eLife

Latest preprint reviews

1. Rubella virus tropism and single-cell responses in human primary tissue and microglia-containing organoids

   This article has 7 authors:

   1. Galina Popova
   2. Hanna Retallack
   3. Chang N Kim
   4. Albert Wang
   5. David Shin
   6. Joseph L DeRisi
   7. Tomasz Nowakowski

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     The manuscript represents an important study on the pathogenesis of rubella virus tropism and neuropathology in human microglia-containing human stem cell derived organoids and human fetal brain slices. The strength of evidence is compelling, employing two different human-relevant models. The findings will be of broad interest to virologists and infectious disease experts, as well as neurodevelopmental biologists. The findings could also be of interest to pediatrics and obstetrics clinical colleagues.

   Reviewed by eLife

2. Fetal influence on the human brain through the lifespan

   This article has 14 authors:

   1. Kristine B Walhovd
   2. Stine K Krogsrud
   3. Inge K Amlien
   4. Øystein Sørensen
   5. Yunpeng Wang
   6. Anne Cecilie S Bråthen
   7. Knut Overbye
   8. Jonas Kransberg
   9. Athanasia M Mowinckel
   10. Fredrik Magnussen
   11. Martine Herud
   12. Asta K Håberg
   13. Anders Martin Fjell
   14. Didac Vidal-Pineiro

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study uses multiple large neuroimaging data sets acquired at different points through the lifespan to provide solid evidence that birthweight (BW) is associated with robust and persistent variations in cortical anatomy, but less-substantial influences on cortical change over time. These findings, supported by robust statistical methods, illustrate the long temporal reach of early developmental influences and carry relevance for how we conceptualize, study, and potentially modify such influences more generally. The paper will be of interest to people interested in brain development and aging.

   Reviewed by eLife

3. Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models

   This article has 10 authors:

   1. Rita Sianga-Mete
   2. Penelope Hartnady
   3. Wimbai Caroline Mandikumba
   4. Kayleigh Rutherford
   5. Christopher Brian Currin
   6. Florence Phelanyane
   7. Sabina Stefan
   8. Steven Weaver
   9. Sergei L Kosakovsky Pond
   10. Darren P Martin

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study revisits the effects of substitution model selection on phylogenetics by comparing reversible and non-reversible DNA substitution models. The authors provide evidence that 1) non time-reversible models sometimes perform better than general time-reversible models when inferring phylogenetic trees out of simulated viral genome sequence data sets, and that 2) non time-reversible models can fit the real data better than the reversible substitution models commonly used in phylogenetics, a finding consistent with previous work. However, the methods are incomplete in supporting the main conclusion of the manuscript, that is that non time-reversible models should be incorporated in the model selection process for these data sets.

   Reviewed by eLife

4. Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis

   This article has 28 authors:

   1. Shintaro Watanuki
   2. Hiroshi Kobayashi
   3. Yuki Sugiura
   4. Masamichi Yamamoto
   5. Daiki Karigane
   6. Kohei Shiroshita
   7. Yuriko Sorimachi
   8. Shinya Fujita
   9. Takayuki Morikawa
   10. Shuhei Koide
   11. Motohiko Oshima
   12. Akira Nishiyama
   13. Koichi Murakami
   14. Miho Haraguchi
   15. Shinpei Tamaki
   16. Takehiro Yamamoto
   17. Tomohiro Yabushita
   18. Yosuke Tanaka
   19. Go Nagamatsu
   20. Hiroaki Honda
   21. Shinichiro Okamoto
   22. Nobuhito Goda
   23. Tomohiko Tamura
   24. Ayako Nakamura-Ishizu
   25. Makoto Suematsu
   26. Atsushi Iwama
   27. Toshio Suda
   28. Keiyo Takubo

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study provides novel strategies to overcome certain limitations when investigating the metabolism of hematopoietic stem cells, mainly due to their low abundance. The study provides compelling evidence suggesting that proliferative hematopoietic stem cells mainly use glycolysis (rather than mitochondrial OXPHOS or TCA cycle) as their primary energy source during emergency hematopoiesis. The article provides direct links between metabolic features and cell proliferation and explores alternative energy sources, and is of great interest to stem cell biologists.

   Reviewed by eLife

5. A randomized multiplex CRISPRi-Seq approach for the identification of critical combinations of genes

   This article has 8 authors:

   1. Nicole A Ellis
   2. Kevin S Myers
   3. Jessica Tung
   4. Anne Davidson Ward
   5. Kathryn Johnston
   6. Katherine E Bonnington
   7. Timothy J Donohue
   8. Matthias P Machner

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important study uses CRISPRi to silence multiple effectors in the pathogen, Legionella pneumophila. It provides a technique that will allow researchers to address functional redundancy amongst effectors, a problem that has persisted even after decades of study. The methodology used is convincing, and further improvement (such as using multiple guides per gene) can lead to the identification of novel virulence factors.

