Evaluated articles

Genomic basis of drought resistance in Fagus sylvatica

1. Markus Pfenninger
2. Friederike Reuss
3. Angelika Kiebler
4. Philipp Schönnenbeck
5. Cosima Caliendo
6. Susanne Gerber
7. Berardino Cocchiararo
8. Sabrina Reuter
9. Nico Blüthgen
10. Karsten Mody
11. Bagdevi Mishra
12. Miklós Bálint
13. Marco Thines
14. Barbara Feldmeyer

• Curated by eLife

  Evaluation Summary:

  This study uses a genome-wide association approach combining pool-seq data with whole-genome resequencing, which provides a cost-effective means to scale genome-wide association studies to a larger number of individuals, to dissect the genetic basis of drought resistance in several German populations of European beech. European beech is an ecologically important forest tree species and drought resistance is a trait that is likely to be becoming increasingly relevant to the survival of these trees as climate change leads to more frequent and prolonged periods of drought. Knowledge of the genetic basis of such variation existing within current populations can help with management of those populations in the face of increasing threats, especially when such information is used to develop tools for predicting individuals that are likely to have the highest chances of survival, and to suggest hypotheses regarding traits and genetic material which will be important for the future of forests.

  (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

Ferroptotic stress promotes the accumulation of pro-inflammatory proximal tubular cells in maladaptive renal repair

1. Shintaro Ide
2. Yoshihiko Kobayashi
3. Kana Ide
4. Sarah A Strausser
5. Koki Abe
6. Savannah Herbek
7. Lori L O'Brien
8. Steven D Crowley
9. Laura Barisoni
10. Aleksandra Tata
11. Purushothama Rao Tata
12. Tomokazu Souma

• Curated by eLife

  Evaluation Summary:

  Ferroptotic cell death underlies tissue dysfunction inflicted by transient ischemia/reperfusion particularly in renal tissue. Here, the authors provide experimental evidence in animal models and human biopsies that mild and severe ischemic stress trigger distinctive cellular responses in proximal tubular cells which decide upon whether or not tissue may regenerate or fail. This is further corroborated in a genetic mouse model with mild ischemic stress-induced ablation of the key ferroptosis regulator glutathione peroxidase 4 (GPX4). These studies will be of significant interest both to those studying acute kidney injury and others interested in ischemic injury in other organ systems.

  (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

Spc1 regulates substrate selection for signal peptidase

1. Chewon Yim
2. Yeonji Chung
3. Jeesoo Kim
4. IngMarie Nilsson
5. Jong-Seo Kim
6. Hyun Kim

• Curated by eLife

  Evaluation Summary:

  This interesting and well-executed work addresses the function of one of the subunits of the signal peptidase, a complex that processes signal peptides in a wide variety of secretory and membrane proteins. This topic is of relevance to the membrane cell biology community, and the study will be of broader interest when the authors demonstrate the relevance of their findings to the natural substrates of the studied enzyme.

  (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

Method development and characterisation of the low-molecular-weight peptidome of human wound fluids

1. Mariena JA van der Plas
2. Jun Cai
3. Jitka Petrlova
4. Karim Saleh
5. Sven Kjellström
6. Artur Schmidtchen

• Curated by eLife

  Evaluation Summary:

  This well-done study establishes a work flow for the analysis of the peptidome of wound fluids. By doing so it enables the identification of peptide patterns associated with wounds that are healing versus non-healing. The method may therefore help to define candidate biomarkers for wound healing. Overall enthusiasm was somewhat dampened by findings previously reported by the same group and also by others.

  (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

Ciliary chemosensitivity is enhanced by cilium geometry and motility

1. David Hickey
2. Andrej Vilfan
3. Ramin Golestanian

• Curated by eLife

  Evaluation Summary:

  The authors consider how the geometry and motility of cilia affect their performance in detecting chemicals in the surrounding fluid. Based on a theoretical model, the authors suggest that the distinctive elongated shape of a cilium may be coupled to its sensory function. The conjectures presented in this work are likely to be of interest to a wide readership, but whether this actually applies to real biological systems requires more careful validation.

