Bioengineering

CRISPR-Edited DPSCs, Constitutively Expressing BDNF Enhance Dentin Regeneration in Injured Teeth

1. Ji Hyun Kim
2. Muhammad Irfan
3. Sreelekshmi Sreekumar
4. Stephanie Kim
5. Atsawasuwan Phimon
6. Seung Chung

• Curated by eLife

  eLife Assessment

  This study provides a potentially useful investigation into the positive role of BDNF/TrkB signaling in implanted dental pulp stem cells to enhance dentin regeneration in the context of dental caries. Some of the key methods used need to be much better documented, and the data should be strengthened and added to in support of several of the claims of functional benefit, which are inadequately supported at present. Additional details for the validation of the reagents and techniques are needed to support the interpretation of the results.

Reviewed by eLife

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

Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines

1. Sujeethkumar Prithiviraj
2. Alejandro Garcia Garcia
3. Karin Linderfalk
4. Bai Yiguang
5. Sonia Ferveur
6. Ludvig Nilsén Falck
7. Agatheeswaran Subramaniam
8. Sofie Mohlin
9. David Hidalgo
10. Steven J Dupard
11. Dimitra Zacharaki
12. Deepak Bushan Raina
13. Paul E Bourgine

• Curated by eLife

  eLife Assessment

  The study presents a potentially valuable approach to genetically modify cells to produce extracellular matrices with altered compositions, termed cell-laid, engineered extracellular matrices (eECM). The evidence supporting the authors' conclusions regarding the utility of eECM for endogenous repair is solid, although there are some disagreements on the chondrogenicity of lyophilized constructs which was viewed as lacking robust evidence for endochondral ossification.

Reviewed by eLife

Coagulative Granular Hydrogels with an Enzyme Catalyzed Fibrin Network for Endogenous Tissue Regeneration

1. Zhipeng Deng
2. Camila B. Tovani
3. Simona Bianco
4. Gianni Comandini
5. Aya Elghajiji
6. Dave J. Adams
7. Fabrizio Scarpa
8. Michael R. Whitehouse
9. Annela M. Seddon
10. James P. K. Armstrong

Reviewed by preLights