Evaluated articles

Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2

1. Salwa Naushin
2. Viren Sardana
3. Rajat Ujjainiya
4. Nitin Bhatheja
5. Rintu Kutum
6. Akash Kumar Bhaskar
7. Shalini Pradhan
8. Satyartha Prakash
9. Raju Khan
10. Birendra Singh Rawat
11. Karthik Bharadwaj Tallapaka
12. Mahesh Anumalla
13. Giriraj Ratan Chandak
14. Amit Lahiri
15. Susanta Kar
16. Shrikant Ramesh Mulay
17. Madhav Nilakanth Mugale
18. Mrigank Srivastava
19. Shaziya Khan
20. Anjali Srivastava
21. Bhawana Tomar
22. Murugan Veerapandian
23. Ganesh Venkatachalam
24. Selvamani Raja Vijayakumar
25. Ajay Agarwal
26. Dinesh Gupta
27. Prakash M Halami
28. Muthukumar Serva Peddha
29. Gopinath M Sundaram
30. Ravindra P Veeranna
31. Anirban Pal
32. Vinay Kumar Agarwal
33. Anil Ku Maurya
34. Ranvijay Kumar Singh
35. Ashok Kumar Raman
36. Suresh Kumar Anandasadagopan
37. Parimala Karuppanan
38. Subramanian Venkatesan
39. Harish Kumar Sardana
40. Anamika Kothari
41. Rishabh Jain
42. Anupama Thakur
43. Devendra Singh Parihar
44. Anas Saifi
45. Jasleen Kaur
46. Virendra Kumar
47. Avinash Mishra
48. Iranna Gogeri
49. Geethavani Rayasam
50. Praveen Singh
51. Rahul Chakraborty
52. Gaura Chaturvedi
53. Pinreddy Karunakar
54. Rohit Yadav
55. Sunanda Singhmar
56. Dayanidhi Singh
57. Sharmistha Sarkar
58. Purbasha Bhattacharya
59. Sundaram Acharya
60. Vandana Singh
61. Shweta Verma
62. Drishti Soni
63. Surabhi Seth
64. Sakshi Vashisht
65. Sarita Thakran
66. Firdaus Fatima
67. Akash Pratap Singh
68. Akanksha Sharma
69. Babita Sharma
70. Manikandan Subramanian
71. Yogendra S Padwad
72. Vipin Hallan
73. Vikram Patial
74. Damanpreet Singh
75. Narendra Vijay Tripude
76. Partha Chakrabarti
77. Sujay Krishna Maity
78. Dipyaman Ganguly
79. Jit Sarkar
80. Sistla Ramakrishna
81. Balthu Narender Kumar
82. Kiran A Kumar
83. Sumit G Gandhi
84. Piyush Singh Jamwal
85. Rekha Chouhan
86. Vijay Lakshmi Jamwal
87. Nitika Kapoor
88. Debashish Ghosh
89. Ghanshyam Thakkar
90. Umakanta Subudhi
91. Pradip Sen
92. Saumya Ray Chaudhury
93. Rashmi Kumar
94. Pawan Gupta
95. Amit Tuli
96. Deepak Sharma
97. Rajesh P Ringe
98. Amarnarayan D
99. Mahesh Kulkarni
100. Dhansekaran Shanmugam
101. Mahesh S Dharne
102. Sayed G Dastager
103. Rakesh Joshi
104. Amita P Patil
105. Sachin N Mahajan
106. Abujunaid Habib Khan
107. Vasudev Wagh
108. Rakesh Kumar Yadav
109. Ajinkya Khilari
110. Mayuri Bhadange
111. Arvindkumar H Chaurasiya
112. Shabda E Kulsange
113. Krishna Khairnar
114. Shilpa Paranjape
115. Jatin Kalita
116. Narahari G Sastry
117. Tridip Phukan
118. Prasenjit Manna
119. Wahengbam Romi
120. Pankaj Bharali
121. Dibyajyoti Ozah
122. Ravi Kumar Sahu
123. Elapavalooru VSSK Babu
124. Rajeev Sukumaran
125. Aiswarya R Nair
126. Prajeesh Kooloth Valappil
127. Anoop Puthiyamadam
128. Adarsh Velayudhanpillai
129. Kalpana Chodankar
130. Samir Damare
131. Yennapu Madhavi
132. Ved Varun Aggarwal
133. Sumit Dahiya
134. Anurag Agrawal
135. Debasis Dash
136. Shantanu Sengupta

