Digital Commons Network^™

Large Animal Genetic Engineering Summit 2016 Proceedings, Utah State University

Animal, Dairy, and Veterinary Science Faculty Publications

It is our great pleasure to welcome you to the first Large Animal Genetic Engineering (LAGE) Summit. Our objectives for the summit are twofold: 1) to provide an update on new approaches to the genetic modification of large animal species for development of better animal models for biomedical research, biomanufacturing, and improved agricultural production; and 2) to provide a forum for discussions on funding mechanisms and regulations effecting development of genetically engineered large animals. Our first summit is being held in Bethesda, Maryland, to facilitate participation by representatives from various federal agencies who either fund or regulate the production of …

The Effects Of Drought On Diets Of Apex Predators In The South African Lowveld Inferred By Fecal Hair Analysis, Shelby Wade

Mahurin Honors College Capstone Experience/Thesis Projects

To properly manage offtake quotas and conservation efforts, Balule Nature Reserve (South Africa) instituted a study in 2014 to determine prey species selection by megapredators. In 2015, Balule Nature Reserve received about 190 mm less rainfall between the months of January and June than in 2014 (116 mm less than average). This study compares the diets of lions and hyaenas between 2014 and 2015. Prey species consumed were determined by fecal analysis, and results were compared to prey availability. Sixteen, 1 km2 plots were chosen from the 400 km2 Reserve. Between June and August 2015, we walked three, 1 km …

A Simplified Direct Lipid Mixing Lipoplex Preparation: Comparison Of Liposomal-, Dimethylsulfoxide-, And Ethanol-Based Methods, Joseph Meisel, George Gokel

Chemistry & Biochemistry Faculty Works

Established transfection methodology often uses commercial reagents, which must be formed into liposomes in a sequence of about half a dozen steps. The simplified method reported here is a direct lipid mixing approach that requires fewer steps, less manipulation, and is less time-consuming. Results are comparable to those obtained with more commonly used methods, as judged by a variety of analytical techniques and by comparisons of transfection results. The method reported here may be applied to non-liposome-forming compounds, thereby greatly expanding the range of structures that can be tested for transfection ability.

The Role Of Epidermal Enhancer 923 In The Chromatin Architecture And Transcriptional Regulation Of The Epidermal Differentiation Complex, Inez Oh

Arts & Sciences Graduate Student Theses and Dissertations

The epidermis covers the surface of the skin and provides a functional barrier across the entire body. Epidermal cells or keratinocytes proliferate in the innermost basal layer and migrate upwards into the suprabasal spinous and granular layers as they differentiate, and finally into the terminally differentiated outermost stratum corneum. Keratinocytes undergoing terminal differentiation are marked by tissue-specific concomitant expression of genes encoded in the Epidermal Differentiation Complex (EDC) locus. The EDC genes are organized into four gene families - S100, Sprr, Lce, and Flg-like, which are coordinately expressed upon activation of the terminal differentiation program in keratinocytes. The molecular mechanisms …

Plasmid Dna Bind And Elute Chromatography Using Borosilicate Filters And Filter Holders, Stacey D. Floyd, Camille S. Baird, Jordan Finnell, Tsz Ming Tsang, Robert C. Davis, Kenneth A. Christensen

Student Works

This research has been completed to determine whether plasmid DNA will bind to a simple borosilicate filter in a reusable filter holder, and whether it can be released in a controlled procedure after a wash has been done to eliminate impurities.

The motivation for this is to help small research groups, both in educational settings as well as in other small research settings be able to study isolated DNA without much of the expense generally associated with purification kits and to remove the limitations on trial numbers imposed by the expense of each individual isolation kit.

Medical research, forensics, and …

The Floral Charms Of Saint John’S: A Survey Of Botanical Communities, Stephen G. Saupe, Paul Melchior

Headwaters

Saint John’s is a “landscape paradise” in central Minnesota. Although no complete checklist of vegetation exists for the campus, various surveys reveal a diverse flora. This floral wealth is the result of several terrestrial biomes converging on campus — prairie, savanna, deciduous forest, and coniferous forest — as well as diverse aquatic habitats including both lakes and wetlands. A 56-acre restored prairie at the entrance of Saint John’s is dominated by big bluestem and little bluestem. A savanna has been restored to the north and east of the Gemini Lakes and is characterized by bur oaks scattered among prairie grasses …

Ecological And Phenotypic Factors Influencing The Movement Dynamics Of The Blackspotted Topminnow, Fundulus Olivaceus, Scott Richard Clark

Dissertations

Movement of individuals throughout a landscape is a complex behavior that has important consequences on numerous ecological and evolutionary processes. Perhaps most notably is the relationship between movement and reproduction, as this has implicit ramifications on individual fitness and consequently, population level processes. Although this relationship has been theoretically and empirically demonstrated across a number of animal taxa, its role in fishes remains understudied and largely unknown. Using a series of outdoor mesocosms, in combination with a field study, I employed passive integrated transponder (PIT) tags to experimentally assess the sex-specific movement dynamics of a small-bodied, sexually-dimorphic stream fish, the …

Reproductive Ecology Of Dragonfishes (Family: Stomiidae) In The Gulf Of Mexico, Alex D. Marks

HCNSO Student Theses and Dissertations

The most speciose group of fishes in the Gulf of Mexico is the dragonfishes (Family: Stomiidae). These fishes are dominant mesopelagic predators occurring throughout the world’s oceans, including the Antarctic seas. Little is known regarding their reproductive ecology, a consequence attributed to insufficient sample sizes of mature adults due to inadequacies of sampling gear; larger, sexually mature stomiid adults are more adept at net avoidance, thereby obfuscating synoptic reproductive biology studies. Between 2010-2011, the Offshore Nekton Sampling and Analysis Program was initiated in the northern Gulf of Mexico over all four seasons using a discrete-depth sampling system (MOCNESS) and a …

Microbubble Generation By Piezoelectric Transducers For Biomedical Studies, Mohammed Alkhazal

Electrical & Computer Engineering Theses & Dissertations

Bubbles induced by blast waves or shocks are speculated as the major cause of damage in biological cells in mild traumatic brain injuries (TBI). Microbubble collapse was found to induce noticeable cell detachment from the cell substrate, changes in focal adhesion, and biomechanics. To better understand the bubble mechanism, a system needs to be constructed which allows clear differentiation on the impact of bubbles from that of shocks. Such a generator needs to be low profile in order to place under a microscope. A piezoelectric transducer system was designed to meet the need. The system uses either a flat or …

Gene Set Enrichment And Projection: A Computational Tool For Knowledge Discovery In Transcriptomes, Karl Douglas Stamm

Dissertations (1934 -)

Explaining the mechanism behind a genetic disease involves two phases, collecting and analyzing data associated to the disease, then interpreting those data in the context of biological systems. The objective of this dissertation was to develop a method of integrating complementary datasets surrounding any single biological process, with the goal of presenting the response to a signal in terms of a set of downstream biological effects. This dissertation specifically tests the hypothesis that computational projection methods overlaid with domain expertise can direct research towards relevant systems-level signals underlying complex genetic disease. To this end, I developed a software algorithm named …

An Indirect Defence Trait Mediated Through Egg-Induced Maize Volatiles From Neighbouring Plants, Daniel M. Mutyambai, Toby J.A. Bruce, Johnnie Van Den Berg, Charles A.O. Midega, John A. Pickett, Zeyaur R. Khan

All Peer-Reviewed Publications

Attack of plants by herbivorous arthropods may result in considerable changes to the plant's chemical phenotype with respect to emission of herbivore-induced plant volatiles (HIPVs). These HIPVs have been shown to act as repellents to the attacking insects as well as attractants for the insects antagonistic to these herbivores. Plants can also respond to HIPV signals from other plants that warn them of impending attack. Recent investigations have shown that certain maize varieties are able to emit volatiles following stemborer egg deposition. These volatiles attract the herbivore's parasitoids and directly deter further oviposition. However, it was not known whether these …

The Explorations Program: Benefits Of Single-Session, Research- Focused Classes For Students And Postdoctoral Instructors, Jeremy L. Hsu, Anna M. Wrona, Sarah E. Brownell, Waheeda Khalfan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present an update to Explorations, a program at Stanford University that allows undergraduates in an introductory biology course to explore specialized topics in the biological sciences while providing graduate students and postdoctoral scholars the unique opportunity to develop and teach single-session, research-focused classes. We provide an assessment of eight iterations of the program, using program attendance, student and instructor evaluations, senior exit surveys, course grades, and completion of undergraduate honors theses to assess the impact of our program on students and instructors. Students rated their experiences highly, and most reported that the program had a positive impact on their …

Determination Of Glut1 Oligomerization Parameters Using Bioluminescent Förster Resonance Energy Transfer, Brendan D. Looyenga, Calvin Vanopstall, Zion Lee, Jed Bell

University Faculty Publications and Creative Works

The facilitated glucose transporter GLUT1 (SLC2A1) is an important mediator of glucose homeostasis in humans. Though it is found in most cell types to some extent, the level of GLUT1 expression across different cell types can vary dramatically. Prior studies in erythrocytes - which express particularly high levels of GLUT1 - have suggested that GLUT1 is able to form tetrameric complexes with enhanced transport activity. Whether dynamic aggregation of GLUT1 also occurs in cell types with more modest expression of GLUT1, however, is unclear. To address this question, we developed a genetically encoded bioluminescent Förster resonance energy transfer (BRET) assay …

Producing Knowledge: The Social Made Visible In The Division Of Environmental Biology Of The National Science Foundation, Patrick Southern

