Biology subjects

Miller, W.

Publications and source records attributed to Miller, W..

13 recordsLinked to original sources

bioRxiv2025

Genomic Analyses of Antibiotic-Resistant Escherichia coli From Extensive Beef Cattle and Sheep Farms Identifies Inter-Species and Farm-Farm Sharing as Clonal Dissemination Pathways

SynopsisO_ST_ABSBackgroundC_ST_ABSGlobally, there is a large gap in our understanding of the prevalence, ecology and transmission dynamics of antibiotic resistance (ABR) in extensively reared ruminants, despite these animals contributing to the food chain and frequently sharing land with humans. MethodsFive hundred and seventy one visits to 33 Welsh beef cattle and/or sheep farms resulted in 1874 samples being collected at faecally contaminated sites from April 2022 to March 2023 (ADGC1) and September 2023 to December 2024 (ADGC2). Samples were tested for resistant Escherichia coli using amoxicillin, streptomycin, spectinomycin, cefotaxime and ciprofloxacin. WGS used Illumina technology. Clonal relationships were determined following core-genome alignment. ResultsA significant reduction in positivity for spectinomycin-resistant E. coli in sheep samples from ADGC1 to ADGC2 was observed, coincident with market withdrawal of a spectinomycin-containing preparation widely used in sheep. Reductions were seen in 19/22 sheep flocks with nine seeing a >50% reduction. Resistance to other tested antibiotics was unchanged. Phenotypic analysis and WGS for 713 E. coli showed that resistance to antibacterials important for human medicine was rare and genetically diverse. We identified 77 E. coli clones (<100 SNP cutoff) circulating among study farms with mixed farms contributing most; clones were also shared between animal species on mixed farms. ConclusionsFor extensively reared ruminants, ABR-reducing efforts can have significant impacts on antibiotic resistance on farms. Focusing these efforts onto farms contributing to the most animal movement and mixing events may generate the greatest reductions in overall on-farm ABR prevalence at regional and national levels.

microbiology↗

bioRxiv2025

RAB1A is a novel vulnerability in uveal melanoma revealed by dual inhibition of MNK1/2 and mTOR.

Uveal melanoma (UM) is an eye cancer that is fatal upon metastasis to the liver. Most treatments trialed in UM fail to provide therapeutic benefit, thus there is an urgent need for novel treatment strategies. The MAPK and PI3K signaling pathways, key molecular drivers found to be hyper-activated in UM, converge on the MNK1/2-eIF4E and mTORC1/2-4EBP axes. Here, we demonstrate that the pharmacologic inhibition of MNK1/2 in combination with an mTOR inhibitor impairs clonogenic outgrowth and UM cell invasion. Using proteomic analyses, we reveal that combined MNK1/2 and mTOR inhibition disrupts Golgi homeostasis and protein vesicle trafficking mainly due to downregulated RAB1A expression, a master regulator of intracellular protein transport. We uncover that the knockdown of RAB1A blocks liver metastasis, a result that is recapitulated by combined pharmacologic inhibition of MNK1/2 and mTOR. Finally, we show that RAB1A expression reshapes the surfaceome by increasing the abundance of plasma membrane proteins associated with poor overall survival in UM, highlighting its potential as a biomarker. This study identifies protein vesicle transport as an unrecognized vulnerability in UM and supports a mechanistic rationale for targeting MNK1/2 and mTOR in metastatic UM.

cancer biology↗

bioRxiv2024

Modeling gene-environment interactions in Parkinson's Disease: Helicobacter pylori infection of Pink1-/- mice induces CD8 T cell-dependent motor and cognitive dysfunction.