• Curated by eLife

  Evaluation Summary:

  The paper presents results of a serological survey done on 10,000+ employees and workers associated with CSIR labs in India during August-September 2020. This is a one of the few surveys with a pan-India footprint, making it a valuable addition to understanding of Covid-19 pandemic evolution in the country. The reviewers felt that the writing could have been tighter and more targeted.

  (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 names with the authors.)

Reviewed by eLife, ScreenIT

Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart

1. Julia Hesse
2. Christoph Owenier
3. Tobias Lautwein
4. Ria Zalfen
5. Jonas F Weber
6. Zhaoping Ding
7. Christina Alter
8. Alexander Lang
9. Maria Grandoch
10. Norbert Gerdes
11. Jens W Fischer
12. Gunnar W Klau
13. Christoph Dieterich
14. Karl Köhrer
15. Jürgen Schrader

• Curated by eLife

  Evaluation Summary:

  The article by Hesse et al. defines heterogeneity of epicardial cells and fibroblasts in a murine model of cardiac injury to analyze the resulting populations through single cell RNA sequencing. Spatial confirmation of associated markers is performed using in-situ RNA hybridization. The work provides new insights into the heterogeneity of epicardial stromal and activated cardiac stromal cells post-injury.

  (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

Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19

1. Courtney Tindle
2. MacKenzie Fuller
3. Ayden Fonseca
4. Sahar Taheri
5. Stella-Rita Ibeawuchi
6. Nathan Beutler
7. Gajanan Dattatray Katkar
8. Amanraj Claire
9. Vanessa Castillo
10. Moises Hernandez
11. Hana Russo
12. Jason Duran
13. Laura E Crotty Alexander
14. Ann Tipps
15. Grace Lin
16. Patricia A Thistlethwaite
17. Ranajoy Chattopadhyay
18. Thomas F Rogers
19. Debashis Sahoo
20. Pradipta Ghosh
21. Soumita Das

• Curated by eLife

  Evaluation Summary:

  The manuscript by Tindle et al describes generation of adult lung organoids (ALO) from human lung biopsies and their use to study the changes in gene expression as a result of SARS-CoV-2 infection. In this particular case the authors report the presence of AT1, AT2 cells, Basal cells, Goblet cells, Ciliated cells and Club cells. The authors were able to cultivate the cells at the air-liquid interface and to establish cultures of predominately proximal and predominately distal airway cells. The main finding is that proximal cells are more prone to viral infection, while distal cells are governing the exuberant inflammatory response, with both cells required for the exuberant response to occur. Useful information provided by the paper is the analysis gene signatures of various cellular models, in comparison to the infected human lung.

  (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, ScreenIT

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

1. Rosemary Yu
2. Egor Vorontsov
3. Carina Sihlbom
4. Jens Nielsen

Reviewed by eLife

T cell self-reactivity during thymic development dictates the timing of positive selection

1. Lydia K Lutes
2. Zoë Steier
3. Laura L McIntyre
4. Shraddha Pandey
5. James Kaminski
6. Ashley R Hoover
7. Silvia Ariotti
8. Aaron Streets
9. Nir Yosef
10. Ellen A Robey

• Curated by eLife

  Evaluation Summary:

  This study is of interest to immunologists as it fills a key knowledge gap in understanding factors involved in determining the duration of intrathymic positive selection of T cells. The findings come from a series of both in vitro and in vivo experiments implicating the self-reactivity of thymocytes in the time to completion of positive selection. An RNA-sequencing analysis suggests that gene expression differences from the pre-selection to the single-positive thymocyte stage is self-reactivity dependent, correlating in particular the level of ion channel expression with positive selection completion rates.

