https://jbmethods.org/jbm/issue/feed Journal of Biological Methods 2022-02-21T20:02:31-08:00 JBM Editorial Office editorial_staff@jbmethods.org Open Journal Systems <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> https://jbmethods.org/jbm/article/view/381 Site-specific nanobody-oligonucleotide conjugation for super-resolution imaging 2021-11-08T22:32:08-08:00 Laura Teodori laura.teodori@inano.au.dk Marjan Omer marjan@inano.au.dk Anders Märcher am@inano.au.dk Mads K. Skaanning mskaanning@inano.au.dk Veronica L. Andersen veronica.andersen@inano.au.dk Jesper S. Nielsen jespersejrupnielsen@gmail.com Emil Oldenburg emil.oldenburg@mbg.au.dk Yuchen Lin yuchen.lin@cbni.ucd.ie Kurt V. Gothelf kvg@chem.au.dk Jørgen Kjems jk@mbg.au.dk <p>Camelid single-domain antibody fragments, also called nanobodies, constitute a class of binders that are small in size (~15 kDa) and possess antigen-binding properties similar to their antibody counterparts. Facile production of recombinant nanobodies in several microorganisms has made this class of binders attractive within the field of molecular imaging. Particularly, their use in super-resolution microscopy has improved the spatial resolution of molecular targets due to a smaller linkage error. In single-molecule localization microscopy techniques, the effective spatial resolution can be further enhanced by site-specific fluorescent labeling of nanobodies owing to a more homogeneous protein-to-fluorophore stoichiometry, reduced background staining and a known distance between dye and epitope. Here, we present a protocol for site-specific bioconjugation of DNA oligonucleotides to three distinct nanobodies expressed with an N- or C-terminal unnatural amino acid, 4-azido-<em>L</em>-phenylalanine (pAzF). Using copper-free click chemistry, the nanobody-oligonucleotide conjugation reactions were efficient and yielded highly pure bioconjugates. Target binding was retained in the bioconjugates, as demonstrated by bio-layer interferometry binding assays and the super-resolution microscopy technique, DNA points accumulation for imaging in nanoscale topography (PAINT). This method for site-specific protein-oligonucleotide conjugation can be further extended for applications within drug delivery and molecular targeting where site-specificity and stoichiometric control are required.</p> 2022-03-01T00:00:00-08:00 Copyright (c) 2022 Laura Teodori, Marjan Omer, Anders Märcher, Mads K. Skaanning, Veronica L. Andersen, Jesper S. Nielsen, Emil Oldenburg, Yuchen Lin, Kurt V. Gothelf , Jørgen Kjems https://jbmethods.org/jbm/article/view/379 Development of a reproducible porcine model of infected burn wounds 2021-10-24T19:39:56-07:00 Sayf Said saids@ccf.org Samreen Jatana jatanas@ccf.org Andras Ponti pontia@ccf.org Erin Johnson exjohnson@jcu.edu Kimberly Such suchk@ccf.org Megan Zangara zangarm@ccf.org Maria Madajka mm892901@ohio.edu Francis Papay papayf@ccf.org Christine McDonald mcdonac2@ccf.org <p>Severe burns are traumatic and physically debilitating injuries with a high rate of mortality. Bacterial infections often complicate burn injuries, which presents unique challenges for wound management and improved patient outcomes. Currently, pigs are used as the gold standard of pre-clinical models to study infected skin wounds due to the similarity between porcine and human skin in terms of structure and immunological response. However, utilizing this large animal model for wound infection studies can be technically challenging and create issues with data reproducibility. We present a detailed protocol for a porcine model of infected burn wounds based on our experience in creating and evaluating full thickness burn wounds infected with <em>Staphylococcus aureus</em> on six pigs. Wound healing kinetics and bacterial clearance were measured over a period of 27 d in this model. Enumerated are steps to achieve standardized wound creation, bacterial inoculation, and dressing techniques. Systematic evaluation of wound healing and bacterial colonization of the wound bed is also described. Finally, advice on animal housing considerations, efficient bacterial plating procedures, and overcoming common technical challenges is provided. This protocol aims to provide investigators with a step-by-step guide to execute a technically challenging porcine wound infection model in a reproducible manner. Accordingly, this would allow for the design and evaluation of more effective burn infection therapies leading to better strategies for patient care.</p> 2022-02-21T00:00:00-08:00 Copyright (c) 2022 Sayf Al-deen Said, Samreen Jatana, Andras K. Ponti, Erin E. Johnson, Kimberly A. Such, Megan T. Zangara, Maria Madajka, Francis Papay, Christine McDonald