eLife

Latest preprint reviews

1. Genetic evidence: zebrafish hoxba and hoxbb clusters are essential for the anterior-posterior positioning of pectoral fins

   This article has 9 authors:

   1. Morimichi Kikuchi
   2. Renka Fujii
   3. Daiki Kobayashi
   4. Yuki Kawabe
   5. Haruna Kanno
   6. Sohju Toyama
   7. Farah Tawakkal
   8. Kazuya Yamada
   9. Akinori Kawamura

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study advances our understanding of vertebrate forelimb development, specifically the contribution of Hox genes to zebrafish pectoral fin formation. While there are reservations about some of the descriptions and interpretations of the data, the results are mostly convincing. The authors have employed a robust and extensive genetic approach to tackle a key and unresolved question. The findings will be of broad interest to developmental and evolutionary biologists.

   Reviewed by eLife

2. Targeted protein degradation by KLHDC2 ligands identified by high-throughput screening

   This article has 9 authors:

   1. Han Zhou
   2. Tonglian Zhou
   3. Wenli Yu
   4. Liping Liu
   5. Yeonjin Ko
   6. Kristen A Johnson
   7. Ian A Wilson
   8. Peter G Schultz
   9. Michael J Bollong

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study aims to advance the toolkit of small molecules used for approaches to targeted protein degradation for research and therapeutic applications. The authors provide solid data demonstrating the use of a high-throughput screen of small molecules to target a specific E3 ligase, KLHDC2 (Kelch-like homology domain containing protein 2); the resulting compounds then form the basis for new PROTAC (proteolysis targeting chimera) reagents. The strength of the work lies in expanding the PROTAC reagent inventory. The current work would be strengthened further by confirming that the PROTAC's activity is dependent on KLHDC2 and by a more thorough examination of off-target effects in cellular applications.

   Reviewed by eLife

3. Ubiquitination-activated TAB–TAK1–IKK–NF-κB axis modulates gene expression for cell survival in the lysosomal damage response

   This article has 5 authors:

   1. Akinori Endo
   2. Chikage Takahashi
   3. Yasumasa Nishito
   4. Keiji Tanaka
   5. Yukiko Yoshida

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents the important finding that lysosomal damage triggers inflammatory signaling through ubiquitination and the TAB-TAK1-IKK-NF-kB axis. The data obtained from the unbiased transcriptomic and proteomic analyses are convincing and provide invaluable information to the field. Although further experiments will be required to clarify how TAB2/3 are activated, this work will be of interest to researchers in the fields of organelle biology and inflammation.

   Reviewed by eLife

4. Epitope Sequence and Modification Fingerprints of Anti-Aβ Antibodies

   This article has 15 authors:

   1. Ivan Talucci
   2. Timon Leske
   3. Hans-Wolfgang Klafki
   4. Mohammed Mehedi Hassan
   5. Annik Steiert
   6. Barbara Morgado
   7. Sebastian Bothe
   8. Lars van Werven
   9. Thomas Liepold
   10. Jochen Walter
   11. Hermann Schindelin
   12. Jens Wiltfang
   13. Oliver Wirths
   14. Olaf Jahn
   15. Hans-Michael Maric

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Antibodies that selectively bind distinct amyloid-beta variants are vital tools for Alzheimer's disease research. This valuable manuscript aims to delineate the epitope specificity in a panel of anti-amyloid-beta antibodies, including some with clinical relevance. The experiments were rigorously conducted, employing an interesting combination of established and state-of-the-art methodologies, yielding mostly robust findings. While the data regarding antibody sequence preferences for distinct amyloid-beta regions and aggregation states are convincing, a thorough revision of the manuscript would help to highlight the key results.

   Reviewed by eLife

5. Endothelial Slit2 guides the Robo1-positive sympathetic innervation during heart development

   This article has 8 authors:

   1. Juanjuan Zhao
   2. Susann Bruche
   3. Konstantinos Lekkos
   4. Carolyn Carr
   5. Joaquim M Vieira
   6. John G Parnavelas
   7. William D Andrews
   8. Mathilda TM Mommersteeg

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study presents a valuable finding on the role of Slit-Robo signaling in cardiac innervation. The evidence supporting the main claims of the authors is solid. The use of several mouse models including constitutive and cell type specific knockout models make the findings more robust. The scope of the presented studies is somewhat limited, as they primarily focus on evaluating the phenotypic changes in cardiac innervation following the loss of various Slit or Robo genes.

