eLife

Latest preprint reviews

1. Deconstructing cold-induced brown adipocyte neogenesis in mice

   This article has 5 authors:

   1. Rayanne B Burl
   2. Elizabeth Ann Rondini
   3. Hongguang Wei
   4. Roger Pique-Regi
   5. James G Granneman

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Burl and Rondini et al. elucidate the transcriptional profile of the stromal vascular fraction of murine brown adipose tissue in the context of thermogenic stimulation. The authors combined systems and reductionist approaches to show the reliance of mature brown adipocytes on adrenergic activation to indirectly stimulate progenitor proliferation and differentiation and the involvement of dendritic cells in this process. Overall, this is a timely and well-rounded work that will provide beneficial data for public use and further resolve the complexities underlying brown adipose physiology.

     (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 name with the authors.)

   Reviewed by eLife

2. MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size

   This article has 9 authors:

   1. Michael J Lafferty
   2. Nil Aygün
   3. Niyanta K Patel
   4. Oleh Krupa
   5. Dan Liang
   6. Justin M Wolter
   7. Daniel H Geschwind
   8. Luis de la Torre-Ubieta
   9. Jason L Stein

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is one of the first demonstrations that expression quantitative trait loci (eQTL) affecting human microRNAs are linked to brain development affecting brain structure and function. These findings will have a broad impact on the genomics, neural development, and microRNA fields. The datasets produced here (developmental changes in miRNAs, new human miRNAs) will likely be used for further discoveries. However, some claims need to be tempered.

     (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

3. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5

   This article has 16 authors:

   1. Ryota Miyashita
   2. Atsuya Nishiyama
   3. Weihua Qin
   4. Yoshie Chiba
   5. Satomi Kori
   6. Norie Kato
   7. Chieko Konishi
   8. Soichiro Kumamoto
   9. Hiroko Kozuka-Hata
   10. Masaaki Oyama
   11. Yoshitaka Kawasoe
   12. Toshiki Tsurimoto
   13. Tatsuro S Takahashi
   14. Heinrich Leonhardt
   15. Kyohei Arita
   16. Makoto Nakanishi

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     DNA methylation inheritance through the UHRF1-DNMT1 signaling axis is becoming increasingly appreciated as a ubiquitin-regulated process. This study builds on the observation that UHRF1 multi mono-ubiquitinates the PCNA-associated protein PAF15, and that, similarly to H3 substrates, these mono-ubiquitin sites are bound by DNMT1 and may contribute to its S-phase chromatin association. The authors focus on players involved in ubiquitin removal and PAF15 release from chromatin and they identify the deubiquitinase USP7 and the DNA replication regulator ATAD5 as important to this termination process. While manipulation of these factors using Xenopus egg extracts shows quite striking effects on DNMT1 chromatin association, effects on DNA methylation are minimal and this brings to question the importance and potential impact of the pathway involving PAF15. In addition, how the findings from Xenopus egg extracts translate to regulation of DNA methylation maintenance in mammalian cells is currently unclear.

     (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

4. Insulin sensitivity is preserved in mice made obese by feeding a high starch diet

   This article has 17 authors:

   1. Amanda E Brandon
   2. Lewin Small
   3. Tuong-Vi Nguyen
   4. Eurwin Suryana
   5. Henry Gong
   6. Christian Yassmin
   7. Sarah E Hancock
   8. Tamara Pulpitel
   9. Sophie Stonehouse
   10. Letisha Prescott
   11. Melkam A Kebede
   12. Belinda Yau
   13. Lake-Ee Quek
   14. Greg M Kowalski
   15. Clinton R Bruce
   16. Nigel Turner
   17. Gregory J Cooney

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study evaluates the effects of two distinct dietary methods that cause obesity in mice (high fat vs high starch) on insulin sensitivity and glucose homeostasis. Through a series of nicely performed physiology experiments, the authors demonstrated that high starch feeding causes obesity without deleterious effects on insulin sensitivity. This work will have an impact in the field and help define the important lipid mediators of metabolic disease.

     (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 #3 agreed to share their name with the authors.)

   Reviewed by eLife

5. Real time, in vivo measurement of neuronal and peripheral clocks in Drosophila melanogaster

   This article has 7 authors:

   1. Peter S Johnstone
   2. Maite Ogueta
   3. Olga Akay
   4. Inan Top
   5. Sheyum Syed
   6. Ralf Stanewsky
   7. Deniz Top

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper presents a novel and potentially highly useful approach to monitor circadian rhythms in specific tissues. The elegant reporter that the authors have built has the potential to become an important tool for understanding how different body clocks respond to various inputs and genetic manipulations. The authors already apply it to show that different clocks appear to be responding differently to loss of signaling from a key circadian neuropeptide in Drosophila melanogaster. However, it is difficult to determine whether these results, as currently presented and analyzed, provide new insight into the relationship between brain and peripheral clocks. The work is of interest to the community of biologists studying biological rhythms.

