Biology subjects

Dunn, J.

Publications and source records attributed to Dunn, J..

14 recordsLinked to original sources

bioRxiv2025

Different dopaminergic circuits defined by D2/D3 receptor availablity patterns show structure-specific links to memory in ageing

Cognitive ageing is marked by progressive decline in episodic memory and dopaminergic function, yet the extent to which individual differences in dopaminergic system integrity influence memory under motivational contexts remains unclear. In this study, we investigated how baseline D2/D3 receptor availability (BPND0) in key dopaminergic pathways relates to reward-modulated memory performance in healthy older adults. Thirty-three healthy seniors (aged 64-85) underwent two session concurrent MR-PET imaging with [1F]fallypride involving scene categorisation task with high- and low-motivational contexts. We quantified BPND0 across nine dopaminergic regions of interest and examined their relationships with recognition memory performance at short ([~]15m) and long ([~]24h) delays. Baseline D2/D3 receptor availability showed high test-retest reliability and regionally distinct profiles, suggesting it reflects a stable neurochemical characteristic in healthy ageing, and principal axis factor analysis revealed two partially independent dopaminergic subsystems (dorsal striatal vs mesolimbic) based on interindividual patterns in receptor densities. Region-specific associations further linked D2/D3 receptor availability to distinct memory outcomes. Higher caudate D2/D3 receptor availability was associated with a liberal response bias (increased hits and false alarms both), whereas higher putamen D2/D3 predicted more durable long-term memory retention. Greater thalamic D2/D3 receptor availability correlated with fewer short-term false memories, while greater D2/D3 receptor availability in the amygdala was associated with better recognition at longer delays. In contrast, higher midbrain (substantia nigra and ventral tegmental area) D2/D3 availability which was linked to poorer reward-related memory performance. These findings suggest several complementary dopaminergic circuits supporting episodic memory. Our results highlight dopaminergic neuromodulation as a key factor in cognitive ageing and a potential target for interventions to bolster memory in late life. Patient consent and ethics approvalAll subjects who were included in this study have provided their consent prior to their participation, following the guidelines of the ethics committee at University Hospital Magdeburg in Magdeburg, Germany.

neuroscience↗

bioRxiv2025

Effects of C3aR activated mast cells in eosinophilic esophagitis

BackgroundEosinophilic esophagitis is a chronic food induced allergic inflammatory disease of the esophagus. Eosinophil-depleting antibodies have not shown significant improvement in clinical symptoms, which has turned attention to mast cells. These cells also accumulate in the esophagus of EoE at levels that correlate with symptoms, demonstrate extensive activation including degranulation, correlate and remain elevated and poised for reactivation even in EoE patients in remission as defined by reduced eosinophil levels. Herein, we examine a mechanism of mast cell activation in EoE. MethodsEsophageal mast cell degranulation was quantitated by CD63 expression by flow cytometry. Mast cell degranulation activity of esophageal biopsies was examined employing a bioassay with human CD34 progenitor cell derived primary human mast cells. Bulk and single cell RNA sequencing data of the esophagus were analyzed for complement dysregulation and mast cell properties as a function of disease state. Human esophageal biopsies were stained for C3 and analyzed for C3a and C3 protein content. Primary human mast cells and fibroblasts were further interrogated by flow cytometry, immunostaining, and RNA sequencing. ResultsEsophageal mast cells demonstrated increased CD63 expression, a measure of degranulation, in subjects with active compared with remission EoE. Esophageal biopsy lysates induced mast cell degranulation. Analysis of esophageal bulk RNA sequencing data demonstrated that the mast cell marker CPA3 strongly correlated with C3AR1. Accordingly, the level of C3a receptor on esophageal mast cells was proportional with CD63 expression. C3AR1 expression was increased in the fibrostenotic endoscopic phenotype compared to normal appearing active EoE patients. Esophageal biopsies were notably enriched in the expression of multiple complement genes (including C3AR1, C3, CFB, C1QA, C1QB, and C1QC) some of which were increased in active vs remission EoE (C3AR1, CFB, C1QA, C1QB, and C1QC). Single cell RNA (scRNA) sequencing data revealed enrichment of C3 in fibroblasts at levels higher in EoE compared with non-EoE controls. The ratio of C3a/C3 protein levels in the esophagus was increased in EoE compared to control. Mast cells and fibroblasts have increased proximity in EoE compared with non-EoE control subjects. Additionally, C3a stimulated mast cells to express increased CD117 and release multiple EoE-relevant cytokines including fibroblast active mediators including granzyme B, which is enriched in esophageal mast cells. ConclusionTaken together, our findings present evidence for the interplay of mast cells and fibroblasts via C3a in the pathogenesis of EoE.

