Biology subjects

Hunter, E.

Publications and source records attributed to Hunter, E..

14 recordsLinked to original sources

bioRxiv2026

SPrOUT: A computational and targeted sequencing approach for mixed plant DNA identification with Angiosperms353

PremiseThe identification of plant species from mixed samples is crucial in various fields, including ecological surveys, conservation efforts, and food and dietary supplement safety. Traditional methods face potential challenges due to the high costs of DNA sequencing, inefficiencies in computational workflows, and incomplete sequence databases. Methods and ResultsThis study introduces a novel approach using the Angiosperms353 target sequencing kit for efficient taxonomic identification of angiosperm DNA in mixed samples. Our method assembles short pair-end reads for each mixed sample. Using gene sets of Angiosperms353 from 871 species, we apply phylogenetic inference to categorize the variance in phylogenetic distance across genes to identify the presence of taxa in mixed plant samples. The pipeline reaches 98.1 to 99.6% accuracy, 92.9 to 100% precision for identifying unknown taxa in in-silico mixes, and 90.7% accuracy and 98.0% precision for mock supplement mixtures. We explored the parameter cutoffs of the pipeline to offer an empirical range for different applications. ConclusionsThe Angiosperms353 and HybPiper assembly proved effective in sorting mixed plant DNA samples. Our method offers a framework for scientific and practical applications in plant species identification in both single and mixed samples.

bioinformatics↗

bioRxiv2025

The Pioneer Transcription Factor Oct4 Differentially Co-opts Bcl11a and Bcl11b to Regulate Reprogramming to Pluripotency

Pioneer transcription factors (TFs) orchestrate development, reprogramming, and cancer. Yet, the molecular mechanisms by which they cooperate with endogenous TFs and chromatin to trigger cell fate conversions remain largely unknown. Here, we identified antagonistic functions in reprogramming to pluripotency for the two paralogous somatic zinc finger TFs Bcl11a and Bcl11b. We reveal that Bcl11a and Bcl11b are initially co-expressed in mouse embryonic fibroblasts and then segregate in cellular intermediates respectively prone or refractory to reprogramming, transdifferentiation, and oncogenic transformation. They exert opposite functions - with Bcl11a promoting and Bcl11b hindering - the efficacy of induced pluripotent stem cells generation. During reprogramming, we uncover that Bcl11b safeguards cellular identity by persistently binding to differentiation genes with Runx1 in refractory intermediates. In contrast, in reprogramming intermediates, Bcl11a interacts with Oct4 and is initially displaced from MEF enhancers. Bcl11a then binds transiently and contributes to activate the E3 ubiquitin ligase Pja1 that regulates Smad3, thus promoting mesenchymal-epithelial transition and constraining senescence. Collectively, our work unveils how the differential repurposing of paralogous TFs by Oct4 orchestrates reprogramming to pluripotency.

cell biology↗

bioRxiv2024

Synaptic targets and cellular sources of CB1 cannabinoid receptor and vesicular glutamate transporter-3 expressing nerve terminals in relation to GABAergic neurons in the human cerebral cortex