Parkinsons disease (PD) is a chronic neurodegenerative disorder characterized by progressive loss of motor function. Diagnosis occurs late: after motor symptom development downstream of the irreparable loss of a large proportion of the dopaminergic neurons in the substantia nigra of the brain. Understanding PD pathophysiology in its pre-motor prodromal phase is needed for earlier diagnosis and intervention. Genetic risk factors, environmental triggers, and dysregulated immunity have all been implicated in PD development. Here, we demonstrate in a mouse model deficient in the PD-associated gene Pink, that infection with the human PD-associated gastric bacterium Helicobacter pylori leads to development of motor and cognitive signs resembling prodromal features of PD. This was also associated with proliferation and activation of primary mitochondria-reactive CD8 T cells and infiltration of CD8 T cells into the brain. Development of the motor and cognitive phenotypes in the infected Pink1-/- mice was abrogated when CD8 T cells were depleted prior to infection. We anticipate that this new model, which integrates genetic PD susceptibility, a PD-relevant environmental trigger, and specific immune changes that are required for symptom development, will be a valuable tool for increasing our understanding of this complex disease.

immunology↗

bioRxiv2023

A glycolytic metabolite restores DNA repair activity of polynucleotide kinase 3-phosphatase in polyglutamine (PolyQ) diseases

Huntingtons disease (HD) and spinocerebellar ataxia type 3 (SCA3) are the two most prevalent polyglutamine (polyQ) neurodegenerative diseases, caused by CAG (encoding glutamine) repeat expansion in the coding region of the huntingtin (HTT) and ataxin-3 (ATXN3) proteins, respectively. We have earlier reported that the activity, but not the protein level, of an essential DNA repair enzyme, polynucleotide kinase 3-phosphatase (PNKP), is severely abrogated in both HD and SCA3 resulting in accumulation of double-strand breaks in patients brain genome. While investigating the mechanistic basis for the loss of PNKP activity and accumulation of DNA double-strand breaks leading to neuronal death, we observed that PNKP interacts with the nuclear isoform of 6-phosphofructo-2-kinase fructose-2,6-bisphosphatase 3 (PFKFB3). Depletion of PFKFB3 markedly abrogates PNKP activity without changing its protein level. Notably, the levels of both PFKFB3 and its product fructose-2,6 bisphosphate (F2,6BP), an allosteric modulator of glycolysis, are significantly lower in the nuclear extracts of post-mortem brain tissues of HD and SCA3 patients. Supplementation of F2,6BP restored PNKP activity in the nuclear extracts of patients brain. Moreover, intracellular delivery of F2,6BP restored both the activity of PNKP and the integrity of transcribed genome in neuronal cells derived from striatum of HD mouse. Importantly, supplementing F2,6BP rescued the HD phenotype in Drosophila, suggesting F2,6BP to serve in vivo as a cofactor for the proper functionality of PNKP and thereby, of brain health. Our results thus provide a compelling rationale for exploring the therapeutic use of F2,6BP and structurally related compounds for treating polyQ diseases. SignificanceTo unravel the biological basis for the loss of PNKP activity in HD and SCA3, the two most prevalent polyglutamine neurodegenerative disorders, we analyzed PNKP interactome and found that the nuclear isoform of a glycolytic enzyme PFKFB3 associated with PNKP and other repair proteins forming a multiprotein complex. Surprisingly, we found that PFKFB3 and its biosynthetic product, F2,6BP are significantly low in the affected region of patients brain. Exogenous addition of F2,6BP restored PNKP activity in patients brain nuclear extract. Moreover, supplementing F2,6BP in HD cells and fruit flies restored genome integrity and rescued the disease symptoms. While there is no curative therapy for HD/SCA3, except symptom management, our discovery suggests that F2,6BP supplementation would be a promising therapeutic option.

biochemistry↗

bioRxiv2023

Saltational episodes of reticulate evolution in the jumping pomace fly Drosophila saltans species group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of investigation. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two of which consisted of windows from pseudo-reference genomes aligned to either an outgroup or ingroup species, and two based on our new assemblies using either conserved genes or [≥]50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed [~]7% of the blocks in the most conflicting species quartets. High incidences of low phylogenetic resolution (polytomy) were restricted to three nodes on the tree, that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.

evolutionary biology↗

bioRxiv2021

Rapid quantification of tissue perfusion properties with a two-stage look-up table: a simulation study

