Biology subjects

Wilkinson, T.

Publications and source records attributed to Wilkinson, T..

14 recordsLinked to original sources

bioRxiv2026

ASO-mediated mRNA silencing enables functional analysis and selective depletion of the human microbiota Prevotellaceae

The Prevotellaceae family comprises abundant, taxonomically diverse bacteria of the human microbiota that exhibit remarkable intraspecies variability and distinct phenotypes during host-microbe interactions. Yet functional investigations are hampered by the limited genetic tractability of this medically important bacterial family, rendering it understudied. Here, we apply antisense oligomer (ASO) technology to selectively inhibit translation of single or multiple mRNAs across nine Prevotellaceae species. Using ftsZ- and mreB-related phenotypes as morphogenic readouts, we demonstrate that ASOs can function as a tunable system to study essential gene function. Further, we show that ASOs can selectively deplete target species from a synthetic Bacteroidales community. These results establish ASOs as practical tools for functional genomics and community modulation in otherwise genetically intractable anaerobic microbiota members.

microbiology↗

bioRxiv2025

Anabolic and catabolic responses to different modes of exercise in patients with chronic kidney disease

BackgroundMuscle wasting is a common complication in individuals with chronic kidney disease (CKD) and contributes to reduced physical function and poor clinical outcomes. While exercise is recommended for CKD patients, the molecular responses to different exercise modalities remain poorly understood. This study aimed to investigate the anabolic, catabolic, and myogenic responses of skeletal muscle to aerobic exercise (AE) and combined exercise (CE; aerobic plus resistance) in people with CKD. MethodsMuscle biopsies were collected from participants in a 12-week randomized controlled trial of supervised exercise training, the ExTRA CKD trial. Samples were obtained at baseline, 24 hours after an initial bout of exercise (untrained), and 24 hours after the final training session (trained). Western blotting and RT-qPCR were used to assess changes in key markers of protein synthesis, degradation, and regeneration. To complement these data, in vitro experiments using mechanically stretched primary skeletal muscle cells from CKD and healthy control donors were used to explore the time course of anabolic signalling. ResultsIn vivo, Akt phosphorylation was blunted following unaccustomed CE but significantly upregulated following training, indicating partial restoration of anabolic signalling. No change was observed in response to AE. Myostatin expression was significantly downregulated following both AE and CE in the untrained state, while Pax7 and myogenic gene expression were upregulated only in response to CE after training. In vitro, mechanical stretch induced significant phosphorylation of Akt and p70S6K in both CKD and control cells, with no group difference in Akt response and a trend toward faster return to baseline of p70S6K phosphorylation in CKD cells. ConclusionThese findings demonstrate that CE, but not AE, induces beneficial anabolic and myogenic responses in skeletal muscle in CKD, and highlight the value of combining in vivo and in vitro models to explore temporal dynamics and mechanistic insight into muscle adaptation. What was knownO_LIPeople with CKD often have impaired skeletal muscle responses to exercise, termed anabolic resistance, which may contribute to muscle wasting and poor outcomes. C_LIO_LIResistance exercise activates anabolic and myogenic pathways in healthy muscle, but the extent of these responses in CKD is unclear. C_LIO_LILimited studies have compared molecular responses to different exercise modalities in CKD, particularly combining in vivo and in vitro approaches. C_LI This study addsO_LICombined aerobic-resistance exercise, but not aerobic exercise alone, restored aspects of anabolic signalling (Akt phosphorylation) in CKD skeletal muscle after training. C_LIO_LIMyogenic gene expression was upregulated following combined exercise but not aerobic exercise, indicating a modality-specific regenerative response. C_LIO_LIIn vitro, primary muscle cells from CKD and healthy donors showed similar early anabolic responses to mechanical stretch, though CKD cells may return to baseline more rapidly. C_LI Potential ImpactO_LISupports inclusion of resistance-based modalities in exercise prescriptions for people with CKD to enhance muscle anabolic and regenerative responses. C_LIO_LISuggests that exercise prescriptions for CKD should prioritise combined modalities to maximise muscle anabolic and regenerative potential. C_LIO_LIProvides mechanistic evidence to inform tailored exercise interventions aimed at preserving muscle health in CKD patients. C_LI

molecular biology↗

bioRxiv2025

The response of the skeletal muscle transcriptome to exercise in chronic kidney disease