  (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

tTARGIT AAVs: A sensitive and flexible method to manipulate intersectional neuronal populations

1. Paul V. Sabatini
2. Jine Wang
3. Alan C. Rupp
4. Alison H. Affinati
5. Jonathan N. Flak
6. Chien Li
7. David P. Olson
8. Martin G. Myers

• Curated by eLife

  Evaluation Summary:

  The combination of Cre and Flp recombinase dependent system is powerful in manipulating specific intersectional neurons and has been successfully used in many systems. However, the system cannot express target genes sufficiently in some neurons, e.g., the LepRb VMH neurons. This paper solved this problem. It is therefore an important technical advance.

  (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

In vivo fluorescence lifetime imaging of macrophage intracellular metabolism during wound responses in zebrafish

1. Veronika Miskolci
2. Kelsey E Tweed
3. Michael R Lasarev
4. Emily C Britt
5. Alex J Walsh
6. Landon J Zimmerman
7. Courtney E McDougal
8. Mark R Cronan
9. Jing Fan
10. John-Demian Sauer
11. Melissa C Skala
12. Anna Huttenlocher

• Curated by eLife

  Evaluation Summary:

  Immunometabolism is an emerging field, and to understand immune cell metabolism during inflammation and infection is of great interest. In this report, cutting edge (label free) microscopy techniques and innovative zebrafish models are used to characterize the metabolism of macrophages in situ. In the future, fluorescence microscopy approaches pioneered using zebrafish may illuminate strategies to therapeutically manipulate metabolism in human immune cells.

  (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

Brainrender : a python-based software for visualizing anatomically registered data

1. F. Claudi
2. A. L. Tyson
3. L. Petrucco
4. T.W. Margrie
5. R. Portugues
6. T. Branco

• Curated by eLife

  Evaluation Summary:

  This paper by Claudi et al. will be of interest to any scientist working in neuroanatomy and related fields. Dissemination of scientific results is one of the key products of science, and the software presented here will help scientists achieve that task more easily than ever before.

  (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

Information flow, cell types and stereotypy in a full olfactory connectome

1. Philipp Schlegel
2. Alexander Shakeel Bates
3. Tomke Stürner
4. Sridhar R Jagannathan
5. Nikolas Drummond
6. Joseph Hsu
7. Laia Serratosa Capdevila
8. Alexandre Javier
9. Elizabeth C Marin
10. Asa Barth-Maron
11. Imaan FM Tamimi
12. Feng Li
13. Gerald M Rubin
14. Stephen M Plaza
15. Marta Costa
16. Gregory S X E Jefferis

• Curated by eLife

  Evaluation Summary:

  This study is a tour-de-force that makes a major contribution to the field. It provides a wealth of information about connectivity in the Drosophila olfactory system, identifying a variety of novel features of its neural organization. The study provides a careful analysis of the practically important and biologically interesting question of stereotypy among animals which previous connectomic studies of the fly brain lacked. A variety of interesting hypotheses are generated. Finally, it establishes a paradigm for the analysis other neural 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

High social status males experience accelerated epigenetic aging in wild baboons

1. Jordan A Anderson
2. Rachel A Johnston
3. Amanda J Lea
4. Fernando A Campos
5. Tawni N Voyles
6. Mercy Y Akinyi
7. Susan C Alberts
8. Elizabeth A Archie
9. Jenny Tung

• Curated by eLife

  Evaluation Summary:

  In this paper, the authors collect epigenomic data from a well-studied wild baboon community, which they use to construct an epigenetic clock, a method of measuring "biological age" that is increasingly used as a tool in human aging research. The authors find that deviations between biological and chronological age can in part be explained by social phenomena. In particular, for male baboons, maintaining social dominance may play an important role in accelerating the dimension of aging indexed by this measure. This is a foundational study for social-biological-health 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 names with the authors.)