Tissue perfusion properties reveal crucial information pertinent to clinical diagnosis and treatment. Multispectral spatial frequency domain imaging (SFDI) is an emerging imaging technique that has been widely used to quantify tissue perfusion properties. However, slow processing speed limits its usefulness in real-time imaging applications. In this study, we present a two-stage look-up table (LUT) approach that accurately and rapidly quantifies optical (absorption and reduced scattering maps) and perfusion (total hemoglobin and oxygen saturation maps) properties using stage-1 and stage-2 LUTs, respectively, based on reflectance images at 660nm and 850nm. The two-stage LUT can be implemented on both CPU and GPU computing platforms. Quantifying tissue perfusion properties using the simulated diffuse reflectance images, we achieved a quantification speed of 266, 174, and 74 frames per second for three image sizes 512x512, 1024x1024, and 2048x2048 pixels, respectively. Quantification of tissue perfusion properties was highly accurate with only 3.5% and 2.5% error for total hemoglobin and oxygen saturation quantification, respectively. The two-stage LUT has the potential to be adopted in existing SFDI applications to enable real-time imaging capability of tissue hemodynamics.

bioengineering↗

bioRxiv2021

Molecular Changes in Prader-Willi Syndrome Neurons Reveals Clues About Increased Autism Susceptibility.

BackgroundPrader-Willi syndrome (PWS) is a neurodevelopmental disorder characterized by hormonal dysregulation, obesity, intellectual disability, and behavioral problems. Most PWS cases are caused by paternal interstitial deletions of 15q11.2-q13.1, while a smaller number of cases are caused by chromosome 15 maternal uniparental disomy (PW-UPD). Children with PW-UPD are at higher risk for developing autism spectrum disorder (ASD) than the neurotypical population. In this study, we used expression analysis of PW-UPD neurons to try to identify the molecular cause for increased autism risk. MethodsDental pulp stem cells (DPSC) from neurotypical control and PWS subjects were differentiated to neurons for mRNA sequencing. Significantly differentially expressed transcripts among all groups were identified. Downstream protein analysis including immunocytochemistry and immunoblots were performed to confirm the transcript level data and pathway enrichment findings. ResultsWe identified 9 transcripts outside of the PWS critical region (15q11.2-q13.1) that may contribute to core PWS phenotypes. Moreover, we discovered a global reduction in mitochondrial transcripts in the PW-UPD +ASD group. We also found decreased mitochondrial abundance along with mitochondrial aggregates in the cell body and neural projections of +ASD neurons. LimitationsDPSC derived neuronal cultures used here were immature (3 weeks old), while important for studying the development of the disorder, it will be critical to confirm these mitochondrial defects in more mature neurons or postmortem brain tissue. Our PW-UPD -ASD group included only females, but the sample size in downstream image analysis was increased to include males for the analysis of mitochondrial phenotypes. The ASD diagnostic tool we use is the Social Communication Questionnaire (SCQ), which has been used extensively, but is not the gold standard for ASD diagnosis. ConclusionsThe 9 transcripts we identified common to all PWS subtypes may reveal PWS specific defects during neurodevelopment. Importantly, we found a global reduction in mitochondrial transcripts in PW-UPD +ASD neurons versus control and other PWS subtypes. We then confirmed mitochondrial defects in neurons from individuals with PWS at the cellular level. Quantification of this phenotype supports our hypothesis that the increased incidence of ASD in PW-UPD subjects may arise from mitochondrial defects in developing neurons.

neuroscience↗

bioRxiv2021

Proxy-based model to assess the relative contribution of ballast water and biofoulings potential propagule pressure and prioritize vessel inspections

Commercial shipping is the primary pathway of introduction for aquatic nonindigenous species, mainly through the mechanisms of ballast water and biofouling. In response to this threat, regulatory programs have been established across the globe to regulate and monitor commercial merchant and passenger vessels to assess compliance with local requirements to reduce the likelihood of NIS introductions. Resource limitations often determine the inspection efforts applied by these regulatory agencies to reduce NIS introductions. We present a simple and adaptable model that prioritizes vessel arrivals for inspection using proxies for potential propagule pressure, namely a ships wetted surface area as a proxy for the likelihood of biofouling-mediated potential propagule pressure and ballast water discharge volume as a proxy for ballast water-mediated potential propagule pressure. We used a California-specific dataset of vessels that arrived at California ports between 2015 and 2018 to test the proposed model and demonstrate how a finite set of inspection resources can be applied to target vessels with the greatest potential propagule pressure. The proposed tool is adaptable by jurisdiction, scalable to different segments of the vessel population, adjustable based on the vector of interest, and versatile because it allows combined or separate analyses of the PPP components. The approach can be adopted in any jurisdiction across the globe, especially jurisdictions without access to, or authority to collect, risk profiling data or direct measurements for all incoming vessel arrivals.

