Biology subjects

Kelly, P.

Publications and source records attributed to Kelly, P..

18 recordsLinked to original sources

bioRxiv2026

Widespread detection of Polyethylene glycol reveals chronic human exposure through pharmaceutical drugs

Polyethylene glycol (PEG) is a synthetic polymer ubiquitous in pharmaceuticals, personal care products, food additives, and industrial manufacturing. Despite its widespread use and potential importance as an exposure chemical, the prevalence of PEG exposure and its excretion in human populations remain largely uncharacterized. Moreover, PEG detected in human biofluids is frequently assumed to arise from analytical contamination during sample preparation, potentially obscuring its contribution to the human exposome and confounding metabolic phenotyping studies. Here, we show that PEG is as component of the human xenobiotic exposome and is further metabolized into PEG hydoxy acid and diacid metabolites in humans. We further find that PEG exposure is associated with alterations in microbiome composition and short-chain fatty acid metabolism, suggesting its biological impact of its exposure. We identify PEG exposure in approximately 2.3% of publicly available metabolomics data files and provide a reusable 85,484 candidate PEG and PEGylated MS/MS spectral library for future use for the metabolomic community. Together, these findings establish PEG signal in human biofluids can reflect genuine exposure, and that PEG exposure is neither metabolically inert nor biologically silent.

biochemistry↗

bioRxiv2026

Minimal Data, Maximal Insight (MDMI): A Structure-guided Pipeline for Discovering Functional Alternatives in Peptide-Protein Interfaces

Discovering functional peptides across vast sequence space remains a formidable challenge, particularly when experimental training data is scarce. We present Minimal Data Maximal Insight (MDMI), a two-stage structure-guided computational pipeline that designs functional peptide variants using only a small, annotated dataset. Rather than relying on sequence information alone, MDMI integrates three-dimensional structural features derived from predicted peptide-protein complexes into a machine learning model that captures interface geometry and binding energetics. This structure-aware predictor, paired with a genetic algorithm for sequence exploration, reduced false positives from 70% to close to zero in an all-negative benchmark panel compared with a sequence-only model in computational benchmarking, and produced approximately four-fold more high-confidence in silico binders than state-of-the-art peptide/protein design baselines. Using the split-GFP system as a testbed, where fluorescence provides a direct functional readout of peptide-protein complementation, MDMI identified peptides with up to 38% sequence divergence from wild-type in Stage 1 while retaining measurable activity. In Stage 2, motif-guided recombination of successful Stage 1 variants produced highly divergent yet functional peptides bearing over 50% sequence difference from wild-type, revealing two distinct functional clusters in sequence space. As further validation, a top-performing candidate expressed as a full-length GFP fusion retained a GFP-like emission profile, supporting formation of a fluorescent GFP-like scaffold. These results demonstrate that structure-informed pipelines can uncover remote functional sequence space from minimal data, with broad implications for peptide and therapeutic analog discovery.

synthetic biology↗

bioRxiv2026

Functional Profiling of Thousands of Sequence-Diverse Protease Homologs with GROQ-seq

High-quality datasets that span broad sequence diversity are essential for understanding protein sequence-function relationships beyond local mutational landscapes. Here, we applied Growth-based Quantitative Sequencing (GROQ-seq) to measure function across an 11,722 member protease library, comprised of natural homologs and AI-shrunken variants. This library spans vast sequence diversity, with Levenshtein distances of up to 245 and a mean pairwise sequence identity of 41% to TEV protease S219V. We identified sequence-divergent TEV protease homologs that preserve function against the native TEV protease substrate. These findings reveal the robustness of protease activity across highly diverse sequences. Here, we demonstrate the aptitude of the GROQ-seq assay for screening large, diverse protein libraries for function, enabling efficient data generation at scale for training machine learning models across broad sequence landscapes.

synthetic biology↗

bioRxiv2026

Pan-repository analysis reveals a drug-activating function of microbial bile acid conjugation

