Biology subjects

Kelly, A.

Publications and source records attributed to Kelly, A..

32 records · Page 2Linked to original sources

bioRxiv2024

Immune-profiling of T helper 1 (Th1), Th2 and Th17 signatures in murine splenocytes by targeting intracellular cytokines

Functional cytokines shape both innate and adaptive immune responses in the host after infection or immunization. Deep immunophenotyping of the key functional cytokine signatures associated with T cells in murine lymphoid tissue, especially in the spleen, is challenging. Using spectral flow cytometry, we developed a 17-parameter panel to profile major immune cell subsets along with T cells, memory phenotypes and functional cytokines in murine splenocytes in steady state as well as in stimulated conditions. This panel dissects the memory T cell compartment via CD62L and CD44 expression after mitogen stimulation. To profile T helper (Th) cells distribution after mitogen stimulation, established Th1 markers IFN{gamma}, TNF and IL-2; Th2 markers IL-4/5 and the Th17 marker, IL-17, are included. This optimized multicolor spectral flow panel allows a detailed immune profiling of functional cytokines in the murine T cell compartment and might be useful for exploratory analysis of how these functional cytokines shape host immunity after infection or vaccination. Our panel could be easily modified, if researchers wish to tailor the panel to their specific needs.

immunology↗

bioRxiv2024

A postnatal molecular switch drives the activity-dependent maturation of parvalbumin interneurons

Cortical neurons are specified during embryonic development but often only acquire their mature properties at relatively late stages of postnatal development. This delay in terminal differentiation is particularly prominent for fast-spiking parvalbumin-expressing (PV+) interneurons, which play critical roles in regulating the function of the cerebral cortex. We found that the maturation of PV+ interneurons is triggered by neuronal activity and mediated by the transcriptional cofactor peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1). Developmental loss of PGC-1 prevents PV+ interneurons from acquiring unique structural, electrophysiological, synaptic, and metabolic features and disrupts their diversification into distinct subtypes. PGC-1 exerts its function as a master regulator of the differentiation of PV+ interneurons by directly controlling gene expression through a transcriptional complex that includes ERR{gamma} and Mef2c. Our results uncover a molecular switch that translates neural activity into a specific transcriptional program promoting the maturation of PV+ interneurons at the appropriate developmental stage.

neuroscience↗

bioRxiv2024

Inhibition of Soluble Epoxide Hydrolase Reduces Inflammation and Myocardial Injury in Arrhythmogenic Cardiomyopathy

Previous studies have implicated persistent innate immune signaling in the pathogenesis of arrhythmogenic cardiomyopathy (ACM), a familial non-ischemic heart muscle disease characterized by life-threatening arrhythmias and progressive myocardial injury. Here, we provide new evidence implicating inflammatory lipid autocoids in ACM. We show that specialized pro-resolving lipid mediators are reduced in hearts of Dsg2mut/mut mice, a well characterized mouse model of ACM. We also found that ACM disease features can be reversed in rat ventricular myocytes expressing mutant JUP by the pro-resolving epoxy fatty acid (EpFA) 14,15-eicosatrienoic acid (14-15-EET), whereas 14,15-EE-5(Z)E which antagonizes actions of the putative 14,15-EET receptor, intensified nuclear accumulation of the desmosomal protein plakoglobin. Soluble epoxide hydrolase (sEH), an enzyme that rapidly converts pro-resolving EpFAs into polar, far less active or even pro-inflammatory diols, is highly expressed in cardiac myocytes in Dsg2mut/mut mice. Inhibition of sEH prevented progression of myocardial injury in Dsg2mut/mut mice and led to recovery of contractile function. This was associated with reduced myocardial expression of genes involved in the innate immune response and fewer pro- inflammatory macrophages expressing CCR2, which mediate myocardial injury in Dsg2mut/mut mice. These results suggest that pro-inflammatory eicosanoids contribute to the pathogenesis of ACM and, further, that inhibition of sEH may be an effective, mechanism-based therapy for ACM patients.