   Reviewed by eLife

6. map3k1 is required for spatial restriction of progenitor differentiation in planarians

   This article has 3 authors:

   1. Bryanna Isela-Inez Canales
   2. Hunter O King
   3. Peter W Reddien

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study examines the role of map3k1, a MAP3K family member that has both kinase and ubiquitin ligase domains, in the differentiation of progenitors in the flatworm Planaria. The convincing analyses demonstrate that map3k1 acts within progenitors to restrict their premature differentiation and to prevent formation of teratomas. This work would be of interest to researchers in the fields of regeneration, developmental biology, and aging.

   Reviewed by eLife

7. Conserved and unique features of terminal telomeric sequences in ALT-positive cancer cells

   This article has 7 authors:

   1. Benura Azeroglu
   2. Wei Wu
   3. Raphael Pavani
   4. Ranjodh Singh Sandhu
   5. Tadahiko Matsumoto
   6. André Nussenzweig
   7. Eros Lazzerini-Denchi

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study demonstrates the application of END-seq, originally developed to study genomewide DNA double-strand breaks, to telomere biology; the work packs a punch, concisely demonstrating the utility of this approach and the new insights that can be gained. The authors confirm that telomeres in telomerase-positive cells terminate with 5'-ATC in a Pot1-dependent manner, and demonstrate that this principle holds true in telomerase-negative ALT cells as well. S1-END-seq is similarly developed for telomeres, showing that ALT cells harbor several regions of ssDNA. The study is well-executed and convincing, the new insights are fundamental and compelling, and the optimized END-seq approaches will be widely utilized. The work will prompt additional studies that the reviewers look forward to, including combining telomeric END-seq with long-read sequencing to address the distribution and origin of variant telomere repeats and ssDNA along telomeres in ALT and telomerase-positive settings.

   Reviewed by eLife

8. Blue-shifted ancyromonad channelrhodopsins for multiplex optogenetics

   This article has 13 authors:

   1. Elena G Govorunova
   2. Oleg A Sineshchekov
   3. Hai Li
   4. Yueyang Gou
   5. Hongmei Chen
   6. Shuyuan Yang
   7. Yumei Wang
   8. Stephen Mitchell
   9. Alyssa Palmateer
   10. Leonid S Brown
   11. François St-Pierre
   12. Mingshan Xue
   13. John L Spudich

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study describes newly identified light-gated ion channel homologs (channelrhodopsins, ChRs) in several protist species, with a primary focus on the biophysical characterization of ChRs of ancyromonads. The authors employed a powerful combination of bioinformatics, manual and automated patch-clamp electrophysiology, absorption spectroscopy, and flash photolysis. Additionally, they evaluated the applicability of the newly discovered anion-conducting ChRs in cortical neurons of mouse brain slices and in living C. elegans worms. The evidence supporting most of the claims is convincing and this work will be of interest to the microbial rhodopsin community and neuro- and cardioscientists utilizing optogenetics in their research.

   Reviewed by eLife

9. Domain coupling in allosteric regulation of SthK measured using time-resolved transition metal ion FRET

   This article has 3 authors:

   1. Pierce Eggan
   2. Sharona E Gordon
   3. William N Zagotta

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This valuable study employs transition-metal FRET (tmFRET) and time-correlated single-photon counting to investigate allosteric conformational changes in both isolated cyclic nucleotide-binding domains (CNBDs) and full-length bacterial CNG channels, demonstrating that transmembrane domains stabilize CNBDs in their active state. By comparing isolated CNBD constructs with full-length channels, the authors reveal how allosteric networks couple domain movements to gating energetics, providing insights into ion channel regulation mechanisms. The rigorous methodology and compelling quantitative analysis establish a framework for applying tmFRET to study conformational dynamics in diverse protein systems.

   Reviewed by eLife

10. Identification and classification of ion-channels across the tree of life: Insights into understudied CALHM channels

    This article has 10 authors:

    1. Rahil Taujale
    2. Sung Jin Park
    3. Nathan Gravel
    4. Saber Soleymani
    5. Rayna Carter
    6. Kennady Boyd
    7. Sarah Keuning
    8. Zheng Ruan
    9. Wei Lü
    10. Natarajan Kannan

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      The first part of this manuscript describes an interdisciplinary approach to mine the human channelome and discover further ion channel orthologues across diverse organisms. Although the findings and data curation enabled by the new approach are valuable to the ion channel community, as well as to those interested in improved methods for mining sequence space for their protein of interest, this part of the work is incomplete because critical methodological information is missing. Further validation of the improvements this approach shows over others is needed. The second part of the manuscript utilizes the approach described in the first part to delineate co-conserved amino acid patterns in CALHM channels, but the evidence provided to support the role of the identified residues in channel gating is currently inadequate.

    Reviewed by eLife