BackgroundChronic kidney disease (CKD) affects approximately 14% of the UK population and is associated with significant exercise intolerance, partly due to skeletal muscle dysfunction. While exercise is a potential therapeutic strategy, the molecular response of skeletal muscle to exercise in CKD remains poorly understood. This study aimed to characterise transcriptomic changes in skeletal muscle 24 hours after aerobic (AE) or combined aerobic and resistance exercise (CE) in non-dialysis CKD. MethodsThis study utilised muscle biopsies from participants in the ExTRA CKD trial with stage 3b-4 CKDages 3b-4 (AE: 24 (15-32) ml/min/1.73m2; CE: 25 (19-31) ml/min/1.73m2). Participants (n=4 per group) were randomised to 12 weeks of thrice-weekly AE or CE. Vastus lateralis skeletal muscle biopsies were collected at baseline and 24h after the first bout of exercise. RNA was extracted for Bulk RNA sequencing. Bulk RNA sequencing was performed, and differentially expressed genes (DEGs) were identified between baseline and post-exercise samples, followed by pathway enrichment analysis. ResultsFollowing AE, 1480 genes were upregulated and 1554 downregulated. CE resulted in 556 upregulated and 115 downregulated genes. The most upregulated gene after AE was CHI3L1 (log2FC 10.7), followed by SAA2 and PTX3, all associated with inflammation. After CE, SFN (log2FC 6.8) and MT1A were among the most highly upregulated. Enrichment analysis showed strong activation of inflammatory and cellular senescence pathways, and downregulation of mitochondrial function-related processes, particularly after AE. ConclusionBoth AE and CE triggered robust inflammatory gene expression responses in CKD skeletal muscle, indicative of early repair processes. Unexpectedly, mitochondrial-related pathways were downregulated, aligning with previous findings of impaired mitochondrial adaptation in CKD. These results highlight mitochondrial dysfunction as a potential barrier to effective exercise adaptation and a possible therapeutic target in this population.

physiology↗

bioRxiv2024

Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations

Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations. We describe a method for robust treatment of alternate protonation states for titratable amino acids, which yields improved correlation with and reduced error compared to experimental binding free energies. Following careful analysis of the largest outlier cases in our dataset, we assess limitations of the default FEP+ protocols and introduce an automated script which identifies probable outlier cases that may require additional scrutiny and calculates an empirical correction for a subset of charge-related outliers. Through a series of three additional case study systems, we discuss how protein FEP+ can be applied to real-world protein design projects, and suggest areas of further study. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/590325v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1c5e607org.highwire.dtl.DTLVardef@1810ee5org.highwire.dtl.DTLVardef@1f8f1acorg.highwire.dtl.DTLVardef@c28053_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIReliable calculation of relative binding free energy changes for most protein mutations to within [~]1 kcal/mol. C_LIO_LIAutomated Protein FEP+ Groups treatment of alternate protonation states for titratable residues. C_LIO_LIApplication of FEP+ methodology to "real-world" protein design projects. C_LI

biophysics↗

bioRxiv2023

The evolution and convergence of mutation spectra across mammals

Despite the key role genetic mutations play in shaping phenotypic differences between species, little is currently known about the evolution of germline mutation spectra across mammals. Domesticated species are likely particularly interesting case studies because of their high mutation rates and complex evolutionary histories, which can span multiple founding events and genetic bottlenecks. Here we have developed a new reusable workflow, nSPECTRa, that can undertake the key steps in characterising mutation spectra, from determining ancestral alleles to characterising multiple forms of variation. We apply nSPECTRa to seven species, including several that have undergone domestication, and highlight how nSPECTRa can provide important novel insights into mutation rate evolution. While mutation spectra most often show marked differences between species and even breeds, certain mutation types have risen to a high frequency in subpopulations of different species, indicative of convergent evolution in mutation rates. This includes the previously characterized TCC->TTC change enriched among European humans, which is also enriched among East Asian cattle. We show Indicine cattle are particularly interesting examples of how different mutation spectra segregate within a population and subsequently spread across the globe. Together, this work has important implications for understanding the control and evolution of mammalian mutation rates.

genetics↗

bioRxiv2023

Continent-wide genomic analysis of the African buffalo (Syncerus caffer).

