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  1. Genome assembly of the hybrid grapevine Vitis ‘Chambourcin’

    1. Sagar Patel
    2. Zachary N. Harris
    3. Jason P. Londo
    4. Allison Miller
    5. Anne Fennell

    • Curated by GigaByte

      Editor’s Assessment

      Hybrid genomes are tricky to assemble, and few genomic resources are available for hybrid grapevines such as ‘Chambourcin’, a French-American interspecific hybrid grape grown in the eastern and midwestern United States. Here is an attempt to assemble Chambourcin’ using a combination of PacBio HiFi long-reads, Bionano optical maps, and Illumina short-read sequencing technologies. Producing an assembly with 26 scaffolds, an N50 length 23.3 Mb and an estimated BUSCO completeness of 97.9% that can be used for genome comparisons, functional genomic analyses, and genome-assisted breeding research. Error correction and pilon polishing was a challenge with this hybrid assembly, but after trying a few different approaches in the review process have improved it, and as they have documented what they did and are clear about the final metrics, users can assess the quality themselves.

      This assessment refers to version 2 of this preprint.

    Reviewed by GigaByte

    2 evaluationsAppears in 4 listsLatest version Latest activity

  8. Sequencing SARS-CoV-2 Genomes from Saliva

    1. Tara Alpert
    2. Chantal B.F. Vogels
    3. Mallery I. Breban
    4. Mary E. Petrone
    5. Yale IMPACT Research Team
    6. Anne L. Wyllie
    7. Nathan D. Grubaugh
    8. Joseph R. Fauver

    Reviewed by ScreenIT

    1 evaluationAppears in 3 listsLatest version Latest activity

  9. Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets with therapeutic potential

    1. Bjoern Meyer
    2. Jeanne Chiaravalli
    3. Stacy Gellenoncourt
    4. Philip Brownridge
    5. Dominic P. Bryne
    6. Leonard A. Daly
    7. Arturas Grauslys
    8. Marius Walter
    9. Fabrice Agou
    10. Lisa A. Chakrabarti
    11. Charles S. Craik
    12. Claire E. Eyers
    13. Patrick A. Eyers
    14. Yann Gambin
    15. Andrew R. Jones
    16. Emma Sierecki
    17. Eric Verdin
    18. Marco Vignuzzi
    19. Edward Emmott

    Reviewed by ScreenIT

    1 evaluationAppears in 2 listsLatest version Latest activity

  10. APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy

    1. James Rae
    2. Charles Ferguson
    3. Nicholas Ariotti
    4. Richard I. Webb
    5. Han-Hao Cheng
    6. James L. Mead
    7. Jamie Riches
    8. Dominic J.B. Hunter
    9. Nick Martel
    10. Joanne Baltos
    11. Arthur Christopoulos
    12. Nicole S. Bryce
    13. Maria Lastra Cagigas
    14. Sachini Fonseka
    15. Edna C. Hardeman
    16. Peter W. Gunning
    17. Yann Gambin
    18. Thomas Hall
    19. Robert G. Parton

    • Curated by eLife

      Summary: The manuscript by Rae et al. reports a new protocol for labeling genetically-tagged proteins of interest with heavy atom particles for visualization by electron microscopy. The optimized protocol builds on the use of the enzyme APEX2, fused to the target protein of interest. The contrast enhancement may be useful in diverse 3D EM techniques. Also, reviewers were enthusiastic about the prospects for quantitative studies, even for low-levels of endogenous expression. Semi-quantitative studies may be enabled because the new method appears to improve the proportionality of the signal such that the number of APEX2 tags in a sample correlates with the number of heavy atom particles. The apparent simplicity of the protocol raises the potential for it to become a standard in the field of EM labeling.

      Reviewer #1, Reviewer #2 and Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

    Reviewed by eLife

    4 evaluationsAppears in 4 listsLatest version Latest activity

  12. Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR

    1. Peter J. Diebold
    2. Felicia N. New
    3. Michael Hovan
    4. Michael J. Satlin
    5. Ilana L. Brito

    • Curated by eLife

      Evaluation Summary:

      Tracking horizontal gene transfer of mobile resistance genes is exceptionally important in the context of AMR and its burden on public health. An accessible high-throughput technique that provides an alternative to Hi-C or single-cell whole genome sequencing for associating mobile antibiotic resistance genes with their bacterial hosts in complex microbial populations is an important development for the field. The method introduced here, which relies on cellular emulsion and fusion PCR in one step, is an improvement over the previously published epicPCR. In addition, the method can be applied to other studies on complex microbial communities beyond antibiotic resistance.

      (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

    5 evaluationsAppears in 3 listsLatest version Latest activity

  13. LAG3 is not expressed in human and murine neurons and does not modulate α-synucleinopathies

    1. Marc Emmenegger
    2. Elena De Cecco
    3. Marian Hruska-Plochan
    4. Timo Eninger
    5. Matthias M. Schneider
    6. Melanie Barth
    7. Elena Tantardini
    8. Pierre de Rossi
    9. Mehtap Bacioglu
    10. Rebekah G. Langston
    11. Alice Kaganovich
    12. Nora Bengoa-Vergniory
    13. AndrĂšs Gonzalez-Guerra
    14. Merve Avar
    15. Daniel Heinzer
    16. Regina Reimann
    17. Lisa M. HĂ€sler
    18. Therese W. Herling
    19. Naunehal S. Matharu
    20. Natalie Landeck
    21. Kelvin Luk
    22. Ronald Melki
    23. Philipp J. Kahle
    24. Simone Hornemann
    25. Tuomas P. J. Knowles
    26. Mark R. Cookson
    27. Magdalini Polymenidou
    28. Mathias Jucker
    29. Adriano Aguzzi

    Reviewed by Review Commons

    4 evaluationsAppears in 2 listsLatest version Latest activity

  16. Nosocomial outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward: virus genome sequencing as a key tool to understand cryptic transmission

    1. VĂ­tor Borges
    2. Joana Isidro
    3. Filipe Macedo
    4. José Neves
    5. LuĂ­s Silva
    6. MĂĄrio Paiva
    7. José Barata
    8. Judite Catarino
    9. Liliana Ciobanu
    10. SĂ­lvia Duarte
    11. LuĂ­s Vieira
    12. Raquel Guiomar
    13. JoĂŁo Paulo Gomes

    Reviewed by NCRC, ScreenIT

    2 evaluationsAppears in 5 listsLatest version Latest activity