eLife

Latest preprint reviews

1. A genome-wide functional genomics approach uncovers genetic determinants of immune phenotypes in type 1 diabetes

   This article has 13 authors:

   1. Xiaojing Chu
   2. Anna WM Janssen
   3. Hans Koenen
   4. Linzhung Chang
   5. Xuehui He
   6. Irma Joosten
   7. Rinke Stienstra
   8. Yunus Kuijpers
   9. Cisca Wijmenga
   10. Cheng-Jian Xu
   11. Mihai G Netea
   12. Cees J Tack
   13. Yang Li

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study examines genetic and non-genetic factors influencing immune responses in type 1 diabetes Key findings are: 1) age and season affect immune cell traits and cytokine production upon stimulation; 2) certain genetic variants that determine susceptibility to T1D significantly affect T cell composition, notably the CCR region that is associated with CCR5+ regulatory T cells; and 3) 15 genetic loci that influence immune responses in T1D, most of which have not been seen previously in healthy populations. The results suggest mechanisms of T1D-specific genetic regulation.

     (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

2. KDM6B interacts with TFDP1 to activate P53 signaling in regulating mouse palatogenesis

   This article has 10 authors:

   1. Tingwei Guo
   2. Xia Han
   3. Jinzhi He
   4. Jifan Feng
   5. Junjun Jing
   6. Eva Janečková
   7. Jie Lei
   8. Thach-Vu Ho
   9. Jian Xu
   10. Yang Chai

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is a tour de force study, with elegant mouse genetics and potentially clinically relevant rescue results using a small molecule inhibitor that can aleriorate cleft palate in a mutant mouse model. The work will be of interest to the craniofacial biology community and to the broader developmental biology community, as well as to all those devoted to the study of the epigenetic and transcriptional regulation of morphogenesis and organogenesis.

     (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. The Arabidopsis SAC9 enzyme is enriched in a cortical population of early endosomes and restricts PI(4,5)P2 at the plasma membrane

   This article has 15 authors:

   1. Alexis Lebecq
   2. Mehdi Doumane
   3. Aurelie Fangain
   4. Vincent Bayle
   5. Jia Xuan Leong
   6. Frédérique Rozier
   7. Maria del Marques-Bueno
   8. Laia Armengot
   9. Romain Boisseau
   10. Mathilde Laetitia Simon
   11. Mirita Franz-Wachtel
   12. Boris Macek
   13. Suayib Üstün
   14. Yvon Jaillais
   15. Marie-Cécile Caillaud

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Phosphoinositide phosphates (PIPs) are lipids that can convey distinct identities to different cellular membranes via different phosphorylation patterns. Here, Doumane and co-authors document the effects of the previously-characterized sac9 mutant, affecting a putative PIP-5-phosphatase in Arabidopsis, on PIP localization and endocytic trafficking. This work confirms that disrupting PI(4,5)P2 localization can affect endocytic trafficking in plants and will be of interest to the plant and cell biology research fields.

     (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

4. Most primary olfactory neurons have individually neutral effects on behavior

   This article has 6 authors:

   1. Tayfun Tumkaya
   2. Safwan Burhanudin
   3. Asghar Khalilnezhad
   4. James Stewart
   5. Hyungwon Choi
   6. Adam Claridge-Chang

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Olfactory coding is still an open question in neuroscience. Therefore, this paper is of potential interest to a broad audience of neuroscientists. It undertakes a thorough investigation of how olfactory sensory neurons drive avoidance or attraction in flies and also addresses how combinations of active ORNs can become behaviorally meaningful. It has great potential value for clarifying how animals map sensory input to valence.

     (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

5. A genetic compensatory mechanism regulated by Jun and Mef2d modulates the expression of distinct class IIa Hdacs to ensure peripheral nerve myelination and repair

   This article has 9 authors:

   1. Sergio Velasco-Aviles
   2. Nikiben Patel
   3. Angeles Casillas-Bajo
   4. Laura Frutos-Rincón
   5. Enrique Velasco
   6. Juana Gallar
   7. Peter Arthur-Farraj
   8. Jose A Gomez-Sanchez
   9. Hugo Cabedo

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This study is of interest to scientists working in the field of genetic control of glial cell differentiation, myelination and repair. The data are extensive, of high quality, support their main conclusions, and provide novel insights into regulation of genetic compensatory mechanisms. The presentation and interpretation of the data can be improved.