The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided surprisingly little support for the currently described four subspecies, but indicated three main lineages, in Western/Central, Eastern and Southern Africa, respectively. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

genomics↗

bioRxiv2021

Beehives possess their own distinct microbiomes

Honey bees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a tremendous amount of microbes, including bacteria that derive from plants and different parts of the honey bees body. In this study, we conducted 16S rDNA metataxonomic analysis on honey and beebread samples that were collected from 15 beehives in the southeast of England in order to quantify the bacteria associated with beehives. The results highlighted that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and pathogens of plants and animals. Remarkably, this bacterial diversity differs amongst the beehives, suggesting a defined fingerprint that is affected, not only by the nectar and pollen gathered from local plants, but also from other environmental sources. In summary, our results show that every hive possesses their own distinct microbiome, and that honeybee products are valuable indicators of the bacteria present in the beehives and their surrounding environment.

microbiology↗

bioRxiv2021

Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands

CD8+ and CD4+ T cells provide cell-mediated cross-protection against multiple influenza strains by recognising epitopes bound as peptides to human leukocyte antigen (HLA) class I and -II molecules respectively. Two challenges in identifying the immunodominant epitopes needed to generate a universal T cell influenza vaccine are: A lack of cell models susceptible to influenza infection which present population-prevalent HLA allotypes, and an absence of a reliable in-vitro method of identifying class II HLA peptides. Here we present a mass spectrometry-based proteomics strategy for identifying viral peptides derived from the A/H3N2/X31 and A/H3N2/Wisconsin/67/2005 strains of influenza. We compared the HLA-I and -II immunopeptidomes presented by ex-vivo influenza challenged human lung tissues. We then compared these with directly infected immortalised macrophage-like cell line (THP1) and primary dendritic cells fed apoptotic influenza-infected respiratory epithelial cells. In each of the three experimental conditions we identified novel influenza class I and II HLA peptides with motifs specific for the host allotype. Ex-vivo infected lung tissues yielded few class-II HLA peptides despite significant numbers of alveolar macrophages, including directly infected ones, present within the tissues. THP1 cells presented HLA-I viral peptides derived predominantly from internal proteins. Primary dendritic cells presented predominantly viral envelope-derived HLA class II peptides following phagocytosis of apoptotic infected cells. The most frequent viral source protein for HLA-I and -II was matrix 1 protein (M1). This work confirms that internal influenza proteins, particularly M1, are a rich source of CD4+ and CD8+ T cell epitopes. Moreover, we demonstrate the utility of two ex-vivo fully human infection models which enable direct HLA-I and -II immunopeptide identification without significant viral tropism limitations. Application of this epitope discovery strategy in a clinical setting will provide more certainty in rational vaccine design against influenza and other emergent viruses. Author SummaryInfluenza infections present a significant global health challenge. High rates of mutation require reformulation of vaccines annually. Vaccines are designed to induce antibody responses to the surface proteins of the influenza virus, but the contribution of T cells to overall immunity is unclear. Here, we used several totally human laboratory models to show how the viral proteins are presented to the T cells to induce immunity. We found that CD8 T cells, which kill infected cells, and CD4 T cells which support the CD8 T cells as well as the antibody-producing B cells, mainly see proteins from inside the viral particle, not the surface ones which are targeted by antibodies. These internal viral proteins are more similar between different viral strains than the surface proteins, and therefore suggest that vaccines designed to induce T cell responses could be better protective if they target internal viral proteins.

immunology↗

bioRxiv2020

Association between vitamin D deficiency and exercise capacity in patients with CKD, a cross-sectional analysis