Reviewed by eLife

Tetrahydroxanthohumol, a xanthohumol derivative, attenuates high-fat diet-induced hepatic steatosis by antagonizing PPARγ

1. Yang Zhang
2. Gerd Bobe
3. Cristobal L Miranda
4. Malcolm B Lowry
5. Victor L Hsu
6. Christiane V Lohr
7. Carmen P Wong
8. Donald B Jump
9. Matthew M Robinson
10. Thomas J Sharpton
11. Claudia S Maier
12. Jan F Stevens
13. Adrian F Gombart

• Curated by eLife

  Evaluation Summary:

  This is a comprehensive study of the effect of xanthohumol and TXN, a xanthohumol derivative, on different pathologies related to the metabolic syndrome. It clearly shows the therapeutic potential of these substances, which has a high translational potential since currently, there are is a lack of effective therapies.

  (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

HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase

1. Johannes Rudolph
2. Genevieve Roberts
3. Uma M Muthurajan
4. Karolin Luger

• Curated by eLife

  Evaluation Summary:

  This manuscript describes a set of biochemical studies on the substrate and reaction specificity of poly(ADP-ribose) polymerase 1 (PARP1), an important antineoplastic drug target and component of DNA damage response. The most significant finding is that histone PARylation factor (HPF1) binding to PARP1 causes a shift from primarily PARylation activity to that of hydrolytic activity, which offers new avenues for understanding and controlling PARP1. While some of the observed effects need a modest amount of further explanation, the findings described in this paper are of broad interest to readers in the fields of DNA damage response, chromatin structure regulation, and to researchers studying PARP1 and issues related to NAD+ metabolism.

  (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

Sex and origin-specific inbreeding effects on flower attractiveness to specialised pollinators

1. Karin Schrieber
2. Sarah Catherine Paul
3. Levke Valena Höche
4. Andrea Cecilia Salas
5. Rabi Didszun
6. Jakob Mößnang
7. Caroline Müller
8. Alexandra Erfmeier
9. Elisabeth Johanna Eilers

• Curated by eLife

  Evaluation Summary:

  This research is relevant for ecologist and evolutionary biologist in the specific fields of plant conservation, chemical ecology, pollination biology and plant sex evolution. The authors test the interesting hypothesis that traits important for plant-insect interactions are directly affected by inbreeding, which in turn may directly impact the plant-insect interaction. The authors test this prediction in a series of experiments on the plant Silene latifolia, and the results largely support the hypothesis that inbreeding reduces plant attractiveness. In short, the results show that there are indeed strong negative effects of inbreeding on multiple plant/floral traits, but that the effects of these traits do not necessarily translate directly into reduced pollinator visitation rates. The data are of high quality, the sampling of populations was markedly geographically broad and balanced, and the experiments were well implemented, leading to a certain robustness of the results and conclusions.

  (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

PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107

1. Holly Fowle
2. Ziran Zhao
3. Qifang Xu
4. Jason S Wasserman
5. Xinru Wang
6. Mary Adeyemi
7. Felicity Feiser
8. Alison N Kurimchak
9. Diba Atar
10. Brennan C McEwan
11. Arminja N Kettenbach
12. Rebecca Page
13. Wolfgang Peti
14. Roland L Dunbrack
15. Xavier Graña

Reviewed by eLife

The Ca2+-activated cation channel TRPM4 is a positive regulator of pressure overload-induced cardiac hypertrophy

1. Yang Guo
2. Ze-Yan Yu
3. Jianxin Wu
4. Hutao Gong
5. Scott Kesteven
6. Siiri E Iismaa
7. Andrea Y Chan
8. Sara Holman
9. Silvia Pinto
10. Andy Pironet
11. Charles D Cox
12. Robert M Graham
13. Rudi Vennekens
14. Michael P Feneley
15. Boris Martinac

• Curated by eLife

  Evaluation Summary:

  In this work, the authors subjected mice with cardiomyocyte-specific deletion of ion channel TRPM4 to transverse aortic constriction-induced pressure overload, which is a well-validated model for heart failure. The study showed that cell-specific loss of TRPM4 in cardiomyocytes could protect against pathological left ventricular hypertrophy which is associated with an attenuation of pathological changes in the expression several genes that become dysregulated during the development pathological hypertrophy. These findings are likely to contribute to understanding of pressure overload-induced hypertrophy heart disease and the pathophysiology of heart failure.

