Evaluated articles

Nanopore-based DNA sequencing in clinical microbiology: preliminary assessment of basic requirements

1. Håvard Harstad
2. Rafi Ahmad
3. Anders Bredberg

Reviewed by Arcadia Science

Deep learning pipeline reveals key moments in human embryonic development predictive of live birth in IVF

1. Camilla Mapstone
2. Helen Hunter
3. Daniel Brison
4. Julia Handl
5. Berenika Plusa

Reviewed by Arcadia Science

The protist ubiquitin ligase effector PbE3-2 targets RD21A to impede plant immunity

1. Chao Li
2. Shaofeng Luo
3. Lu Feng
4. Qianqian Wang
5. Jiasen Cheng
6. Jiatao Xie
7. Yang Lin
8. Yanping Fu
9. Daohong Jiang
10. Tao Chen

Reviewed by Arcadia Science

Uncovering novel endolysins against methicillin-resistant Staphylococcus aureus using microbial single-cell genome sequencing

1. Takuya Yoda
2. Ayumi Matsuhashi
3. Ai Matsushita
4. Shohei Shibagaki
5. Yukie Sasakura
6. Kazuteru Aoki
7. Masahito Hosokawa
8. Soichiro Tsuda

Reviewed by Arcadia Science

Pathogenic Huntingtin aggregates alter actin organization and cellular stiffness resulting in stalled clathrin-mediated endocytosis

1. Surya Bansi Singh
2. Shatruhan Singh Rajput
3. Aditya Sharma
4. Sujal Kataria
5. Priyanka Dutta
6. Vaishnavi Ananthanarayanan
7. Amitabha Nandi
8. Shivprasad Patil
9. Amitabha Majumdar
10. Deepa Subramanyam

Reviewed by Review Commons, Arcadia Science

ImmuNet: a segmentation-free machine learning pipeline for immune landscape phenotyping in tumors by multiplex imaging

1. Shabaz Sultan
2. Mark A J Gorris
3. Evgenia Martynova
4. Lieke L van der Woude
5. Franka Buytenhuijs
6. Sandra van Wilpe
7. Kiek Verrijp
8. Carl G Figdor
9. I Jolanda M de Vries
10. Johannes Textor

Reviewed by Arcadia Science

Novel role for peptidoglycan carboxypeptidases in maintaining the balance between bacterial cell wall synthesis and degradation

1. Manuela Alvarado Obando
2. Tobias Dörr

Reviewed by Arcadia Science

Replaying the tape of ecology to domesticate wild microbiota

1. Alberto Pascual-García
2. Damian Rivett
3. Matt L. Jones
4. Thomas Bell

Reviewed by Arcadia Science

The Landscape of Maize-Associated Bacteria and Fungi Across the United States

1. Corey R Schultz
2. Hanish Desai
3. Jason G Wallace

Reviewed by Arcadia Science

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

1. Lauren M. Lui
2. Torben N. Nielsen

Reviewed by Arcadia Science

Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias

1. Kangjin Kim
2. Sungho Won

Reviewed by Arcadia Science

A class of secreted mammalian peptides with potential to expand cell-cell communication

1. Amanda L. Wiggenhorn
2. Hind Z. Abuzaid
3. Laetitia Coassolo
4. Veronica L. Li
5. Julia T. Tanzo
6. Wei Wei
7. Xuchao Lyu
8. Katrin J. Svensson
9. Jonathan Z. Long

Reviewed by Arcadia Science

Spatiotemporal Mapping of Brain Cilia Reveals Region-Specific Oscillation of Length and Orientation

1. Roudabeh Vakil Monfared
2. Sherif Abdelkarim
3. Pieter Derdeyn
4. Kiki Chen
5. Hanting Wu
6. Kenneth Leong
7. Tiffany Chang
8. Justine Lee
9. Sara Versales
10. Surya M. Nauli
11. Kevin Beier
12. Pierre Baldi
13. Amal Alachkar

Reviewed by Arcadia Science

Monitoring norepinephrine release in vivo using next-generation GRAB _NE sensors

1. Jiesi Feng
2. Hui Dong
3. Julieta Lischinsky
4. Jingheng Zhou
5. Fei Deng
6. Chaowei Zhuang
7. Xiaolei Miao
8. Huan Wang
9. Hao Xie
10. Guohong Cui
11. Dayu Lin
12. Yulong Li

Reviewed by Arcadia Science

Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small datasets 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 and uterine fluids proteomics

1. Adrien Dufour
2. Cyril Kurylo
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