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Synthetic Biology Open Language (Sbol) Version 2.1.0, Zhen Zhang

Integrative Biology Faculty and Staff Publications

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 …

Effects Of Nutrient Supplementation On Host-Pathogen Dynamics Of The Amphibian Chytrid Fungus: A Community Approach, Julia C. Buck, Jason R. Rohr, Andrew R. Blaustein

Integrative Biology Faculty and Staff Publications

1. Anthropogenic stressors may influence hosts and their pathogens directly or may alter host–pathogen dynamics indirectly through interactions with other species. For example, in aquatic ecosystems, eutrophication may be associated with increased or decreased disease risk. Conversely, pathogens can influence community structure and function and are increasingly recognised as important members of the ecological communities in which they exist.
2. In outdoor mesocosms, we experimentally manipulated nutrients (nitrogen and phosphorus) and the presence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), and examined the effects on Bd abundance on larval amphibian hosts (Pseudacris regilla: Hylidae), amphibian traits and community dynamics. We …

An Experiment In Graduate Education: A Marine Science Adventure Across The Indian Ocean, Vicki Buchsbaum Pearse, John C. Ogden, Sharon J. Proctor

Integrative Biology Faculty and Staff Publications

In the fall of 1964, Stanford University’s R/V Te Vega Cruise 5 crossed the equatorial Indian Ocean from Mombasa to Singapore, one of many ships participating in the International Indian Ocean Expedition. The cruise achieved two goals: (1) it provided hands-on oceanography training for graduate students in marine sciences, and (2) it documented the deep scattering layers of the Indian Ocean, only poorly known at the time. Taking place on the other side of the globe from the United States, the cruise also exposed students to cultural and personal experiences that shaped their lives and professions. It demonstrated the importance …

Chronic Pancreatitis, Pain, And Anxiety In An Alcohol And High Fat Mouse Model, Tiffanie Clinkinbeard

Theses and Dissertations--Gerontology

Homeodynamic space (HDS) shrinks as vulnerability increases with aging and repeated damage to the cells. HDS is lost in alcoholic pancreatitis patients due to overconsumption of alcohol, smoking, and high fat diets. Etiologically relevant animal models for study of chronic pancreatitis (CP) are needed. In order to begin filling this gap a central purpose of this dissertation research was to examine relationships between the alcohol and high fat diet (AHF) and pancreatitis with attention to hypersensitivity and anxiety-like behaviors. The AHF diet induced pancreatitis described here etiologically mimics human risk factors of AHF consumption for advancement to alcoholic CP.

In …

Spatial Spread Of The West Africa Ebola Epidemic, Andrew M. Kramer, J. Tomlin Pulliam, Laura W. Alexander, Andrew W. Park, Pejman Rohani, John M. Drake

Integrative Biology Faculty and Staff Publications

Controlling Ebola outbreaks and planning an effective response to future emerging diseases are enhanced by understanding the role of geography in transmission. Here we show how epidemic expansion may be predicted by evaluating the relative probability of alternative epidemic paths. We compared multiple candidate models to characterize the spatial network over which the 2013–2015 West Africa epidemic of Ebola virus spread and estimate the effects of geographical covariates on transmission during peak spread. The best model was a generalized gravity model where the probability of transmission between locations depended on distance, population density and international border closures between Guinea, Liberia …

Ordination Obscures The Influence Of Environment On Plankton Metacommunity Structure, Tad A. Dallas, Andrew M. Kramer, Marcus Zokan, John M. Drake

Integrative Biology Faculty and Staff Publications

The composition of plankton communities in individual habitats is often influenced by environmental conditions like pH or hydroperiod. At larger scales, environmental gradients can influence community structure across interconnected local communities. Detecting the role of environmental and spatial factors on metacommunity structure depends on the ordering of sites and species prior to analysis. We investigated this ordination in two wetland metacommunities; a well-sampled, hyper-diverse zooplankton metacommunity, and a Central American phytoplankton metacommunity. We calculated coherence, turnover, and boundary clumping to classify the structure of the metacommunity, and we propose a statistic that responds to variation in both coherence and turnover. …

