https://jbmethods.org/jbm/issue/feed Journal of Biological Methods 2022-06-08T14:58:59-07:00 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/386 An experimental method for evoking and characterizing dynamic color patterning of cuttlefish during prey capture 2022-01-05T22:26:46-08:00 Danbee Kim danbee@danbeekim.org Kendra C. Buresch kburesch@mbl.edu Roger T. Hanlon rhanlon@mbl.edu Adam R. Kampff adam.kampff@gmail.com <p>Cuttlefish are active carnivores that possess a wide repertoire of body patterns that can be changed within milliseconds for many types of camouflage and communication. The forms and functions of many body patterns are well known from ethological studies in the field and laboratory. Yet one aspect has not been reported in detail: the category of rapid, brief and high-contrast changes in body coloration (“Tentacle Shot Patterns” or TSPs) that always occur with the ejection of two ballistic tentacles to strike live moving prey (“Tentacles Go Ballistic” or TGB moment). We designed and tested a mechanical device that presented prey in a controlled manner, taking advantage of a key stimulus for feeding: motion of the prey. High-speed video recordings show a rapid transition into TSPs starting 114 ms before TGB (<em>N</em> = 114). TSPs are then suppressed as early as 470–500 ms after TGB (<em>P</em> &lt; 0.05) in unsuccessful hunts, while persisting for at least 3 s after TGB in successful hunts. A granularity analysis revealed significant differences in the large-scale high-contrast body patterning present in TSPs compared to the camouflage body pattern deployed beforehand. TSPs best fit the category of secondary defense called deimatic displaying, meant to briefly startle predators and interrupt their attack sequence while cuttlefish are distracted by striking prey. We characterize TSPs as a pattern category for which the main distinguishing feature is a high-contrast signaling pattern with aspects of Acute Conflict Mottle or Acute Disruptive Pattern. The data and methodology presented here open opportunities for quantifying the rapid neural responses in this visual sensorimotor set of behaviors.</p> 2022-06-14T00:00:00-07:00 Copyright (c) 2022 Danbee Kim, Kendra C. Buresch, Roger T. Hanlon, Adam R. Kampff https://jbmethods.org/jbm/article/view/374 Methodology for measuring oxidative capacity of isolated peroxisomes in the Seahorse assay 2021-09-01T14:04:50-07:00 Brittany A. Stork stork@bcm.edu Adam Dean amdean@bcm.edu Brian York york@bcm.edu <p>The regulation of cellular energetics is a complex process that requires the coordinated function of multiple organelles. Historically, studies focused on understanding cellular energy utilization and production have been overwhelmingly concentrated on the mitochondria. While mitochondria account for the majority of intracellular energy production, they alone are incapable of maintaining the variable energetic demands of the cell. The peroxisome has recently emerged as a secondary metabolic organelle that complements and improves mitochondrial performance. Although mitochondria and peroxisomes are structurally distinct organelles, they share key functional similarities that allows for the potential to repurpose readily available tools initially developed for mitochondrial assessment to interrogate peroxisomal metabolic function in a novel manner. To this end, we report here on procedures for the isolation, purification and real-time metabolic assessment of peroxisomal β-oxidation using the Agilent Seahorse® system. When used together, these protocols provide a straightforward, reproducible and highly quantifiable method for measuring the contributions of peroxisomes to cellular and organismal metabolism.</p> 2022-06-08T00:00:00-07:00 Copyright (c) 2022 Brittany A. Stork, Adam Dean, Brian York