Evidence is growing for a role of vitamin D in regulating skeletal muscle mass, strength and functional capacity. Given the role the kidneys play in activating total vitamin D, and the high prevalence of vitamin D deficiency in Chronic Kidney Disease (CKD), it is possible that deficiency contributes to the low levels of physical function and muscle mass in these patients. This is a secondary cross-sectional analysis of previously published interventional study, with ex vivo follow up work. 34 CKD patients at stages G3b-5 (eGFR 25.5 {+/-} 8.3ml/min/1.73m2; age 61 {+/-} 12 years) were recruited, with a sub-group (n=20) also donating a muscle biopsy. Vitamin D and associated metabolites were analysed in plasma by liquid chromatography tandem-mass spectroscopy and correlated to a range of physiological tests of muscle size, function, exercise capacity and body composition. The effects of 1,25(OH)2D3 supplementation on myogenesis and myotube size was investigated in primary skeletal muscle cells from vitamin D deficient donors. In vivo, there was no association between total or active vitamin D and muscle size or strength, but a significant correlation with [Formula] was seen with the total form. Ex vivo, 1,25(OH)2D3 supplementation reduced IL-6 mRNA expression, but had no effect upon proliferation, differentiation or myotube diameter. This early preliminary work suggests that vitamin D deficiency is not a prominent factor driving the loss of muscle mass in CKD, but may play a role in reduced exercise capacity.

cell biology↗

bioRxiv2019

In silico identification of novel peptides with antibacterial activity against multidrug resistant Staphylococcus aureus

Herein we report the identification and characterisation of two linear antimicrobial peptides (AMPs), HG2 and HG4, with activity against a wide range of multidrug resistant (MDR) bacteria, especially methicillin resistant Staphylococcus aureus (MRSA) strains, a highly problematic group of Gram-positive bacteria in the hospital and community environment. To identify the novel AMPs presented here, we employed the classifier model design, a feature extraction method using molecular descriptors for amino acids for the analysis, visualization, and interpretation of AMP activities from a rumen metagenomic dataset. This allowed for the in silico discrimination of active and inactive peptides in order to define a small number of promising novel lead AMP test candidates for chemical synthesis and experimental evaluation. In vitro data suggest that the chosen AMPs are fast acting, show strong biofilm inhibition and dispersal activity and are efficacious in an in vivo model of MRSA USA300 infection, whilst showing little toxicity to human erythrocytes and human primary cell lines ex vivo. Observations from biophysical AMP-lipid-interactions and electron microscopy suggest that the newly identified peptides interact with the cell membrane and may be involved in the inhibition of other cellular processes. Amphiphilic conformations associated with membrane disruption are also observed in 3D molecular modelling of the peptides. HG2 and HG4 both preferentially bind to MRSA total lipids rather than with human cell lipids indicating that HG4 may form superior templates for safer therapeutic candidates for MDR bacterial infections.\n\nAuthor SummaryWe are losing our ability to treat multidrug resistant (MDR) bacteria, otherwise known as superbugs. This poses a serious global threat to human health as bacteria are increasingly acquiring resistance to antibiotics. There is therefore urgent need to intensify our efforts to develop new safer alternative drug candidates. We emphasise the usefulness of complementing wet-lab and in silico techniques for the rapid identification of new drug candidates from environmental samples, especially antimicrobial peptides (AMPs). HG2 and HG4, the AMPs identified in our study show promise as effective therapies for the treatment of methicillin resistant Staphylococcus aureus infections both in vitro and in vivo whilst having little cytotoxicity against human primary cells, a step forward in the fight against MDR infections.

microbiology↗

bioRxiv2019

Islands in the desert: Environmental distribution modelling of endemic flora reveals the extent of Pleistocene tropical relict vegetation in southern Arabia

