Biology subjects

Clarke, E.

Publications and source records attributed to Clarke, E..

11 recordsLinked to original sources

bioRxiv2025

Effect of prescribing and deprescribing oxycodone on pain and function in a mouse model of osteoarthritis: impact of polypharmacy and sex on response

Osteoarthritis and polypharmacy are common in older adults. While not consistent with guidelines, opioid analgesia is commonly prescribed to older adults with osteoarthritis and other causes of chronic non-cancer pain. Long term use of opioids is associated with tolerance, addiction, loss of efficacy and adverse events. Thus, deprescribing (reducing or ceasing) opioids is often required. The effect of polypharmacy on the efficacy and safety of opioid prescribing and deprescribing in this setting is poorly understood. Here we aimed to assess the effects of chronic oxycodone, as monotherapy and in polypharmacy (oxycodone, citalopram, simvastatin, oxybutynin, and metoprolol), and of deprescribing oxycodone, on allodynia, physical and cognitive function, and daily activities in middle-aged, osteoarthritic male and female C57BL/6J mice (n=11-15/ group). Only oxycodone monotherapy reduced mechanical allodynia after 6 weeks of treatment. Chronic polypharmacy with oxycodone transiently increased mechanical allodynia in the injured limb and caused marked reductions in mobility, maximum walking speed, activities of daily living, and increased anxiety. Polypharmacy also altered daily activities detected by an automated animal behaviour recognition cage. Sex differences in treatment response were observed in frailty measurements and activity over 23 hours. Deprescribing oxycodone was well tolerated and did not alter physical or cognitive function but did reverse some of the daily activity changes and mechanical allodynia in polypharmacy treated animals only. This clinically relevant preclinical model provides an opportunity to understand the effects of prescribing and deprescribing opioids in older adults with osteoarthritis, including the impact of comedications and sex.

pharmacology and toxicology↗

bioRxiv2024

A New Approach to Monitoring Protein Transfer via Extracellular Vesicles

Extracellular vesicles (EVs) allow the exchange of protein, lipids and genetic material for communication between cells. We developed a method to track protein exchange between cells via EVs, using stable isotope labelling of amino acids in cell culture (SILAC). We compared EV isolation methods: ultracentrifugation and size exclusion chromatography (SEC) and undertook characterisation through nanoparticle tracking analysis (NTA), then optimised the requirement (0-10%) for foetal calf serum (FCS) and EV application concentration (6.5 million-200 EVs/cell seeded). We employed heavy amino acids L-Arg-HCl and L-Lys-2HCl to label donor cells and subsequent EV proteins. Unlabelled recipient cells were treated for 12 hours with EVs, at various concentrations. Mass spectrometry proteomics was used to assess uptake of heavy labelled EVs into recipient cells. A labelling efficiency of 62% was achieved. There was no relationship between the number of EVs applied to cells and the number of heavy proteins detected in the recipient cells. Pathway analysis indicated an inflammatory effect of applying EVs to cells, but the potential cause of this was unclear. We identified transferred protein cargo from EVs in recipient cells. Further optimisation of this method is still necessary.

molecular biology↗

bioRxiv2024

Searching for Jouvence SnoRNA in the Horse Genome

In humans, various pathologies have been associated with snoRNAs. Others have shown that the expression of a non-canonical snoRNA Jouvence is involved in lifespan determination in relation to gut homeostasis. As snoRNAs are evolutionary conserved, both structurally and functionally, a jouvence orthologue has been identified in humans. This study aimed to locate the Jouvence snoRNA in the horse genome. Using our previous snoRNA data in ageing equine cartilage along with equine genome data we identified a putative equine Jouvence snoRNA gene. ECABCGRLG0000000730 was the primary candidate horse Jouvence snoRNA. The expression of equine Jouvence snoRNA was increased in ageing equine cartilage.

molecular biology↗

bioRxiv2024

Allogenic platelet-rich plasma and platelet-rich plasma extracellular vesicles alter the proteome of tenocytes in an in vitro equine model of tendon inflammation: A pilot study

BackgroundTendon injuries are common in horses, often resulting in a high risk of reinjury. Hemoderivative therapeutics including platelet-rich plasma (PRP) show promise but outcomes vary due to inconsistent composition. PRP is rich in soluble growth factors and extracellular vesicles (EVs), the latter facilitate cell-to-cell communication by delivering biologically active cargo. This pilot study profiled the proteome of PRP and PRP-derived EVs and examined their effects on an equine tendon inflammatory model in vitro. MethodsPlasma was isolated via double centrifugation and PRP produced using a commercial filtration kit. EVs were isolated from PRP and plasma using differential ultracentrifugation and characterised with the Exoview Tetraspanin assay. Equine tenocytes were stimulated with interleukin 1{beta} and tumor necrosis factor , then treated with PRP or PRP-derived EVs. Proteomic analysis was conducted on cell lysates, PRP and PRP-EVs using data-dependent acquisition liquid chromatography-tandem mass spectrometry and the data analyzed using multivariate and univariate approaches. ResultsPRP contained 575 quantifiable proteins and PRP-derived EVs 209 proteins. When compared to plasma and plasma derived EVs respectively, PRP and PRP-EVs were enriched in proteins associated with cellular waste disposal and inhibition of lipid metabolism. Experimental factors (inflammatory stimulation and/or treatments) significantly affected the abundance of 18 proteins as expressed in equine tenocytes including col1a1 (col1a1) and sequestosome 1, associated with collagen metabolism and nuclear factor kappa B signaling. DiscussionThe findings from this study suggest PRP-derived EVs influence inflammatory tenocytes and may be crucial to the efficacy of PRP.

