Microbiology

Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients

1. André Moreira-Rosário
2. Cláudia Marques
3. Hélder Pinheiro
4. João Ricardo Araújo
5. Pedro Ribeiro
6. Rita Rocha
7. Inês Mota
8. Diogo Pestana
9. Rita Ribeiro
10. Ana Pereira
11. Maria José de Sousa
12. José Pereira-Leal
13. José de Sousa
14. Juliana Morais
15. Diana Teixeira
16. Júlio César Rocha
17. Marta Silvestre
18. Nuno Príncipe
19. Nuno Gatta
20. José Amado
21. Lurdes Santos
22. Fernando Maltez
23. Ana Boquinhas
24. Germano de Sousa
25. Nuno Germano
26. Gonçalo Sarmento
27. Cristina Granja
28. Pedro Póvoa
29. Ana Faria
30. Conceição Calhau

Reviewed by ScreenIT

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection

1. Hejun Liu
2. Meng Yuan
3. Deli Huang
4. Sandhya Bangaru
5. Fangzhu Zhao
6. Chang-Chun D. Lee
7. Linghang Peng
8. Shawn Barman
9. Xueyong Zhu
10. David Nemazee
11. Dennis R. Burton
12. Marit J. van Gils
13. Rogier W. Sanders
14. Hans-Christian Kornau
15. S. Momsen Reincke
16. Harald Prüss
17. Jakob Kreye
18. Nicholas C. Wu
19. Andrew B. Ward
20. Ian A. Wilson

Reviewed by ScreenIT

Toxoplasma gondii injected neurons localize to the cortex and striatum and have altered firing

1. Oscar A. Mendez
2. Emiliano Flores Machado
3. Jing Lu
4. Anita A. Koshy

• Curated by eLife

  Evaluation Summary:

  This study uses a new approach to map all neurons in the brain that have been infected with Toxoplasma gondii or injected with parasite proteins. The authors show that Toxoplasma injected neurons are heterogeneously distributed in murine brain tissues, that excitatory neurons are the primary targets, and that injection of parasite proteins leads to neuronal death. This work provides new insights into Toxoplasma-neuron interactions that underlie the pathology and potential changes in behaviour of infected individuals. The manuscript will be of interest to those working in neuroscience and/or parasitic infections.

  (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. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes

1. Benjamin H Meyer
2. Panagiotis S Adam
3. Ben A Wagstaff
4. George E Kolyfetis
5. Alexander J Probst
6. Sonja V Albers
7. Helge C Dorfmueller

• Curated by eLife

  Evaluation Summary:

  The authors identified the enzyme involved in the transfer of the second GlcNAC residue on the nascent oligosaccharide in protein N-glycosylation of the thermophilic Crenarchaeon Sulfolobus acidocaldarius. Although N-glycosylation is well-known in Euryarchaeota, the enzymes involved in this process, their substrates, and the mechanisms followed to produce the mature glycan are still elusive in Crenarchaeota. This work will impact the community interested in glycoprotein biogenesis and evolution. The experiments reported in this study were well-performed and the results are solid, but text and figure editing is required to enhance the accuracy, readability and strengthen the message of the work.

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

Reviewed by eLife

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

1. Hong Zhou
2. Jingkai Ji
3. Xing Chen
4. Yuhai Bi
5. Juan Li
6. Qihui Wang
7. Tao Hu
8. Hao Song
9. Runchu Zhao
10. Yanhua Chen
11. Mingxue Cui
12. Yanyan Zhang
13. Alice C. Hughes
14. Edward C. Holmes
15. Weifeng Shi

Reviewed by NCRC, ScreenIT

Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life

1. Raphaël Méheust
2. Shuo Huang
3. Rafael Rivera-Lugo
4. Jillian F. Banfield
5. Samuel H. Light

• Curated by eLife

  Evaluation Summary:

  Light and coworkers provide evidence from mining 31,910 prokaryotic genomes for the widespread occurrence of extracytosolic flavinylated FMN-binding domains in bacteria. They discovered extracytosolic flavinylation of five protein classes potentially involved in transmembrane electron transfer. The study also proposes new connections between respiration and iron assimilation and identifies two novel substrates of ApbE enzymes. This work should inspire further work in the fields of redox enzymology and bioenergetics to characterize the suggested involvement of flavinylated protein complexes in prokaryotes.