Cannabinoid receptor 1 (CB1) regulates synaptic transmission through presynaptic receptors in nerve terminals, and its physiological roles are of clinical relevance. The cellular sources and synaptic targets of CB1-expressing terminals in the human cerebral cortex are undefined. We demonstrate a variable laminar pattern of CB1-immunorective axons and electron microscopically show that CB1-positive GABAergic terminals make type-2 synapses innervating dendritic shafts (69%), dendritic spines (20%) and somata (11%) in neocortical layers 2-3. Of the CB1-immunopositive GABAergic terminals, 25% were vesicular-glutamate-transporter-3 (VGLUT3)-immunoreactive, suggesting GABAergic/glutamatergic co-transmission on dendritic shafts. In vitro recorded and labelled VGLUT3 or CB1-positive GABAergic interneurons expressed cholecystokinin, vasoactive-intestinal-polypeptide and calretinin, had diverse firing, axons and dendrites, and included rosehip, neurogliaform and basket cells, but not double bouquet or axo-axonic cells. CB1-positive interneurons innervated pyramidal cells and GABAergic interneurons. Most glutamatergic synaptic terminals formed type-1 synapses and some were positive for CB1 receptor concentrated in the presynaptic active zone, unlike in GABAergic terminals. From the sampled VGLUT3-positive terminals, 60% formed type-1 synapses with dendritic spines (80%) or shafts (20%) and 52% were also positive for VGLUT1, suggesting intracortical origin. Some VGLUT3-positive terminals were immunopositive for vesicular-monoamine-transporter-2, suggesting 5-HT/glutamate co-transmission. Overall, the results show that CB1 regulates GABA release mainly to dendritic shafts of both pyramidal cells and interneurons, and predict CB1-regulated co-release of GABA and glutamate from single cortical interneurons. We also demonstrate the co-existence of multiple vesicular glutamate transporters in a select population of terminals probably originating from cortical neurons and innervating dendritic spines in the human cerebral cortex.

neuroscience↗

bioRxiv2024

Whole Genome 3D Blood Biopsy Profiling of Canine Cancers: Development and Validation of EpiSwitch Multi-Choice Array-Based Diagnostic Test.

Veterinary oncology has a critical need for an accurate, specific, and sensitive non-invasive (blood) biomarker assay to assess multiple canine oncological indications early to better inform therapeutic interventions. Extended from clinical applications in human oncology, here we report on a novel 3D genomics approach to identify systemic blood biomarkers for canine diffuse large B-cell lymphoma (DLBCL), T-zone lymphoma (TZL), hemangiosarcoma (HSA), histiocytic sarcoma, osteosarcoma, and canine malignant melanoma, in a single assay format that encompasses multiple classes and phenotypes of cancer. In the validation of the independent test cohort the 3D whole-genome profiling in peripheral blood demonstrated high sensitivity and specificity for lymphomas and sarcomas as a class, with accuracy >80%; and high sensitivity and specificity for individual indications, with accuracy >89%. This study demonstrates a 3D genomic approach can be used to develop a non-invasive, blood-based test for multiple choice diagnosis of canine oncological indications. The modular EpiSwitch(R) Specific Canine Blood (EpiSwitch SCB) test promises to help veterinary specialists to diagnose the disease, make more informed treatment decisions, better utilize alternative effective treatments, minimize or avoid unnecessarily toxicity, and efficiently manage costs and resources.

molecular biology↗

bioRxiv2023

Gene Expression Changes in Cultured Reactive Rat Astrocyte Models and Comparison to Device-Associated Effects in the Brain

Implanted microelectrode arrays hold immense therapeutic potential for many neurodegenerative diseases. However, a foreign body response limits long-term device performance. Recent literature supports the role of astrocytes in the response to damage to the central nervous system (CNS) and suggests that reactive astrocytes exist on a spectrum of phenotypes, from beneficial to neurotoxic. The goal of our study was to gain insight into the subtypes of reactive astrocytes responding to electrodes implanted in the brain. In this study, we tested the transcriptomic profile of two reactive astrocyte culture models (cytokine cocktail or lipopolysaccharide, LPS) utilizing RNA sequencing, which we then compared to differential gene expression surrounding devices inserted into rat motor cortex via spatial transcriptomics. We interpreted changes in the genetic expression of the culture models to that of 24 hour, 1 week and 6 week rat tissue samples at multiple distances radiating from the injury site. We found overlapping expression of up to [~]250 genes between in vitro models and in vivo effects, depending on duration of implantation. Cytokine-induced cells shared more genes in common with chronically implanted tissue ([≥]1 week) in comparison to LPS-exposed cells. We revealed localized expression of a subset of these intersecting genes (e.g., Serping1, Chi3l1, and Cyp7b1) in regions of device-encapsulating, glial fibrillary acidic protein (GFAP)-expressing astrocytes identified with immunohistochemistry. We applied a factorization approach to assess the strength of the relationship between reactivity markers and the spatial distribution of GFAP-expressing astrocytes in vivo. We also provide lists of hundreds of differentially expressed genes between reactive culture models and untreated controls, and we observed 311 shared genes between the cytokine induced model and the LPS-reaction induced control model. Our results show that comparisons of reactive astrocyte culture models with spatial transcriptomics data can reveal new biomarkers of the foreign body response to implantable neurotechnology. These comparisons also provide a strategy to assess the development of in vitro models of the tissue response to implanted electrodes.