cell biology↗

bioRxiv2024

Genetic network analysis uncovers spatial variation in diversity and connectivity of a species presenting a continuous distribution

The conservation of genetic diversity and connectivity is essential for the long-term persistence and adaptive ability of a species. Recent calls have been made for the inclusion of genetic diversity and differentiation measures in the assessment, management, and conservation of species. However, the literature often lacks direction on how to do so for species with continuous distributions or no distinct breaks in genetic connectivity. There are many considerations to overcome when investigating genetic diversity and connectivity of such species. We combine multiple genetic network methodologies with more traditional population genetic analyses within a single framework to address the challenges of investigating population structure and quantifying variation in genetic diversity and connectivity of wide-ranging species with continuous distributions. We demonstrate the efficacy and applicability of our framework through a study on woodland caribou (Rangifer tarandus) occupying the boreal forest of Canada; a species of significant conservation concern. The dataset consisted of 4911 unique individuals genotyped at 9 microsatellite loci, which were subsequently partitioned into 103 spatial nodes to create a population-based genetic network. The Walktrap community detection algorithm was used to detect hierarchical population genetic structure within the study area and node-based network metrics such as mean inverse edge weight and clustering coefficient were used to quantify the variation in genetic connectivity across the range. Lastly, genetic diversity was assessed by calculating allelic richness and heterozygosity of the nodes making up the network. The community detection analysis identified two communities at the coarsest scale to nine communities at the optimal partition. A strong pattern of Isolation by Distance (IBD) was found across the range at multiple scales. Furthermore, signs of genetic erosion along the study areas southern boundaries were depicted by nodes presenting low genetic diversity and low centrality values. These results are important to the species status assessments in providing previously unavailable information on connectivity and diversity within and beyond the current local population units used in management. Our approach to quantify the patterns and extent of connectivity across the boreal range is comprehensive and could easily be adapted to other species. The results are robust and provide a solid foundation for the continued monitoring and recovery of the species.

ecology↗

bioRxiv2023

Monoclonal antibodies against human coronavirus NL63 spike

The COVID-19 pandemic has illustrated the potential for monoclonal antibody therapeutics as prophylactic and therapeutic agents against pandemic viruses. No such therapeutics currently exist for other human coronaviruses. NL63 is a human alphacoronavirus that typically causes the common cold and uses the same receptor, ACE2, as the highly pathogenic SARS-CoV and SARS-CoV-2 pandemic viruses. In a cohort of healthy adults, we characterised humoral responses against the NL63 spike protein. While NL63 spike and receptor binding domain-specific binding antibodies and neutralisation activity could be detected in plasma of all subjects, memory B cells against NL63 spike were variable and relatively low in frequency compared to that against SARS-CoV-2 spike. From these donors, we isolated a panel of antibodies against NL63 spike and characterised their neutralising potential. We identified potent neutralising antibodies that recognised the receptor binding domain (RBD) and other non-RBD epitopes within spike.

microbiology↗

bioRxiv2022

Continent-wide phylogenomic framework reveals introgression as a driver of intra-specific diversity and enriched molecular pathways in caribou

High intra-specific genetic diversity is associated with adaptive potential which is key for resilience to global change. However, high variation may also support deleterious alleles through genetic load, unless purged, thereby increasing the risk of inbreeding depression if population sizes decrease rapidly. Purging of deleterious variation has now been demonstrated in some threatened species. However, less is known about the costs of population declines and inbreeding in species with large population sizes and high genetic diversity even though this encompasses many species globally that have or are expected to undergo rapid population declines. Caribou is a species of ecological and cultural significance in North America with a continental-wide distribution supporting extensive phenotypic variation, but with some populations undergoing significant declines resulting in their at-risk status in Canada. We assessed intra-specific genetic variation, adaptive divergence, inbreeding, and genetic load across populations with different demographic histories using an annotated chromosome-scale reference genome and 66 whole genome sequences. We found high genetic diversity and nine phylogenomic lineages across the continent with adaptive diversification of genes, but also high genetic load among lineages. We also found highly divergent levels of inbreeding across individuals including the loss of alleles by drift (genetic erosion) but not purging, likely due to rapid population declines not allowing time for purging of deleterious alleles. As a result, further inbreeding may need to be mitigated through conservation efforts. Our results highlight the double-edged sword of genetic diversity that may be representative of other species-at-risk affected by anthropogenic activities.

