eLife

Latest preprint reviews

1. Mitochondrial respiration contributes to the interferon gamma response in antigen-presenting cells

   This article has 7 authors:

   1. Michael C Kiritsy
   2. Katelyn McCann
   3. Daniel Mott
   4. Steven M Holland
   5. Samuel M Behar
   6. Christopher M Sassetti
   7. Andrew J Olive

   Reviewed by eLife

2. Evolution of cytokine production capacity in ancient and modern European populations

   This article has 11 authors:

   1. Jorge Domínguez-Andrés
   2. Yunus Kuijpers
   3. Olivier B Bakker
   4. Martin Jaeger
   5. Cheng-Jian Xu
   6. Jos WM Van der Meer
   7. Mattias Jakobsson
   8. Jaume Bertranpetit
   9. Leo AB Joosten
   10. Yang Li
   11. Mihai G Netea

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Dominguez-Andrés et al. collect a large amount of immune-related trait association data from a cohort made up of 534 individuals of Western European ancestry. The goal was to track the evolutionary trajectories of cytokine production capacity over time in a number of patients with different exposure to infectious organisms, infectious disease, autoimmune and inflammatory diseases, using the 500 Functional Genomics cohort of the Human Functional Genomics Project. From this analysis it was hypothesized that the Neolithic transition was characterized by strong changes in the adaptive response to pathogens in human biology. Overall, the manuscript is interesting but could be improved by significant enhancements to statistical methodology.

     (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

3. A genetic screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation

   This article has 9 authors:

   1. Michael C Kiritsy
   2. Laurisa M Ankley
   3. Justin Trombley
   4. Gabrielle P Huizinga
   5. Audrey E Lord
   6. Pontus Orning
   7. Roland Elling
   8. Katherine A Fitzgerald
   9. Andrew J Olive

   Reviewed by eLife

4. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

   This article has 10 authors:

   1. Daniel R Knight
   2. Korakrit Imwattana
   3. Brian Kullin
   4. Enzo Guerrero-Araya
   5. Daniel Paredes-Sabja
   6. Xavier Didelot
   7. Kate E Dingle
   8. David W Eyre
   9. César Rodríguez
   10. Thomas V Riley

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: We appreciate this study and find that the conclusions that reclassify Clostridiodes are largely justified by the data/analysis. The major concern is that the work represents the application of standard approaches to refine species classification, as opposed to either proposing a novel approach to classify species or defining a split that might be more surprising and/or clinically significant (e.g. Kumar et al. Nature Genetics, 2019). Consequently, despite being a useful contribution to the literature we believe it is more suitable for a specialized audience.

     Reviewer #1 opted to reveal their name to the authors in the decision letter after review.

   Reviewed by eLife

5. Restored TDCA and valine levels imitate the effects of bariatric surgery

   This article has 23 authors:

   1. Markus Quante
   2. Jasper Iske
   3. Timm Heinbokel
   4. Bhavna N Desai
   5. Hector Rodriguez Cetina Biefer
   6. Yeqi Nian
   7. Felix Krenzien
   8. Tomohisa Matsunaga
   9. Hirofumi Uehara
   10. Ryoichi Maenosono
   11. Haruhito Azuma
   12. Johann Pratschke
   13. Christine S Falk
   14. Tammy Lo
   15. Eric Sheu
   16. Ali Tavakkoli
   17. Reza Abdi
   18. David Perkins
   19. Maria-Luisa Alegre
   20. Alexander S Banks
   21. Hao Zhou
   22. Abdallah Elkhal
   23. Stefan G Tullius

   Reviewed by eLife

6. Improving oligo-conjugated antibody signal in multimodal single-cell analysis

   This article has 10 authors:

   1. Terkild B Buus
   2. Alberto Herrera
   3. Ellie Ivanova
   4. Eleni Mimitou
   5. Anthony Cheng
   6. Ramin S Herati
   7. Thales Papagiannakopoulos
   8. Peter Smibert
   9. Niels Odum
   10. Sergei B Koralov

   Reviewed by eLife

7. Functional specialization within the inferior parietal lobes across cognitive domains

   This article has 3 authors:

   1. Ole Numssen
   2. Danilo Bzdok
   3. Gesa Hartwigsen

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: Overall the reviewers felt that the manuscript had a fair amount of promise but raised some issues about the specific tasks used and some details of the analysis. One reviewer in particular felt that the manuscript should be reworked around the functional connectivity results, which would strengthen the manuscript. I tend to agree with this assessment, particularly as concerns the lateralization framing which is not very well explored by these tasks.

   Reviewed by eLife

8. How subtle changes in 3D structure can create large changes in transcription

   This article has 3 authors:

   1. Jordan Yupeng Xiao
   2. Antonina Hafner
   3. Alistair N Boettiger

   This article has been curated by 1 group:

   • Curated by eLife

     Summary: The work describes a simple theoretical model for enhancer action that explains several major controversies in the field of long-range gene regulation and the role of topologically associating domains and insulating boundaries in modulating enhancer-promoter interactions. Further, the model makes predictions that can be experimentally tested. This is valuable for the field of gene regulation.

     Reviewer #2 and Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

   Reviewed by eLife

9. The role of sigma 1 receptor in organization of endoplasmic reticulum signaling microdomains

   This article has 7 authors:

   1. Vladimir Zhemkov
   2. Jonathon A Ditlev
   3. Wan-Ru Lee
   4. Mikaela Wilson
   5. Jen Liou
   6. Michael K Rosen
   7. Ilya Bezprozvanny

   Reviewed by eLife

10. Spatial modulation of visual responses arises in cortex with active navigation

    This article has 7 authors:

    1. E Mika Diamanti
    2. Charu Bai Reddy
    3. Sylvia Schröder
    4. Tomaso Muzzu
    5. Kenneth D Harris
    6. Aman B Saleem
    7. Matteo Carandini

    This article has been curated by 1 group:

    • Curated by eLife

      Summary: This paper investigates the modulation of spatial signals in higher order visual areas in mice navigating virtual reality environments. Previous work demonstrated that the spatial position of an animal modulates neural activity in the primary visual cortex (V1). Here, the authors demonstrate that this spatial modulation however, is not a general feature of the visual circuit. Similar spatial modulation occurs in higher visual areas but not in lower visual areas, such as the lateral geniculate nucleus. Moreover, this work finds that spatial modulation was stronger when animals had more experience on the track and when the animals were actively performing a task, rather than when the animal was passively viewing the same virtual track. Since the first reports that visual neurons show modulation by spatial position during spatial navigation tasks, similar to that observed in hippocampal place cells, the source of this modulation has been an open question. This work adds new insight regarding this question, suggesting that it is likely either generated within the visual cortex itself or propagated in a top-down manner from higher brain areas, rather than in a bottom-up manner from the thalamus.

    Reviewed by eLife