Dataset Search: A lightweight, community-built tool to support research data discovery

Objective: Promoting discovery of research data helps archived data realize its potential to advance knowledge. Montana State University (MSU) Dataset Search aims to support discovery and reporting for research datasets created by researchers at institutions. Methods and Results: The Dataset Search application consists of five core features: a streamlined browse and search interface, a data model based on dataset discovery, a harvesting process for finding and vetting datasets stored in external repositories, an administrative interface for managing the creation, ingest, and maintenance of dataset records, and a dataset visualization interface to demonstrate how data is produced and used by MSU researchers. Conclusion: The Dataset Search application is designed to be easily customized and implemented by other institutions. Indexes like Dataset Search can improve search and discovery for content archived in data repositories, therefore amplifying the impact and benefits of archived data

Biphasic alterations in coronary smooth muscle Ca2+ regulation in a repeat cross-sectional study of coronary artery disease severity in metabolic syndrome

BACKGROUND AND AIMS: Coronary artery disease (CAD) is progressive, classified by stages of severity. Alterations in Ca(2+) regulation within coronary smooth muscle (CSM) cells in metabolic syndrome (MetS) have been observed, but there is a lack of data in relatively early (mild) and late (severe) stages of CAD. The current study examined alterations in CSM Ca(2+) regulation at several time points during CAD progression. METHODS: MetS was induced by feeding an excess calorie atherogenic diet for 6, 9, or 12 months and compared to age-matched lean controls. CAD was measured with intravascular ultrasound (IVUS). Intracellular Ca(2+) was assessed with fura-2. RESULTS: IVUS revealed that the extent of atherosclerotic CAD correlated with the duration on atherogenic diet. Fura-2 imaging of intracellular Ca(2+) in CSM cells revealed heightened Ca(2+) signaling at 9 months on diet, compared to 6 and 12 months, and to age-matched lean controls. Isolated coronary artery rings from swine fed for 9 months followed the same pattern, developing greater tension to depolarization, compared to 6 and 12 months (6 months = 1.8 ± 0.6 g, 9 months = 5.0 ± 1.0 g, 12 months = 0.7 ± 0.1 g). CSM in severe atherosclerotic plaques showed dampened Ca(2+) regulation and decreased proliferation compared to CSM from the wall. CONCLUSIONS: These CSM Ca(2+) regulation data from several time points in CAD progression and severity help to resolve the controversy regarding up-vs. down-regulation of CSM Ca(2+) regulation in previous reports. These data are consistent with the hypothesis that alterations in sarcoplasmic reticulum Ca(2+) contribute to progression of atherosclerotic CAD in MetS

Metabolic Syndrome Abolishes Glucagon-Like Peptide 1 Receptor Agonist Stimulation of SERCA in Coronary Smooth Muscle

Metabolic syndrome (MetS) doubles the risk of adverse cardiovascular events. Glucagon-like peptide 1 (GLP-1) receptor agonists induce weight loss, increase insulin secretion, and improve glucose tolerance. Studies in healthy animals suggest cardioprotective properties of GLP-1 receptor agonists, perhaps partially mediated by improved sarco-endoplasmic reticulum Ca(2+) ATPase (SERCA) activity. We examined the acute effect of GLP-1 receptor agonists on coronary smooth muscle cells (CSM) enzymatically isolated from lean, healthy Ossabaw miniature swine. Intracellular Ca(2+) handling was interrogated with fura-2. The GLP-1 receptor agonist exenatide activated SERCA but did not alter other Ca(2+) transporters. Further, we tested the hypothesis that chronic, in vivo treatment with GLP-1 receptor agonist AC3174 would attenuate coronary artery disease (CAD) in swine with MetS. MetS was induced in 20 swine by 6 months' feeding of a hypercaloric, atherogenic diet. Swine were then randomized (n = 10/group) into placebo or AC3174 treatment groups and continued the diet for an additional 6 months. AC3174 treatment attenuated weight gain, increased insulin secretion, and improved glucose tolerance. Intravascular ultrasound and histology showed no effect of AC3174 on CAD. MetS abolished SERCA activation by GLP-1 receptor agonists. We conclude that MetS confers vascular resistance to GLP-1 receptor agonists, partially through impaired cellular signaling steps involving SERCA