Mathematical Models Are A Powerful Method To Understand And Control The Spread Of Huanglongbing, Rachel A. Taylor, Erin Mordecai, Christopher A. Gilligan, Jason R. Rohr, Leah R. Johnson

Integrative Biology Faculty and Staff Publications

Huanglongbing, or citrus greening, is a global citrus disease occurring in almost all citrus growing regions and causing substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof, it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of Huanglongbing. We adapt a malaria model to Huanglongbing, by including temperature-dependent psyllid traits and economic costs, to …

Role Of The Chondroitin Sulfate Proteoglycan, Neurocan, In Inhibition Of Sensory Neurite Regeneration, Madison Klump, Umang Khandpur, Chris Calulot, Adrian Centers, Diane M. Snow

Lewis Honors College Capstone Collection

In the adult mammalian brain and spinal cord, neuronal injury results in failed neurite regeneration, in part due to the up-regulation of chondroitin sulfate proteoglycans (CSPGs). CSPGs are molecules consisting of a protein core with covalently bound glycosaminoglycans (GAGS), specifically, chondroitin sulfate side-chains. The majority of CSPGs produced after injury originate from reactive astrocytes found in the glial scar surrounding the injury site. Although this milieu is very complex and involves more than just CSPGs, axonal regrowth may be improved if the expression of specific, highly inhibitory CSPGs produced after injury were attenuated selectively. Neurocan is one type of CSPG …

How Hostile Was The Space Race? An Examination Of Soviet-American Antagonism And Cooperation In Space, Mitchell Mundorff

Lewis Honors College Capstone Collection

It is commonly accepted that the United States and the Soviet Union competed, and did not cooperate, with one and other between World War II and the collapse of the USSR in the early 1990s. This is problematic, due to several joint projects undertaken by the two nations during this period, and especially the Apollo-Soyuz Experimental Test Project. Analysis of contemporary and secondary sources shows that though there was a large degree of competition between these superpowers, the idea of working together was proposed several times before it became a reality. Once the nations decided to move forward with Apollo-Soyuz, …

The Role Of Rapgap1 In Sxl Activation In Drosophila Melanogaster, Katherine M. Barnes

Lewis Honors College Capstone Collection

The master switch of the sexual differentiation and dosage compensation pathway in Drosophila is the sex lethal gene, Sxl. The early promoter, SxlPe, is activated in females, resulting in female-specific splicing of later transcripts (notably the late Sxl transcript SxlPm), while inactive in males. Chromatin immunoprecipitation (ChIP) assays have previously shown association of two conventionally heterochromatin-localized proteins, HOAP and HP1, at SxlPe, and in situ hybridization as well as RT-PCR assays have confirmed a repressive role for HOAP and both repressive and activating roles for HP1. The mechanism for the activity shift of HP1 is currently unknown. Deletions in the …

Molecular Genetics Of Ms4a6a And Alzheimer's Disease, Ryan Harpole

Lewis Honors College Capstone Collection

Increased Alzheimer’s disease (AD) risk has previously been associated with a SNP called rs610932 near the gene MS4A6A. The goal of this experiment was to quantify the expression of two MS4A6A isoforms in the brains of AD and non-AD subjects, particularly as a function of rs610932 genotype. According to an article titled “Alzheimer’s Disease Susceptibility Variants in the MS4A6A Gene are Associated with Altered Levels of MS4A6A Expression in Blood”, MS4A6A has four different isoforms that have been reported to be differentially expressed in the blood of AD subjects compared to non-AD subjects (Petroula et al., 2014). After statistically …

The Daily Gamecock, Thursday, April 14, 2016, University Of South Carolina, Office Of Student Media

April

No abstract provided.

The Daily Gamecock, Thursday, August 25, 2016, University Of South Carolina, Office Of Student Media

August

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The Daily Gamecock, Thursday, August 18, 2016, University Of South Carolina, Office Of Student Media

August

No abstract provided.