neuroscience↗

bioRxiv2022

Digital twins and hybrid modelling for simulation of physiological variables and stroke risk

One of the more interesting ideas for achieving personalized, preventive, and participatory medicine is the concept of a digital twin. A digital twin is a personalized computer model of a patient. So far, digital twins have been constructed using either mechanistic models, which can simulate the trajectory of physiological and biochemical processes in a person, or using machine learning models, which for example can be used to estimate the risk of having a stroke given a cross-section profile at a given timepoint. These two modelling approaches have complementary strengths which can be combined into a hybrid model. However, even though hybrid modelling combining mechanistic modelling and machine learning have been proposed, there are few, if any, real examples of hybrid digital twins available. We now present such a hybrid model for the simulation of ischemic stroke. On the mechanistic side, we develop a new model for blood pressure and integrate this with an existing multi-level and multi-timescale model for the development of type 2 diabetes. This mechanistic model can simulate the evolution of known physiological risk factors (such as weight, diabetes development, and blood pressure) through time, under different intervention scenarios, involving a change in diet, exercise, and certain medications. These forecast trajectories of the physiological risk factors are then used by a machine learning model to calculate the 5-year risk of stroke, which thus also can be calculated for each timepoint in the simulated scenarios. We discuss and illustrate practical issues with clinical implementation, such as data gathering and harmonization. By improving patients understanding of their body and health, the digital twin can serve as a valuable tool for patient education and as a conversation aid during the clinical encounter. As such, it can facilitate shared decision-making, promote behavior change towards a healthy lifestyle, and improve adherence to prescribed medications.

systems biology↗

bioRxiv2022

Differential effects of group III metabotropic glutamate receptors on spontaneous inhibitory synaptic currents in spine-innervating double bouquet and parvalbumin-expressing dendrite-targeting GABAergic interneurons in human neocortex

Diverse neocortical GABAergic neurons specialise in synaptic targeting and their effects are modulated by presynaptic metabotropic glutamate receptors (mGluRs) suppressing neurotransmitter release in rodents, but their effects in human neocortex are unknown. We tested whether activation of group III mGluRs by L-AP4 changes GABAA receptor-mediated spontaneous inhibitory postsynaptic currents (sIPSCs) in two distinct dendritic spine-innervating GABAergic interneurons recorded in vitro in human neocortex. Calbindin-positive double bouquet cells (DBC) had columnar "horsetail" axons descending through layers II-V innervating dendritic spines (48%) and shafts, but not somata of pyramidal and non-pyramidal neurons. Parvalbumin-expressing dendrite-targeting cell (PV-DTC) axons extended in all directions innervating dendritic spines (22%), shafts (65%) and somata (13%). As measured, 20% of GABAergic neuropil synapses innervate spines, hence DBCs, but not PV-DTCs, preferentially select spine targets. Group III mGluR activation paradoxically increased the frequency of sIPSCs in DBCs (to median 137% of baseline), but suppressed it in PV-DTCs (median 92%), leaving the amplitude unchanged. The facilitation of sIPSCs in DBCs may result from their unique GABAergic input being disinhibited via network effect. We conclude that dendritic spines receive specialised, diverse GABAergic inputs, and group III mGluRs differentially regulate GABAergic synaptic transmission to distinct GABAergic cell types in human cortex.