     (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

6. DNA methylome combined with chromosome cluster-oriented analysis provides an early signature for cutaneous melanoma aggressiveness

   This article has 18 authors:

   1. Arnaud Carrier
   2. Cécile Desjobert
   3. Loic Ponger
   4. Laurence Lamant
   5. Matias Bustos
   6. Jorge Torres-Ferreira
   7. Rui Henrique
   8. Carmen Jeronimo
   9. Luisa Lanfrancone
   10. Audrey Delmas
   11. Gilles Favre
   12. Antoine Daunay
   13. Florence Busato
   14. Dave SB Hoon
   15. Jorg Tost
   16. Chantal Etievant
   17. Joëlle Riond
   18. Paola B Arimondo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Predicting if a tumour has aggressive or metastatic characteristics would be of great utility in the clinic as it would help patient stratification and management. In this manuscript, Carrier and collaborators derive a signature for melanoma aggressiveness relying on methylated regions of tumour and cell line genomes. The identification of a 4-gene methylation biomarker for melanoma aggressiveness and survival is an important contribution. This manuscript is of relevance to clinicians and melanoma researchers interested in biomarker research.

     (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 #2 agreed to share their name with the authors.)

   Reviewed by eLife

7. Mapping odorant sensitivities reveals a sparse but structured representation of olfactory chemical space by sensory input to the mouse olfactory bulb

   This article has 7 authors:

   1. Shawn D Burton
   2. Audrey Brown
   3. Thomas P Eiting
   4. Isaac A Youngstrom
   5. Thomas C Rust
   6. Michael Schmuker
   7. Matt Wachowiak

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This is an important paper querying odor responses in the olfactory bulb at low concentrations. Classical studies have revealed a 'combinatorial code' for odorant recognition, with individual odorants represented by combinations of broadly tuned and low-affinity olfactory receptors. Here, the authors perform a large-scale analysis of odor responses across glomeruli and surprisingly observe that odorant receptors instead generally display remarkably narrow tuning profiles.

     (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 #2 agreed to share their name with the authors.)

   Reviewed by eLife

8. Higher-order unimodal olfactory sensory preconditioning in Drosophila

   This article has 4 authors:

   1. Juan Martinez-Cervantes
   2. Prachi Shah
   3. Anna Phan
   4. Isaac Cervantes-Sandoval

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper shows that Drosophila can perform olfactory unimodal sensory preconditioning, an example of higher-order conditioning that may guide behaviour through inferred value. This is of conceptual significance for the brain, behavioural, and to some extent, the social sciences, because it shows that a conditioned response to a stimulus can occur even when the stimulus itself was never paired with punishment, for example.

     (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

9. Regulation of inflammation and protection against invasive pneumococcal infection by the long pentraxin PTX3

   This article has 18 authors:

   1. Rémi Porte
   2. Rita Silva-Gomes
   3. Charlotte Theroude
   4. Raffaella Parente
   5. Fatemeh Asgari
   6. Marina Sironi
   7. Fabio Pasqualini
   8. Sonia Valentino
   9. Rosanna Asselta
   10. Camilla Recordati
   11. Marta Noemi Monari
   12. Andrea Doni
   13. Antonio Inforzato
   14. Carlos Rodriguez-Gallego
   15. Ignacio Obando
   16. Elena Colino
   17. Barbara Bottazzi
   18. Alberto Mantovani

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This submission represents a holistic approach to how pentraxin 3 (PTX3) modulates susceptibility to experimental infection by Streptococcus pneumoniae. The authors have built robust findings on the importance of PTX3 for the survival of mice and they have extensively investigated all different aspects of the mechanism of PTX3 protection. One main strength of the manuscript is its usage of bone marrow chimeras in addition to total as well as tissue-specific mouse strains that support their claims.

     (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 #2 agreed to share their name with the authors.)

   Reviewed by eLife

10. On the flexibility of the cellular amination network in E coli

    This article has 9 authors:

    1. Helena Schulz-Mirbach
    2. Alexandra Müller
    3. Tong Wu
    4. Pascal Pfister
    5. Selçuk Aslan
    6. Lennart Schada von Borzyskowski
    7. Tobias J Erb
    8. Arren Bar-Even
    9. Steffen N Lindner

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      In this paper, the authors demonstrate that a reversible amination network that allows nitrogen transfer via transaminases for synthesis of several amino acids can be constructed in laboratory strains through clever and carefully designed experiments. As a result, this work should be of interest to microbiologists, biochemists, synthetic biologists, and biotechnologists.

      (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 and Reviewer #3 agreed to share their name with the authors.)

    Reviewed by eLife