molecular biology↗

bioRxiv2023

Persistent immune imprinting after XBB.1.5 COVID vaccination in humans

Immune imprinting - also known as original antigenic sin - describes how the first exposure to a virus shapes the immunological outcome of subsequent exposures to antigenically related strains. SARS-CoV-2 Omicron breakthrough infections and bivalent COVID-19 vaccination were shown to primarily recall cross-reactive memory B cells and antibodies induced by prior mRNA vaccination with the Wuhan-Hu-1 spike rather than priming naive B cells that recognize Omicron-specific epitopes. These findings underscored a strong immune imprinting resulting from repeated Wuhan-Hu-1 spike exposures. To understand if immune imprinting can be overcome, we investigated memory and plasma antibody responses after administration of the updated XBB.1.5 COVID mRNA vaccine booster. Our data show that the XBB.1.5 booster elicits neutralizing antibody responses against current variants that are dominated by recall of pre-existing memory B cells previously induced by the Wuhan-Hu-1 spike. These results indicate that immune imprinting persists even after multiple exposures to Omicron spikes through vaccination and infection, including post XBB.1.5 spike booster mRNA vaccination, which will need to be considered to guide the design of future vaccine boosters.

immunology↗

bioRxiv2021

Expression of soluble methane monooxygenase in Escherichia coli enables methane conversion

Natural gas and biogas provide an opportunity to harness methane as an industrial feedstock. Bioconversion is a promising alternative to chemical catalysis, which requires extreme operating conditions and exhibits poor specificities. Though methanotrophs natively utilize methane, efforts have been focused on engineering platform organisms like Escherichia coli for synthetic methanotrophy. Here, a synthetic E. coli methanotroph was developed by engineering functional expression of the Methylococcus capsulatus soluble methane monooxygenase in vivo via expression of its cognate GroESL chaperone. Additional overexpression of E. coli GroESL further improved activity. Incorporation of an acetone formation pathway then enabled the conversion of methane to acetone in vivo, as validated via 13C tracing. This work provides the first reported demonstration of methane bioconversion to liquid chemicals in a synthetic methanotroph.

bioengineering↗

bioRxiv2020

TrkB agonist antibody delivery to the brain using a TfR1 specific BBB shuttle provides neuroprotection in a mouse model of Parkinson's Disease

Single domain shark antibodies that bind to the transferrin receptor 1 (TfR1) on brain endothelial cells can be used to shuttle antibodies and other cargos across the blood brain barrier (BBB). We have fused one of these (TXB4) to differing regions of TrkB and TrkC neurotrophin receptor agonist antibodies (AAb) and determined the effect on agonist activity, brain accumulation and engagement with neurons in the mouse brain following systemic administration. The TXB4-TrkB and TXB4-TrkC fusion proteins retain agonist activity at their respective neurotrophin receptors and in contrast to their parental AAb they rapidly accumulate in the brain reaching nM levels following a single IV injection. Following SC administration, the most active TrkB fusion protein, TXB4-TrkB1, associates with and activates ERK1/2 signalling in TrkB positive cells in the cortex and tyrosine hydroxylase (TH) positive dopaminergic neurons in the substantia nigra pars compacta (SNc). When tested in the 6-hydroxydopamine (6-OHDA) mouse model of Parkinsons disease (PD) TXB4-TrkB1, but not the parental TrkB AAb or a TXB4-TrkC1 fusion protein, completely prevented the 6-OHDA induced death of TH positive neurons in the SNc. In conclusion, the fusion of the TXB4 TfR1 binding module allows a TrkB AAb to reach neuroprotective concentrations in the brain parenchyma following systemic administration.

neuroscience↗

bioRxiv2019

Use of a pandemic H1N1 strain with updated haemagglutinin and neuraminidase results in increased nasopharyngeal shedding and improved immunogenicity to Russian-backbone live attenuated influenza vaccine among children aged 2 - 4 years old: an open label, prospective, observational, phase 4 study in The Gambia.