     (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. Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays

   This article has 13 authors:

   1. Konrad H Stopsack
   2. Svitlana Tyekucheva
   3. Molin Wang
   4. Travis A Gerke
   5. J Bailey Vaselkiv
   6. Kathryn L Penney
   7. Philip W Kantoff
   8. Stephen P Finn
   9. Michelangelo Fiorentino
   10. Massimo Loda
   11. Tamara L Lotan
   12. Giovanni Parmigiani
   13. Lorelei A Mucci

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Tissue microarrays (TMA) have become a mainstay in clinical and basic research, for both discovery and validation of biomarkers. This manuscript provides relevant methodologic considerations for cancer researchers investigating tissue-biomarkers using TMAs. A comprehensive investigation was conducted using a combination of analytic approaches using empirical data and simulated data to support key findings and conclusions. The authors approach the possible sampling variation in a thoughtful way, not only quantifying the issue systematically, but working towards a solution.

     (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. Tracking cell lineages in 3D by incremental deep learning

   This article has 3 authors:

   1. Ko Sugawara
   2. Çağrı Çevrim
   3. Michalis Averof

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Sugawara et al describe a new interactive tool for 3D cell tracking in time that allows the user to retrain models quickly with updated labels. The utility of a tool like this for biologists is great: many experiments require tracking cell division over time or cell movements. With clear comparison to the latest developments in cellular segmentation and an improved procedure enabling the use of the tool, this paper would make an interesting contribution to the image analysis field.

     (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. Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

   This article has 4 authors:

   1. Katelyn Mika
   2. Camilla M Whittington
   3. Bronwyn M McAllan
   4. Vincent J Lynch

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Mika and colleagues reconstruct the evolution of uterine endometrial transcriptomes during pregnancy from 23 diverse species of mammals that differ with respect to their degree of placental invasiveness. Through this analysis the authors infer that the eutherian mammal ancestor had an invasive mode of placentation and that the degree of invasiveness of placentation is reflected on uterine endometrial gene expression during pregnancy. Thus, phylogenetic analysis of gene expression profiles of different mammals groups them on the basis of degree of placental invasiveness, a quite striking finding.

     (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

9. Mutation saturation for fitness effects at human CpG sites

   This article has 2 authors:

   1. Ipsita Agarwal
   2. Molly Przeworski

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Diminishing returns on sampling new variable sites with increasing samples sizes is a classic limitation of population genomics and one that limits the power of population genomic approaches to make site-specific inferences of natural selection. This timely study demonstrates that methylated CpG sites, which have a mutation rate an order of magnitude higher than other sites in the genome, are saturated with polymorphisms in modern human genomic datasets. They can thus serve as a starting point for understanding the effects of natural selection at the resolution of single nucleotide sites. The manuscript is a clearly written presentation of the state of the field and the claims are supported by a variety of thoughtful analyses. Additional work will be needed to take full advantage of the insights from this study.

     (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

10. Local field potentials reflect cortical population dynamics in a region-specific and frequency-dependent manner

    This article has 5 authors:

    1. Cecilia Gallego-Carracedo
    2. Matthew G Perich
    3. Raeed H Chowdhury
    4. Lee E Miller
    5. Juan Álvaro Gallego

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      This paper will be of interest to electrophysiologists, systems neuroscientists and neural engineers. The authors describe a framework for evaluating the comparison between LFP dynamics and spikes and perform this comparison for several datasets recorded from motor, premotor, and sensory areas of cortex in rhesus macaque monkeys. These results serve as an important benchmark for the information content of LFP recordings, which is relevant to data collection in neuroscientific investigations and to designing brain computer interfaces.

      (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