ecology↗

bioRxiv2020

Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci

The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we demonstrated that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding, in a B cell line that was 1) uninfected, 2) infected with a strain of EBV lacking EBNA2, or 3) infected with a strain that expresses EBNA2. We identified >400 EBNA2-dependent differentially expressed human genes and >5,000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed >2,000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP-seq data revealed >1,700 regions where EBNA2 altered chromatin looping interactions. Importantly, autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.

genomics↗

bioRxiv2020

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium fitti. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of the coral hybrids in Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). In the workflow the users data is compared to the database of previously genotyped samples and generates a report of genet identification. The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning as well as be applied to downstream genomic analyses.

genetics↗

bioRxiv2018

Relaxed constraint and thermal desensitization of the cold-sensing ion channel TRPM8 in mammoths

Unlike the living elephants, which live in warm tropical and subtropical habitats, mammoths lived in extreme cold environments where average winter temperatures ranged from -30{degrees} to -50{degrees}C. Like other cold adapted and artic species, mammoths evolved of suite of morphological and molecular adaptations that facilitated life in the cold. Here we reanalyze mammoth genomes and find that genes with mammoth-specific amino acid substitutions are enriched in functions related to temperature sensation. Among the genes with mammoth-specific amino acid substitutions is TRPM8, which mediates sensitivity to nonnoxious cool temperatures from 25- 28{degrees}C and cooling sensations induced by the chemical agonists menthol and icilin. We find that TRPM8 evolved rapidly in the mammoth stem-lineage, likely because of an episode of relaxed purifying selection. Functional characterization of resurrected mammoth and ancestral TRPM8 indicates that the mammoth TRPM8 is desensitized to cold but maintains sensitivity to menthol and icilin. These data suggest that as mammoths evolved into a cold tolerant species they lost the need for a cold-sensitive TRPM8.

evolutionary biology↗

bioRxiv2018

Genomic variants among threatened Acropora corals

Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora. We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the Pacific A. digitifera. A subset of predicted nucleotide variants were verified using restriction length polymorphism assays and proved useful in distinguishing the two Caribbean Acroporids and the hybrid they form (\"A. prolifera\"). Nucleotide variants are freely available from the Galaxy server (usegalaxy.org), and can be analyzed there with computational tools and stored workflows that require only an internet browser. We describe these data and some of the analysis tools, concentrating on fixed differences between A. cervicornis and A. palmata. In particular, we found that fixed amino acid differences between these two species were enriched in proteins associated with development, cellular stress response and the hosts interactions with associated microbes, for instance in the Wnt pathway, ABC transporters and superoxide dismutase. Identified candidate genes may underlie functional differences in the way these threatened species respond to changing environments. Users can expand the presented analyses easily by adding genomic data from additional species as they become available.\n\nArticle SummaryWe provide the first comprehensive genomic resources for two threatened Caribbean reef-building corals in the genus Acropora. We identified genetic differences in key pathways and genes known to be important in the animals response to the environmental disturbances and larval development. We further provide a list of candidate loci for large scale genotyping of these species to gather intra- and interspecies differences between A. cervicornis and A. palmata across their geographic range. All analyses and workflows are made available and can be used as a resource to not only analyze these corals but other non-model organisms.

genomics↗

bioRxiv2017

Accumulation And Functional Architecture Of Deleterious Genetic Variants During The Extinction Of Wrangel Island Mammoths

Woolly mammoths were among the most abundant cold adapted species during the Pleistocene. Their once large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ~5,600 years ago and Wrangel Island ~4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here we show that the Wrangel Island mammoth accumulated many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of Wrangel Island mammoth genes carrying these substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These results suggest that Wrangel Island mammoths may have suffered adverse consequences from their reduced population sizes and isolation.

genetics↗