BackgroundPoor efficacy and effectiveness of the pandemic H1N1 (pH1N1) component in intranasal live attenuated influenza vaccine (LAIV) has been demonstrated in several studies. The reasons for this are unclear, but may be due to impaired replicative fitness of pH1N1 A/California/07/2009-like (Cal09) LAIV strains. MethodsIn an open-label, prospective, observational, phase 4 study, we evaluated the impact of updating the pH1N1 component in the Russian-backbone trivalent LAIV from Cal09 in 2016-17 (n=118) to an A/Michigan/45/2015-like strain (A/17/New York/15/5364, NY15) in 2017-18 (n=126), on shedding and immunogenicity in Gambian children aged 2-4 years old. The study was nested within a larger randomised controlled trial investigating LAIV-microbiome interactions (ClinicalTrials.gov NCT02972957). FindingsCal09 showed impaired nasopharyngeal shedding compared to H3N2 and influenza B, along with sub-optimal serum antibody and T-cell responses. Following the switch to NY15, a significant increase in pH1N1 shedding was seen, along with improvements in seroconversion and influenza-specific CD4+ T-cell responses. Viral kinetics in vitro mirrored these findings, with NY15 showing greater replicative ability than Cal09 in human nasal epithelial cells. Persistent shedding to day 7 was independently associated with both seroconversion and CD4+ T cell response in multivariable logistic regression. InterpretationOur results suggest that the pH1N1 component switch in LAIV may have overcome problems in prior formulations. LAIV effectiveness against pH1N1 should therefore improve in upcoming influenza seasons. Our data also highlight the importance of evaluating replicative fitness, in addition to antigenicity, when selecting annual LAIV components and design of potentially more effective vaccines. FundingThe Wellcome Trust.

clinical trials↗

bioRxiv2018

Cities of the future, visualizing climate change to inspire actions

Combating against climate change requires unified action across all sectors of society. However, this collective action is precluded by the consensus gap between scientific knowledge and public opinion. A growing body of evidence suggests that facts do not persuade people to act. Instead, it is visualization - the ability to simulate relatable scenarios - is the most effective approach for motivating behavior change. Here, we exemplify this approach, using current climate projections to enable people to visualize cities of the future, rather than describing intangible climate variables. Analyzing city pairs for 520 major cities of the world, we characterize which cities will most closely resemble the climate conditions of which other major cities by 2050. On average, most cities will resemble cities that are over 1000km south, and 22% of cities will experience climate conditions that are not currently experienced by any existing major cities. We predict that Londons climate in 2050 will resemble Barcelonas climate today, Madrid will resemble to Marrakesh, Moscow to Sofia, Seattle to San Francisco, Stockholm to Budapest, Tokyo to Changsha, etc. Our approach illustrates how complex climate data can be packaged to provide tangible information. By allowing people to visualize their own climate futures, we hope to empower citizens, policy makers and scientists to visualize expected climate impacts and adapt decision making accordingly.

scientific communication and education↗

bioRxiv2018

Genome wide association study of hippocampal subfield volume in PTSD cases and trauma-exposed controls

Behavioral, structural, and functional neuroimaging have implicated the hippocampus as a critical brain region in PTSD pathogenesis. We conducted a GWAS of hippocampal subfield volumes in a sample of recent military veteran trauma survivors (n=157), including some with PTSD (n=66). Covariates in our analysis included lifetime PTSD diagnosis, sex, intracranial volume, genomic estimates of ancestry, and childhood trauma. Interactions between genetic variants and lifetime PTSD or childhood trauma were interrogated for SNPs with significant main effects. Several genetic associations surpassed correction for multiple testing for several hippocampal subfields, including fimbria, subiculum, cornu ammonis-1(CA1), and hippocampal amygdala transition area (HATA). One association replicated in an independent cohort of civilians with PTSD (rs12880795 in TUNAR with L-HATA volume, p=3.43 x 10-7 in the discovery and p=0.0004 in the replication cohort). However, the most significant association in the discovery data set was between rs6906714 in LINC02571 and R-fimbria volume (p=5.99 x10-8, q=0.0056). Interestingly, the effect of rs6906714 on R-fimbria volume increased with childhood trauma (G*E interaction p=0.022). In addition to variants in long intergenic non-coding RNAs (lincRNAs), we identified SNPs associated with hippocampal subfield volume, which are also quantitative trait loci (QTLs) for genes involved in RNA editing of glutamate receptor subunits (GluRs), oxidative stress, and autoimmune disorders. Genomic regions, some with putative regulatory roles, influence the volume of hippocampal subfields. Neuroimaging phenotypes may offer important insight into the genetic architecture and neurobiological pathways relevant to PTSD, as well as in the identification of potential biomarkers and drug targets for PTSD.

neuroscience↗

bioRxiv2018

Sunbeam: a pipeline for next-generation metagenomic sequencing experiments

BackgroundAnalysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes. ResultsWe present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. Unique components of the Sunbeam pipeline include direct analysis of data from NCBI SRA and an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated. ConclusionsSunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic low complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.

bioinformatics↗