  (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

Understanding the evolution of multiple drug resistance in structured populations

1. David V McLeod
2. Sylvain Gandon

• Curated by eLife

  Evaluation Summary:

  This paper addresses the important question of multidrug resistance evolution, which is of both theoretical and applied interest. The authors efforts to carefully distinguish population and metapopulation linkage disequilibrium and to develop a framework to rigorously analyze the relationship between the two has promise, although we have noted concerns about the modeling framework used and results interpretation. If these concerns can be sufficiently addressed, then this paper has the potential to represent a clear advance in our understanding of microbial population dynamics.

  (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 names with the authors.)

Reviewed by eLife

Toxoplasma gondii injected neurons localize to the cortex and striatum and have altered firing

1. Oscar A. Mendez
2. Emiliano Flores Machado
3. Jing Lu
4. Anita A. Koshy

• Curated by eLife

  Evaluation Summary:

  This study uses a new approach to map all neurons in the brain that have been infected with Toxoplasma gondii or injected with parasite proteins. The authors show that Toxoplasma injected neurons are heterogeneously distributed in murine brain tissues, that excitatory neurons are the primary targets, and that injection of parasite proteins leads to neuronal death. This work provides new insights into Toxoplasma-neuron interactions that underlie the pathology and potential changes in behaviour of infected individuals. The manuscript will be of interest to those working in neuroscience and/or parasitic infections.

  (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

Stress diminishes outcome but enhances response representations during instrumental learning

1. Jacqueline Katharina Meier
2. Bernhard P Staresina
3. Lars Schwabe

• Curated by eLife

  Evaluation Summary:

  The authors used EEG-based multivariate pattern analysis and acute stress induction to assess the neural representations mediating a previously demonstrated influence of stress on the balance between goal-directed and habitual responding. While the results should be of interest to a wide range of neuroscientists, the temporal alignment of clinical, behavioral, and neural measures somewhat obscures the underlying causal mechanisms.

  (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

SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc-SMPDL3B

1. Wei Fan
2. Shuang Tang
3. Xiaojuan Fan
4. Yi Fang
5. Xiaojiang Xu
6. Leping Li
7. Jian Xu
8. Jian-Liang Li
9. Zefeng Wang
10. Xiaoling Li

• Curated by eLife

  Evaluation Summary:

  This paper will be of broad interest to cell biologists and advances the current understanding of the connection between lipid metabolism and stem cell function. The data generated from multiple complementary experimental approaches are of high quality and convincingly support the claims made.

  (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

LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells

1. Bo-Ruei Chen
2. Yinan Wang
3. Anthony Tubbs
4. Dali Zong
5. Faith C Fowler
6. Nicholas Zolnerowich
7. Wei Wu
8. Amelia Bennett
9. Chun-Chin Chen
10. Wendy Feng
11. Andre Nussenzweig
12. Jessica K Tyler
13. Barry P Sleckman

• Curated by eLife

  Evaluation summary:

  This manuscript will be of interest for scientists interested in cell cycle, DNA repair, transcription and genome stability opening a new chapter in studies of cell cycle dependent regulation of DSB repair. Much of the prior work has focused on cell cycle-driven post-translational regulatory modification of DSB end resection, whereas the current work finds transcriptional programs are equally, if not more, important in controlling resection in G0. This could open possibilities for gene therapy in post-mitotic tissues. The data are of high quality and the conclusions drawn are supported by the experimental evidence.

  (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

Oxaliplatin resistance in colorectal cancer enhances TRAIL sensitivity via death receptor 4 upregulation and lipid raft localization

1. Joshua D Greenlee
2. Maria Lopez-Cavestany
3. Nerymar Ortiz-Otero
4. Kevin Liu
5. Tejas Subramanian
6. Burt Cagir
7. Michael R King

• Curated by eLife

  Evaluation Summary:

  The study investigates the molecular characteristics of chemotherapy-resistant colorectal cancer cells and proposes a therapeutic alternative for chemo-resistant cancer. The authors provide evidence in vitro that chemo-resistant cells are pro-apoptotic in the presence of the death receptor ligand TRAIL due to the enhanced localization of the death receptor DR4 in the lipid rafts of their plasma membrane. Based on this finding, the authors treat blood samples from 5 colorectal cancer patients with TRAIL-conjugated liposomes and observed reduction in the number of circulating cancer cells in the blood draws.

