Journal of Biological Methods https://polscientific.com/jbm/index.php/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><em>JBM</em> 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><em>JBM</em> has 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> POL Scientific, LLC en-US Journal of Biological Methods 2326-9901 <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> SpheroidAnalyseR—an online platform for analyzing data from 3D spheroids or organoids grown in 96-well plates https://polscientific.com/jbm/index.php/jbm/article/view/388 <p>Spheroids and organoids are increasingly popular three-dimensional (3D) cell culture models. Spheroid models are more physiologically relevant to a tumor compared to two-dimensional (2D) cultures and organoids are a simplified version of an organ with similar composition. Spheroids are often only formed from a single cell type which does not represent the situation <em>in vivo</em>. However, despite this, both spheroids and organoids can be used in cell migration studies, disease modelling and drug discovery. A drawback of these models is, however, the lack of appropriate analytical tools for high throughput imaging and analysis over a time course. To address this, we have developed an R Shiny app called SpheroidAnalyseR: a simple, fast, effective open-source app that allows the analysis of spheroid or organoid size data generated in a 96-well format. SpheroidAnalyseR processes and analyzes datasets of image measurements that can be obtained <em>via</em> a bespoke software, described herein, that automates spheroid imaging and quantification using the Nikon A1R Confocal Laser Scanning Microscope. However, templates are provided to enable users to input spheroid image measurements obtained by user-preferred methods. SpheroidAnalyseR facilitates outlier identification and removal followed by graphical visualization of spheroid measurements across multiple predefined parameters such as time, cell-type and treatment(s). Spheroid imaging and analysis can, thus, be reduced from hours to minutes, removing the requirement for substantial manual data manipulation in a spreadsheet application. The combination of spheroid generation in 96-well ultra-low attachment microplates, imaging using our bespoke software, and analysis using SpheroidAnalyseR toolkit allows high throughput, longitudinal quantification of 3D spheroid growth whilst minimizing user input and significantly improving the efficiency and reproducibility of data analysis. Our bespoke imaging software is available from https://github.com/GliomaGenomics. SpheroidAnalyseR is available at https://spheroidanalyser.leeds.ac.uk, and the source code found at https://github.com/GliomaGenomics.</p> Rhiannon Barrow Joseph Wilkinson Yichen He Martin Callaghan Anke Brüning-Richardson Mark Dunning Lucy Stead Copyright (c) 2022 Rhiannon Barrow, Joseph N. Wilkinson, Yichen He, Martin Callaghan, Anke Brüning-Richardson, Mark Dunning, Lucy F. Stead https://creativecommons.org/licenses/by-nc-sa/4.0 2022-11-23 2022-11-23 9 4 e163 e163 10.14440/jbm.2022.388 Multiplexed tape-stabilized cryohistology of mineralized large animal specimens https://polscientific.com/jbm/index.php/jbm/article/view/389 <p>Tape-stabilized cryohistology is a powerful histological method to reinforce tissue samples during and after sectioning, enhancing the overall image quality. This technique has widely been applied to section mineralized small animal (i.e., mice, rat, rabbit) specimens, but has only been sparsely implemented for large animal samples that have a greater tendency to tear due to their increased surface area. Here, we present an optimized protocol for tape-stabilized cryohistology of undecalcified minipig vertebral body, femoral head, and temporomandibular joint samples. This protocol further develops a pipeline for sequential staining and imaging of the tape-stabilized cryosections. Images from multiple rounds of staining (endogenous bone mineral labels, aligned collagen (polarized light), tartrate resistant phosphatase (TRAP), alkaline phosphatase (AP), and toluidine blue) are overlaid to provide insight into dynamic bone remodeling. Overall, the established multiplexed tape-stabilized cryohistology protocol provides step-by-step instructions and guidance to cryosection large, mineralized tissues, and maximize data output from a single histological section.</p> Hannah M. Zlotnick Xi Jiang Robert L. Mauck Nathaniel A. Dyment Copyright (c) 2022 Hannah M. Zlotnick, Xi Jiang, Robert L. Mauck, Nathaniel A. Dyment https://creativecommons.org/licenses/by-nc-sa/4.0 2022-11-17 2022-11-17 9 4 e166 e166 10.14440/jbm.2022.389