Evaluated articles

A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data

1. Florence Débarre
2. Zach Hensel

Reviewed by Arcadia Science

The ion channel TRPM8 is a direct target of the immunosuppressant rapamycin in primary sensory neurons

1. José Miguel Arcas
2. Khalid Oudaha
3. Alejandro González
4. Jorge Fernández‐Trillo
5. Francisco Andrés Peralta
6. Júlia Castro‐Marsal
7. Seyma Poyraz
8. Francisco Taberner
9. Salvador Sala
10. Elvira de la Peña
11. Ana Gomis
12. Félix Viana

Reviewed by Arcadia Science

Centriolar satellites are sites of translation of centrosomal and ciliary proteins

1. Claudia Pachinger
2. Jeroen Dobbelaere
3. Cornelia Rumpf-Kienzl
4. Shiviya Raina
5. Júlia Garcia-Baucells
6. Marina Sarantseva
7. Andrea Brauneis
8. Alexander Dammermann

Reviewed by Arcadia Science

Benchmarking reverse docking through AlphaFold2 human proteome

1. Qing Luo
2. Sheng Wang
3. Hoi Yeung Li
4. Liangzhen Zheng
5. Yuguang Mu
6. Jingjing Guo

Reviewed by Arcadia Science

OmniNA: A foundation model for nucleotide sequences

1. Xilin Shen
2. Xiangchun Li

Reviewed by Arcadia Science

LazyAF, a pipeline for accessible medium-scale in silico prediction of protein-protein interactions

1. Thomas C. McLean

Reviewed by Arcadia Science

Discovery of highly active kynureninases for cancer immunotherapy through protein language model

1. Hyunuk Eom
2. Sukhwan Park
3. Kye Soo Cho
4. Jihyeon Lee
5. Hyunbin Kim
6. Stephanie Kim
7. Jinsol Yang
8. Young-Hyun Han
9. Juyong Lee
10. Chaok Seok
11. Myeong Sup Lee
12. Woon Ju Song
13. Martin Steinegger

Reviewed by Arcadia Science

Freshwater ‘microcroissants’ shed light on a novel higher-level clade within Trebouxiophyceae and reveal the genus Chlorolobion as a trebouxiophyte

1. Dovilė Barcytė
2. Ladislav Hodač
3. Marek Eliáš

Reviewed by Arcadia Science

Raman microscopy of cryofixed biological specimens for high-resolution and high-sensitivity chemical imaging

1. Kenta Mizushima
2. Yasuaki Kumamoto
3. Shoko Tamura
4. Masahito Yamanaka
5. Kentaro Mochizuki
6. Menglu Li
7. Syusuke Egoshi
8. Kosuke Dodo
9. Yoshinori Harada
10. Nicholas I. Smith
11. Mikiko Sodeoka
12. Hideo Tanaka
13. Katsumasa Fujita

Reviewed by Arcadia Science

A thin-film optogenetic visual prosthesis

1. Eric B Knudsen
2. Kara Zappitelli
3. Jennifer Brown
4. Jonathan Reeder
5. Kevin Sean Smith
6. Marat Rostov
7. Jaebin Choi
8. Amy Rochford
9. Nate Slager
10. Satoru K Miura
11. Kyle Rodgers
12. Ansel Reed
13. Yonatan R Lewis Israeli
14. Seton Shiraga
15. Kyung Jin Seo
16. Corey Wolin
17. Paul Dawson
18. Mohamed Eltaeb
19. Arvind Dasgupta
20. Max Rothman
21. Eugene Yoon
22. Paul Chong
23. Seleipiri Charles
24. Jay M. Stewart
25. Ruwan A Silva
26. Tyson Kim
27. Yifan Kong
28. Alan R Mardinly
29. Max Hodak

Reviewed by Arcadia Science

A fungi hotspot deep down the ocean: explaining the presence of Gjaerumia minor in Equatorial Pacific bathypelagic waters

1. Massimo C. Pernice
2. Irene Forn
3. Ramiro Logares
4. Ramon Massana

Reviewed by Arcadia Science

A treasure trove of 1,034 actinomycete genomes

1. Tue Sparholt Jørgensen
2. Omkar Mohite
3. Eva B Sterndorff
4. Maria Alvarez-Arevalo
5. Kai Blin
6. Thomas J Booth
7. Pep Charusanti
8. David Faurdal
9. Troels Ø Hansen
10. Matin Nuhamunada
11. Anna-Sophie Mourched
12. Bernhard Ø Palsson
13. Tilmann Weber

