the study is mostly convincing, as conclusions are supported by a variety of mutational strategies and cellular systems to look at interactions among signaling pathways.

   Reviewed by eLife

6. Disassembly of embryonic keratin filaments promotes pancreatic cancer metastases

   This article has 12 authors:

   1. Ryan R. Kawalerski
   2. Mariana Torrente Gonçalves
   3. Chun-Hao Pan
   4. Robert Tseng
   5. Lucia Roa-Peña
   6. Cindy V. Leiton
   7. Luke A. Torre-Healy
   8. Taryn Boyle
   9. Sumedha Chowdhury
   10. Natasha T. Snider
   11. Kenneth R. Shroyer
   12. Luisa F. Escobar-Hoyos

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The authors address the function of keratin 17 (K17), a marker of the most aggressive pancreatic ductal adenocarcinomas (PDACs). While this potentially useful study addresses a significant area of pancreatic cancer research, the lack of evidence demonstrating nuclear localization of K17 in human PDAC and the excessive reliance on a single cell line reduce the significance of the work. Moreover, the weak phenotypes of K17 phosphosite mutants provide incomplete support for the authors' mechanistic model.

   Reviewed by eLife

7. Theoretical principles explain the structure of the insect head direction circuit

   This article has 3 authors:

   1. Pau Vilimelis Aceituno
   2. Dominic Dall'Osto
   3. Ioannis Pisokas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important work suggests that the observed cosine-like activity in the head direction circuit of insects not only subserves vector addition but also minimizes noise in the representation. The authors provide solid evidence using the locust and fruit fly connectomes. The work raises important theoretical questions about the organization of the navigation system and will be of interest to theoretical and experimental researchers studying navigation.

   Reviewed by eLife

8. Early evolution of the ecdysozoan body plan

   This article has 13 authors:

   1. Deng Wang
   2. Yaqin Qiang
   3. Junfeng Guo
   4. Jean Vannier
   5. Zuchen Song
   6. Jiaxin Peng
   7. Boyao Zhang
   8. Jie Sun
   9. Yilun Yu
   10. Yiheng Zhang
   11. Tao Zhang
   12. Xiaoguang Yang
   13. Jian Han

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study provides a fundamental advance in palaeontology by reporting the fossils of a new invertebrate, Beretella spinosa, and inferring its relationship with already described species. The analysis placed the newly described species in the earliest branch of moulting invertebrates. The study, supported by convincing fossil observation, hypothesizes that early moulting invertebrate animals were not vermiform.

   Reviewed by eLife

9. Functional characterization of all CDKN2A missense variants and comparison to in silico models of pathogenicity

   This article has 4 authors:

   1. Hirokazu Kimura
   2. Kamel Lahouel
   3. Cristian Tomasetti
   4. Nicholas Jason Roberts

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This is a saturation mutagenesis screening of CDKN2A gene, successfully assessing the functionality of the missense variants. The work is solid and well-prosecuted. The manuscript was improved during the revision process and this work will serve as a valuable resource for diagnostic labs as well as cancer geneticists.

   Reviewed by eLife

10. Remodeling of skeletal muscle myosin metabolic states in hibernating mammals

    This article has 23 authors:

    1. Christopher TA Lewis
    2. Elise G Melhedegaard
    3. Marija M Ognjanovic
    4. Mathilde S Olsen
    5. Jenni Laitila
    6. Robert AE Seaborne
    7. Magnus Gronset
    8. Changxin Zhang
    9. Hiroyuki Iwamoto
    10. Anthony L Hessel
    11. Michel N Kuehn
    12. Carla Merino
    13. Nuria Amigo
    14. Ole Frobert
    15. Sylvain Giroud
    16. James F Staples
    17. Anna V Goropashnaya
    18. Vadim B Fedorov
    19. Brian Barnes
    20. Oivind Toien
    21. Kelly Drew
    22. Ryan J Sprenger
    23. Julien Ochala

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      The work by Lewis and co-workers presents important findings on the role of myosin structure/energetics on the molecular mechanisms of hibernation by comparing muscle samples from small and large hibernating mammals. The solid methodological approaches have revealed insights into the mechanisms of non-shivering thermogenesis and energy expenditure.

    Reviewed by eLife