Genomics

Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

1. Ching-Ho Chang
2. Lauren E Gregory
3. Kathleen E Gordon
4. Colin D Meiklejohn
5. Amanda M Larracuente

Reviewed by Review Commons

Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

1. José L. Oliver
2. Pedro Bernaola-Galván
3. Francisco Perfectti
4. Cristina Gómez-Martín
5. Silvia Castiglione
6. Pasquale Raia
7. Miguel Verdú
8. Andrés Moya

Reviewed by ScreenIT

Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines

1. Kazuhiro Konishi
2. Toshiyuki Yamaji
3. Chisato Sakuma
4. Fumio Kasai
5. Toshinori Endo
6. Arihiro Kohara
7. Kentaro Hanada
8. Naoki Osada

Reviewed by ScreenIT

A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity

1. Alberto Gómez-Carballa
2. Irene Rivero-Calle
3. Jacobo Pardo-Seco
4. José Gómez-Rial
5. Carmen Rivero-Velasco
6. Nuria Rodríguez-Núñez
7. Gema Barbeito-Castiñeiras
8. Hugo Pérez-Freixo
9. Miriam Cebey-López
10. Ruth Barral-Arca
11. Carmen Rodriguez-Tenreiro
12. Ana Dacosta-Urbieta
13. Xabier Bello
14. Sara Pischedda
15. María José Currás-Tuala
16. Sandra Viz-Lasheras
17. Federico Martinón-Torres
18. Antonio Salas
19. Aguilera Guirao Antonio
20. Álvarez Escudero Julián
21. Antela López Antonio
22. Barbeito Castiñeiras Gema
23. Bello Paderne Xabier
24. Ben García Miriam
25. Carral García María Victoria
26. Cebey López Miriam
27. Coira Nieto Amparo
28. Conde Pájaro Mónica
29. Costa Alcalde José Javier
30. Currás Tuala María José
31. Dacosta Urbieta Ana Isabel
32. Díaz Esteban Blanca
33. Domínguez Santalla María Jesús
34. Fernández Pérez Cristina
35. Fernández Villaverde Juan
36. Galbán Rodríguez Cristóbal
37. García Allut José Luis
38. García Vicente Luisa
39. Giráldez Vázquez Elena
40. Gómez Carballa Alberto
41. Gómez Rial José
42. González Barcala Francisco Javier
43. Guerra Liñares Beatriz
44. Leboráns Iglesias Pilar
45. Lence Massa Beatriz
46. López Franco Montserrat
47. López Lago Ana
48. Martinón-Torres Federico
49. Antonio Salas
50. Navarro De la Cruz Daniel
51. Núñez Masid Eloína
52. Ortolá Devesa Juan Bautista
53. Pardo Seco Jacobo
54. Pazo Núñez María
55. Pérez del Molino Bernal Marisa
56. Pérez Freixo Hugo
57. Piñeiro Rodríguez Lidia
58. Pischedda Sara
59. Portela Romero Manuel
60. Pose Reino Antonio
61. Prada Hervella Gloria María
62. Queiro Verdes Teresa
63. Redondo Collazo Lorenzo
64. Regueiro Casuso Patricia
65. Rey García Susana
66. Rey Vázquez Sara
67. Riveiro Blanco Vanessa
68. Rivero Calle Irene
69. Rivero Velasco Carmen
70. Rodríguez Núñez Nuria
71. Rodríguez-Tenreiro Sánchez Carmen
72. Saborido Paz Eva
73. Sadiki Orayyou José Miguel
74. Saito Villanueva Carla
75. Serén Fernández Sonia
76. Souto Sanmartín Pablo
77. Taboada Muñiz Manuel
78. Trastoy Pena Rocío
79. Treviño Castellano Mercedes
80. Valdés Cuadrado Luis
81. Varela García Pablo
82. Vilas Iglesias María Soledad
83. Viz Lasheras Sandra
84. Ferreiro-Iglesias Rocio
85. Bastón-Rey iria
86. Calviño-Suárez Cristina

