Biology subjects

Doyle, A.

Publications and source records attributed to Doyle, A..

10 recordsLinked to original sources

bioRxiv2026

Pancreatic progenitor cells respond to laminar shear stress with transcriptomic changes, accompanied by reduced YAP1 activity

The human pancreas secretes digestive fluid that flows through an extensive ductal network before emptying into the duodenum. However, little is known about how hydrodynamic forces influence pancreatic function and development. We hypothesized that pancreatic cells respond to physiological levels of fluid shear stress. In this study, we developed a microfluidic system featuring reversible sealing between the device layer and the cell culture substrate, enabling (1) conventional open-well cell culture prior to fluid shear stress application and (2) selective patterning of proteins and cells for migration studies. Channel dimensions were chosen to support 24-hour perfusion using standard syringe pumps. Using this platform, we investigated effects of physiological shear stress levels representing basal and activated pancreatic function (2, 8 and 33 mPa) on human iPSC-derived pancreatic progenitor cells. Pancreatic progenitor cells exhibit graded sensitivity to shear stress at the transcriptomic level. Specifically, shear stress upregulated expression of cell cycle-related gene sets; endocrine-associated genes including NEUROG3; and Notch receptor ligands (DLL1, DLL3) in a magnitude-dependent manner. The exposure to unidirectional fluid flow also resulted in a reduction in YAP1 protein content, decreased WWTR1 gene expression, and downregulation of YAP/TAZ target genes. Furthermore, barrier-based migration assays under shear stress revealed that cell patches expanded their boundaries both along and against the flow, with greater distance in the direction of flow. Our system and findings may help lay the foundation for understanding biophysical regulation of developmental processes in a physiologically important, yet hard-to-access, epithelial model system.

bioengineering↗

bioRxiv2024

Manipulation of Host Cholesterol by SARS-CoV-2

Cholesterol homeostasis relies on lysosomes, which release free cholesterol from degraded lipids. We show that SARS-CoV-2 blocks lysosomal cholesterol export through its protein ORF3a. ORF3a binds the HOPS subunit VPS39, and disrupting this interaction restores cholesterol trafficking. Two mechanisms underlie this defect. First, ORF3a-VPS39 interaction traps the sorting receptor CI-MPR and the retrieval complex retromer in endosomes/lysosomes, impairing trafficking of the cholesterol transporter NPC2. Retromer deletion reproduced these defects. Second, ORF3a reduces bis(monoacylglycerol)phosphates (BMPs), lysosomal lipids required for cholesterol export. Lipidomics and proteomics revealed altered metabolism of BMP precursors, mitochondrial phosphatidylglycerols (PGs), and reduced mitochondrial proteins at lysosomes. ORF3a-VPS39 interaction decreased lysosome-mitochondrion membrane contact sites (MCS), excluding autophagy or mitochondrion-derived vesicles as routes for PG transfer. VPS39 deletion decreased the MCS and BMPs. These findings identify VPS39 as a regulator of NPC2 trafficking and BMP biosynthesis and reveal that ORF3a disrupts both pathways to block cholesterol egress.

cell biology↗

bioRxiv2024

Inferring the composition of the blood plasma proteome by a human proteome distribution atlas

The plasma proteome is maintained by the influx and efflux of proteins from surrounding organs and cells. To quantify the extent different organs and cells contribute to the plasma proteome composition, we developed a mass spectrometry-based proteomics strategy to infer the origin of proteins detected in human plasma in health and disease. First, we constructed an extensive human proteome atlas from 18 vascularized organs and the most abundant cell types in blood. Second, the atlas was interfaced with previous RNA/protein atlases to objectively define proteome wide protein-organ associations to enable both the inference of origin and the reproducible quantification of organ-specific proteins in plasma. We demonstrate that the resource can determine disease-specific quantitative changes of organ-enriched protein panels in three separate patient cohorts with infection, pancreatitis, and myocardial injury. The strategy can be extended to other diseases to advance our understanding of the processes contributing to plasma proteome dynamics.

systems biology↗

bioRxiv2022

Validity of Optical Heart Rate Measurement in Commercially Available Wearable Fitness Tracking Devices