genomics↗

bioRxiv2022

Incorporating selection pressures into risk predictions of chemical resistance evolution in pest organisms

Chemical resistance in pest organisms threatens global food security and human health, yet resistance issues are mostly dealt with reactively. Predictive models of resistance risk provide an avenue for field practitioners to implement proactive pest management but require knowledge of factors that drive resistance evolution. Despite the importance of chemical selection pressure on resistance evolution, poor availability of chemical usage data has limited the use of a general multi-species measure of selection pressure in predictive models. We demonstrate the use of pesticide product registrations as a predictor of resistance status and potential proxy of chemical selection pressure. Pesticide product registrations were obtained for 427 USA and 209 Australian agricultural arthropod pests, for 42 and 39 chemical Mode of Action (MoA) groups, respectively. We constructed Bayesian logistic regressions of resistance status as a function of the number of pesticide product registrations and two ecological traits, phagy and voltinism. Our models were well-supported with demonstrated power to discriminate between resistant and susceptible observations in both USA and Australian species sets using cross-validation. Importantly, we observed strong support for a positive association between pesticide products and resistance status. Our work expands the horizon for proactive management by quantitatively linking a proxy for selection pressure on pest species to different chemical MoAs. This proxy for selection pressure can be combined with ecological information to predict the resistance risk in agricultural pests. Because pesticide product registrations can typically be derived from publicly available data, we believe there is broad applicability to other agricultural pests such as weeds and fungi, and to other geographical regions beyond the USA and Australia.

evolutionary biology↗

bioRxiv2021

A multimodal study of a first episode psychosis cohort: potential markers of antipsychotic treatment resistance

Treatment resistant (TR) psychosis is considered to be a significant cause of disability and functional impairment. Numerous efforts have been made to identify the clinical predictors of TR. However, the exploration of molecular and biological markers is still at an early stage. To understand the TR condition and identify potential molecular and biological markers, we analyzed demographic information, clinical data, structural brain imaging data, and molecular brain imaging data in 7 Tesla magnetic resonance spectroscopy, from a first episode psychosis cohort that includes 138 patients. Age, gender, race, smoking status, duration of illness, and antipsychotic dosages were controlled in the analyses. We found that TR patients had a younger age at onset, more hospitalizations, more severe negative symptoms, a significant reduction in the volumes of the hippocampus (HP) and superior frontal gyrus (SFG), and a significant reduction in glutathione (GSH) levels in the anterior cingulate cortex (ACC), when compared to non-TR patients. The combination of multiple markers provided a better classification between TR and non-TR patients compared to any individual marker. Our study shows that ACC GSH, HP and SFG volumes, and age at onset could potentially be trait biomarkers for TR diagnosis, while hospitalization and negative symptoms could be used to evaluate the progression of the disease. Multimodal cohorts are essential in obtaining a comprehensive understanding of brain disorders.

neuroscience↗

bioRxiv2020

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

Pleistocene glacial cycles influenced the diversification of high-latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. For many taxa, research has focused on genetic patterns since the Last Glacial Maximum (LGM), however glacial cycles before the LGM likely impacted genomic variation which may influence contemporary genetic patterns. We investigate diversification and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 high-coverage whole genomes coupled with larger-scale mitochondrial data. Contrary to the well-established paradigm that caribou ecotypes and contemporary genetic diversity arose from two major lineages in separate refugia during the LGM, a Beringian-Eurasian (BEL) and a North American (NAL) lineage, we found that the major diversifications of caribou occurred much earlier at around 110 kya, the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20-30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results highlight the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high-latitude species.