neuroscience↗

bioRxiv2021

3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome

Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.

biochemistry↗

bioRxiv2020

Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response

Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, diversity metric of the HLA profile of individuals within a population and consideration of sequence diversity in the context of an individuals CD8 T-cell immune repertoire to assess the HIV proteome for defined regions of immunogenicity. Using this approach, Analysis of HLA adaptation and functional immunogenicity data enabled the identification of regions within the proteome that offer significant conservation, HLA recognition within a population, low prevalence of HLA adaptation and demonstrated immunogenicity. We believe this unique and novel approach to vaccine design that, in combination with in vitro functional assays, offers a bespoke pipeline for expedited and rational CD8 T-cell vaccine design for HIV and potentially other pathogens with the potential for both global and local coverage.

immunology↗

bioRxiv2020

Negative interplay between biofilm formation and competence in the environmental strains of Bacillus subtilis

Environmental strains of the soil bacterium Bacillus subtilis have valuable applications in agriculture, industry, and biotechnology. They are capable of forming robust biofilms and demonstrate excellent biological control activities in plant protection. However, environmental strains are genetically less accessible, a sharp contrast to the laboratory strains well known for their natural competence and a limitation toward their application. In this study, we observed that robust biofilm formation of the environmental strains greatly reduces the rate of competent cells within the biofilm. By using the model strain 3610, we reveal a cross-pathway regulation that allows biofilm matrix producers and competence-developing cells to undergo mutually exclusive cell differentiation. We show that the competence activator ComK represses the key biofilm regulatory gene sinI by directly binding to the sinI promoter, thus blocking competent cells from simultaneously becoming matrix producers. In parallel, the biofilm activator SlrR represses competence through three distinct mechanisms, involving both genetic regulation and cell morphological changes. We discuss potential implications of limiting competence in a bacterial biofilm. ImportanceThe soil bacterium Bacillus subtilis is capable of forming robust biofilms, a multicellular community important for its survival in the environment. B. subtilis also exhibits natural competence, the ability of cells to acquire genetic materials directly from the environment. By investigating competence development in situ during B. subtilis biofilm formation, we reveal that robust biofilm formation, an important feature of the environmental strains of B. subtilis, often greatly reduces the rate of competent cells within the biofilm. We characterize a cross-pathway regulation that allows cells associated with these two developmental events to undergo mutually exclusive cell differentiation during biofilm formation. Finally, we discuss potential biological implications of limiting competence in a bacterial biofilm.

microbiology↗

bioRxiv2020

A systematic review of European farmer and non-farmer attitudes towards landscapes, ecosystem services, and agricultural management practices: Implications for permanent grassland management.

Permanent grassland (PG) is an important agricultural land use for the delivery of multiple ecosystem services (ES), including carbon sequestration, water quality protection, food production, habitat provision, and cultural activities. However, PG environments are threatened by sub-optimal management, cultivation, and abandonment that are influenced by context, land managers attitudes and societal demand for ES. Therefore, the perceptions and attitudes of key decision-makers (farmers) and other stakeholders (non-farmers, including citizens and consumers of the products of permanent grasslands, and ES) need to be understood to ensure the sustainability of PGs and the ES they provide. A systematic review of the literature identified 135 scholarly articles. Application of thematic analysis, allowed the organization, and synthesis of current research related to (different) stakeholder attitudes, and how these influence PG management and the delivery of ES. The results suggest that different stakeholders hold different views towards permanent grassland, with farmers in particular having to balance economic with other (potentially conflicting) drivers. The types of knowledge held by different groups of stakeholders, access to sources of information, as well as the influence of knowledge on behaviour; and environmental values (for example in relation to aesthetics or conservation of biodiversity) explained why certain motivations for attitudes and behaviours are held. A major gap, however, was identified in relation to PG as opposed to other types of landscape.

