Developing Methods for Access to High Quality Genome Sequences from Wild Ape Populations

Modern evolutionary study of wild ape populations requires the collection of genomic DNA from individuals living in their natural habitat. In order to be maximally useful, these samples must be robust enough for the amplification and subsequent assembly of genomic sequences, which are driving much of modern evolutionary research. Additionally, conservation efforts require that these samples be collected with zero intervention on the study species, because all great apes are now critically endangered. Consequently, the conventional method for genomic DNA collection has been extraction from cells present in fecal samples. However, this approach presents multiple difficulties to investigators, including extensive contamination of sequences from gut microbiota and limited storage time. The purpose of this study is to explore alternative procedures of noninvasive DNA collection to overcome these challenges. Specifically, the study looks at DNA extraction from hair follicle cells and from cells present in urine. These sources of genomic information confer a number of advantages over feces, such as smaller volumes of collection, much lower levels of microbial contamination, and relative ease of storage and transport. In this study, a method for isolating genomic DNA from chimpanzee (Pan troglodytes) hair follicle cells is developed and tested for limit of detection using a decreasing number of hairs per extraction. Validation of the method is then established through the determination of the frequency of polymorphisms due genomic amplification error by comparing sequences obtained from three identically handled samples. After laying out the next steps of development for this method, the study also suggests a similar investigation for samples derived from urine. The overall aim of these studies is a future incorporation of these procedures into the suite of DNA collection techniques available to researchers working with natural populations of great apes and other mammals.Honors Thesis submitted in partial fulfillment of the requirements for graduation with Distinction in Biology in Trinity College of Duke Universit

What\u27s in your Cup? Increasing Transparency and Confidence in Alcohol Use Screening and Brief Intervention

19% of Vermonters report drinking alcohol at levels which puts their health at risk, but many healthcare providers do not feel confident in addressing their patients\u27 usage. This can stem from lack of experience with alcohol use, worries about stigma, and time constraints. However, data has shown that even 5-15 minute interventional conversations can significantly reduce a patient\u27s risky drinking. This project aims to provide real-world, practical advice for having conversations around alcohol, and provides a conversion chart converting popular alcoholic beverages into standard drink equivalents.https://scholarworks.uvm.edu/fmclerk/1597/thumbnail.jp

Training: Key in Recognizing Potential Trafficking Victims in a Healthcare Setting

Background • Human Trafficking (HT) is a crime that involves exploiting a person for labor, services, or commercial sex. • HT can happen in any industry, to persons of any gender, age, economic status, religion, and nationality. • In FY 2018, service agencies in the State of Vermont submitted over 180 reports of HT. • HT has a profound negative impact on survivors’ physical and mental health. • 25-88% of HT victims interact with a healthcare professional while they are being exploited. • Providers have cited a lack of confidence and knowledge on HT as a major barrier to proper care of potential victims, stemming from a lack of adequate training. • There is a need to assess healthcare workers’ knowledge in recognizing and providing appropriate care and options to potential victims of HT. Objectives • Assess awareness of University of Vermont Medical Center (UVMMC) and affiliated primary care staff and providers regarding the recent implementation of a UVMMC policy on providing support to victims of HT. • Understand current behaviors of staff and providers when providing care to a patient suspected of being a victim of HT.https://scholarworks.uvm.edu/comphp_gallery/1277/thumbnail.jp

A genome-wide CRISPR screen identifies a restricted set of HIV host dependency factors

Host proteins are essential for HIV entry and replication and can be important nonviral therapeutic targets. Large-scale RNA interference (RNAi)-based screens have identified nearly a thousand candidate host factors, but there is little agreement among studies and few factors have been validated. Here we demonstrate that a genome-wide CRISPR-based screen identifies host factors in a physiologically relevant cell system. We identify five factors, including the HIV co-receptors CD4 and CCR5, that are required for HIV infection yet are dispensable for cellular proliferation and viability. Tyrosylprotein sulfotransferase 2 (TPST2) and solute carrier family 35 member B2 (SLC35B2) function in a common pathway to sulfate CCR5 on extracellular tyrosine residues, facilitating CCR5 recognition by the HIV envelope. Activated leukocyte cell adhesion molecule (ALCAM) mediates cell aggregation, which is required for cell-to-cell HIV transmission. We validated these pathways in primary human CD4 + T cells through Cas9-mediated knockout and antibody blockade. Our findings indicate that HIV infection and replication rely on a limited set of host-dispensable genes and suggest that these pathways can be studied for therapeutic intervention

Effects of a new hospital building on patient outcomes

In June 2019, the University of Vermont Medical Center opened the Miller building as part of an initiative to improve patient experiences by providing private rooms, hotel-like amenities, and family-centered features. However, it remains to be seen if this effort has had an effect on patient outcomes compared to those patients admitted to the older “legacy” buildings. Our objective was to identify any difference in mortality, readmission, and/or length of stay outcomes for adult medicine patients admitted to the Miller building compared to contemporaneous controls assigned to the legacy buildings. We analyzed all patients admitted to the Adult Hospital Medicine service, who are randomly assigned to either Miller or legacy buildings, from the Miller building’s opening to the beginning of the COVID-19 pandemic in March 2020 and compared outcomes for patients matched by diagnosis. We found no significant differences between outcomes, indicating non-inferiority of the new hospital building

HLA class-I-peptide stability mediates CD8+ T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV

Defining factors that govern CD8+ T cell immunodominance is critical for the rational design of vaccines for viral pathogens. Here, we assess the contribution of human leukocyte antigen (HLA) class-I-peptide stability for 186 optimal HIV epitopes across 18 HLA alleles using transporter associated with antigen processing (TAP)-deficient mono-allelic HLA-expressing cell lines. We find that immunodominant HIV epitopes increase surface stabilization of HLA class-I molecules in comparison to subdominant epitopes. HLA class-I-peptide stability is also strongly correlated with overall immunodominance hierarchies, particularly for epitopes from high-abundance proteins (e.g., Gag). Moreover, HLA alleles associated with HIV protection are preferentially stabilized by epitopes derived from topologically important viral regions at a greater frequency than neutral and risk alleles. These findings indicate that relative stabilization of HLA class-I is a key factor for CD8+ T cell epitope immunodominance hierarchies, with implications for HIV control and the design of T-cell-based vaccines