Reviewed by Arcadia Science

Temporal and spatial dynamics within the fungal microbiome of grape fermentation

1. Cristobal A. Onetto
2. Chris M. Ward
3. Steven Van Den Heuvel
4. Laura Hale
5. Kathleen Cuijvers
6. Anthony R. Borneman

Reviewed by Arcadia Science

Mast cell activation disrupts interactions between endothelial cells and pericytes during early life allergic asthma

1. Régis Joulia
2. Franz Puttur
3. Helen Stölting
4. William J. Traves
5. Lewis J. Entwistle
6. Anastasia Voitovich
7. Minerva Garcia Martín
8. May Al-Sahaf
9. Katie Bonner
10. Elizabeth Scotney
11. Philip L. Molyneaux
12. Richard J. Hewitt
13. Simone A. Walker
14. Laura Yates
15. Sejal Saglani
16. Clare M. Lloyd

Reviewed by Arcadia Science

A constraint-based framework to reconstruct interaction networks in microbial communities

1. Omid Oftadeh
2. Asli Sahin
3. Evangelia Vayena
4. Vassily Hatzimanikatis

Reviewed by Arcadia Science

CDK-4 regulates nucleolar size and metabolism at the cost of late-life fitness in C. elegans

1. Rachel Webster
2. Maria Quintana
3. Bin Yu
4. Stacey Fluke
5. Ran Kafri
6. W. Brent Derry

Reviewed by Arcadia Science

Evolution of novel sensory organs in fish with legs

1. Corey A.H. Allard
2. Amy L. Herbert
3. Stephanie P. Krueger
4. Qiaoyi Liang
5. Brittany L. Walsh
6. Andrew L. Rhyne
7. Allex N. Gourlay
8. Agnese Seminara
9. Maude W. Baldwin
10. David M. Kingsley
11. Nicholas W. Bellono

Reviewed by Arcadia Science

Recording γ-secretase activity in living mouse brains

1. Steven S Hou
2. Yuya Ikegawa
3. Yeseo Kwon
4. Natalia Wieckiewicz
5. Mei CQ Houser
6. Brianna Lundin
7. Brian J Bacskai
8. Oksana Berezovska
9. Masato Maesako

• Curated by eLife

  eLife assessment

  Hou and colleagues describe the the use of a previously characterized FRET sensor for use in determining gamma secretase activity in the brain of living mice. In an approach that targeted the sensor to neurons, they observe patterns of fluorescent sensor readout suggesting clustered regions of secretase activity. These results once validated would be valuable in the field of Alzheimer's Disease research, yet further validation of the approach is required, as the current evidence provided is inadequate to support the conclusions.

Reviewed by eLife, Arcadia Science

Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity

1. Sasmita Panda
2. Yahani P Jayasinghe
3. Dhananjay D Shinde
4. Emilio Bueno
5. Amanda Stastny
6. Blake P Bertrand
7. Sujata S Chaudhari
8. Tammy Kielian
9. Felipe Cava
10. Donald R Ronning
11. Vinai C Thomas

• Curated by eLife

  eLife Assessment

  In this useful study, the authors present convincing evidence linking the enzyme D-alanine-D-alanine ligase (Ddl), crucial for cell wall fortification, to organic acid exposure in Staphylococcus aureus. While it's established that organic acids impede bacterial growth, the researchers reveal a novel coping mechanism where S. aureus maintains elevated levels of D-alanine, the substrate for Ddl, to counteract this inhibition. This discovery illuminates a bacterial strategy for organic acid tolerance, offering new insights for microbiologists and potentially informing future antimicrobial approaches.

Reviewed by eLife, Arcadia Science

Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns

1. Ken-ichiro F Kamei
2. Koseki J Kobayashi-Kirschvink
3. Takashi Nozoe
4. Hidenori Nakaoka
5. Miki Umetani
6. Yuichi Wakamoto

• Curated by eLife

  eLife Assessment

  This paper reports the fundamental finding of how Raman spectral patterns correlate with proteome profiles using Raman spectra of E. coli cells from different physiological conditions and found global stoichiometric regulation on proteomes. The authors' findings provide compelling evidence that stoichiometric regulation of proteomes is general through analysis of both bacterial and human cells. In the future, similar methodology can be applied on various tissue types and microbial species for studying proteome composition with Raman spectral patterns.

Reviewed by eLife, Arcadia Science