ecology↗

bioRxiv2019

Low Replication Capacity Virus Is Preferentially Transmitted In Mother-To-Child-Transmission But Not In Adult-To-Adult-Transmission Of HIV-1

Previous studies of the transmitted/founder virus compared to viral quasispecies in the donor have yielded conflicting results. In heterosexual adult-to-adult transmission (ATAT), the viral replicative capacity (VRC) of transmitted virus is reportedly either similar to, or somewhat higher than, that of donor virus, whilst transmitted virus in mother-to-child transmission (MTCT) has a significantly lower VRC than that of maternal virus. These discrepancies may be explained by the different methodologies used in these studies, or they may reflect true differences in the transmission bottleneck. To resolve this question, we here use the same methodology to compare transmitted versus donor virus in MTCT and ATAT. We show that, in a South African mother-child cohort, infant virus samples obtained at 1-2 days after birth had VRC significantly lower than in the mothers (p=0.0003). By contrast, in Zambian ATAT transmission pairs, VRC of transmitted virus was similar to or somewhat higher than donor virus (p=ns). The VRC of virus transmitted to the recipient, compared to that in the donor, was significantly lower in MTCT versus heterosexual ATAT (p=0.01). These studies demonstrate that fundamental differences exist between the viruses transmitted via the MTCT and ATAT bottlenecks that are not explained by methodological factors. This result is of importance since transmission of low replicative capacity virus results in low immune activation and a small viral reservoir, and therefore the preferential transmission of low fitness viruses in MTCT might be expected to increase cure potential in in utero infected infants and children.\n\nIMPORTANCEUnderstanding the factors determining which viruses are preferentially transmitted in HIV infection is critical to the development of new, effective strategies to prevent transmission. Despite this, much remains unknown in this respect, both with regard to adult-to-adult transmission (ATAT) but especially with respect to mother-to-child transmission (MTCT). The finding here that fundamental differences exist in the genetic bottleneck of HIV transmission between heterosexual ATAT and MTCT is an important initial step to help define the viral mechanisms contributing to transmission in each case. In addition, we show that viruses of low viral replicative capacity are preferentially transmitted in MTCT. This suggests the possibility that a window of opportunity exists following in utero infection in which early anti-viral intervention not only reduces the size and diversity of the viral reservoir, but additionally maintains a reservoir comprising low viral replicative capacity HIV. Low replicative capacity of transmitted virus has previously been shown to result in low immune activation and low proviral DNA load in central memory cells, factors likely to be directly relevant to increasing cure potential in HIV-infected infants and children.

immunology↗

bioRxiv2018

Evaluation of whole genome sequencing for the identification and typing of Vibrio cholerae

Epidemiological and microbiological data on Vibrio cholerae isolated between 2004 and 2017 (n=836) and held in the Public Health England culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome derived species identification and serotype for a sub-set of isolates (n=152). Of the 836 isolates, 750 (89.7%) were from faecal specimens, 206 (24.6%) belonged to serogroup O1 and seven (0.8%) were serogroup O139, and 792 (94.7%) isolates from patients reporting recent travel abroad, most commonly to India (n=209) and Pakistan (n=104). Of the 152 isolates of V. cholerae speciated by kmer identification, 149 (98.1%) were concordant with the traditional biochemical approach. Traditional serotyping results were 100% concordant with the whole genome sequencing (WGS) analysis for identification of serogroups O1 and O139 and Classical and El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor and O139 belonging to sequence type (ST) 69, and in V. cholerae O1 Classical variants belonging to ST73. A phylogeny of isolates belonging to ST69 from UK travellers clustered geographically, with isolates from India and Pakistan located on separate branches. Moving forward, WGS data from UK travellers will contribute to global surveillance programs, and the monitoring of emerging threats to public health and the global dissemination of pathogenic lineages. At the national level, these WGS data will inform the timely reinforcement of direct public health messaging to travellers and mitigate the impact of imported infections and the associated risks to public health.

microbiology↗

bioRxiv2018

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

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

bioinformatics↗