  (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 names with the authors.)

Reviewed by eLife

Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane

1. Akshay Sabnis
2. Katheryn LH Hagart
3. Anna Klöckner
4. Michele Becce
5. Lindsay E Evans
6. R Christopher D Furniss
7. Despoina AI Mavridou
8. Ronan Murphy
9. Molly M Stevens
10. Jane C Davies
11. Gérald J Larrouy-Maumus
12. Thomas B Clarke
13. Andrew M Edwards

Reviewed by eLife

OPA1 deletion in brown adipose tissue improves thermoregulation and systemic metabolism via FGF21

1. Renata O Pereira
2. Alex Marti
3. Angela Crystal Olvera
4. Satya Murthy Tadinada
5. Sarah Hartwick Bjorkman
6. Eric Thomas Weatherford
7. Donald A Morgan
8. Michael Westphal
9. Pooja H Patel
10. Ana Karina Kirby
11. Rana Hewezi
12. William Bùi Trân
13. Luis Miguel García-Peña
14. Rhonda A Souvenir
15. Monika Mittal
16. Christopher M Adams
17. Kamal Rahmouni
18. Matthew J Potthoff
19. E Dale Abel

• Curated by eLife

  Evaluation Summary:

  The new work utilizes several elegant genetic mouse models to evaluate the importance of the mitochondrial fusion protein OPA1 in thermogenic brown adipocytes. This well-written and rigorous study sheds insight into the importance of OPA1 in brown adipocytes and also uncovers an unexpected compensatory mechanism that ensures thermoregulation in mice.

  (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

Host-associated microbe PCR (hamPCR): accessing new biology through convenient measurement of both microbial load and community composition

1. Derek S. Lundberg
2. Pratchaya Pramoj Na Ayutthaya
3. Annett Strauß
4. Gautam Shirsekar
5. Wen-Sui Lo
6. Thomas Lahaye
7. Detlef Weigel

• Curated by eLife

  Evaluation Summary:

  Overall, we agree that this new method is potentially impactful although the full versatility of the approach is currently unclear for several reasons. We appreciated the application of the approach to distinct systems and also the relatively low cost of this technique. The diagrams presented (particularly in Figure 3) nicely convey the steps in the protocol with expected sample outcomes to further facilitate the ability of other researchers to employ hamPCR. Overall, we are very positive about this work, but given that the impact of this paper rests on whether or not the technique is widely adopted, some revisions will lower the barrier to entry for future researchers to adopt this approach.

  (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

BonVision – an open-source software to create and control visual environments

1. Gonçalo Lopes
2. Karolina Farrell
3. Edward A. B. Horrocks
4. Chi-Yu Lee
5. Mai M. Morimoto
6. Tomaso Muzzu
7. Amalia Papanikolaou
8. Fabio R. Rodrigues
9. Thomas Wheatcroft
10. Stefano Zucca
11. Samuel G. Solomon
12. Aman B. Saleem

• Curated by eLife

  Evaluation Summary:

  Increasingly, neuroscience experiments require immersive virtual environments that approximate natural sensory motor loops while permitting high-bandwidth measurements of brain activity. BonVision is an open-source graphics programming library that allows experimenters to quickly implement immersive 3D visual environments across display hardware and geometry with automated calibration and integration with hundreds of different neural recording technologies, behavioral apparatuses, etc. BonVision standardizes sharing complex, closed-loop visual tasks between labs with vastly different equipment, provides a concrete and easy way to do so, and should be of interest to a wide array of visual systems neuroscientists.

Reviewed by eLife

GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo

1. Marissa M Gaskill
2. Tyler J Gibson
3. Elizabeth D Larson
4. Melissa M Harrison

• Curated by eLife

  Evaluation Summary:

  This paper will be of interest to a broad audience of developmental biologists and molecular biologists in the field of transcriptional control and epigenetics. It evaluates the pioneer factor activity associated with GAGA-Factor during the process of zygotic genome activation. The experiments are rigorously performed and the data analysis supports the conclusions.

  This manuscript is in revision at eLife.

  (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