immunology↗

bioRxiv2025

Phylogeographic clustering of Salmonella enterica serovar Mississippi in the Southeastern United States indicates regional transmission pathways

Salmonella enterica subspecies enterica serovar Mississippi (S. Mississippi) is a polyphyletic serovar endemic in Australia, New Zealand, the United Kingdom, and the United States (USA). From 2018 to 2024, it was the 13th most frequently reported clinical Salmonella serovar in the USA. Its incidence in the USA is geographically focused on the Southeast. From 2018 to 2024, 78% of all S. Mississippi cases in the USA occurred in Southeastern states. The objective of this study was to determine the phylogeographic patterns of clinical S. Mississippi in the Southeastern USA using clinical S. Mississippi isolate sequencing data and metadata from ten state public health laboratories in the region. The resulting phylogeny, based on core single nucleotide polymorphism (SNP) differences, showed that S. Mississippi has five major clades (Ai, Aii, Bi, Bii, C), four of which are consistent with the results of previous studies. Clade Ai, which comprised 99% of study isolates, was systematically divided into seven subclades. County-level mapping of the clade Ai isolates revealed distinct geographical distributions at the clade and subclade levels. For example, subclade Ai1 was predominantly identified along the East Coast, while subclade Ai3 was primarily found in Western Tennessee. Simple linear regression showed a significant positive association (p < 0.01) between isolate-to-isolate genomic distance (SNP differences) and county-to-county geographic distance (km) at the clade and subclade levels. These findings provide insight into the transmission of S. Mississippi and may inform public health hypothesis generation. IMPORTANCEThis study enhances understanding of S. Mississippi transmission pathways and reveals localized phylogeographic clustering within the Southeastern USA. Classification of this serovar with consideration to geographical clustering may improve surveillance, investigation, and control efforts. Geographical clustering of this serovar within this region suggests local or regional transmission pathways and enzootic reservoirs, which could be related to environmental or regional food exposures. Identifying possible environmental sources, enzootic reservoirs, or climate factors contributing to human infection with this serovar within the Southeastern USA could lead to prevention recommendations. Knowledge of exposure patterns for S. Mississippi may facilitate development and implementation of targeted control strategies and interventions locally that can limit further exposure and prevent illness.

genomics↗

bioRxiv2024

Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets

Soil-transmitted helminths (STHs) are intestinal pathogens affecting over a billion people worldwide. STH control relies on microsopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance, however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remains unclear. Using low-coverage genome sequencing, we assessed the presence of STHs in worm, faecal and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We defined substancial copy number and sequence variants in current diagnostic targets and validated the impact of genetic variants on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.

genomics↗

bioRxiv2024

Thalamic blood flow and EEG frequency band power during hyperventilation in idiopathic generalized epilepsy