Microbially modified bile acids shape host physiology by regulating nutrient absorption, glucose homeostasis, circadian rhythms and thermoregulation. Here we identify a previously unrecognized drug-activating function of microbial bile acid conjugation. By systematically mining human LC-MS/MS datasets across public repositories and linking uncharacterized bile acid spectra to health-associated metadata, we discovered conjugates of the >75-year-old anti-inflammatory drug 5-aminosalicylic acid (5-ASA) with primary and secondary bile acids, including cholic, deoxycholic and lithocholic acids. These bile acid-drug conjugates were detected specifically in individuals treated with 5-ASA or its prodrugs. Multiple gut bacteria, including members of the Bacteroidota and Bacillota, generated cholyl-5-ASA in vitro, and bile salt hydrolase-associated transaminase activity was required for conjugate formation. In a mouse model of colitis, cholyl-5-ASA was associated with reduced intestinal inflammatory pathology and showed markedly enhanced activation of PPAR-{gamma} in cell-based reporter assays compared with 5-ASA alone. Consistent with this activity, cholyl-5-ASA elicited selective immunophenotypic changes in CD4 T cells in vitro, including increased Foxp3+ regulatory T cells. Together with prior evidence that 5-ASA efficacy depends on the microbiome, these findings support a model in which microbial bile acid conjugation represents a key activation step for 5-ASA therapy. More broadly, this work demonstrates how pan-repository metabolomics can uncover previously unrecognized microbiome-dependent chemical functions with direct therapeutic relevance.

biochemistry↗

bioRxiv2026

Body size, wing area, and wing loading follow a pattern of trait conservatism in Drosophila

Wing loading is a metric of flight performance that captures the relationship between body mass and wing area and reflects how much weight each unit of wing surface supports during flight. Comparative studies have documented substantial differences in wing loading among individuals and across species. However, no study has evaluated the extent of this variation when species are reared under identical, controlled conditions. Here, we address that gap by measuring wing loading in 30 species of drosophilids raised in a common lab environment. We applied comparative phylogenetic methods to assess the extent to which the evolution of body mass, wing area, and wing loading is structured by shared ancestry. We find that wing area and body mass exhibit moderate phylogenetic signal, but wing loading does not. In addition, all three traits are best explained by a model of evolution in which most trait divergence occurs during speciation events. More conservative analyses provide no support for adaptive peaks in wing loading within drosophilids. Together, our results indicate that the evolutionary dynamics of wing loading in Drosophila differ from those described in birds and bats, and raise the question of whether similar patterns characterize other insect lineages.

evolutionary biology↗

bioRxiv2025

A META-ANALYSIS OF GUT MICROBIOME RESEARCH IN MALNOURISHED AFRICAN POPULATIONS: A NATURAL LANGUAGE PROCESSING APPROACH

BackgroundMalnutrition still affects millions of children in Africa. Changes in the gut microbiome have been implicated in malnutrition, but there has been inconsistent nomenclature of microbes. This meta-analysis reviews the microbiome literature using natural language processing (NLP) methods. MethodologyWe searched PubMed for gut microbiome studies of undernourished children living in low-middle-income countries (LMICs). The primary analysis focused on continental coverage and study characteristics of microbiome research in sub-Saharan Africa. We also employed an NLP tool for normalising primary data from full-text publications in ss-Africa compared to other LMICs, and between diseased and healthy children. ResultsWe identified 16 studies. Most studies were conducted in Malawi and characterised the faecal microbiome using 16S rRNA sequencing. For comparison, 18 studies conducted in Bangladesh, India, Pakistan and Peru were included. With this, we identified frequently reported microbes that were distinctly identified in sub-Saharan Africa and highlighted possible signatures of an undernourished faecal microbiome across the globe. ConclusionThe consistent associations between elevated Pseudomonadota levels and severe acute malnutrition provides new insights into host-microbiome interactions in African contexts. However, the overlap between taxa associated with healthy and stunting underscores the need for further research to better inform potential targeted interventions in Africa.

genomics↗

bioRxiv2025

The effect of vitamin D and calcium supplementation on gut microbiota composition in adolescents living with HIV in Southern Africa