The Daily Gamecock, Monday, February 15, 2016, University Of South Carolina, Office Of Student Media

February

No abstract provided.

The Daily Gamecock, Wednesday, February 10, 2016, University Of South Carolina, Office Of Student Media

February

No abstract provided.

The Daily Gamecock, Wednesday, January 20, 2016, University Of South Carolina, Office Of Student Media

January

No abstract provided.

The Daily Gamecock, Monday, October 24, 2016, University Of South Carolina, Office Of Student Media

October

No abstract provided.

The Daily Gamecock, Thursday, October 20, 2016, University Of South Carolina, Office Of Student Media

October

No abstract provided.

The Daily Gamecock, Monday, September 26, 2016, University Of South Carolina, Office Of Student Media

September

No abstract provided.

The Daily Gamecock, Monday, September 12, 2016, University Of South Carolina, Office Of Student Media

September

No abstract provided.

Evaluation Of Resin Sealer Penetration Of Dentin Following Different Final Rinses For Endodontic Irrigation Using Confocal Laser Scanning Microscopy, Omar Ezzaldin Abusteit

MUSC Theses and Dissertations

Introduction: The aim of the study was to directly assess the depth of sealer penetration into dentinal tubules following different final rinses and indirectly evaluate precipitation of irrigating solutions. Materials and Methods: 52 extracted maxillary incisors were prepared to size 40/04 crown down with 6% sodium hypochlorite irrigating solution. Teeth were randomly divided into 4 groups (n=13) according to the final rinse. Group 1- 17% EDTA, saline and 2% Chlorhexidine solution; Group 2- SmearOFFâ„¢; Group 3- QMix®; Group 4- control with saline. Each final rinse was 3 ml over 1 minute placed with a 30-gauge needle 3 mm short from …

The Fli-1 Transcription Factor Regulates The Expression Of Ifn-Gamma Inducible Protein 10 (Ip-10), Tomika Shanta' Caldwell

MUSC Theses and Dissertations

The innate immune system is the primary line of defense to protect the host from pathogen infection. Mammalian cells produce inflammatory cytokines and chemokines in response to innate immune signals and their expression is tightly regulated. IFN-gamma Inducible Protein (IP-10), also known as C-X-C motif chemokine 10 (CXCL10), is an inflammatory chemokine belonging to the CXC chemokine family. CXCL10 is chemotactic for many inflammatory cells, including macrophages, and altered expression of CXCL10 is associated with inflammatory diseases, including lupus nephritis and other autoimmune diseases. The Fli-1 transcription factor is a member of the Ets gene family and regulates the immune …

Hop, The Heat Shock Link Between Hsp90 And The Piwi-Pirna Pathway, Joseph A. Karam

MUSC Theses and Dissertations

The Piwi-piRNA pathway is an RNA interference pathway that is conserved across eukaryotes; it is involved with the maintenance of genomic stability through its actions on the germline. We have studied the relationship between a protein complex involving factors in the Piwi-piRNA pathway, Piwi and Aubergine, and the Hsp90-Hop-Hsp70 molecular chaperone machinery. Through a series of in vitro experiments and previous data, we have shown that an interaction between Piwi, Hop, and Hsp90 occurs, when all three proteins are present. Shedding light on this interaction could give us insight on how the PiwipiRNA pathway functions. Through in vivo experiments performed, …

Effects Of Predator Odor-Induced Stress On The Rodent Prefrontal Cortex And Cocaine Self-Administration, Jonathon Alan Koerber

MUSC Theses and Dissertations

Post-traumatic stress disorder (PTSD) and substance use disorder (SUD) affect a combined 30 million Americans as of 2014 (Hedden et. al., 2015). An individual who is diagnosed with one has a greatly increased risk of being diagnosed with the other later in life. This suggests some type of biological link between the two. Unfortunately, it is difficult to study the molecular underpinnings of either disease in humans because of ethical concerns. Therefore it would be prudent to develop an animal model that allows for a standardized examination of both disorders. This investigation was designed as an attempt to create an …