Absence seizures in idiopathic generalised epilepsy (IGE) involve thalamo-cortical circuits. Hyperventilation (HV) is a standard technique to trigger epileptiform discharges and absence seizures in IGE. HV also increases electroencephalography (EEG) delta band power and decreases global cerebral blood flow (CBF). The relationships between HV, EEG band power, and regional CBF have not been investigated in the same patients at the same time. We compared the effects of hyperventilation between 13 individuals with IGE and 18 healthy controls on thalamic CBF assessed with pseudo-continuous Arterial Spin Labelling (pCASL) simultaneously to EEG frequency band power during three periods of hyperventilation interleaved with three periods of rest, normalised to each participants pre-HV values. Pre-HV, there were no differences between patients and controls. During the three rest periods combined, patients had higher normalised respiratory rates but no difference in CBF or EEG band power compared with controls. During HV, CBF decreases were similar in controls and IGE patients in cortical gray matter (37.1{+/-}1.3% in controls, 37.9{+/-}2.0% in patients) and basal ganglia (35.6{+/-}2.0% in controls, 33.3{+/-}2.3% in patients). In the thalamus, CBF decreased by 35.5{+/-}1.9% in controls, but only by 27.1{+/-}2.5% in patients (p=0.011). Delta band power increased by 42% in patients, but only by 27% in patients (p<0.045). Both controls and patients thalamic CBF significantly decreased as a function of respiratory rate, but the relationship was weaker in patients (rho -0.38 [0.95 confidence interval lower limit -0.629; upper limit -0.059] vs -0.51 [-0.698; -0.255] in controls). Delta power correlated with thalamic CBF only in controls (rho -0.21 [-0.388; -0.017]) but not in patients (rho -0.1 [-0.345; 0.157]). EEG power and respiratory rate were not significantly correlated in either group. This first study of the interrelationships between HV, blood flow, and EEG band power suggests that regional thalamic abnormalities of blood flow regulation, or a neurophysiological abnormality leading to smaller reactive blood flow changes, may underlie HV-associated EEG activation. Graphical abstract textIn this first investigation of combined hyperventilation, blood flow and EEG band power measurements in idiopathic generalised epileptic patients and healthy subjects, we revealed that localized thalamic blood flow regulatory problems or neurophysiological disorders caused minor reactive blood flow variations and may cause hyperventilation-associated EEG activation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/586742v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@12a5ebeorg.highwire.dtl.DTLVardef@b22944org.highwire.dtl.DTLVardef@b335dforg.highwire.dtl.DTLVardef@195c5e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Single-Cell Peripheral Immunoprofiling of Lewy Body Disease in a Multi-site Cohort

Studies implicated peripheral organs involvement in the development of Lewy body disease (LBD), a spectrum of neurodegenerative diagnoses that include Parkinsons Disease (PD) without or with dementia (PDD) and dementia with Lewy bodies (DLB). This study characterized peripheral immune responses unique to LBD at single-cell resolution. Peripheral mononuclear cell (PBMC) samples were collected from sites across the U.S. The diagnosis groups comprise healthy controls (HC, n=164), LBD (n=132), Alzheimers disease dementia (ADD, n=98), other neurodegenerative disease controls (NDC, n=21), and immune disease controls (IDC, n=14). PBMCs were activated with three stimulants, stained by surface and intracellular signal markers, and analyzed by flow cytometry, generating 1,184 immune features. Our model classified LBD from HC with an AUROC of 0.90{+/-}0.06. The same model distinguished LBD from ADD, NDC, IDC, or other common conditions associated with LBD. Model predictions were driven by pPLC{gamma}2, p38, and pSTAT5 signals from specific cell populations and activations.

neuroscience↗

bioRxiv2023

Spiral NeuroString: High-Density Soft Bioelectronic Fibers for Multimodal Sensing and Stimulation

Bioelectronic fibers hold promise for both research and clinical applications due to their compactness, ease of implantation, and ability to incorporate various functionalities such as sensing and stimulation. However, existing devices suffer from bulkiness, rigidity, limited functionality, and low density of active components. These limitations stem from the difficulty to incorporate many components on one-dimensional (1D) fiber devices due to the incompatibility of conventional microfabrication methods (e.g., photolithography) with curved, thin and long fiber structures. Herein, we introduce a fabrication approach, "spiral transformation'', to convert two-dimensional (2D) films containing microfabricated devices into 1D soft fibers. This approach allows for the creation of high density multimodal soft bioelectronic fibers, termed Spiral NeuroString (S-NeuroString), while enabling precise control over the longitudinal, angular, and radial positioning and distribution of the functional components. We show the utility of S-NeuroString for motility mapping, serotonin sensing, and tissue stimulation within the dynamic and soft gastrointestinal (GI) system, as well as for single-unit recordings in the brain. The described bioelectronic fibers hold great promises for next-generation multifunctional implantable electronics.

bioengineering↗

bioRxiv2023

Deep Whole-Genome Resequencing of Marek's Disease Virus Strains Reveals Intrastrain Variation

Current strategies to understand the molecular basis of Mareks disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988GenBank.BAC diverged from CVI988Pirbright.lab and CVI988USDA.PA.field. Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988GenBank.BAC that were not present in either CVI988Pirbright.lab or CVI988USDA.PA.field. Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.