Adolescents living with HIV are at risk of delayed growth and of increased susceptibility to infections, potentially linked to vitamin D insufficiency, which is common in people living with HIV. We analyzed rectal swab microbiota compositions before and after 48 weeks supplementation with high-dose vitamin D and calcium, or placebo, embedded in a randomized controlled trial conducted in Zambia and Zimbabwe (Pan African Clinical Trials Registry PACTR20200989766029). In a sub-cohort of 244 participants, we first assessed baseline associations of the rectal swab microbiota with vitamin D metabolites, parathyroid hormone (PTH), and bone mineral density (BMD). We then analyzed longitudinal changes in rectal swab microbiota and intestinal barrier integrity during supplementation and examined whether the baseline microbiota influenced the treatment response. At baseline, anaerobic taxa within the class Clostridia were positively associated with PTH, 1,25(OH)2D, and BMD, and negatively associated with 24,25(OH)2D. After supplementation, Shannon diversity was decreased ({beta}Std=-0.495, CI [-0.802, -0.188], p=0.0018), median Bray-Curtis dissimilarity from baseline samples was increased ({beta}Std=0.399, CI [0.086, 0.712], p=0.013), and abundance of Clostridia_vadinBB60_group was decreased (log2fc=-1.715, CI [-2.596, -0.835], q=0.043) in the intervention arm. The intervention did not affect the intestinal barrier integrity, measured by intestinal fatty acid binding protein (iFABP) concentration in blood plasma. On average, PTH concentrations decreased and BMD increased during supplementation. However, higher baseline abundance of Clostridia-member UCG-009 predicted a smaller reduction in PTH concentrations during supplementation (log2fcstd=1.200 CI [0.656, 1.744], q=0.012), while higher baseline abundances of Enterococcus (log2fcstd=-1.220 CI [-1.807, -0.632], q=0.022) and Fournierella (log2fcstd=-1.122 CI [-1.694, -0.551], q=0.025) predicted a smaller increase in BMD. In conclusion, there was a reduction of an anaerobic taxon of the class Clostridia following vitamin D supplementation. Further, the microbiota appeared to moderate the effect of the intervention on PTH and bone density.

microbiology↗

bioRxiv2025

Telomeric assemblies of Paracoccidioides genomes

Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the brasiliensis complex (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis) and P. lutzii. These include the first complete telomere-to-telomere assemblies for P. brasiliensis (Pb18) and P. americana (Pb03), each with five chromosomes. Comparative analyses revealed chromosomal fusion and fission events distinguishing P. brasiliensis and P. americana, and a 90 kb tandem duplication in P. americana containing siderophore biosynthesis genes (sid1, sid3, sid4), a cluster of putative virulence factors. Mitochondrial genomes showed conserved gene order but a phylogenetic topology inconsistent with the nuclear tree, suggesting mitochondrial introgression between P. lutzii and P. venezuelensis. RNA transposable elements were enriched near telomeres, correlated with genome size, and most abundant in P. lutzii. These assemblies provide key resources for understanding genome evolution and introgression in Paracoccidioides. SIGNIFICANCESpecies of Paracoccidioides cause paracoccidioidomycosis, a systemic mycosis that remains a major public health problem in Latin America. Despite their clinical importance, genome evolution across the genus is poorly understood owing to the lack of complete reference assemblies. Here, we present the first telomere-to-telomere reference genomes for P. brasiliensis and P. americana, enabling a comprehensive comparison of chromosomal structure across the genus. Our analyses reveal that the nuclear genome is highly dynamic and shaped by large-scale rearrangements and structural variants, including the duplication of a siderophore biosynthesis-related gene cluster linked to virulence. In contrast, the mitochondrial genome is structurally conserved but shows introgression between species, revealing hidden evolutionary exchange. Together, these genomic resources redefine our understanding of Paracoccidioides evolution and provide a foundation for advances in molecular diagnostics, epidemiological surveillance, and studies of fungal pathogenicity.