Background and AimsSouthern Arabia is a global biodiversity hotspot with a high proportion of endemic desert-adapted plants. Here we examine evidence for a Pleistocene climate refugium in the southern Central Desert of Oman, and its role in driving biogeographical patterns of endemism. MethodsDistribution data for seven narrow-range endemic plants were collected systematically across 195 quadrats, together with incidental and historic records. Important environmental variables relevant to arid coastal areas, including night time fog and cloud cover were developed for the study area. Environmental niche models were built and tuned for each species and spatial overlap examined. Key ResultsA region of the Jiddat Al Arkad reported independent high model suitability for all species. Examination of environmental data across southern Oman indicates that the Jiddat Al Arkad displays a regionally unique climate with higher intra-annual stability, due in part to the influence of the southern monsoon. Despite this, relative importance of environmental variables was highly differentiated among species, suggesting characteristic variables such as coastal fog are not major cross-species predictors at this scale. ConclusionsThe co-occurrence of a high number of endemic study species within a narrow monsoon-influenced region is indicative of a refugium with low climate change velocity. Combined with climate analysis, our findings provide strong evidence for a southern Arabian Pleistocene refugium in the Omans Central Desert. We suggest this refugium has acted as an isolated temperate and mesic island in the desert, resulting in the evolution of these narrow-range endemic flora. Based on the composition of species, this system may represent the northernmost remnant of a continuous belt of mesic vegetation formerly ranging from Africa to Asia, with close links to the flora of East Africa. This has significant implications for future conservation of endemic plants in an arid biodiversity hotspot.

ecology↗

bioRxiv2018

Adherence to the iDSI reference case among published cost-per-DALY averted studies

BackgroundThe iDSI reference case, originally published in 2014, aims to improve the quality and comparability of cost-effectiveness analyses (CEAs). This study assesses whether the development of the guideline has improved the reporting and methodology for CEAs using disability-adjusted life-years (DALYs).\n\nMethodsWe analyzed the Tufts Medical Center Global Health CEA Registry to identify cost-per-DALY averted studies published from 2011 to 2017. Among each of 11 principles in the iDSI reference case, we translated all reporting standards and methodological specifications into quantifiable yes/no questions and awarded articles one point for each item satisfied. We then separately calculated reporting and methods scores, measured as percent adherence (0%=no adherence, 100%=full adherence). Using the year 2014 as the dissemination period, we conducted a pre-post analysis. Additionally, we conducted an analysis stratified by the 11 principles and examined different scoring strategies and dissemination periods in sensitivity analyses.\n\nResultsArticles averaged 74% adherence to reporting standards and 60% adherence to methodological specifications. Adherence to reporting standards increased slightly over time (72% pre-2014 vs. 75% post-2014, p<0.01), but methodological adherence did not significantly improve (59% pre-2014 vs. 60% post-2014, p=0.53). Overall, reporting adherence scores exceeded methodology adherence scores (74% vs. 60%, p<0.001). Articles seldom addressed budget impact (9% reporting, 10% methodology) or equity (7% reporting, 7% methodology).\n\nConclusionsThe iDSI reference case has substantial potential to serve as a useful resource for researchers and policy-makers in global health settings, but greater effort to promote adherence and awareness is needed to achieve its potential.

scientific communication and education↗

bioRxiv2018

Identifying Parkinson’s disease and parkinsonism cases using routinely-collected healthcare data: a systematic review

BackgroundPopulation-based, prospective studies can provide important insights into Parkinsons disease (PD) and other parkinsonian disorders. Participant follow-up in such studies is often achieved through linkage to routinely-collected healthcare datasets. We systematically reviewed the published literature on the accuracy of these datasets for this purpose.\n\nMethodsWe searched four electronic databases for published studies that compared PD and parkinsonism cases identified using routinely-collected data to a reference standard. We extracted study characteristics and two accuracy measures: positive predictive value (PPV) and/or sensitivity.\n\nResultsWe identified 18 articles, resulting in 27 measures of PPV and 14 of sensitivity. For PD, PPVs ranged from 56-90% in hospital datasets, 53-87% in prescription datasets, 81-90% in primary care datasets and was 67% in mortality datasets. Combining diagnostic and medication codes increased PPV. For parkinsonism, PPVs ranged from 36-88% in hospital datasets, 40-74% in prescription datasets, and was 94% in mortality datasets. Sensitivities ranged from 15-73% in single datasets for PD and 43-63% in single datasets for parkinsonism.\n\nConclusionsIn many settings, routinely-collected datasets generate good PPVs and reasonable sensitivities for identifying PD and parkinsonism cases. Further research is warranted to investigate primary care and medication datasets, and to develop algorithms that balance a high PPV with acceptable sensitivity.

epidemiology↗

bioRxiv2017

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, 2 and 3) were effective against numerous bacterial pathogens, including methicillin resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.

microbiology↗