BackgroundWearable fitness tracking devices have risen in popularity for athletes and the general population and are increasingly integrated into smartwatch technology. Many devices incorporate optical heart rate (HR) measurement by photoplethysmography which provides data used to monitor and track exercise training intensities, progress, and other health and fitness related parameters. ObjectiveTo determine the validity of optical heart rate measurement in three fitness tracking devices while resting, walking, and running. MethodsTwenty subjects (10 male, 10 female) completed the research study based on the ANSI/CTI standards for physical activity monitoring of heart rate under 4 different conditions: sedentary (SED), treadmill walking (WLK), running (RUN), and dynamic running/walking (DYN). Subjects wore 3 optical heart rate devices: Polar OH1 (OH1) on the right forearm, Apple Watch 4 (AW4) on the right wrist and Garmin Forerunner 945 (FR945) on the left wrist. A Polar H10 (H10), a chest strap device, was the criterion HR measurement device. SED, WLK, and RUN were all 7-minute protocols with 1 minute of standing, 5 minutes of prescribed activity, and 1 final minute of standing. The DYN protocol was a 12-minute protocol with 1 minute of standing, 10 minutes of variable intensity walking and running, and 1 minute of standing. Raw HR data was extracted from each device and temporally aligned with the criterion H10 HR data for analysis. ResultsThe mean absolute deviation (MAD, measured in beats per minute) for the three experimental devices (OH1, AW4, FR945, respectively) for SED was 1.31, 1.33, and 2.03; for WLK was 2.79, 2.58, and 5.19; for RUN were 4.00, 4.29, and 6.51; and for DYN was 2.60, 2.44, and 2.44. The mean absolute percent error (MAPE) for the three experimental devices (OH1, AW4, FR945, respectively) for SED was 1.78%, 1.89%, and 2.81%; for WLK was 3.15%, 3.18%, and 5.93%; for RUN was 3.43%, 3.51%, and 5.25%; and for DYN was 2.05%, 1.95%, and 5.47%. The intraclass correlation for each device across all conditions was .991 (OH1), .984 (AW4), and .697 (FR945). ConclusionsAt rest, and during both steady-state and variable-speed treadmill walking and running, the Polar OH1, Garmin Forerunner 945, and Apple Watch 4 optical HR monitors demonstrated a level of accuracy well within that required by the ANSI/CTA Standard (2018) for physical activity monitoring devices for heart rate measurement (i.e., <10% Mean Absolute Percent Error). Therefore, consumers can have confidence that these devices provide HR data with accuracy that conforms to the performance criteria recommended for consumer electronics.

physiology↗

bioRxiv2022

Classification of electrically-evoked compound action potentials in the parkinsonian subthalamic nucleus of non-human primates

Electrically evoked compound action potentials (ECAPs) generated in the subthalamic nucleus (STN) contain features that may be useful for titrating deep brain stimulation (DBS) therapy for Parkinsons disease. Delivering a strong therapeutic effect with DBS therapies, however, relies on selectively targeting neural pathways to avoid inducing side effects. In this study, we investigated the spatiotemporal features of ECAPs in and around the STN across parameter sweeps of stimulation current amplitude, pulse width, and electrode configuration, and used a linear classifier of ECAP responses to predict electrode location. Four non-human primates were implanted unilaterally with either a directional (n=3) or non-directional (n=1) DBS lead targeting the sensorimotor STN. ECAP responses were characterized by primary features (within 1.6 ms after a stimulus pulse) and secondary features (between 1.6-7.4 ms after a stimulus pulse). Using these ECAP features, a linear classifier was able to accurately differentiate electrodes within the STN versus dorsal to the STN in all four subjects. ECAP responses varied systematically with recording and stimulating electrode locations, which provides a subject-specific neuroanatomical basis for selecting electrode configurations in the treatment of Parkinsons disease with DBS therapy.

neuroscience↗

bioRxiv2021

Visualization of trigeminal ganglion sensory neuronal signaling regulated by Cdk5