microbiology↗

bioRxiv2025

Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers

Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers frequently acquire AMR organisms, and thus may provide a window into AMR dynamics in otherwise poorly monitored regions and environments. To assess the utility of travelers as global AMR sentinels, we collected pre- and post-travel stool samples from 608 travelers, which were screened for the presence of extended-spectrum beta-lactamase producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales. A total of 307 distinct AMR organisms were sequenced in order to determine genotypic patterns and their association with travel region and behavior. Travel-associated AMR organisms were overwhelmingly E. coli, which exhibited considerable phylogenetic diversity regardless of travel region. However, the prevalence of resistance genes varied by region, with blaCTX-M-55 and blaCTX-M-27 significantly more common in travelers returning from South America and South-Eastern Asia, respectively. Hybrid assembly and plasmid reconstruction revealed the genomic neighborhood of blaCTX-M-55 frequently matched a motif previously linked to animal populations. Contact with animals was also associated with virulence factors in acquired AMR organisms, including carriage of the ColV plasmid, a driver of avian pathogenic E. coli. We identified novel variants of the mcr-1 gene in strains acquired from Western Africa, highlighting the potential for traveler surveillance to detect emerging clinical threats. Ongoing efforts to track travel-acquired organisms could complement existing global AMR surveillance frameworks. ImportanceWe collected pre- and post-travel stool samples from 608 U.S. international travelers, which were screened for the presence of three clinically relevant antimicrobial-resistant organisms, with the goal of understanding the utility of travelers as sentinels for emerging AMR and identifying regional resistance patterns. We sequenced 307 organisms and uncovered significant diversity and geographic heterogeneity in AMR organisms. We found significant differences in certain resistance gene alleles of travelers returning from South America and South-Eastern Asia, traveler contact with animals associated with virulence factors, including a plasmid that is a known driver of avian pathogenic E. coli, and novel variants of the colistin resistance mcr-1 gene in strains acquired from Western Africa. This work emphasizes the value of monitoring international travelers as a proxy for understanding AMR patterns globally and could be an important addition to existing global AMR surveillance frameworks.

genomics↗

bioRxiv2023

Unveiling the Role of Endoplasmic Reticulum Stress Pathways in Canine Demodicosis

Canine demodicosis is a prevalent skin disease caused by overpopulation of a commensal species of Demodex mite, yet its precise cause remains unknown. Research suggests that T cell exhaustion, increased immunosuppressive cytokines, induction of regulatory T cells, and increased expression of immune checkpoint inhibitors may contribute to its pathogenesis. This study aimed to gain a deeper understanding of the molecular changes occurring in canine demodicosis using mass spectrometry and pathway enrichment analysis. The results indicate that endoplasmic reticulum stress is promoting canine demodicosis through regulation of three linked signalling pathways: eIF2, mTOR, and eIF4 and p70S6K. These pathways are involved in the modulation of Toll-like receptors, most notably TLR2, and have been shown to play a role in the pathogenesis of skin diseases in both dogs and humans. Moreover, these pathways are also implicated in the promotion of immunosuppressive M2 phenotype macrophages. Immunohistochemical analysis, utilizing common markers of dendritic cells and macrophages, verified the presence of M2 macrophages in canine demodicosis. The proteomic analysis also identified immunological disease, organismal injury and abnormalities, and inflammatory response as the most significant underlying diseases and disorders associated with canine demodicosis. This study demonstrates that Demodex mites, through ER stress, unfolded protein response and M2 macrophages contribute to an immunosuppressive microenvironment thereby assisting in their proliferation.

immunology↗

bioRxiv2022

Found in translation: Microproteins are a new class of potential host cell impurity in mAb drug products

Chinese hamster ovary (CHO) cells are used to produce almost 90% of therapeutic monoclonal antibodies (mAbs). The annotation of non-canonical translation events in these cellular factories remains incomplete, limiting not only our ability to study CHO cell biology but also detect host cell protein (HCP) contaminants in the final mAb drug product. We utilised ribosome footprint profiling (Ribo-seq) to identify novel open reading frames (ORFs) including N-terminal extensions and thousands of short ORFs (sORFs) predicted to encode microproteins. Mass spectrometry-based HCP analysis of four commercial mAb drug products using the extended protein sequence database revealed the presence of microprotein impurities for the first time. We also show that microprotein abundance varies with growth phase and can be affected by the cell culture environment. In addition, our work provides a vital resource to facilitate future studies of non-canonical translation as well as the regulation of protein synthesis in CHO cell lines.