evolutionary biology↗

bioRxiv2020

Longitudinal changes in brain metabolites in healthy subjects and patients with first episode psychosis (FEP): a 7-Tesla MRS study

Objective7 Tesla (T) longitudinal magnetic resonance spectroscopy (MRS) offers a precise measurment of metabolic levels in human brain via a non-invasive approach. Studying longitudinal changes in neurometabolites could help identify trait and state markers for diseases and understand inconsistent findings from different researchers due to differences in the age of study participants and duration of illness. This study is the first to report novel longitudinal patterns in young adulthood from both physiological and pathological viewpoints using 7T MRS. MethodsUtilizing a four-year longitudinal cohort with 38 first episode psychosis (FEP) patients (onset within 2 years) and 48 healthy controls (HC), the authors examined the annual percentage changes of 9 neurometabolites in 5 brain regions. ResultsBoth FEP patients and HC subjects were found to have significant longitudinal reductions in glutamate (Glu) in the anterior cingulate cortex (ACC). Only FEP patients were found to have a significant decrease over time in {gamma}-aminobutyric acid (GABA), N-acetyl aspartate (NAA), myo-inositol (mI), and total choline (tCho: phosphocholine plus glycerophosphocholine) in the ACC. Uniquely, glutathione (GSH) was found to have a near zero annual percentage change in both FEP patients and HC subjects in all 5 brain regions over a four-year timespan in young adulthood. ConclusionsGSH could be a trait marker for diagnostic applications at least in young adulthood. Glu, GABA, NAA, mI, and tCho in the ACC are associated with the patients status and could be state markers for mechanistic studies of psychotic disorders, including those for progressive pathological changes and medication effects in young adulthood.

neuroscience↗

bioRxiv2020

An autocrine Vitamin D-driven Th1 shutdown program can be exploited for COVID-19

Pro-inflammatory immune responses are necessary for effective pathogen clearance, but cause severe tissue damage if not shut down in a timely manner1,2. Excessive complement and IFN-{gamma}-associated responses are known drivers of immunopathogenesis3 and are among the most highly induced immune programs in hyper-inflammatory SARS-CoV2 lung infection4. The molecular mechanisms that govern orderly shutdown and retraction of these responses remain poorly understood. Here, we show that complement triggers contraction of IFN-{gamma} producing CD4+ T helper (Th) 1 cell responses by inducing expression of the vitamin D (VitD) receptor (VDR) and CYP27B1, the enzyme that activates VitD, permitting T cells to both activate and respond to VitD. VitD then initiates the transition from pro-inflammatory IFN-{gamma}+ Th1 cells to suppressive IL-10+ Th1 cells. This process is primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating superenhancers and recruiting c-JUN and BACH2, a key immunoregulatory transcription factor5-7. Accordingly, cells in psoriatic skin treated with VitD increased BACH2 expression, and BACH2 haplo-insufficient CD4+ T cells were defective in IL-10 production. As proof-of-concept, we show that CD4+ T cells in the bronchoalveolar lavage fluid (BALF) of patients with COVID-19 are Th1-skewed and that VDR is among the top regulators of genes induced by SARS-CoV2. Importantly, genes normally down-regulated by VitD were de-repressed in CD4+ BALF T cells of COVID-19, indicating that the VitD-driven shutdown program is impaired in this setting. The active metabolite of VitD, alfacalcidol, and cortico-steroids were among the top predicted pharmaceuticals that could normalize SARS-CoV2 induced genes. These data indicate that adjunct therapy with VitD in the context of other immunomodulatory drugs may be a beneficial strategy to dampen hyperinflammation in severe COVID-19.

