eLife

Latest preprint reviews

1. RNA localization mechanisms transcend cell morphology

   This article has 4 authors:

   1. Raeann Goering
   2. Ankita Arora
   3. Megan C Pockalny
   4. J Matthew Taliaferro

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Goering and colleagues investigate subcellular RNA localization across different cell types and species. The major insight is that there may be general mechanisms and specifically conserved proteins that regulate RNA localization in diverse cell types and morphologies. This manuscript will be of interest to those studying gene expression and how its regulation occurs within the cell.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

2. The proportion of randomized controlled trials that inform clinical practice

   This article has 4 authors:

   1. Nora Hutchinson
   2. Hannah Moyer
   3. Deborah A Zarin
   4. Jonathan Kimmelman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This article constructs a four-step assessment of the informativeness of a clinical trial that measures its feasibility, reporting, importance, and risk of bias. This is a potentially highly relevant methodology for the class of trials for which it is defined, namely 'clinically directed randomized controlled trials'. It could also be translated and validated in other areas, using data from a wider set of sources beyond the trial registry clinicaltrials.gov. However, the extended longitudinal nature of the assessment and its potential subjectivity limit this tool's utility to being a retrospective diagnostic rather than as a prospective diagnostic and/or fix for at-risk designs.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. All three Reviewers agreed to share their names with the authors.)

   Reviewed by eLife

3. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins

   This article has 2 authors:

   1. Eric B Zheng
   2. Li Zhao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     By integrating in silico predictions and mass-spectrometry, this manuscript tackles the problem of annotating the currently nameless stretches of genomic sequence that actually code for proteins. The hundreds of protein coding fruit fly genes described here offer new inroads for studying some of the very youngest functional elements in genomes, particularly those that have recently emerged from non-coding DNA sequences. To clarify the biological significance of the present study, the authors should both highlight the genes mostly like to encode functional products and conduct a comparison to published datasets that used different methods to identify such genes in fruit flies.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by Arcadia Science, eLife

4. A dopamine-gated learning circuit underpins reproductive state-dependent odor preference in Drosophila females

   This article has 11 authors:

   1. Ariane C Boehm
   2. Anja B Friedrich
   3. Sydney Hunt
   4. Paul Bandow
   5. KP Siju
   6. Jean Francois De Backer
   7. Julia Claussen
   8. Marie Helen Link
   9. Thomas F Hofmann
   10. Corinna Dawid
   11. Ilona C Grunwald Kadow

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this manuscript, the authors explore the circuit mechanism underlying mating-induced change of odor preference in Drosophila. Olfactory cues during mating induce a long-lasting increase in attraction to polyamines in female flies. The authors use a combination of neurogenetics, imaging, and behaviour to identify elements of the mushroom body and lateral horn circuitry involved in this behaviour. The importance of mushroom body plasticity in female postmating changes highlights a novel pathway for these changes and reveals the variety of mechanisms by which the brain can encode experience and adapt behavior. This paper will be of interest to scientists within the field of reproductive behaviors and neuroscience of internal states.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

5. Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies

   This article has 17 authors:

   1. Stella Tamana
   2. Maria Xenophontos
   3. Anna Minaidou
   4. Coralea Stephanou
   5. Cornelis L Harteveld
   6. Celeste Bento
   7. Joanne Traeger-Synodinos
   8. Irene Fylaktou
   9. Norafiza Mohd Yasin
   10. Faidatul Syazlin Abdul Hamid
   11. Ezalia Esa
   12. Hashim Halim-Fikri
   13. Bin Alwi Zilfalil
   14. Andrea C Kakouri
   15. ClinGen Hemoglobinopathy Variant Curation Expert Panel
   16. Marina Kleanthous
   17. Petros Kountouris

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The increased use of gene and exome sequencing of individuals for diagnostic purposes has led to the identification of numerous single nucleotide variants (SNVs). However, annotating the probable clinical significance of every newly identified variant relies on multiple criteria, and in silico predictions can be used by curation experts to classify variants in databases. Since the reliability of such predictions is of paramount importance, this study compares the performance of 31 computational tools in classifying the pathogenicity of SNVs in the human adult globin genes and proposes an improved approach to achieve balanced predictions. The paper will be of interest to scientists and clinicians in the field of hemoglobinopathies.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

   Reviewed by eLife

6. Transcriptional heterogeneity and cell cycle regulation as central determinants of Primitive Endoderm priming

   This article has 7 authors:

