Evaluated articles

Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small data sets with class imbalance and hierarchical grouping

1. Stefan Stiller
2. Juan F. Dueñas
3. Stefan Hempel
4. Matthias C. Rillig
5. Masahiro Ryo

Reviewed by Arcadia Science

Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB

1. Joseph L Basalla
2. Claudia A Mak
3. Jordan A Byrne
4. Maria Ghalmi
5. Y Hoang
6. Anthony G Vecchiarelli

• Curated by eLife

  Evaluation Summary:

  Carboxysomes enable the efficient fixation of carbon dioxide in specific bacteria. Phase separation has been invoked as a mechanism that drives the formation of carboxysomes. The current work focuses on the biophysical principles of how one of two essential specific protein components enable spatial regulation over carboxysomes. This important work highlights the connection between oligomerization via specific molecular interactions and phase separation. The work is of interest to the areas of biochemistry and carbon dioxide fixation as well as phase separation.

  (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 #3 agreed to share their name with the authors.)

Reviewed by Arcadia Science, eLife

zDB: bacterial comparative genomics made easy

1. Bastian Marquis
2. Trestan Pillonel
3. Alessia Carrara
4. Claire Bertelli

Reviewed by Arcadia Science

Cell specification and functional interactions in the pig blastocyst inferred from single cell transcriptomics

1. Adrien Dufour
2. Cyril Kurilo
3. Jan B. Stöckl
4. Denis Laloë
5. Yoann Bailly
6. Patrick Manceau
7. Frédéric Martins
8. Ali G. Turhan
9. Stéphane Ferchaud
10. Bertrand Pain
11. Thomas Fröhlich
12. Sylvain Foissac
13. Jérôme Artus
14. Hervé Acloque

Reviewed by Arcadia Science

IntAct: a non-disruptive internal tagging strategy to study actin isoform organization and function

1. M.C. van Zwam
2. A. Dhar
3. W. Bosman
4. W. van Straaten
5. S. Weijers
6. E. Seta
7. B. Joosten
8. S. Palani
9. K. van den Dries

Reviewed by Review Commons, Arcadia Science

ESMFold Hallucinates Native-Like Protein Sequences

1. Jeliazko R. Jeliazkov
2. Diego del Alamo
3. Joel D. Karpiak

Reviewed by Arcadia Science

Enterococcus faecalis strains with compromised CRISPR-Cas defense emerge under antibiotic selection for a CRISPR-targeted plasmid

1. Wenwen Huo
2. Valerie J. Price
3. Ardalan Sharifi
4. Michael Q. Zhang
5. Kelli L. Palmer

Reviewed by Arcadia Science

Thermoprotection by a cell membrane–localized metacaspase in a green alga

1. Yong Zou
2. Igor Sabljić
3. Natalia Horbach
4. Adrian N Dauphinee
5. Anna Åsman
6. Lucia Sancho Temino
7. Elena A Minina
8. Marcin Drag
9. Simon Stael
10. Marcin Poreba
11. Jerry Ståhlberg
12. Peter V Bozhkov

Reviewed by Arcadia Science

SPLIT HAND/FOOT VARIANTS FAIL TO RESCUE PRDM1A MUTANT CRANIOFACIAL DEFECTS

1. Brittany T. Truong
2. Lomeli C. Shull
3. Ezra Lencer
4. Kristin B. Artinger

Reviewed by Arcadia Science

TANGO-Light - optogenetic control of transcriptional modulators

1. Alicja Przybyszewska-Podstawka
2. Joanna Kałafut
3. Jakub Czapiński
4. Thu Ha Ngo
5. Arkadiusz Czerwonka
6. Adolfo Rivero-Müller

Reviewed by Arcadia Science

RaMALDI: Enabling simultaneous Raman and MALDI imaging of the same tissue section

1. Ethan Yang
2. Jeong Hee Kim
3. Caitlin M. Tressler
4. Xinyi Elaine Shen
5. Dalton R. Brown
6. Cole C. Johnson
7. Tae-Hun Hahm
8. Ishan Barman
9. Kristine Glunde

Reviewed by PREreview, Arcadia Science

Perturb-tracing enables high-content screening of multiscale 3D genome regulators

1. Yubao Cheng
2. Mengwei Hu
3. Bing Yang
4. Tyler B Jensen
5. Tianqi Yang
6. Ruihuan Yu
7. Zhaoxia Ma
8. Jonathan S D Radda
9. Shengyan Jin
10. Chongzhi Zang
11. Siyuan Wang

Reviewed by Arcadia Science

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

1. Yanay Rosen
2. Maria Brbić
3. Yusuf Roohani
4. Kyle Swanson
5. Ziang Li
6. Jure Leskovec

Reviewed by Arcadia Science

Bioactive exometabolites drive maintenance competition in simple bacterial communities

1. John L. Chodkowski
2. Ashley Shade

Reviewed by Arcadia Science

Convergent evolution of noxious heat sensing by TRPA5, a novel class of heat sensor in Rhodnius prolixus

1. Marjorie A. Liénard
2. David Baez-Nieto
3. Cheng-Chia Tsai
4. Wendy A. Valencia-Montoya
5. Balder Werin
6. Urban Johanson
7. Jean-Marc Lassance
8. Jen Q. Pan
9. Nanfang Yu
10. Naomi E. Pierce

Reviewed by Arcadia Science

Massive genome reduction occurred prior to the origin of coral algal symbionts

1. Sarah Shah
2. Katherine E. Dougan
3. Yibi Chen
4. Rosalyn Lo
5. Gemma Laird
6. Michael D. A. Fortuin
7. Subash K. Rai
8. Valentine Murigneux
9. Anthony J. Bellantuono
10. Mauricio Rodriguez-Lanetty
11. Debashish Bhattacharya
12. Cheong Xin Chan

Reviewed by Arcadia Science

Syntenin and CD63 Promote Exosome Biogenesis from the Plasma Membrane by Blocking Cargo Endocytosis

1. Yiwei Ai
2. Chenxu Guo
3. Marta Garcia-Contreras
4. Laura S. Sánchez B.
5. Andras Saftics
6. Oluwapelumi Shodubi
7. Shankar Raghunandan
8. Junhao Xu
9. Shang Jui Tsai
10. Yi Dong
11. Rong Li
12. Tijana Jovanovic-Talisman
13. Stephen J. Gould

Reviewed by Arcadia Science

EMT induces cell-cycle-dependent changes of Rho GTPases and downstream effectors

1. Kamran Hosseini
2. Annika Frenzel
3. Elisabeth Fischer-Friedrich

Reviewed by Arcadia Science

Reconstructing cell type evolution across species through cell phylogenies of single-cell RNAseq data

1. Jasmine L. Mah
2. Casey W. Dunn

Reviewed by Arcadia Science

Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

1. Samuel E. Barnett
2. Ashley Shade

Reviewed by Arcadia Science