immunology↗

bioRxiv2020

Brain capillary pericytes exert a substantial but slow influence on blood flow

The majority of the brains vasculature is comprised of intricate capillary networks lined by capillary pericytes. However, it remains unclear whether capillary pericytes contribute to blood flow control. Using two-photon microscopy to observe and manipulate single capillary pericytes in vivo, we find their optogenetic stimulation decreases lumen diameter and blood flow, but with slower kinetics than mural cells of upstream pial and pre-capillary arterioles. This slow, optogenetically-induced vasoconstriction was inhibited by the clinically-used vasodilator fasudil, a Rho kinase inhibitor that blocks contractile machinery. Capillary pericytes were also slower to constrict back to baseline following hypercapnia-induced dilation, and relax towards baseline following optogenetically-induced vasoconstriction. In a complementary approach, optical ablation of single capillary pericytes led to sustained local dilation and a doubling of blood cell flux in capillaries lacking pericyte contact. Altogether these data indicate that capillary pericytes contribute to basal blood flow resistance and slow modulation of blood flow throughout the capillary bed.

neuroscience↗

bioRxiv2018

Learning dynamical information from static protein and sequencing data

Many complex processes, from protein folding and virus evolution to brain activity and neuronal network dynamics, can be described as stochastic exploration of a high-dimensional energy landscape. While efficient algorithms for cluster detection and data completion in high-dimensional spaces have been developed and applied over the last two decades, considerably less is known about the reliable inference of state transition dynamics in such settings. Here, we introduce a flexible and robust numerical framework to infer Markovian transition networks directly from time-independent data sampled from stationary equilibrium distributions. Our approach combines Gaussian mixture approximations and self-consistent dimensionality reduction with minimal-energy path estimation and multi-dimensional transition-state theory. We demonstrate the practical potential of the inference scheme by reconstructing the network dynamics for several protein folding transitions, gene regulatory network motifs and HIV evolution pathways. The predicted network topologies and relative transition time scales agree well with direct estimates from time-dependent molecular dynamics data, stochastic simulations and phylogenetic trees, respectively. The underlying numerical protocol thus allows the recovery of relevant dynamical information from instantaneous ensemble measurements, effectively alleviating the need for time-dependent data in many situations. Owing to its generic structure, the framework introduced here will be applicable to high-throughput RNA and protein sequencing datasets and future cryo-electron-microscopy data, and can guide the design of new experimental approaches towards studying complex multiphase phenomena.

bioinformatics↗

bioRxiv2018

Genome-wide profiling of an enhancer-associated histone modification reveals the influence of asthma on the epigenome of the airway epithelium.

Asthma is a chronic airway disease driven by complex genetic-environmental interactions. The role of epigenetic modifications in bronchial epithelial cells (BECs) in asthma is poorly understood. We undertook genome-wide profiling of the enhancer-associated histone modification H3K27ac in BECs from people with asthma and healthy controls. We identified 49,903 regions exhibiting differential H3K27ac enrichment in asthma, clustered at genes associated with type-2-high asthma (CLCA1) and epithelial processes (EMT). Asthma dramatically influenced the BEC enhancer landscape and we identified asthma-associated Super-Enhancers encompassing genes encoding transcription factors (TP63) and enzymes regulating lipid metabolism (NOX4). We integrated published protein, epigenomic and transcriptomic datasets and identified epithelium-specific transcription factors associated with H3K27ac in asthma (TP73) and dynamic relationships between asthma-associated changes in H3K27ac, DNA methylation, genetic susceptibility and transcriptional profiles. Finally, we used a CRISPR-based approach to recapitulate the H3K27ac-asthma landscape in vitro and provide proof of principal that asthma-associated gene expression (SERPINB2) is driven in part by aberrant histone acetylation, validating the combination of genome-wide and epigenome-editing approaches in deciphering the molecular mechanisms underlying asthma pathogenesis.

genomics↗