   1. Marta Perera
   2. Silas Boye Nissen
   3. Martin Proks
   4. Sara Pozzi
   5. Rita S Monteiro
   6. Ala Trusina
   7. Joshua M Brickman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study uses media-based conversion of stem cell cultures towards to investigate how cell cycle regulation affects the transition of cell populations between pluripotent and differentiated states. Through a detailed analysis of cell cycle properties in different primed subpopulations, under a range of growth conditions, the authors propose that both the maintenance of pluripotency as well as the conversion towards a more differentiated state is influenced by selective shortening of the cell cycle in different primed subpopulations. By using new reporter systems and long-term imaging, this study thus sheds new light on the old question of whether extracellular signals control differentiation in cell populations through selection or induction.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

7. Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis

   This article has 14 authors:

   1. Julie Paxman
   2. Zhen Zhou
   3. Richard O'Laughlin
   4. Yuting Liu
   5. Yang Li
   6. Wanying Tian
   7. Hetian Su
   8. Yanfei Jiang
   9. Shayna E Holness
   10. Elizabeth Stasiowski
   11. Lev S Tsimring
   12. Lorraine Pillus
   13. Jeff Hasty
   14. Nan Hao

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The idea of individual aging trajectories of single cells is important and the authors provide sufficient evidence that there is some stochasticity that directs individual cells towards certain routes of aging - at least in budding yeast. Investigating the link between rDNA silencing and protein homeostasis, this study thus addresses an interesting and exciting question. The authors show how age-dependent loss of rDNA silencing might contribute to protein aggregation. Importantly, the paper furthers the understanding of distinct aging trajectories and raises important questions about how these processes might be relevant in multicellular organisms.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

8. Ear pinnae in a neotropical katydid (Orthoptera: Tettigoniidae) function as ultrasound guides for bat detection

   This article has 9 authors:

   1. Christian A Pulver
   2. Emine Celiker
   3. Charlie Woodrow
   4. Inga Geipel
   5. Carl D Soulsbury
   6. Darron A Cullen
   7. Stephen M Rogers
   8. Daniel Veitch
   9. Fernando Montealegre-Z

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Remarkably, Katydids, insects related to grasshoppers and crickets, have ears in their left and right forelegs. Pulver and colleagues show convincingly how two specialized chambers lining the hearing organs function as sound resonators that effectively boost the perception of high ultrasonic frequencies. This enables Katydids to detect the echolocating pulses of their bat predators before they home in on them for a meal. This study uses an impressive combination of approaches, but the manuscript would be improved by greater clarity.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)

   Reviewed by eLife

9. Resurrecting essential amino acid biosynthesis in mammalian cells

   This article has 14 authors:

   1. Julie Trolle
   2. Ross M McBee
   3. Andrew Kaufman
   4. Sudarshan Pinglay
   5. Henri Berger
   6. Sergei German
   7. Liyuan Liu
   8. Michael J Shen
   9. Xinyi Guo
   10. J Andrew Martin
   11. Michael E Pacold
   12. Drew R Jones
   13. Jef D Boeke
   14. Harris H Wang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     In this study, Trolle et al aimed to introduce methionine, threonine, isoleucine, and valine biosynthetic pathways into Chinese Hamster Ovary (CHO) cells. While this was unsuccessful for methionine, threonine, and isoleucine, introduction of valine synthesis rendered CHO cells partially independent on exogenous valine. Although introduction of essential amino acid biosynthetic pathways into mammalian cells is of potentially broad interest to the fields of synthetic biology, biotechnology and metabolism, there were concerns regarding incomplete demonstration that the introduction of valine pathway into CHO cells is sufficient to sustain homeostasis in the absence of exogenous valine. Further metabolic/biochemical characterization of valine-producing CHO cells is warranted.

     (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

10. Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for label-free detection of molecules across entire cell sections

    This article has 4 authors:

    1. Johannes Elferich
    2. Giulia Schiroli
    3. David T Scadden
    4. Nikolaus Grigorieff

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      The work details a new acquisition method of defocus corrected large area cryo-EM (DeCo-LACE). The data-acquisition approach is highly complementary to the research group's previous work of using high-resolution 2D template-matching (2DTM) to identify macromolecular complexes in dense and heterogeneous cellular specimens. Notably and importantly, the data-acquisition approach minimizes sampling bias. Overall, DeCo-LACE is a very interesting approach to locating large ribosomal subunits in FIB-lamella at scale.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife