Journal of Biological Methods https://jbmethods.org/jbm <p>The <em>Journal of Biological Methods (JBM) </em>(ISSN 2326-9901) is a multidisciplinary and open-access journal committed to publishing peer-reviewed papers on cutting-edge and innovative biological techniques, methods and protocols.</p> <p>JBM has been included by the following indexing and archiving services: Google Scholar, CrossRef, OCLC, Portico and SHERPA/RoMEO, BIOSIS Previews and Biological Abstracts.</p> <p><sup><span style="background-color: #ffff00;">New</span></sup> JBM has now been indexed by PubMed Central (PMC) and all papers are also searchable in PubMed.</p> <div style="margin: 0 auto; text-align: center; overflow: hidden; border-radius: 0px; background: #367e32; border: 0px solid #000000; padding: 5px; max-width: calc(100% - 10px); width: 740px;"> <div style="display: inline-block; text-shadow: #decf1b 4px 4px 4px; position: relative; vertical-align: middle; padding: 9px; font-size: 30px; color: #ffffff; font-weight: bold;">COVID 19 Special Issue - Call for Papers</div> <div style="display: inline-block; position: relative; vertical-align: middle; padding: 17px; font-size: 16px; color: #ffffff; font-weight: normal;">JBM is now accepting manuscripts to be published in a COVID 19 Special Issue</div> </div> en-US <p>Authors who publish with JBM agree to the following terms:</p> <ol> <li>Authors retain copyright and grant JBM right of first publication with the work simultaneously licensed under a <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution License</a> that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.</li> <li>Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.</li> <li>Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See <a href="http://opcit.eprints.org/oacitation-biblio.html" target="_new">The Effect of Open Access</a>).</li> </ol> editorial_staff@jbmethods.org (JBM Editorial Office) support@jbmethods.org (JBM Technical Support) Wed, 26 May 2021 00:00:00 -0700 OJS 3.2.1.4 http://blogs.law.harvard.edu/tech/rss 60 High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples https://jbmethods.org/jbm/article/view/360 <p>In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using established visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable "how-to" reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and long-read nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.</p> Adrian A. Pater, Michael S. Bosmeny, Adam A. White, Rourke J. Sylvain, Seth B. Eddington, Mansi Parasrampuria, Katy N. Ovington, Paige E. Metz, Abadat O. Yinusa, Christopher L. Barkau, Ramadevi Chilamkurthy, Scott W. Benzinger, Madison M. Hebert, Keith T. Gagnon Copyright (c) 2021 Adrian A. Pater, Michael S. Bosmeny, Adam A. White, Rourke J. Sylvain, Seth B. Eddington, Mansi Parasrampuria, Katy N. Ovington, Paige E. Metz, Abadat O. Yinusa, Christopher L. Barkau, Ramadevi Chilamkurthy, Scott W. Benzinger, Madison M. Hebert, Keith T. Gagnon https://creativecommons.org/licenses/by-nc-sa/4.0 https://jbmethods.org/jbm/article/view/360 Mon, 27 Sep 2021 00:00:00 -0700 Special issue editorial: Methods to facilitate SARS-CoV-2 and COVID-19 research https://jbmethods.org/jbm/article/view/387 <p>This special issue of&nbsp;<em>Journal of Biological Methods</em>&nbsp;presents methods related to SARS- CoV-2 research in responding to the current global COVID-19 pandemic.</p> Keith T Gagnon; Vera Huang Copyright (c) 2021 Keith T Gagnon; Vera Huang https://creativecommons.org/licenses/by-nc-sa/4.0 https://jbmethods.org/jbm/article/view/387 Thu, 30 Dec 2021 00:00:00 -0800 Virtual screening on the web for drug repurposing: a primer https://jbmethods.org/jbm/article/view/351 <p><span lang="EN-GB">We describe a procedure of performing <em>in silico</em> (virtual) screening using a web-based service, the MTiOpenScreen, which<br />is freely accessible to non-commercial users. We shall use the SARS-CoV-2 main protease as an example. Starting from a structure downloaded from the Protein Data Bank, we discuss how to prepare the coordinates file, taking into account the known biochemical background information of the target protein. The reader will find that this preparation step takes up most of the effort before the target is ready for screening. The steps for uploading the target structure and defining the search volume by critical residues, and the main parameters to use, are outlined. When this protocol is followed, the user will expect to obtain a ranked list of small approved drug compounds docked into the target structure. The results can be readily examined graphically on the web site or downloaded for studying in a local molecular graphics program such as PyMOL.</span></p> Yu Wai Chen, Chin-Pang Bennu Yiu, Kwok-Yin Wong Copyright (c) 2021 Yu Wai Chen, Chin-Pang Bennu Yiu, Kwok-Yin Wong https://creativecommons.org/licenses/by-nc-sa/4.0 https://jbmethods.org/jbm/article/view/351 Wed, 26 May 2021 00:00:00 -0700