Biology subjects

Barker, D.

Publications and source records attributed to Barker, D..

11 recordsLinked to original sources

bioRxiv2026

Regional cerebral arterial elasticity is associated with cardiovascular health in cognitively healthy older adults

Ageing is often associated with a decline in cardiovascular and cerebrovascular health. This study examines the relationship between cerebral arterial elasticity and measures of cardiovascular health, as well as longitudinal changes in cerebral arterial elasticity over a 1.5 year interval. The pulse relaxation function (PReFx) is a measure of regional cerebral arterial elasticity derived using diffuse optical tomography (pulse-DOT). PReFx was measured over the anterior brain, including the frontal lobes and anterior sections of temporal and parietal regions that are especially vulnerable to vascular and cognitive ageing. We examined relationships between PReFx and measures of four cardiovascular risk factors (CVRF; i.e., hypertension, cholesterol, diabetes, obesity), as well as CVRF burden (i.e., number of CVRFs) in the highly active and cognitively healthy ACTIVate cohort (60-70 years). We replicated the well-established relationship between PReFx and both age and cardiorespiratory fitness, and examined associations between PReFx, measures of cardiovascular health and CVRF burden. Higher CVRF burden was linearly associated with lower cerebral arterial elasticity. The relationship between age and cerebral arterial elasticity was partially mediated by pulse pressure, an index of hypertension. PReFx declined significantly in as little as 1.5 years, and the effect did not vary with baseline level of any of the four CVRFs. We conclude that PReFx shows promise as a putative biomarker for monitoring cerebrovascular ageing in healthy older adults.

neuroscience↗

bioRxiv2025

Region-specific associations between cerebral arterial elasticity and grey matter volume: Evidence for lateral prefrontal vulnerability

BackgroundAgeing is associated with increased cardiovascular health risks and disproportionate atrophy in frontotemporal brain. Regional cerebral arterial elasticity correlates with regional grey matter volume, with stronger associations frontally and in older adults. Cardiorespiratory fitness (CRF) is linked to preserved brain structure and greater arterial elasticity, while sex differences exist in the timing of vascular versus structural changes. This study examines whether regional cerebral arterial elasticity in frontotemporal cortex mediates the association between age and corresponding grey matter volume decline, and whether sex and/or CRF moderate this relationship. MethodsWe analysed data from 162 healthy adults (60-70 years) with structural MRI and diffuse optical tomography of the cerebral arterial pulse (Pulse-DOT) from the ACTIVate cohort. CRF was estimated from demographic and physiological measures. Pulse Relaxation Function (PReFx), an optical index of regional arterial elasticity, was measured across 28 frontal, temporal, and parietal regions of interest (ROI). Grey matter (GM) volume was quantified for corresponding ROIs. Mediation and moderated mediation models tested whether PReFx mediated the relationship between age and GM volume at bilateral frontal and temporal ROIs, and whether biological sex or CRF moderated this relationship. ResultsRegional bivariate correlations identified associations between age, PReFx and GM volume across multiple ROIs, which PReFx and GM volume being associated primarily in left frontal and temporal areas. PReFx partially mediated the effect of age on GM volume in a left mid-inferior frontal ROI, accounting for approximately 16% of the total age effect and this relationship was only evident in females. Although higher CRF was associated with greater PReFx, it did not moderate the relationship between age, PReFx and GM volume. ConclusionsConsistent with cascade models of neurovascular aging, cerebral arterial stiffening was found to partially explain the effect of increasing age on frontal GM volume, even in this highly age-restricted and high functioning cohort. This effect was only significant over the left prefrontal cortex, consistent with greater vulnerability of frontal brain and associated cognitive functions. It was also exclusively present in females, who had better cardiovascular health, larger grey matter volume and greater arterial elasticity than males. These findings are consistent with pulse-DOT measures of cerebral arterial elasticity being more sensitive to subclinical brain structural variability.

neuroscience↗

bioRxiv2025

A Mycobacterium tuberculosis Mbox controls a conserved, small upstream ORF via a translational expression platform and rho-dependent termination of transcription

