eLife

Latest preprint reviews

1. DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

   This article has 6 authors:

   1. Vincent Gardeux
   2. Roel PJ Bevers
   3. Fabrice PA David
   4. Emily Rosschaert
   5. Romain Rochepeau
   6. Bart Deplancke

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Genetic analysis of complex traits in Drosophila provides a resource for exploring the relationship between genetic and phenotypic variation. The web tool DGRPool presented in this paper makes data and results from the Drosophila Genetic Reference Panel accessible that will enable downstream analyses of genetic association. The findings of this paper are considered to be important, with practical implications beyond a single subfield, supported by convincing evidence using appropriate and validated methodology in line with current state of the art.

   Reviewed by eLife

2. Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

   This article has 11 authors:

   1. Roberto Efraín Díaz
   2. Andrew K Ecker
   3. Galen J Correy
   4. Pooja Asthana
   5. Iris D Young
   6. Bryan Faust
   7. Michael C Thompson
   8. Ian B Seiple
   9. Steven Van Dyken
   10. Richard M Locksley
   11. James S Fraser

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This structural and biochemical study of the mouse homolog of acidic mammalian chitinase (AMCase) enhances our understanding of the pH-dependent activity and catalytic properties of mouse AMCase, and it sheds light on its adaptation to different physiological pH environments. The methods and analysis of data are solid, providing several lines of evidence to support the development of mechanistic hypotheses. While the findings and interpretation will be valuable to those studying AMCase in mice, the broader significance, including extension of the results to other species including human, remain less clear.

   Reviewed by eLife

3. Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and promote Dbp5-mediated tRNA export in vivo in Saccharomyces cerevisiae

   This article has 3 authors:

   1. Arvind Arul Nambi Rajan
   2. Ryuta Asada
   3. Ben Montpetit

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The work is a valuable contribution to understanding the mechanism of nuclear export of tRNA in budding yeast. The authors present solid evidence that Dbp5 functions in parallel with Los1 and Msn5 in tRNA export, in a manner dependent on Gle1 for activation of its ATPase activity but independently of Mex67, Dbp5's partner in mRNA export. It further presents biochemical evidence that Dbp5 can bind tRNA but that Gle1 and InsP6 are required for activating ATP hydrolysis by the Dbp5-tRNA complex, suggesting a possible mechanism for tRNA export by Dbp5.

   Reviewed by eLife

4. Deep Batch Active Learning for Drug Discovery

   This article has 14 authors:

   1. Michael Bailey
   2. Saeed Moayedpour
   3. Ruijiang Li
   4. Alejandro Corrochano-Navarro
   5. Alexander Kötter
   6. Lorenzo Kogler-Anele
   7. Saleh Riahi
   8. Christoph Grebner
   9. Gerhard Hessler
   10. Hans Matter
   11. Marc Bianciotto
   12. Pablo Mas
   13. Ziv Bar-Joseph
   14. Sven Jager

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study reports novel active learning batch selection methods that have been applied to optimization tasks related to ADMET and affinity properties relevant within the drug discovery field. While the evidence is solid, the paper could have benefited from a clearer and deeper description of methods as well as interpretation of the obtained models, and a wider comparison to existing methods. The article will be of general interest to scientist working in the field of drug discovery and, in general, to researchers within the fields of machine learning and data analysis.

   Reviewed by eLife

5. CLOCK evolved in cnidaria to synchronize internal rhythms with diel environmental cues

   This article has 6 authors:

   1. Raphael Aguillon
   2. Mieka Rinsky
   3. Noa Simon-Blecher
   4. Tirza Doniger
   5. Lior Appelbaum
   6. Oren Levy

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This fundamental study for the first time defines genetically the role of the Clock gene in basal metazoa, using the cnidarian Nematostella vectensis. With convincing evidence, the study provides insight into the early evolution of circadian clocks. Clock in this species is necessary for daily rhythms under constant conditions, but not under a rhythmic light/dark cycle, suggesting that the major role of the circadian oscillator in this species could be a stabilizing function under non-rhythmic environmental conditions.