genomics↗

bioRxiv2021

Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease

Environmental enteropathy (EE) is a subclinical condition of the small intestine that is highly prevalent in low- and middle-income countries. It is thought to be a key contributing factor to childhood malnutrition, growth-stunting, and diminished oral vaccine responses. While EE has been shown to be the by-product of recurrent enteric infection, its full pathophysiology remains unclear. Here, we mapped the cellular and molecular correlates of EE severity by performing high-throughput single-cell RNA-sequencing on 33 small intestinal biopsies from 11 adults with EE from Lusaka, Zambia (8 HIV-negative, 3 HIV-positive), 6 adults without EE in Boston, USA, and 2 adults from Durban, South Africa, which we complemented with published data from 3 additional South African adults from the same clinical site. By using these data to reanalyze previously-defined bulk-transcriptomic signatures of reduced villus height and decreased plasma LPS levels in EE, we found that these signatures may be driven by an increased abundance of surface mucosal cells - a gastric-like subset previously implicated in epithelial repair in the gastrointestinal tract. In addition, we identified several cell subsets whose fractional abundances associate with histologically determined EE severity, small intestinal region, and HIV infection. Furthermore, by comparing distal duodenal EE samples with those from three control cohorts, we identified dysregulated WNT and MAPK signaling in the EE epithelium and a T cell subset highly expressing a transcriptional signature of tissue-resident memory cells but with increased pro-inflammatory cytokine expression in the EE cohort. Altogether, our work illuminates epithelial and immune correlates of EE and provides new molecular targets for intervention. One Sentence SummaryUsing single-cell RNA-sequencing, we characterize the pathophysiology of environmental enteropathy (EE) - a highly prevalent condition of the small intestine that is thought to be a primary cause of global growth-stunting cases and a key contributing factor to childhood malnutrition and diminished oral vaccine responses - to derive insights into the epithelial and immune correlates of disease severity, suggesting new therapeutic targets for future investigation.

genomics↗

bioRxiv2021

Leishmania infantum xenodiagnosis from vertically infected dogs reveals significant skin tropism

BackgroundDogs are the primary reservoir for human visceral leishmaniasis due to Leishmania infantum. Phlebotomine sand flies maintain zoonotic transmission of parasites between dogs and humans. A subset of dogs is infected transplacentally during gestation, but at what stage of the clinical spectrum vertically infected dogs contribute to the infected sand fly pool is unknown. Methodology/Principal FindingsWe examined infectiousness of dogs vertically infected with L. infantum from multiple clinical states to the vector Lutzomyia longipalpis using xenodiagnosis and found that vertically infected dogs were infectious to sand flies at differing rates. Dogs with moderate disease showed significantly higher transmission to the vector than dogs with very mild or severe disease. We documented a substantial parasite burden in the skin of vertically infected dogs by RT-qPCR, despite these dogs not having received intradermal parasites via sand flies. There was a highly significant correlation between skin parasite burden at the feeding site and sand fly parasite uptake. This suggests dogs with high skin parasite burden contribute the most to the infected sand fly pool. Although skin parasite load and parasitemia correlated with one another, the average parasite number detected in skin was significantly higher compared to blood in matched subjects. Thus, dermal resident parasites were infectious to sand flies from dogs without detectable parasitemia. Conclusions/SignificanceTogether, our data implicate skin parasite burden and earlier clinical status as stronger indicators of outward transmission potential than blood parasite burden. Our studies of a population of dogs without vector transmission highlights the need to consider canine vertical transmission in surveillance and prevention strategies. AUTHOR SUMMARYSand flies transmit Leishmania parasites between infected dogs and humans leading to the life-threatening tropical disease Visceral Leishmaniasis (VL). Identifying which dogs transmit parasites well to sand flies is important to curb disease spread. The offspring of both dogs and humans can also be infected vertically while in utero. Despite this, the infectiousness of dogs that receive parasites in utero to sand flies has not been thoroughly investigated. Thus, we allowed sand flies to feed on a group of vertically infected dogs at varying stages of VL disease severity and measured sand fly parasite uptake. We found vertically infected dogs were readily able to transmit parasites to the sand flies. Dogs that were most infectious had moderate clinical disease and relatively high levels of parasite infection in their blood and skin. However, the level of skin infection was significantly higher than that observed in the blood, and the skin parasite load had the strongest correlation with sand fly parasite uptake. This implicates the skin may be an underappreciated driver of canine infectiousness to the sand fly vector. In addition, this work highlights that vertically infected dogs are very important parts of the transmission cycle and must be considered in all public health efforts addressing VL.