The mechanisms underlying facial and oral pain are still incompletely understood, posing major therapeutic challenges. Cyclin-dependent kinase 5 (Cdk5) is a key neuronal kinase involved in pain signaling. However, the regulatory roles of Cdk5 in orofacial pain signaling and the possibility of therapeutic intervention at the level of mouse trigeminal ganglion primary neurons remain elusive. In this study, we used optimized intravital imaging to directly compare trigeminal neuronal activities after mechanical, thermal, and chemical stimulation. We then tested whether facial inflammatory pain in mice could be alleviated by the Cdk5 inhibitor peptide TFP5. We demonstrated regulation of total Ca2+ intensities by Cdk5 activity using transgenic and knockout mouse models. In mice with orofacial inflammation, application of TFP5 specifically decreased total Ca2+ intensities in response to noxious stimuli. It also alleviated inflammation-induced allodynia by inhibiting activation of trigeminal peripheral sensory neurons. Cdk5 inhibitors may provide promising non-opioid candidates for pain treatment.

neuroscience↗

bioRxiv2020

Linking scales of life-history variation with population structure in Atlantic cod

It is increasing recognised that sustainable exploitation of marine fish requires the consideration of population diversity and associated productivity. This study used a combination of genotypic screening and phenotypic traits to define the scale of population structuring in Atlantic cod inhabiting the northern North Sea (ICES 4a) and Scottish west coast (6a). The genetic analysis indicated an isolation by distance pattern with an even finer scale structuring than previously reported, that persisted over a decade and between feeding and spawning seasons. Spatial variation in phenotypic traits reflected genetic variation with cod maturing later and at a larger size near the Viking Bank in 4a. The identified population structuring provides an explanation for differences in historic changes in maturation schedules and the temperature exposure recorded in previous electronic tagging studies. The study also highlights how the mismatch between stock divisions and population units is leading to a misunderstanding about stock recovery.

ecology↗

bioRxiv2019

Dose-dependent effects of transcranial alternating current stimulation on spike timing in awake nonhuman primates

Weak extracellular electric fields can influence spike timing in neural networks. Approaches to impose such fields on the brain in a noninvasive manner have high potential for novel treatments of neurological and psychiatric disorders. One of these methods, transcranial alternating current stimulation (TACS), is hypothesized to affect spike timing and cause neural entrainment. However, the conditions under which these effects occur in-vivo are unknown. Here, we show that TACS modulates spike timing in awake nonhuman primates (NHPs) in a dose-dependent fashion. Recording single-unit activity from pre-and post-central gyrus regions in NHPs during TACS, we found that a larger population of neurons became entrained to the stimulation waveform for higher stimulation intensities. Performing a cluster analysis of changes in interspike intervals, we identified two main types of neural responses to TACS - increased burstiness and phase entrainment. Our results demonstrate the ability of TACS to affect spike-timing in the awake primate brain and identify fundamental neural mechanisms. Concurrent electric field recordings demonstrate that spike-timing changes occur with stimulation intensities readily achievable in humans. These results suggest that novel TACS protocols tailored to ongoing brain activity may be a potent tool to normalize spike-timing in maladaptive brain networks and neurological disease.

neuroscience↗

bioRxiv2019

A molecular gradient along the longitudinal axis of the human hippocampus informs large-scale behavioral systems

The functional organization of the hippocampus is distributed as a gradient along its longitudinal axis that explains its differential interaction with diverse brain systems. We show that the location of human tissue samples extracted along the longitudinal axis of the hippocampus can be predicted within 2mm using the expression pattern of less than 100 genes. When variation in this specific gene expression pattern was observed across the whole brain, a distinct anterioventral-posteriodorsal gradient was observed. Frontal, anterior temporal and brainstem regions involved in social and motivational behaviors, selectively vulnerable to frontotemporal dementia and more functionally connected to the anterior hippocampus could be clearly differentiated from posterior parieto-occipital and cerebellar regions involved in spatial cognition, selectively vulnerable to Alzheimers disease, and more functionally connected to the posterior hippocampus. These findings place the human hippocampus at the interface of two major brain systems defined by a single distinct molecular gradient. (148/150)

neuroscience↗

bioRxiv2018

NeuroMTL iSEG challenge methods

We propose a tissue classification method for MRI scans of 6-month old infants, and used it to process the iSeg-2017 challenge data. The method relies on a deep-learning 3D U-Net network, trained with MRI scans of 216 infants, aged 6-24 months, from the ACE-IBIS longitudinal database.

neuroscience↗