Evaluated articles

Co-option of lysosomal machinery shapes the symbiosis supporting coral reefs

1. Shumpei Maruyama
2. Catherine F Henderson
3. Natalie Swinhoe
4. Griffin P Kowalewski
5. Emily K Meier
6. Ty R Engelke
7. Phillip A Cleves

Reviewed by Arcadia Science

Coalescence and Translation: A Language Model for Population Genetics

1. Kevin Korfmann
2. Nathaniel S. Pope
3. Melinda Meleghy
4. Auélien Tellier
5. Andrew D. Kern

Reviewed by Arcadia Science

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models

1. Etowah Adams
2. Liam Bai
3. Minji Lee
4. Yiyang Yu
5. Mohammed AlQuraishi

Reviewed by Arcadia Science

IRF2 degradation tunes the innate immune response

1. Cristhian Cadena
2. Rohit Reja
3. Emma Bolech
4. Joshua D. Webster
5. Vasumathi Kameswaran
6. Marco de Simone
7. Cynthia Chen
8. Jian Jiang
9. Kathy Hotzel
10. Kamela Alegre
11. Zhenyu Tan
12. Raymond Newland
13. Ryan Kelly
14. Spyros Darmanis
15. Bence Daniel
16. Ishan Deshpande
17. Kim Newton
18. Nobuhiko Kayagaki
19. Vishva M. Dixit

Reviewed by Arcadia Science

JIP4 deficiency causes a lysosomal storage disease arising from impaired cystine efflux

1. Layla M. Nassar
2. Xiaojian Shi
3. Agnes Roczniak-Ferguson
4. Hongying Shen
5. Shawn M. Ferguson

Reviewed by Arcadia Science

Stress response of membrane-based cell organelles in budding yeast

1. Sheng Peng
2. Bai Li-zhe
3. Cao Hong
4. Li Dan

Reviewed by Arcadia Science

Stool Dynamics and the Developing Gut Microbiome During Infancy

1. Mohammed Al-Andoli
2. Sarah Schoch
3. Andjela Markovic
4. Christophe Mühlematter
5. Matthieu Beaugrand
6. Oskar G. Jenni
7. Rabia Liamlahi
8. Jean-Claude Walser
9. Dennis Nielsen
10. Salome Kurth

Reviewed by Arcadia Science

The Implications of Alternative Splicing Regulation for Maximum Lifespan

1. Wei Jiang
2. Sika Zheng
3. Liang Chen

Reviewed by Arcadia Science

Targeting a novel chloroquine derivative to lysosomes induces massive and irreversible damage to lysosomes and suppresses autophagosomes and lysosomes assembly in cancer

1. Nitish Chauhan
2. Ananda Guha Majumdar
3. Sujit Kumar Bhutia
4. Papiya Dey
5. Mahesh Subramanian
6. Birija Sankar Patro

Reviewed by Arcadia Science

Quantifying a trait-mediated indirect effect of an environmental stressor on population dynamics

1. Shota Shibasaki
2. Masato Yamamichi

Reviewed by Arcadia Science

Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context

1. Sung Yun Park
2. Arlo Sheridan
3. Bobae An
4. Erin Jarvis
5. Julia Lyudchik
6. William Patton
7. Jun Y. Axup
8. Stephanie W. Chan
9. Hugo G.J. Damstra
10. Daniel Leible
11. Kylie S. Leung
12. Clarence A. Magno
13. Aashir Meeran
14. Julia M. Michalska
15. Franz Rieger
16. Claire Wang
17. Michelle Wu
18. George M. Church
19. Jan Funke
20. Todd Huffman
21. Kathleen G.C. Leeper
22. Sven Truckenbrodt
23. Johan Winnubst
24. Joergen M.R. Kornfeld
25. Edward S. Boyden
26. Samuel G. Rodriques
27. Andrew C. Payne

Reviewed by Arcadia Science

Extracellular adenosine deamination primes tip organizer development in Dictyostelium

1. Pavani Hathi
2. Baskar Ramamurthy

• Curated by eLife

  eLife Assessment

  During the development of the unicellular eukaryote Dictyostelium discoideum, cells aggregate into mounds, which then form protrusions called tips, and the tips then become the front of migrating slugs and the top of fruiting bodies. This valuable study identifies a protein called adenosine deaminase-related growth factor (ADGF) as a key regulator of tip formation, and the authors convincingly show that ADGF catalyses the formation of ammonia from adenosine, allowing ammonia to initiate tip formation, and they then elucidate pathways upstream and downstream from ADGF. The authors discuss the intriguing possibility that mammalian ADGF may also regulate development in a similar manner.

Reviewed by Arcadia Science, eLife

Haploinsufficiency of lysosomal enzyme genes in Alzheimer’s disease

1. Bruno A. Benitez
2. Clare E. Wallace
3. Maulikkumar Patel
4. Niko-Petteri Nykanen
5. Carla M. Yuede
6. Samantha L. Eaton
7. Cyril Pottier
8. Arda Cetin
9. Matthew Johnson
10. Mia T. Bevan
11. Woodrow D. Gardiner
12. Hannah M. Edwards
13. Brookelyn M. Doherty
14. Ryan T. Harrigan
15. Dominic Kurian
16. Thomas M. Wishart
17. Colin Smith
18. John R. Cirrito
19. Mark S. Sands

Reviewed by Arcadia Science

Unsupervised Representation Learning of C. elegans Poses and Behavior Sequences From Microscope Video Recordings

1. Maurice Deserno
2. Katarzyna Bozek

• Curated by eLife

  eLife Assessment

  This valuable study introduces a self-supervised machine learning method to classify C. elegans postures and behaviors directly from video data, offering an alternative to the skeleton-based approaches that rely on often error-prone tracking. This novel approach holds promise for advancing ethology research. That said, the strength of evidence is currently incomplete, as key aspects - including measuring head-tail orientation, increased behavioral interpretability, and quantitative comparisons to established methods - are underdeveloped and would benefit from further validation.

Reviewed by Arcadia Science, eLife

The reproductive microbiome inhibits pollen germination in milkweed

1. Harmony J. Dalgleish
2. Joshua R. Puzey
3. Katie Barlow
4. Olivia Cunningham
5. Elizabeth M. Davies
6. Hannah Machiorlete
7. Geneva Waynick
8. Kurt E. Williamson

Reviewed by Arcadia Science

Isolation of functional lysosomes from skeletal muscle

1. Thulasi Mahendran
2. Anastasiya Kuznyetsova
3. Neushaw Moradi
4. David A. Hood

Reviewed by Arcadia Science

Leaffooted bugs enrich local soil with their horizontally acquired symbiont

1. Bibek Singh Parajuli
2. John Teodosio
3. Alison Ravenscraft

Reviewed by Arcadia Science

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

1. Chengzhong Ye
2. Gonzalo Benegas
3. Carlos Albors
4. Jianan Canal Li
5. Sebastian Prillo
6. Peter D. Fields
7. Brian Clarke
8. Yun S. Song

Reviewed by Arcadia Science

Scaling down protein language modeling with MSA Pairformer

1. Yo Akiyama
2. Zhidian Zhang
3. Milot Mirdita
4. Martin Steinegger
5. Sergey Ovchinnikov

Reviewed by Arcadia Science