microbiology↗

bioRxiv2021

West Nile virus in crocodiles and mosquitoes in Zimbabwe

We detected, for the first time, West Nile virus lineages 1 and 2 in Zimbabwe in mosquitoes and crocodile tissue samples, including fluid from egg waste. Our results provide evidence of WNV circulation in Zimbabwe, suggesting that an evaluation of the risk to humans and susceptible animals should be considered.

microbiology↗

bioRxiv2019

Sub physiological temperature induces pervasive alternative splicing in Chinese hamster ovary cells

RNA sequencing (RNASeq) has been widely used to associate alterations in Chinese hamster ovary (CHO) cell gene expression with bioprocess phenotypes, however alternative mRNA splicing, has thus far, received little attention. In this study, we utilised RNASeq for transcriptomic analysis of a monoclonal antibody producing CHOK1 cell line subjected to a temperature shift. More than 2,365 instances of differential splicing were observed 24hrs after the reduction of cell culture temperature. 1,163 of these alternative splicing events were identified in genes where no changes in abundance were detected by standard differential expression analysis. Ten examples of alternative splicing were selected for independent validation using qPCR in the monoclonal antibody producing CHOK1 line used for RNASeq and a further 2 CHOK1 cell lines. This analysis provided evidence that exon skipping and mutually exclusive splicing events occur in genes linked to the cellular response to changes in temperature and mitochondrial function. While further work is required to determine the impact of changes in mRNA sequence on cellular phenotype, this study demonstrates that alternative splicing analysis can be utilised to gain a deeper understanding of post-transcriptional regulation in CHO cells during biopharmaceutical production.

cell biology↗

bioRxiv2019

Biofilm Associated Genotypes of Multidrug-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitous environmental microorganism that is also a common cause of nosocomial infections that vary in severity from chronic wound infections to pneumonia, bloodstream infections and sepsis. Its ability to survive in many different environments and persistently colonize human tissue is linked to its presence within biofilms that form on indwelling device surfaces such as plastics and stainless steel. Biofilm promotes bacterial adhesion and survival on surfaces, reduces susceptibility to desiccation, and the actions of antibiotics and disinfectants. Recent genome sequencing studies demonstrate that P. aeruginosa is a highly diverse species with a very large pan-genome consistent with its adaptability to differing environments. However, most MDR infections are caused by a small number of \"high-risk\" clones or lineages that recently emerged and spread globally.\n\nIn our 2017 study of the resistome of P. aeruginosa we confirmed the power of genome-wide association (GWAS) techniques to explore the genetic basis of several antibiotic resistance phenotypes and discovered 46 novel putative resistance polymorphisms. In this study we sought to examine genetic associations within a subset of these isolates with simple biofilm phenotypes. We examined the genetic basis for biofilm production on polystyrene at room temperature (22{degrees}C) and body temperature (37{degrees}C) within a total of 280 isolates. 69% of isolates (n=193) produced more biofilm mass at 22{degrees}C, whilst those producing more biofilm at 37{degrees}C had reduced optical density 540 variation. We found statistically significant associations with IpxO and other genes associated with arsenic resistance to be significantly associated with this trait. IpxO which encodes a lipid A hydroxylase and arsenic reduction genes have previously been found to be associated with biofilm production in this species. We analyzed 260 ST111 and ST235 genomes and found considerable genetic variation between isolates in their content of genes previously found associated with biofilm production. This is indicative of a highly variable and flexible population within these clades with frequent emergence of successful sub-lineages. Analysis of 48 of these isolates ability to form biofilm on stainless steel surfaces showed that a good biofilm-forming phenotype had significant intra-clone variation, independent of core genome phylogeny with pan-genome analysis, suggesting a possible association and involvement of components of the type IV secretion system. However, GWAS and pan-GWAS analyses yielded weaker statistical significance. This study confirms GWAS and pan-GWAS trait associations can be performed for biofilm phenotype and produce data in agreement with each other. This panel of 280 study isolates, matched to genomic data has potential for the investigation of other phenotypes in P. aeruginosa perhaps as part of a growing database / collection. A representative, curated, genome sequenced collection should increase in usefulness as it grows offering increasing statistical power.\n\nImportanceP. aeruginosa is a major cause of multiply antibiotic infections worldwide but it is also found in many hospital and natural environments, especially aquatic ones. In this study we examined genetic polymorphism associated with biofilm production at room temperature and at body temperature, the biofilm associated gene repertoire of two major MDR clones and also genetic polymorphisms associated with biofilm production on stainless steel. Using these genome-wide and pan-genome wide association methods we identified / confirmed potential key genes involved in biofilm production and survival of P. aeruginosa. The study demonstrates the potential usefulness of large, genome sequenced isolate collections such as ours, to better understand the genetics underlying phenotypic diversity in this species.