DNA Extraction Method Development for Ocular Tissues

Purpose: DNA extraction kits are traditionally developed to work with liquid tissues such as blood, saliva, and swabs, but some have been proposed to work with solid tissues. Somatic variation in cancers can be important for tumor subtyping and treatment guidance, including ocular tumors. Additionally, epigenetic marks such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are tissue-specific and change in disease states, particularly evident in diabetic retinopathy and age-related macular degeneration. Commercial DNA extraction kits are available from several vendors, but the various kits have different strengths and weaknesses, and the removal of PCR inhibitors will vary with each kit. This project investigates the yield and purity of DNA from ocular tissues using commercial DNA extraction kits. Methods: Cornea, neural retina, RPE/choroid layer, optic nerve, and capsular bag were collected and aliquoted into 15 mg aliquots. Extractions were performed using the following kits: DNEasy Blood and Tissue Kit (Qiagen;), GeneJET Genomic DNA Purification Kit (ThermoFisher Scientific), Monarch HMW DNA Extraction Kit for Tissue (New England Biosciences), and genomicPrep Mini Spin Kit (Cytiva). DNA was quantified using the Qubit Fluorometer and molecular weight was checked by agarose gel. Several more kits are currently being tested. Results: All four kits yielded high molecular weight DNA (above 20 kbp). The Monarch HMW kit yielded DNA with significantly higher molecular weights. The DNA yields per milligram of tissue were highest using the DNEasy Blood and Tissue Kit for optic nerve, neural retina, and RPE/choroid. The yield was highest for the cornea using the genomicPrep Mini Spin Kit. Only the genomicPrep Mini Spin Kit yielded sufficient DNA for quantification from the capsular bag, and total yields were minimal (600 ng or less). Additional kits are currently being tested, but initial results indicate that several commercial kits will be sufficient for DNA extraction of ocular tissues. Further work is needed to purify epithelial cells and stem cells from the intraocular lens. Conclusions: Of the kits tested, all are sufficient to obtain significant amounts of DNA from all ocular tissues aside from the capsular bag. The Monarch HMW yielded the highest molecular weight, but significantly lower quantities of DNA than the other kits, indicating that it may not be ideal for most purposes. Protocol development for the capsular bag is still underway

Epicardial adipose excision slows the progression of porcine coronary atherosclerosis

BACKGROUND: In humans there is a positive association between epicardial adipose tissue (EAT) volume and coronary atherosclerosis (CAD) burden. We tested the hypothesis that EAT contributes locally to CAD in a pig model. METHODS: Ossabaw miniature swine (n = 9) were fed an atherogenic diet for 6 months to produce CAD. A 15 mm length by 3–5 mm width coronary EAT (cEAT) resection was performed over the middle segment of the left anterior descending artery (LAD) 15 mm distal to the left main bifurcation. Pigs recovered for 3 months on atherogenic diet. Intravascular ultrasound (IVUS) was performed in the LAD to quantify atheroma immediately after adipectomy and was repeated after recovery before sacrifice. Coronary wall biopsies were stained immunohistochemically for atherosclerosis markers and cytokines and cEAT was assayed for atherosclerosis-related genes by RT-PCR. Total EAT volume was measured by non-contrast CT before each IVUS. RESULTS: Circumferential plaque length increased (p < 0.05) in the proximal and distal LAD segments from baseline until sacrifice whereas plaque length in the middle LAD segment underneath the adipectomy site did not increase. T-cadherin, scavenger receptor A and adiponectin were reduced in the intramural middle LAD. Relative to control pigs without CAD, 11β-hydroxysteroid dehydrogenase (11βHSD-1), CCL19, CCL21, prostaglandin D(2) synthase, gp91phox [NADPH oxidase], VEGF, VEGFGR1, and angiotensinogen mRNAs were up-regulated in cEAT. EAT volume increased over 3 months. CONCLUSION: In pigs used as their own controls, resection of cEAT decreased the progression of CAD, suggesting that cEAT may exacerbate coronary atherosclerosis

Annual Student Exhibition 2015: Senior Capstone Gallery Guide

We are pleased to present the inaugural edition of the Senior Capstone Gallery Guide, a collaboration between the graduating Studio Art and Art History Majors. This publication and the exhibition it accompanies celebrate the achievements of the Department\u27s Class of 2015

Development of a Protocol for Obtaining Biological Samples for Genetic Testing from Remote Individuals

Pharmacogenomic sequencing allows individuals to learn more about how they will respond to certain medications but requires shipping of a biological sample. One complication of sending biological samples to remote laboratories is stability. Blood generally yields sufficient quantities of high-quality DNA but requires a clinic visit. Saliva and buccal swabs are routinely used for DNA extractions, but the DNA quality is notoriously low due to the presence of bacteria in the mouth. Additionally, elderly individuals have difficulty producing enough saliva for testing, and the tubes contain several milliliters of liquid and shipping requires special considerations. Dried blood spot cards, which serve as an alternative to saliva and buccal swabs, yield high-quality DNA and ship easily, but may produce a lower yield. This project aims to determine which biological sample methods can reasonably be obtained from remote individuals

DNA Extraction Method Development for Solid Tissues

Although germline variation testing is traditionally performed using DNA obtained from blood or other liquid samples, determining somatic variation in cancer samples requires DNA extraction directly from tissues. Additionally, epigenetic markers, such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are tissue-specific and change in selected disease states. However, several substances present in tissues are known to inhibit downstream reactions, including polymerase chain reaction PCR). For this project, we are assessing the quantity and quality of DNA obtained from extractions of various vital organs using 30 different commercially available DNA extraction kits to determine optimal kits for each tissue