   Reviewed by eLife

6. Multiple repeat regions within mouse DUX recruit chromatin regulators to facilitate an embryonic gene expression program

   This article has 4 authors:

   1. Christina M. Smith
   2. Edward J. Grow
   3. Sean C. Shadle
   4. Bradley R. Cairns

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This useful study provides a systematic mutational analysis to elucidate mechanisms involved in transcriptional activation by the murine DUX protein, DUX is a master transcription factor regulating mammalian early embryonic gene activation and its human homolog DUX4 is also involved in a muscular disease, fascioscapulohumeral dystrophy (FSHD). The data are solid and the interpretations of the findings are reasonable. The work will be of interest to colleagues studying early embryonic development or FSHD.

   Reviewed by eLife

7. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ

   This article has 6 authors:

   1. Zhi Yang Tan
   2. Shujun Cai
   3. Alex J Noble
   4. Jon K Chen
   5. Jian Shi
   6. Lu Gan

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This important paper exploits new cryo-EM tomography tools to examine the state of chromatin in situ. The experimental work is meticulously performed, with a vast amount of data collected, with convincing interpretation of possible nucleosomal structures in yeast. The majority of these nucleosomes appear not to possess stable octameric configurations. Although it cannot be excluded that there could be an unknown bias in class detection, we agree that the authors have gone as far as is possible, given constraints in current technology and analysis, to support their model. Despite the provocative nature of this report, it is our hope that such work will spark debate, and further the development of exciting new tools that can interrogate the dynamic nature of the nucleosome, and its associated functions in situ.

   Reviewed by eLife

8. Inositol pyrophosphate dynamics reveals control of the yeast phosphate starvation program through 1,5-IP8 and the SPX domain of Pho81

   This article has 8 authors:

   1. Valentin Chabert
   2. Geun-Don Kim
   3. Danye Qiu
   4. Guizhen Liu
   5. Lydie Michaillat Mayer
   6. Muhammed Jamsheer K
   7. Henning J Jessen
   8. Andreas Mayer

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This fundamental study describes the mechanisms for regulation of the phosphate starvation response in baker's yeast, clarifies the interpretations of prior data, and suggests a unifying mechanism across eukaryotes. The study provides compelling data, based on biochemical analyses, protein localization by fluorescence, and genetic approaches that 1,5-InsP8 is the phosphate nutrient messenger in yeast.

   Reviewed by eLife

9. Genetic validation of PfFKBP35 as an antimalarial drug target

   This article has 13 authors:

   1. Basil T Thommen
   2. Jerzy M Dziekan
   3. Fiona Achcar
   4. Seth Tjia
   5. Armin Passecker
   6. Katarzyna Buczak
   7. Christin Gumpp
   8. Alexander Schmidt
   9. Matthias Rottmann
   10. Christof Grüring
   11. Matthias Marti
   12. Zbynek Bozdech
   13. Nicolas MB Brancucci

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     FKBP35 is the only FK506-binding protein present in the malaria-causing parasite Plasmodium falciparum, and has been considered a promising drug target due to its high affinity to the macrolide compound FK506, an immunosuppressant with antiplasmodial activity. This study demonstrates the essentiality of FKBP35 in parasite growth, based on compelling genetic evidence. The data also suggest that FK506 may exert its antimalarial activity through FKBP35-independent mechanisms that have not yet been characterised. This important study will be of interest to scientists working on the parasite biology and antimalarial drug development.

   Reviewed by eLife

10. Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5

    This article has 7 authors:

    1. Sarah E McComas
    2. Tom Reichenbach
    3. Darko Mitrovic
    4. Claudia Alleva
    5. Marta Bonaccorsi
    6. Lucie Delemotte
    7. David Drew

    This article has been curated by 1 group:

    • Curated by eLife

      eLife assessment

      The current manuscript investigates the energy landscape of the mammalian sugar porter GLUT5 using enhanced molecular dynamics simulations and biochemical assays. The approach generates important insights into the mechanism of GLUT5 conformational change, and into mechanistic diversity among the GLUT sugar porters more generally. The overall strategy is solid, but without an additional error analysis, the computational components remain incomplete. These findings will be of interest to the transporter and membrane biology communities.

    Reviewed by eLife