Bioengineering

Isolating Small Extracellular Vesicles from Small Volumes of Blood Plasma using size exclusion chromatography and density gradient ultracentrifugation: A Comparative Study

1. Fang Kong
2. Megha Upadya
3. Andrew See Wong Weng
4. Rinkoo Dalan
5. Ming Dao

• Curated by eLife

  eLife Assessment

  This work provides a simple, rapid and valuable protocol for the isolation of small extracellular vesicles from small volumes of plasma, using two well-known methodologies, in tandem: size exclusion chromatography (SEC) and density gradient ultracentrifugation (DGUC). The authors exhaustively test these methodologies separately and in combination, showing superior results for the SEC-DGUC in terms of purity and yield. The results obtained in this work are convincing, using multiple state-of-art methodologies for the characterization of the isolates that support their conclusions.

Reviewed by eLife

Development of antigen-dextramers for detection and evaluation of CAR T cells

1. Rasmus U. W. Friis
2. Maria Ormhøj
3. Cecilie S. Krüger-Jensen
4. Markus Barden
5. Keerthana Ramanathan
6. Mikkel R. Hansen
7. Hinrich Abken
8. Sine R. Hadrup

Reviewed by Arcadia Science

Lab-in-the-loop therapeutic antibody design with deep learning

1. Nathan C. Frey
2. Isidro Hötzel
3. Samuel D. Stanton
4. Ryan Kelly
5. Robert G. Alberstein
6. Emily K. Makowski
7. Karolis Martinkus
8. Daniel Berenberg
9. Jack Bevers
10. Tyler Bryson
11. Pamela Chan
12. Yongmei Chen
13. Alicja Czubaty
14. Tamica D’Souza
15. Henri Dwyer
16. Anna Dziewulska
17. James W. Fairman
18. Allen Goodman
19. Jennifer Hofmann
20. Henry Isaacson
21. Aya Ismail
22. Samantha James
23. Taylor Joren
24. Simon Kelow
25. James R. Kiefer
26. Matthieu Kirchmeyer
27. Joseph Kleinhenz
28. James T. Koerber
29. Julien Lafrance-Vanasse
30. Andrew Leaver-Fay
31. Jae Hyeon Lee
32. Edith Lee
33. Donald Lee
34. Wei-Ching Liang
35. Joshua Yao-Yu Lin
36. Sidney Lisanza
37. Andreas Loukas
38. Jan Ludwiczak
39. Sai Pooja Mahajan
40. Omar Mahmood
41. Homa Mohammadi-Peyhani
42. Santrupti Nerli
43. Ji Won Park
44. Jaewoo Park
45. Stephen Ra
46. Sarah Robinson
47. Saeed Saremi
48. Franziska Seeger
49. Imee Sinha
50. Anna M. Sokol
51. Natasa Tagasovska
52. Hao To
53. Edward Wagstaff
54. Amy Wang
55. Andrew M. Watkins
56. Blair Wilson
57. Shuang Wu
58. Karina Zadorozhny
59. John Marioni
60. Aviv Regev
61. Yan Wu
62. Kyunghyun Cho
63. Richard Bonneau
64. Vladimir Gligorijević

Reviewed by Arcadia Science

Mitochondrial adenine base editing of mouse somatic tissues via adeno-associated viral delivery

1. Christian D Mutti
2. Lindsey Van Haute
3. Lucia Luengo-Gutierrez
4. Keira Turner
5. Pedro Silva-Pinheiro
6. Michal Minczuk

• Curated by eLife

  eLife Assessment

  The authors have demonstrated the use of adenine base editors delivered via adeno-associated viruses to introduce edits in the mitochondrial genome. The manuscript describes the methodology well, and the conclusions are convincingly supported by the results. The valuable results highlight the potential of these base editors to model mtDNA variations in somatic tissues in animal models.

Reviewed by eLife

Scaly-tail organ enhances static stability during Pel’s scaly-tailed flying squirrels’ arboreal locomotion

1. Andrew K. Schulz
2. Mrudul Chellapurath
3. Pranav C. Khandelwal
4. SeyedReza Rezaei
5. Stefan Merker
6. Ardian Jusufi

Reviewed by preLights

Semantical and geometrical protein encoding toward enhanced bioactivity and thermostability

1. Yang Tan
2. Bingxin Zhou
3. Lirong Zheng
4. Guisheng Fan
5. Liang Hong

• Curated by eLife

  eLife Assessment

  ProtSSN is a valuable approach that generates protein embeddings by integrating sequence and structural information, demonstrating improved prediction of mutation effects on thermostability compared to competing models. The evidence supporting the authors' claims is compelling, with well-executed comparisons. This work will be of particular interest to researchers in bioinformatics and structural biology, especially those focused on protein function and stability.

Reviewed by eLife

DyAb: sequence-based antibody design and property prediction in a low-data regime

1. Joshua Yao-Yu Lin
2. Jennifer L. Hofmann
3. Andrew Leaver-Fay
4. Wei-Ching Liang
5. Stefania Vasilaki
6. Edith Lee
7. Pedro O. Pinheiro
8. Natasa Tagasovska
9. James R. Kiefer
10. Yan Wu
11. Franziska Seeger
12. Richard Bonneau
13. Vladimir Gligorijevic
14. Andrew Watkins
15. Kyunghyun Cho
16. Nathan C. Frey

Reviewed by Arcadia Science

Gut-on-Chip Methodology Based on 3D-Printed Molds: A Cost-Effective and Accessible Approach

1. Elise Delannoy
2. Aurélie Burette
3. Sébastien Janel
4. Catherine Daniel
5. Alexandre Grassart

Reviewed by Arcadia Science

Discovery of Expression-Governing Residues in Proteins

1. Fan Jiang
2. Mingchen Li
3. Banghao Wu
4. Liang Zhang
5. Bozitao Zhong
6. Yuanxi Yu
7. Liang Hong

Reviewed by Arcadia Science

AI-enabled alkaline-resistant evolution of protein to apply in mass production

1. Liqi Kang
2. Banghao Wu
3. Bingxin Zhou
4. Pan Tan
5. Yun (Kenneth) Kang
6. Yongzhen Yan
7. Yi Zong
8. Shuang Li
9. Zhuo Liu
10. Liang Hong

• Curated by eLife

  eLife Assessment

  This important work demonstrates the application of Pro-PRIME, a large language model, to engineer VHH antibodies with enhanced stability for extreme industrial environments. The evidence is convincing, showing through two rounds of design and experimental validation that AI-guided approaches can outperform traditional rational design methods. The solid methodology and results establish a foundation for further exploration of LLM-assisted protein engineering.

Reviewed by eLife