  (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 #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Biosynthesis of a sulfated exopolysaccharide, synechan, and bloom formation in the model cyanobacterium Synechocystis sp. strain PCC 6803

1. Kaisei Maeda
2. Yukiko Okuda
3. Gen Enomoto
4. Satoru Watanabe
5. Masahiko Ikeuchi

• Curated by eLife

  Evaluation Summary:

  The authors have elucidated the biochemical and regulatory apparatus for the biosynthesis of sulfated exopolysaccharides, an entire class of molecules not previously studied in cyanobacteria. The work has broad implications for the microbiology and ecology of these organisms and also opens the possibility to use these compounds in biotechnology and modify their structures by combinatorial synthesis.

  (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 #1, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

Reviewed by eLife

Dynamic persistence of UPEC intracellular bacterial communities in a human bladder-chip model of urinary tract infection

1. Kunal Sharma
2. Neeraj Dhar
3. Vivek V Thacker
4. Thomas M Simonet
5. Francois Signorino-Gelo
6. Graham W Knott
7. John D McKinney

• Curated by eLife

  Evaluation Summary:

  Reviewers value the development and characterization of a bladder-on-chip infection model for recapitulating the multiples factors involved in UPEC driven UTIs. Notably, it consists of human bladder epithelial cells, bladder microvascular endothelial cells, neutrophils and urine that are also subjected to mechanical changes mimicking those occurring during bladder filling and micturition. This model is a lot more complex than in vitro tissue culture models and more amenable to analysis such as imaging than animal models and therefore constitute a distinct advance for in vitro modeling of UTI that has potential to reveal key aspects of UTIs and reasons for the difficulty to clear these infections with antibiotics.

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

Reviewed by eLife

HIV-1 uncoating by release of viral cDNA from capsid-like structures in the nucleus of infected cells

1. Thorsten G Müller
2. Vojtech Zila
3. Kyra Peters
4. Sandra Schifferdecker
5. Mia Stanic
6. Bojana Lucic
7. Vibor Laketa
8. Marina Lusic
9. Barbara Müller
10. Hans-Georg Kräusslich

• Curated by eLife

  Evaluation Summary:

  The authors use a variety of complementary approaches to visualize and characterize events in the first half of the HIV life cycle, with some overlap between the latter studies and the recent (and cited) Zila et al. bioRxiv paper from some of the same authors. The data are generally of high quality, and many findings are in line with recent field advances indicating that reverse transcription completes in the nucleus, that intact/nearly intact cores are imported into the nucleus, and that nuclear uncoating likely occurs immediately prior to integration. The results provide the best evidence to date that intact capsids can enter the nucleus of target cells during infection, and will generally be of interest to the field, although the impact is diminished somewhat by similar recent publications from a number of other groups (including one case that used nearly identical labeling methods to follow viral complexes during infection). Issues that should be addressed include missing controls in some cases, some examples of over-interpretation and uneven citation, and the need for additional images to help bolster some of the claims. Strengths of the study include the rigorous characterization of infection using sophisticated imaging methods and, most importantly, the use of CLEM-ET to visualize viral capsids in the nucleus.

  (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 eLife, PREreview

Human airway cells prevent SARS-CoV-2 multibasic cleavage site cell culture adaptation

1. Mart M Lamers
2. Anna Z Mykytyn
3. Tim I Breugem
4. Yiquan Wang
5. Douglas C Wu
6. Samra Riesebosch
7. Petra B van den Doel
8. Debby Schipper
9. Theo Bestebroer
10. Nicholas C Wu
11. Bart L Haagmans

• Curated by eLife

  Evaluation Summary:

  This manuscript follows up on work documenting the relevance of the multi-basic cleavage site (MBCS) in the spike (S) protein of SARS-CoV-2 for determining cell tropism and mode of cell entry. The paper describes a number of important findings: 1) That SARS-CoV-2 grown in Vero cells rapidly acquires MBCS mutations, where as virus grown in airway epithelial cells or Vero-TMPRSSR2 cells do not; 2) that deep sequencing is necessary to see mutations emerging that are not apparent in consensus sequence reads; 3) that factors such as fetal calf serum can influence the selection of mutant phenotypes, and 4) that cultures derived from differentiated stem cells can provide reproducible systems for virus culture. Together, the work sets out clear guidelines for the propagation of SARS-CoV-2 to avoid adaptations to laboratory cell-lines/conditions and maintain the authenticity of clinical isolates. The work has relevance to other viruses and the use of permissive transformed cell lines.

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

Reviewed by eLife, ScreenIT