  (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

Fully autonomous mouse behavioral and optogenetic experiments in home-cage

1. Yaoyao Hao
2. Alyse Marian Thomas
3. Nuo Li

• Curated by eLife

  Evaluation Summary:

  This manuscript describes extensively a fully automated procedure to train mice to perform voluntary head-fixation, and a whisker-based tactile discrimantion task. In addition the authors demonstrate that with this procedure, light illumination of red-shifted opsins expressed in inhibitory neurons can be used to selectively silence targeted brain regions during the task in a non-invasive manner. Together, although volontary head-fixation training and automated behavior has been readily implemented in different contexts, this study elegantly delineates important steps to boost the acceptancy and duration of head-fixations and thereby train more complex tasks. The demonstration of transcranial optogenetics in this context also opens the possibility to perform precise brain inactivations during well-controlled sensory stimulations, in self-initiated behavior.

  (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

Increased theta/alpha synchrony in the habenula-prefrontal network with negative emotional stimuli in human patients

1. Yongzhi Huang
2. Bomin Sun
3. Jean Debarros
4. Chao Zhang
5. Shikun Zhan
6. Dianyou Li
7. Chencheng Zhang
8. Tao Wang
9. Peng Huang
10. Yijie Lai
11. Peter Brown
12. Chunyan Cao
13. Huiling Tan

• Curated by eLife

  Evaluation Summary:

  Since DBS of the habenula is a new treatment, these are the first data of its kind and potentially of high interest to the field. Although the study mostly confirms findings from animal studies rather than bringing up completely new aspects of emotion processing, it certainly closes a knowledge gap. This paper is of interest to neuroscientists studying emotions and clinicians treating psychiatric disorders. Specifically the paper shows that the habenula is involved in processing of negative emotions and that it is synchronized to the prefrontal cortex in the theta band. These are important insights into the electrophysiology of emotion processing in the human brain.

  (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Metal microdrive and head cap system for silicon probe recovery in freely moving rodent

1. Mihály Vöröslakos
2. Peter C Petersen
3. Balázs Vöröslakos
4. György Buzsáki

• Curated by eLife

  Evaluation Summary:

  The manuscript describes an improved methodology for performing electrophysiological experiments (involving recording of the activity of tens or hundreds of neurons in the brain simultaneously) in freely behaving mice and rats using silicon probes. By providing a versatile microdrive and head cap design for rodents, this paper may contribute to ease silicon probe chronic recording and recovery, thus reducing experimental costs and making the technique more accessible. The paper is expected to appeal to a broad range of systems neuroscientists who seek to understand how the brain commands movement and behavior.

  (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

Integrative transcriptomic analysis of tissue-specific metabolic crosstalk after myocardial infarction

1. Muhammad Arif
2. Martina Klevstig
3. Rui Benfeitas
4. Stephen Doran
5. Hasan Turkez
6. Mathias Uhlén
7. Maryam Clausen
8. Johannes Wikström
9. Damla Etal
10. Cheng Zhang
11. Malin Levin
12. Adil Mardinoglu
13. Jan Boren

• Curated by eLife

  Evaluation Summary:

  This paper will be of considerable interest to researchers studying the interactions between metabolic responses in myocardial infarction. Ultimately increased understanding of these interactive metabolic responses could lead to exploration of new avenues of treatment.

  (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 names with the authors.)

Reviewed by eLife

Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status

1. Ilhame Diboun
2. Sachin Wani
3. Stuart H Ralston
4. Omar ME Albagha

• Curated by eLife

  Evaluation Summary:

  Paget disease of bone (PDB) results in focal areas of disorganized bone, leading to bone deformities and fragility. There is substantial interest in finding circulating biomarkers that might be of use for possible diagnostic applications and towards this end, these authors identified novel DNA methylation patterns in peripheral blood mononuclear cells that are able to differentiate PDB cases from controls with a high level of accuracy. This prediction model has functional relevance as these candidate methylation sites and regions are associated with osteological and immunologic processes and in the longer term, has future clinical potential.

  (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

Quantitative mapping of dense microtubule arrays in mammalian neurons

1. Eugene A Katrukha
2. Daphne Jurriens
3. Desiree M Salas Pastene
4. Lukas C Kapitein

• Curated by eLife

  Evaluation Summary:

  In this manuscript, Katrukha et al. use STED and Expansion Microscopy techniques to map the distribution of different microtubule populations within the dendrites of neurons, a challenging task due to the tight bundling of microtubules along neuronal processes. They are able to show that dendritic microtubules are either acetylated or tyrosinated, but rarely have both or neither of these post-translational modifications. The strength of this paper is the quality of the experiments, the thoroughness of the analyses, and most importantly the transparent and critical discussion of the limitations the authors have encountered. This manuscript is of broad interest to the cytoskeletal and neurobiology 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 #3 agreed to share their name with the authors.)