   Reviewed by eLife

6. Improved inference of population histories by integrating genomic and epigenomic data

   This article has 3 authors:

   1. Thibaut Sellinger
   2. Frank Johannes
   3. Aurélien Tellier

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study extends existing sequentially Markovian coalescent approaches to include the combined use of SNPs and hypervariable loci such as epimutations. This is an intriguing addition to infer population size history in the recent past, and the authors provide solid validation of their methods via simulation and analysis of empirical data in Arabidopsis thaliana. Given the increasing availability of such data, this work is a timely contribution and represents a foundation for further developments to explore when and where these methods will be best used.

   Reviewed by eLife

7. ROM1 is redundant to PRPH2 as a molecular building block of photoreceptor disc rims

   This article has 9 authors:

   1. Tylor R Lewis
   2. Mustafa S Makia
   3. Carson M Castillo
   4. Ying Hao
   5. Muayyad R Al-Ubaidi
   6. Nikolai P Skiba
   7. Shannon M Conley
   8. Vadim Y Arshavsky
   9. Muna I Naash

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study is focused on the requirement of the photoreceptor-specific tetraspanins, ROM1 and PRPH2, for the formation of light-sensitive membrane discs. The evidence supporting the claim that deficiency in one of the proteins can be compensated by the other is convincing, with both established and advanced techniques yielding results that will be of interest to those studying photoreceptor development and membrane curvature.

   Reviewed by eLife

8. The reciprocal regulation between mitochondrial-associated membranes and Notch signaling in skeletal muscle atrophy

   This article has 6 authors:

   1. Yurika Ito
   2. Mari Yamagata
   3. Takuya Yamamoto
   4. Katsuya Hirasaka
   5. Takeshi Nikawa
   6. Takahiko Sato

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This interesting and important manuscript combines in vitro and in vivo experiments to investigate the reciprocal regulation between mitochondria-associated membranes and Notch signaling in skeletal muscle atrophy, with implications beyond the single subfield of muscle atrophy. The methods, data, and analyses are solid and broadly support the claims.

   Reviewed by eLife

9. What fraction of cellular DNA turnover becomes cfDNA?

   This article has 4 authors:

   1. Ron Sender
   2. Elad Noor
   3. Ron Milo
   4. Yuval Dor

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This manuscript describes a model to estimate what fraction of DNA from specific human tissues becomes cell-free DNA in plasma. This fundamental study, supported by convincing evidence, will be of great interest to the community, as the amount of DNA from a certain tissue (for example, a tumor) that becomes available for detection in the blood has significant implications for disease detection.

   Reviewed by eLife

10. Vitamin D constrains inflammation by modulating the expression of key genes on Chr17q12-21.1

    This article has 21 authors:

    1. Ayse Kilic
    2. Arda Halu
    3. Margherita De Marzio
    4. Enrico Maiorino
    5. Melody G Duvall
    6. Thayse Regina Bruggemann
    7. Joselyn J Rojas Quintero
    8. Robert Chase
    9. Hooman Mirzakhani
    10. Ayse Özge Sungur
    11. Janine Koepke
    12. Taiji Nakano
    13. Hong Yong Peh
    14. Nandini Krishnamoorthy
    15. Raja-Elie Abdulnour
    16. Katia Georgopoulos
    17. Augusto A Litonjua
    18. Marie Demay
    19. Harald Renz
    20. Bruce D Levy
    21. Scott T Weiss

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      The effect of Vitamin D supplementation in reducing asthma via anti-inflammatory mechanisms is a topic of wide interest, with somewhat conflicting published data. Here, bioinformatic approaches help to identify a role of VDR in inducing the expression of the key regulator Ikzf3, which possibly suppresses the IL-2/STAT5 axis, consequently blunting the Th2 response and mitigating allergic airway inflammation. These are important findings based on convincing evidence.

    Reviewed by eLife