Hospital Acquired Infections In Patients Admitted To The Icu: Impact On Length Of Stay, Mortality, And Cost, Shakthi Kumar

MUSC Theses and Dissertations

Objective: To explore the clinical and financial impact of hospital-acquired infections (HAIs) in patients admitted to the Intensive Care Unit (ICU) using statewide representative databases for Washington (WA), New Jersey (NJ), Florida (FL) and New York (NY). Specifically, the following questions will be addressed: 1) Is there an association between HAIs and hospital Length of Stay (LOS) in patients who have an ICU stay ?, 2) Is there an association between HAIs and hospital mortality in patients who have an ICU stay ?, 3) Is there an association between HAIs and hospital cost in patients who have an ICU stay …

Shortened Poly-N-Acetyl Glucosamine (Snag) Nanofibers Induce Rapid Vascular Assembly In 3-Dimensional Microtissue Spheroids, Michael G. Sarson

MUSC Theses and Dissertations

Tissue vascularization and integration with host circulation remains a key barrier to the successful translation of engineered tissues into clinically relevant therapies. Current efforts to implant large engineered structures are limited by insufficient delivery of oxygen and nutrients, and waste removal. Work presented in this thesis focus on the use of a naturally derived nanofiber for improving molecular interactions between vascular endothelial cells and smooth muscle cells for application to vascular bioengineering. We hypothesize optimization of instructive interactions between vascular cell types can improve formation of microtissue spheroids for application to vascular bioengineering. Toward this goal, I use shortened poly-N-acetyl …

The Impact Of Cardiovascular Disease Risk Factors On Late Graft Outcome Disparities In Adult African American Kidney Transplant Recipients, David J. Taber

MUSC Theses and Dissertations

Introduction: Although outcome disparities for non-Hispanic Black (NHB) kidney transplant recipients are well known and documented, there is paucity in the data assessing the impact of cardiovascular disease (CVD) risk factors and risk control on racial disparities in kidney transplantation. Methods: Longitudinal study of a national cohort of veteran kidney recipients transplanted between Jan 2001 and Dec 2007 (follow up through Dec 2010) with the aim of determining the prevalence and impact of CVD risk factor and control, compared between NHB and non-Hispanic White (NHW) recipients, on death-censored graft loss (DCGL), overall graft loss and mortality. Data included comprehensive baseline …

Investigation Of Motivational Interviewing Techniques To Address Health Disparities For Low-Income Hispanic Women Either At Risk For Or Diagnosed With Diabetes Type-2, Patricia Davern Soderlund

MUSC Theses and Dissertations

Hispanic adults are almost twice as likely to have been diagnosed with diabetes than non-Hispanic whites, and Hispanic women have a 1.5 times greater chance of dying from the disease than non-Hispanic white women. Diabetes type 2 (DM2) is the most common type, and accounts for up to 95% of newly diagnosed cases. Although physical activity (PA) is an essential component to DM2 self-management, Hispanic women are less physically active than Hispanic men, and over 40% of these women do not engage in leisure-time PA. Motivational Interviewing (MI) has been found to improve PA levels for non-Hispanic adults with DM2, …

Improving Health Outcomes In Persons With Sickle Cell Disease, Lori L. Vick

MUSC Theses and Dissertations

Purpose: The purpose of this compendium is to identify strategies that influence health outcomes of persons with sickle cell disease (SCD) by investigating available pain instruments, current use of genetic testing to personalize therapies, and the associations of psychosocial characteristics with quality of life. Problem: Suboptimal care for patients with SCD is associated with non-comprehensive pain assessment instruments, limited use of available genetic tests to prescribe the potentially most effective pharmaceuticals in a personalized plan of care, and the absence of national evidence-based guidelines for the psychosocial care of this population. Approach: The research designs used were an integrative review …