Reviewed by eLife

Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels compared to protease inhibitor-based therapy

1. Alexander O Pasternak
2. Jelmer Vroom
3. Neeltje A Kootstra
4. Ferdinand WNM Wit
5. Marijn de Bruin
6. Davide De Francesco
7. Margreet Bakker
8. Caroline A Sabin
9. Alan Winston
10. Jan M Prins
11. Peter Reiss
12. Ben Berkhout
13. The Co-morBidity in Relation to Aids (COBRA) Collaboration
14. P Reiss
15. FWNM Wit
16. J Schouten
17. KW Kooij
18. RA van Zoest
19. BC Elsenga
20. FR Janssen
21. M Heidenrijk
22. W Zikkenheiner
23. M van der Valk
24. NA Kootstra
25. T Booiman
26. AM Harskamp-Holwerda
27. I Maurer
28. MM Mangas Ruiz
29. AF Girigorie
30. J Villaudy
31. E Frankin
32. AO Pasternak
33. B Berkhout
34. T van der Kuyl
35. P Portegies
36. BA Schmand
37. GJ Geurtsen
38. JA ter Stege
39. M Klein Twennaar
40. CBLM Majoie
41. MWA Caan
42. T Su
43. K Weijer
44. PHLT Bisschop
45. A Kalsbeek
46. M Wezel
47. I Visser
48. HG Ruhé
49. C Franceschi
50. P Garagnani
51. C Pirazzini
52. M Capri
53. F Dall'Olio
54. M Chiricolo
55. S Salvioli
56. J Hoeijmakers
57. J Pothof
58. M Prins
59. M Martens
60. S Moll
61. J Berkel
62. M Totté
63. S Kovalev
64. M Gisslén
65. D Fuchs
66. H Zetterberg
67. A Winston
68. J Underwood
69. L McDonald
70. M Stott
71. K Legg
72. A Lovell
73. O Erlwein
74. N Doyle
75. C Kingsley
76. DJ Sharp
77. R Leech
78. JH Cole
79. S Zaheri
80. MMJ Hillebregt
81. YMC Ruijs
82. DP Benschop
83. D Burger
84. M de Graaff-Teulen
85. G Guaraldi
86. A Bürkle
87. T Sindlinger
88. M Moreno-Villanueva
89. A Keller
90. C Sabin
91. D de Francesco
92. C Libert
93. S Dewaele

• Curated by eLife

  Evaluation Summary:

  This study addresses how antiviral treatment regimens impact persistence of an HIV reservoir in individuals who are treated for a long period. The authors examine measures of viral reservoir to understand how different antiviral treatment regimens impact residual virus in HIV infection. They find that NNRTI-based treatments are associated with lower viral reservoirs and better viral suppression than PI-based regimens, suggesting they may have some advantage at reducing HIV levels long term.

  (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

Evidence for a deep, distributed and dynamic code for animacy in human ventral anterior temporal cortex

1. Timothy T Rogers
2. Christopher R Cox
3. Qihong Lu
4. Akihiro Shimotake
5. Takayuki Kikuchi
6. Takeharu Kunieda
7. Susumu Miyamoto
8. Ryosuke Takahashi
9. Akio Ikeda
10. Riki Matsumoto
11. Matthew A Lambon Ralph

• Curated by eLife

  Evaluation Summary:

  This manuscript will be of interest to neuroscientists and psychologists interested in how semantic information is encoded in the brain. It provides a framework for a model driven comparison of semantic encoding in recurrent neural networks and neural data. Limitations in the ways the neural data are analyzed and compared to the model provide only limited support for the major claim regarding the nature of the semantic code in human anterior temporal lobe.

  (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

Constructing an adult orofacial premotor atlas in Allen mouse CCF

1. Jun Takatoh
2. Jae Hong Park
3. Jinghao Lu
4. Shun Li
5. PM Thompson
6. Bao-Xia Han
7. Shengli Zhao
8. David Kleinfeld
9. Beth Friedman
10. Fan Wang

Reviewed by eLife