Reviewed by ScreenIT

Novel insights from a multiomics dissection of the Hayflick limit

1. Michelle Chan
2. Han Yuan
3. Ilya Soifer
4. Tobias M Maile
5. Rebecca Y Wang
6. Andrea Ireland
7. Jonathon J O'Brien
8. Jérôme Goudeau
9. Leanne JG Chan
10. Twaritha Vijay
11. Adam Freund
12. Cynthia Kenyon
13. Bryson D Bennett
14. Fiona E McAllister
15. David R Kelley
16. Margaret Roy
17. Robert L Cohen
18. Arthur D Levinson
19. David Botstein
20. David G Hendrickson

• Curated by eLife

  Evaluation Summary:

  This manuscript presents a well-done integrative analysis of data from many genome-wide technologies for the study of replicative senescence, contrasting the data to non-senescence and acute senescence controls. The time-course study design and the combinatorial analyses have revealed many interesting features of senescence that were previously unknown. Data mining by scientists in the future promises to unlock other aspects of senescence biology and hence this study serves as a great resource to the community. This paper and resource will be invaluable not only for researchers specifically studying the molecular biology of cell senescence but should also be more broadly relevant for researchers studying aging, inflamm-aging, cancer, regeneration, and other fields where senescence plays a role.

  (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

A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk

1. Jessamyn I Perlmutter
2. Jane E Meyers
3. Seth R Bordenstein

• Curated by eLife

  Evaluation Summary:

  This study aims to find the genetic mechanisms underlying sex-ratio distortion through male-killing in Drosophila melanogaster flies infected with the endosymbiont Wolbachia. The endosymbiont carries the prophage WO, which is in the center of interested in this study. The key result of this study is that a synonymous mutation in a prophage gene can explain the differences between sex-ratio distorting and not distorting symbionts.

  (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

Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe

1. Daniel Garcia-Souto
2. Alicia L Bruzos
3. Seila Diaz
4. Sara Rocha
5. Ana Pequeño-Valtierra
6. Camila F Roman-Lewis
7. Juana Alonso
8. Rosana Rodriguez
9. Damian Costas
10. Jorge Rodriguez-Castro
11. Antonio Villanueva
12. Luis Silva
13. Jose Maria Valencia
14. Giovanni Annona
15. Andrea Tarallo
16. Fernando Ricardo
17. Ana Bratoš Cetinić
18. David Posada
19. Juan Jose Pasantes
20. Jose MC Tubio

• Curated by eLife

  Evaluation Summary:

  This paper is of broad interest to biologists and oncologists who study tumour evolution. The study provides new insights into the propagation of a transmissible cancer in clams. Remarkably, based on the analysis of mitochondrial DNA, the transmissible cancer seems to have jumped species. The findings reported have implications to understand the conditions that allow this cancer to spread across huge regions, threatening certain clam species.

  (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 name with the authors.)

Reviewed by eLife

Intensive single-cell analysis reveals immune-cell diversity among healthy individuals

1. Yukie Kashima
2. Keiya Kaneko
3. Patrick Reteng
4. Nina Yoshitake
5. Lucky Ronald Runtuwene
6. Satoi Nagasawa
7. Masaya Onishi
8. Masahide Seki
9. Ayako Suzuki
10. Sumio Sugano
11. Mamiko Sakata-Yanagimoto
12. Yumiko Imai
13. Kaori Nakayama-Hosoya
14. Ai Kawana-Tachikawa
15. Taketoshi Mizutani
16. Yutaka Suzuki

Reviewed by ScreenIT

Covid-19 genomic analysis reveals clusters of emerging sublineages within the delta variant

1. Evans K. Rono

Reviewed by ScreenIT

A test of the pioneer factor hypothesis using ectopic liver gene activation

1. Jeffrey L Hansen
2. Kaiser J Loell
3. Barak A Cohen

• Curated by eLife

  Evaluation Summary:

  How transcription factors access their DNA binding motifs in chromatin and cooperate with other transcription factors in DNA binding remains a contentious question. It is clear that some transcription factors ("pioneer transcription factors") play a dominant role in opening chromatin during development and reprogramming, but it has also been clear that the ability of transcription factors to do so lies on a spectrum, that pioneer transcription factors may mutually interact with other transcription factors in their pioneering activity and that their mode of binding is still poorly understood. This manuscript's presentation attempts to refute an overly simplified pioneer factor hypothesis. Overall, this is an important topic and the authors use a good experimental approach, but the analyses are limited and the interpretation too simplified.

  (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