Magnesium is vital for bacterial survival, and its homeostasis is tightly regulated. Intracellular pathogens like Mycobacterium tuberculosis (Mtb) often face host-mediated magnesium limitation, which can be counteracted by upregulating the expression of Mg2+ transporters. This upregulation may be via Mg2+-sensing regulatory RNA such as the Bacillus subtilis ykoK Mbox riboswitch, which acts as a transcriptional "OFF-switch" under high Mg2+ conditions. Mtb encodes two Mbox elements with strong similarity to the ykoK Mbox. In the current study, we characterize the Mbox encoded upstream of the Mtb pe20 operon, which is required for growth in low Mg2+ combined with low pH. We show that this switch operates via a translational expression platform and Rho-dependent transcription termination, which is the first such case reported for an Mbox. Moreover, we show that the switch directly controls a small ORF (uORF2) encoded upstream of pe20. We have annotated this highly expressed and highly conserved uORF as rv1805A, but its role remains unclear. Interestingly, a homologous gene exists outside the Mbox-regulated context, suggesting functional importance beyond magnesium stress. Overall, this study uncovers a dual mechanism of riboswitch regulation in Mtb, combining translational control with Rho-mediated transcription termination. These findings expand our understanding of RNA-based gene regulation in mycobacteria, with implications for pathogenesis and stress adaptation.

molecular biology↗

bioRxiv2024

Novel wheat germ agglutinin-based mass cytometry cell barcoding reagent for heterogeneous, live or fixed sample

Sample multiplexing in flow cytometry is a powerful technique which allows for reduction of error, inclusion of control samples for batch effect correction, and reduction in both time and consumable usage. Current industry standard for barcoding in mass cytometry is an intracellular reagent, which requires fixation and permeabilization of sample prior to barcoding. We developed a barcode using the ubiquitous and well-tolerated membrane labeling lectin, wheat germ agglutinin. This barcode effectively labels all tested cell types, both live and fixed. We determine that barcode yields, or the ratio of debarcoded cells to total input cells, is stable in live pooled sample for at least an hour. This barcode does not show differential performance across major PBMC lineages. Thus, this universal wheat germ agglutinin-based barcode represents an advance in gentle, non-reactive cell surface barcoding for live cells.

cell biology↗

bioRxiv2023

Mycobacterium tuberculosis employs atypical and different classes of B12 switches to control separate operons

Vitamin B12 (B12), an essential cofactor in all domains of life, is produced de novo by only a small subset of prokaryotes, but B12-sensing riboswitches are some of the most widely distributed riboswitches in bacteria. Mycobacterium tuberculosis, the causative agent of the ongoing tuberculosis pandemic, encodes two distinct vitamin B12 riboswitches. One controls the expression of metE, encoding a B12-independent methionine synthase, while the other is located upstream of ppe2, a PE/PPE family gene whose function is still unresolved. Here, we analyse ligand sensing, secondary structure architecture, and gene expression control mechanisms of these two riboswitches. Our results provide the first evidence of direct ligand binding by metE and ppe2 riboswitches and show that the two switches exhibit different preferences for natural isoforms of B12, use distinct regulatory and structural elements, and act as translational OFF switches. Based on our results, we propose that the ppe2 switch represents a new Class IIc of B12-sensing riboswitches. Moreover, we have identified small translated open reading frames (uORFs) upstream of both metE and ppe2, which modulate the expression of the respective downstream genes in opposite directions. Translation of the metE riboswitch uORF suppresses MetE expression, while translation of the uORF in the ppe2 switch is essential for PPE2 expression via the synthesis of a uORF-PPE2 fusion protein. In summary, our findings reveal an unexpected diversity and complexity of B12-dependent cis-regulation in M. tuberculosis, with potential implications for host-pathogen interactions.

molecular biology↗

bioRxiv2023

Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from leader- over cryptic promoters

CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbor extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposasons. Cbp1 recruits Cren7 forming together chimeric chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third HTH domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.

microbiology↗

bioRxiv2022

Huntingtin turnover: Modulation of huntingtin degradation by cAMP-dependent protein kinase A (PKA) phosphorylation of C-HEAT domain Ser2550

Huntingtons disease (HD) is a neurodegerative disorder caused by an inherited unstable HTT CAG repeat that expands further, thereby eliciting a disease process that may be initiated by polyglutamine-expanded huntingtin or a short polyglutamine-product. Phosphorylation of selected candidate residues is reported to mediate polyglutamine-fragment degradation and toxicity. Here to support the discovery of phospho-sites involved in the life-cycle of (full-length) huntingtin, we employed mass spectrometry-based phosphoproteomics to systematically identify sites in purified huntingtin and in the endogenous protein, by proteomic and phospho-proteomic analyses of members of an HD neuronal progenitor cell panel. Our results bring total huntingtin phospho-sites to 95, with more located in the N-HEAT domain relative to numbers in the Bridge and C-HEAT domains. Moreover, phosphorylation of C-HEAT Ser2550 by cAMP-dependent protein kinase (PKA), the top hit in kinase activity screens, was found to hasten huntingtin degradation, such that levels of the catalytic subunit (PRKACA) were inversely related to huntingtin levels. Taken together these findings highlight categories of phospho-sites that merit further study and provide a phospho-site kinase pair (pSer2550-PKA) with which to investigate the biological processes that regulate huntingtin degradation and thereby influence the steady state levels of huntingtin in HD cells.