microbiology↗

bioRxiv2021

Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19

Previous reports show that Ly49+CD8+ T cells can suppress autoimmunity in mouse models of autoimmune diseases. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various autoimmune diseases. Moreover, KIR+CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from Celiac disease (CeD) patients leukocytes in vitro. Furthermore, we observe elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Expanded KIR+CD8+ T cells from these different diseases display shared phenotypes and similar T cell receptor sequences. These results characterize a regulatory CD8+ T cell subset in humans, broadly active in both autoimmune and infectious diseases, which we hypothesize functions to control self-reactive or otherwise pathogenic T cells. One-Sentence SummaryHere we identified KIR+CD8+ T cells as a regulatory CD8+ T cell subset in humans that suppresses self-reactive or otherwise pathogenic CD4+ T cells.

immunology↗

bioRxiv2021

The evolutionary origins of primate scleral coloration

Primate gaze following behaviors are of great interest to evolutionary scientists studying social cognition. The ability of an organism to determine a conspecifics likely intentions from their gaze direction may confer an advantage to individuals in a social group. This advantage could be cooperative and/or competitive. Humans are unusual in possessing depigmented sclerae whereas most other extant primates, including the closely related chimpanzee, possess dark scleral pigment. The origins of divergent scleral morphologies are currently unclear, though human white sclerae are often assumed to underlie our hyper-cooperative behaviors. Here, we use phylogenetic generalized least squares (PGLS) analyses with previously generated species-level scores of proactive prosociality, social tolerance (both n=15 primate species), and conspecific lethal aggression (n=108 primate species) to provide the first quantitative, comparative test of three complementary hypotheses. The cooperative eye [M. Tomasello, B. Hare, H. Lehmann, J. Call, J. Hum. Evol. 52, 314-320 (2007)] and self-domestication [B. Hare, Annu. Rev. Psychol. 68, 155-186 (2017)] explanations predict white sclerae to be associated with cooperative, rather than competitive, environments. The gaze camouflage hypothesis [H. Kobayashi, S. Kohshima, J. Hum. Evol. 40, 419-435 (2001)] predicts that dark scleral pigment functions as gaze direction camouflage in competitive social environments. We show that white sclerae in primates are associated with increased cooperative behaviors whereas dark sclerae are associated with reduced cooperative behaviors and increased intra-specific lethal aggression. Our results lend support to all three hypotheses of scleral evolution, suggesting that primate scleral morphologies evolve in relation to variation in social environment.

animal behavior and cognition↗

bioRxiv2019

A machine learning based approach to the segmentation of micro CT data in archaeological and evolutionary sciences

Segmentation of high-resolution tomographic data is often an extremely time-consuming task and until recently, has usually relied upon researchers manually selecting materials of interest slice by slice. With the exponential rise in datasets being acquired, this is clearly not a sustainable workflow. In this paper, we apply the Trainable Weka Segmentation (a freely available plugin for the multiplatform program ImageJ) to typical datasets found in archaeological and evolutionary sciences. We demonstrate that Trainable Weka Segmentation can provide a fast and robust method for segmentation and is as effective as other leading-edge machine learning segmentation techniques.

evolutionary biology↗

bioRxiv2019

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in \"fed\" mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome.

genomics↗

bioRxiv2017

High Frequency Actionable Pathogenic Exome Mutations in an Average-Risk Cohort

Whole exome sequencing (WES) is increasingly utilized in both clinical and non-clinical settings, but little is known about the utility of WES in healthy individuals. In order to determine the frequency of both medically actionable and non-actionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multi-omics profiling study at Stanford University. We assessed exomes for rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We used American College of Medical Genetics (ACMG) guidelines were used for the classification of rare sequence variants, and additionally we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes, including 6 (9%) with mutations in genes not currently included in the ACMGs list of 59 actionable genes. This number is higher than that reported in previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 60 participants (89%) had non-actionable findings identified including 57 who were found to be mutation carriers for recessive diseases and 21 who have increased Alzheimers disease risk due to heterozyg ous or homozygous APOE e4 alleles (18 participants had both). These results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.

genomics↗

bioRxiv2017

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of two distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Our analyses discern two biologically distinct variants of anaplastic meningioma with potential prognostic and therapeutic significance.

genomics↗