Biology subjects

Tamayo, A.

Publications and source records attributed to Tamayo, A..

4 recordsLinked to original sources

bioRxiv2022

Mini-IsoQLR: a pipeline for isoform quantification using long-reads sequencing data for single locus analysis

DNA variants altering the pre-mRNA splicing process represent an underestimated cause of human genetic diseases. Their association with disease traits should be confirmed using functional assays from patient cell lines or other alternative models to detect the formation of aberrant mRNAs. Long-read sequencing is a suitable technique to identify and quantify mRNA isoforms. Available isoform clusterization and/or quantification tools are generally designed for the whole transcriptome analysis. Experiments focusing on a single locus analysis need more precise data fine-tuning and visualization tools. Here we describe VIsoQLR, an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies isoforms. Users can edit splice sites through dynamic and interactive graphics and tables as part of their manual curation. Known transcripts, or isoforms detected by other methods, can also be imported as references for comparison. Here, we explain VIsoQLR principles and features, and show its applicability in a case study example using Nanopore sequencing. VIsoQLR is available at https://github.com/TBLabFJD/VIsoQLR.

bioinformatics↗

bioRxiv2021

Pericyte control of pancreatic islet blood flow impacts glucose homeostasis

The pancreatic islet depends on blood supply to efficiently sense plasma glucose levels and deliver insulin and glucagon into the circulation. Long thought to be passive conduits of nutrients and hormones, islet capillaries were recently found to be densely covered with contractile pericytes, suggesting local control of blood flow. Here we determined the contribution of islet pericytes to the regulation of islet blood flow, plasma insulin and glucagon levels, and glycemia. Selective optogenetic activation of pericytes in intraocular islet grafts contracted capillaries and diminished blood flow. In awake mice, acute clamping of islet blood flow by optogenetic or pharmacological activation of pericytes disrupted hormonal responses, glycemia, and glucose tolerance. Our findings indicate that pericytes mediate vascular responses in the islet that are required for adequate hormone secretion and glucose homeostasis. Vascular deficiencies commonly seen in the islets of people with type 2 diabetes may impair regulation of islet blood flow and thus precipitate islet dysfunction.

physiology↗

bioRxiv2021

FAILURE OF PANCREATIC ALPHA CELLS TO RESPOND TO HYPOGLYCEMIA IS LINKED TO IMPAIRED GLUTAMATE RECEPTOR SIGNALING IN DIABETES

Glucagon secretion from pancreatic alpha cells is crucial to prevent hypoglycemia. For reasons still unknown, people with type 1 diabetes lose this glucoregulatory mechanism and are susceptible to dangerous hypoglycemia. Here we show that alpha cells in living pancreas slices from donors with type 1 diabetes failed to secrete glucagon in response to decreases in glucose concentration, thus mirroring the in vivo unresponsiveness to hypoglycemia. Glucagon content and responses to KCl depolarization were not affected, suggesting that alpha cells retained their secretory potential. By contrast, alpha cells had severely impaired signaling via glutamate receptors of the AMPA/kainate type. Under healthy conditions, activating these receptors was required to elicit full glucagon responses to decreases in glucose levels. In type 1 diabetes, reactivating residual glutamate receptor function with the positive allosteric modulators cyclothiazide and aniracetam restored glucagon secretion in response to hypoglycemia. These positive allosteric modulators are already approved to treat other conditions and could be repurposed to prevent hypoglycemia and improve management of diabetes.

physiology↗

bioRxiv2019

PANCREATIC ISLETS COMMUNICATE WITH THE BRAIN VIA VAGAL SENSORY NEURONS

Depleting visceral sensory nerves affects pancreatic islet function, glucose metabolism and diabetes onset, but how islet endocrine cells interact with sensory neurons has not been studied. Here we show that the pancreatic islet is innervated by vagal sensory axons expressing substance P, calcitonin-gene related peptide, and serotonin receptor 5HT3R. Vagal neurons projecting to the pancreas terminate in the commissural nucleus of the solitary tract. These neurons respond to chemical but not mechanical stimulation of the pancreas. By recording activity from nodose neurons in vivo and from sensory axons in living pancreas slices, we show that sensory nerves respond to serotonin secreted from stimulated beta cells. Serotonin is co-released with insulin and therefore conveys information about the secretory state of beta cells via vagal afferent nerves. Our study thus establishes that pancreatic islets communicate with the brain using the neural route and identifies serotonin signaling as a peripheral transduction mechanism.

neuroscience↗