Biology subjects

Clark, J. M.

Publications and source records attributed to Clark, J. M..

5 recordsLinked to original sources

bioRxiv2026

Spinal microglia are dispensable for the development of opioid-induced hyperalgesia

Adverse side effects of chronic opioid use, including analgesic tolerance, opioid-induced hyperalgesia, and addiction, are serious clinical challenges for pain management and opioid deprescribing. Microglia have been implicated in the development of these adverse effects, but the extent to which opioids alter microglia and the mechanisms behind opioid effects on microglia are poorly understood. We performed morphological and single-cell transcriptomic analysis on spinal microglia from opioid-withdrawn and saline-treated mice, and found that while morphological changes recapitulated prior reports, transcriptomic changes in these cells were modest. Furthermore, peripherally, but not centrally, restricted opioid administration was sufficient to induce both hyperalgesia and microglial morphological changes in mice. Finally, complete loss of microglia in Csf1r{Delta}{Delta}FIRE mice did not prevent the development of opioid-induced hyperalgesia, analgesic tolerance, and somatic withdrawal symptoms. These data argue against any microglial involvement in the development of these phenomena.

neuroscience↗

bioRxiv2023

Lack of paternal silencing and ecotype-specific expression in head and body lice hybrids.

Paternal genome elimination (PGE) is a non-Mendelian inheritance system in which males develop from fertilised eggs but their paternally-inherited chromosomes are eliminated before or during spermatogenesis. Therefore, PGE males only transmit their maternally inherited set of chromosomes to their offspring. PGE has been described in numerous arthropod species, many of which are pests or parasites, posing a severe economic burden on crop production and/or with implications for human health. In order to understand how PGE has evolved on the molecular level, to potentially develop novel control strategies, we need to examine species which display basal forms of PGE. The human louse, Pediculus humanus, represents an ideal model system to understand the molecular underpinnings of PGE. In this study we analysed parent-of-origin allele specific expression patterns in male offspring of crosses between head and body lice ecotypes. We have shown that hybrid adult males of P. humanus display biparental gene expression, which constitutes the first known case of a species with PGE in which genetic activity of paternal chromosomes in the soma is not affected by embryonic heterochromatinization or (partial or complete) elimination. We have also identified maternally-biased genes (potentially imprinted genes) which may be involved in the elimination of paternal chromosomes during spermatogenesis. Finally, we have identified genes which show ecotype-specific expression bias. Given the low genetic diversity between ecotypes this is suggestive for a role of epigenetic processes in ecotype differences. These findings have implications for models of pediculicide resistance in human lice and for the development of novel epigenetic-mediated control strategies.

evolutionary biology↗

bioRxiv2021

Machine Learning to Summarize and Provide Context for Sleep and Eating Schedules.

The relative timing of sleep and of eating within the circadian day is important for human health. Despite much data on sleep, and a growing data set for eating, there remains a need for an interpretative framework for the understanding of this data for health decisions. This study provides a new statistical and machine learning analysis of more than 500 participants in the Daily24 project. From their data, and the analysis, we propose a framework for determining the classification of participants into different chronotypes and with that the ability to realize the potential impact of daily circadian habits on health. We propose that our resulting distribution curves could be used, similar to NHANES (National Health and Nutrition Examination Survey) data for pediatric growth, as a measure for circadian misalignment and used to help guide re-entrainment schedules. Author summaryDaily habits can be positive, negative or neutral for human health. Generally sleep and eating schedules are assumed without thought for their potential to help or interfere with health. In this study we propose a framework, based on data from more than 500 participants, for evaluating the relative timing of meals and sleep schedules. This evaluation, similar to pediatric growth charts, can guide clinical suggestions for those at the extremes, while helping others to realize that they are unusual relative to the population average

bioinformatics↗

bioRxiv2020

Relationships between the Bone Expression of Alzheimer Disease-Related Genes, Bone Remodelling Genes and Cortical Bone Structure in Neck of Femur Fracture

Neck of femur (NOF) fracture is a prevalent fracture type amongst the ageing and osteoporotic populations, commonly requiring total hip replacement (THR) surgery. Increased fracture risk has also been associated with Alzheimer disease (AD) in the aged. Here, we sought to identify possible relationships between the pathologies of osteoporosis and dementia by analysing bone expression of neurotropic or dementia-related genes in patients undergoing THR surgery for NOF fracture. Femoral bone samples from 66 NOF patients were examined for expression of the neurotropic genes amyloid precursor protein (APP), APP-like protein-2 (APLP2), Beta Secretase Cleaving Enzyme-1 (BACE1) and nerve growth factor (NGF). Relationships were examined between the expression of these and of bone regulatory genes, systemic factors and bone structural parameters ascertained from plain radiographs. We found strong relative levels of expression and positive correlations between APP, APLP2, BACE1 and NGF levels in NOF bone. Significant correlations were found between APP, APLP2, BACE1 mRNA levels and bone remodelling genes TRAP, RANKL, and the RANKL:OPG mRNA ratio, indicative of potential functional relationships at the time of fracture. Analysis of the whole cohort, as well as non-dementia and dementia sub-groups, revealed structural relationships between APP and APLP2 mRNA expression and lateral femoral cortical thickness. These findings suggest that osteoporosis and AD may share common molecular pathways of disease progression, perhaps explaining the common risk factors associated with these diseases. The observation of a potential pathologic role for AD-related genes in bone may also provide alternative treatment strategies for osteoporosis and fracture prevention.

physiology↗

bioRxiv2018

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control

MOTIVATIONParticle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al., 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would eliminate the need for manual transfer of data to diverse downstream analysis tools. At the same time, it would lay the foundation for shared trajectory data, particle tracking, and motion analysis standards. RESULTSHere, we present Open Microscopy Environment inteGrated Analysis (OMEGA), a cross-platform data management, analysis, and visualization system, for particle tracking data, with particular emphasis on results from viral and vesicular trafficking experiments. OMEGA provides intuitive graphical interfaces to implement integrated particle tracking and motion analysis workflows while providing easy to use facilities to automatically keep track of error propagation, harvest data provenance and ensure the persistence of analysis results and metadata. Specifically, OMEGA: 1) imports image data and metadata from data management tools such as the Open Microscopy Environment Remote Objects (OMERO; Allan et al., 2012); 2) tracks intracellular particles movement; 3) facilitates parameter optimization and trajectory results inspection and validation; 4) performs downstream trajectory analysis and motion type classification; 5) estimates the uncertainty propagating through the motion analysis pipeline; and, 6) facilitates storage and dissemination of analysis results, and analysis definition metadata, on the basis of our newly proposed FAIRsharing.org complainant Minimum Information About Particle Tracking Experiments (MIAPTE; Rigano and Strambio-De-Castillia, 2016; 2017) guidelines in combination with the OME-XML data model (Goldberg et al., 2005). In so doing, OMEGA maintains a persistent link between raw image data, intermediate analysis steps, the overall analysis output, and all necessary metadata to repeat the analysis process and reproduce its results. Availability and implementationOMEGA is a cross-platform, open-source software developed in Java. Source code and cross-platform binaries are freely available on GitHub at https://github.com/OmegaProject/Omega (doi: 10.5281/zenodo.2535523), under the GNU General Public License v.3. Contactcaterina.strambio@umassmed.edu and alex.rigano@umassmed.edu Supplementary informationSupplementary Material is available at BioRxiv.org

bioinformatics↗