biochemistry↗

bioRxiv2021

Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding

Antimicrobial resistance in Gram-negative bacteria is one of the greatest threats to global health. New antibacterial strategies are urgently needed, and the development of antibiotic adjuvants that either neutralize resistance proteins or compromise the integrity of the cell envelope is of ever-growing interest. Most available adjuvants are only effective against specific resistance proteins. Here we demonstrate that disruption of cell envelope protein homeostasis simultaneously compromises several classes of resistance determinants. In particular, we find that impairing DsbA-mediated disulfide bond formation incapacitates diverse {beta}-lactamases and destabilizes mobile colistin resistance enzymes. Furthermore, we show that chemical inhibition of DsbA sensitizes multidrug-resistant clinical isolates to existing antibiotics and that the absence of DsbA, in combination with antibiotic treatment, substantially increases the survival of Galleria mellonella larvae infected with multidrug- resistant Pseudomonas aeruginosa. This work lays the foundation for the development of novel antibiotic adjuvants that function as broad-acting resistance breakers. IMPACT STATEMENTDisruption of disulfide bond formation sensitizes resistant Gram- negative bacteria expressing {beta}-lactamases and mobile colistin resistance enzymes to currently available antibiotics.

microbiology↗

bioRxiv2021

Lateral Preoptic Area Neurons Signal Cocaine Self-Administration Behaviors

The lateral preoptic area is implicated in numerous aspects of substance use disorder. In particular, the lateral preoptic area is highly sensitive to the pharmacological properties of psychomotor stimulants, and its activity promotes drug-seeking in the face of punishment and reinstatement during abstinence. Despite the lateral preoptic areas complicity in substance use disorder, how precisely lateral preoptic area neurons encode the individual components of drug self-administration has not been ascertained. To bridge this gap, we examined how the firing of single lateral preoptic area neurons correlates with three discrete elements of cocaine self-administration: 1) drug-seeking (pre-response), 2) drug-taking (response), and 3) receipt of the cocaine infusion. A significant subset of lateral preoptic area neurons responded to each component with a mix of increases and decreases in firing-rate. A majority of these neurons encoded the operant response with increases in spiking, though responses during the drug-seeking, taking, and reciept windows were highly correlated.

neuroscience↗

bioRxiv2019

Genetic overlap between psychiatric disorders and neuropsychiatric symptoms in HD

Huntingtons disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized exam of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor symptoms in HD, but genetic factors influencing cognitive and psychiatric presentations are unknown. We tested the hypothesis that psychiatric and cognitive symptoms in HD are influenced by the same common genetic variation as in the general population by constructing polygenic risk scores from large genome-wide association studies of psychiatric and neurodegenerative disorders, and of intelligence, and testing for correlation with the presence of psychiatric and cognitive symptoms in a large sample (n=5160) of HD patients. Polygenic risk score for major depression was associated specifically with increased risk of depression in HD, as was schizophrenia risk score with psychosis and irritability. Cognitive impairment and apathy were associated with reduced polygenic risk score for intelligence. In general, polygenic risk scores for psychiatric disorders, particularly depression and schizophrenia, are associated with increased risk of the corresponding psychiatric symptoms in HD, suggesting a common genetic liability. However, the genetic liability to cognitive impairment and apathy appears to be distinct from other psychiatric symptoms in HD. No associations were observed between HD symptoms and risk scores for other neurodegenerative disorders. These data provide a rationale for treatments effective in depression and schizophrenia to be used to treat depression and psychotic symptoms in HD.

genetics↗

bioRxiv2019

Huntington's disease onset is determined by length of uninterrupted CAG, not encoded polyglutamine, and is modified by DNA maintenance mechanisms

The effects of variable, glutamine-encoding, CAA interruptions indicate that a property of the uninterrupted HTT CAG repeat sequence, distinct from huntingtins polyglutamine segment, dictates the rate at which HD develops. The timing of onset shows no significant association with HTT cis-eQTLs but is influenced, sometimes in a sex-specific manner, by polymorphic variation at multiple DNA maintenance genes, suggesting that the special onset-determining property of the uninterrupted CAG repeat is a propensity for length instability that leads to its somatic expansion. Additional naturally-occurring genetic modifier loci, defined by GWAS, may influence HD pathogenesis through other mechanisms. These findings have profound implications for the pathogenesis of HD and other repeat diseases and question a fundamental premise of the "polyglutamine disorders".

genetics↗