genomics↗

bioRxiv2019

Targeting tRNA-Synthetase Interactions towards Novel Therapeutic Discovery Against Eukaryotic Pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and eight clades of trypanosomes, identifying parasite-specific informative features (including base-pairs and base mis-pairs) that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. These findings support a systems biology model in which combination chemotherapies that target multiple tRNA-synthetase interactions should be comparatively less prone to the emergence of resistance than conventional single drug therapies.\n\nAuthor SummaryTrypanosome parasites pose a significant health risk worldwide. Conventional drug development strategies have proven challenging given the high conservation between humans and pathogens, with off-target toxicity being a common problem. Protein synthesis inhibitors have historically been an attractive target for antimicrobial discovery against bacteria, and more recently for eukaryotic pathogens. Here we propose that exploiting pathogen-specific tRNA-synthetase interactions offers the potential for highly targeted drug discovery. To this end, we improved tRNA gene annotations in trypanosome genomes, identified functionally informative trypanosome-specific tRNA features, and showed that these features are highly conserved over approximately 250 million years of trypanosome evolution. Highlighting the species-specific and broad-spectrum potential of our approach, we identified natural product inhibitors against the parasite translational machinery that have no effect on the homologous human enzyme.

microbiology↗

bioRxiv2018

Different analysis methods of Scottish and English child physical activity data explain the majority of the difference between the national prevalence estimates

BackgroundThe percentage of children in Scotland and England meeting the aerobic physical activity recommendation differ greatly according to the estimates derived from the respective national health surveys. The Scottish Health Survey (SHeS) usually estimates that over 70% meet the guidelines; Health Survey for England (HSE) estimates are usually below 25%. It is plausible that these differences originate from different analysis methods. The HSE monitor the percentage of children that undertake 60 minutes of moderate-to-vigorous physical activity on each day of the week ( the daily minimum method (DMM)). The SHeS monitor the proportion that undertake at least seven sessions of moderate-to-vigorous physical activity, with an average daily duration over 60 minutes ( the average method (WAM)). We aimed to establish how great an influence this difference in analysis methods has on the prevalence estimates.\n\nMethodsPhysical activity data from 5-15 year olds in the 2015 HSE and SHeS were reanalysed (weighted n=3840 and 965, respectively). Two comparable pairs of estimates were derived: a DMM and WAM estimate from the HSE not including travel to/from school, and WAM estimates from the HSE and the SHeS including travel to/from school. It is not possible to calculate a DMM estimate from the SHeS due to the way the questions are asked. Results were presented for the total samples, and by sex and age sub-groups.\n\nResultsThe HSE WAM estimate was 31.7 (95% CI: 30.2-33.3) percentage points higher than the DMM estimate (54.3% (95% CI: 52.6-56.0) and 22.6% (95% CI: 21.2-24.1) respectively). The magnitude of this difference differed by age group but not sex. When comparable WAM estimates were derived from the SHeS and the HSE, the SHeS was 11.8 percentage points higher (73.6% (95% CI: 69.8-77.1) and 61.8% (95% CI: 60.2-63.5) respectively). The magnitude of this difference differed by age group and sex.\n\nConclusionsThe results indicate that the difference in the analysis method explains the majority (approximately 30 percentage points) of the difference in the child physical activity prevalence estimates between Scotland and England. These results will help those involved in national surveillance to determine how to increase comparability between the U.K. home nations.

epidemiology↗