Capstone Collection

This inquiry explores how knowledge is produced in the Division of Environmental Biology (DEB) of the National Science Foundation. Beginning from a poststructuralist understanding of science as firmly embedded in the unequal relations of society, this study sought to examine how the policies and procedures of funding research proposals in DEB influence and are influenced by those relations. Using an institutional ethnography approach to analysis, data were collected from analyzing publicly available texts from the division, NSF, Congress, the Office of Management and Budget, and the research community. The analysis demonstrates how the activities of DEB could maintain or exacerbate …

Assessment Of Behavior And Social Dynamics In A Newly-Forming Group Of Captive Western Lowland Gorillas, Sarah Murphey Huskisson

Graduate Theses

This study presents behavioral data of a recently-formed western lowland gorilla (Gorilla gorilla gorilla) group at Riverbanks Zoo and Garden in Columbia, South Carolina, from the initial stages of group formation through the first several months after introduction. The group consists of a male (19 years), two half-sisters (both 10 years), and an unrelated female (20 years). I collected 15-minute focal animal samples for three hours twice a week in two observation blocks, the first lasting from 7/17/15 to 9/11/15, and the second lasting from 10/30/15 to 1/3/16. A total of 99.25 observation hours were collected. It was predicted that …

Species-Recognition Program: A Computer-Assisted Approach To Recognizing Species, Steve Kelsch, Jeffrey Carmichael

Biology Faculty Publications

Species recognition is a crucial component for many types of biological studies. To that end, broadly trained students must be able to accurately identify many different types of organisms. Courses that focus on learning the names of different species traditionally rely on preserved specimens viewed during class or laboratory time. Unfortunately, reliance on preserved specimens comes with many challenges in providing students with an optimal learning experience. The curriculum activity described here uses a modified PowerPoint file (species-recognition program—SRP) as a means of helping students learn to recognize and identify fishes based on subtle visual cues. Our results indicate that …

Affinity Cryo-Electron Microscopy: Methods Development And Applications, Guimei Yu

Open Access Dissertations

Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies. Although less concentrated and smaller amounts of samples are required for single particle cryo-EM compared to X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques holds great promise to tackle these challenging samples by combining the sample purification and freezing on TEM grids steps in cryo-EM grid preparation into a single step, revolutionize the grid preparation of cryo-EM, and extend single particle cryo-EM to a routine structural biology tool to characterize structures …

Molecular Mechanisms Regulating Pathogen Defense: The Role Of Jmj3 In Arabidopsis Thaliana, Nelson Trysler

Renée Crown University Honors Thesis Projects - All

The Raina lab studies plant-pathogen interactions through genetics and molecular biology by using the model organism, Arabidopsis thaliana. A group of genes in A. thaliana, the Jumonji gene family, regulates gene expression by epigenetic mechanisms. Jumonji genes influence histone demethylation. Previous research in the Raina lab has shown that some Jumonji (JMJ) genes play a role in immune signaling in A. thaliana in response to pathogens. My project is to characterize JMJ3 gene, and see if there was any role that JMJ3 played in pathogen defense in A. thaliana.

The goal of my study was …

Evaluating College Biology Laboratory Accommodations For Students With Blindness And Visual Impairments, Barbara Rae Heard

All Theses And Dissertations

Studies show that active participation in science laboratory activities promotes student learning. However, students with blindness and visual impairments (BVI) often confront obstacles to active participation in the required activities of the college biology laboratory. Legislation requires institutions of higher education to provide accommodations for students with disabilities, yet the institutions must also maintain the academic integrity of their courses and programs. While college biology instructors provide specific accommodations, such as tactile models and audible devices, to enable active participation by students with BVI, they do so without research-supported guidelines for best practices. This mixed methods study sought to evaluate …

Insights Into Determinants That Contribute To Colonization, Virulence And Antibiotic Resistance In Enterococci, Maria Camila Montealegre

Dissertations and Theses (Open Access)

Enterococcus faecalis and Enterococcus faecium are increasingly common as causative agents of human infections, many of which are very difficult to treat due to multi-drug resistance. The work presented in the first part of this dissertation elucidates a mechanism for the regulation of pilus expression. I showed that ATT is the initiation codon of ebpA, the first gene of an operon that codes for the endocarditis and biofilm-associated pili (Ebp), a recognized virulence factor in E. faecalis. The presence of this rare start codon downregulates EbpA translation and protein levels, diminishing biofilm and binding abilities of …

In Vitro Investigation Of The Effect Of Exogenous Ubiquitin On Processes Associated With Atherosclerosis, Chase W. Mussard

Undergraduate Honors Theses

Atherosclerosis, characterized by the build-up of cholesterol, immune cells and cellular debris within arterial walls, is accelerated following myocardial infarction by poorly understood mechanisms. Ubiquitin, a small, well-studied intracellular protein involved in protein turnover via the proteasome pathway, has recently been shown to exert extracellular effects on cardiac myocytes, in vitro, and in mice undergoing myocardial remodeling. This study investigates the potential role of extracellular ubiquitin in atherosclerosis by determining its effects on two critical atherosclerotic processes: the migration of vascular smooth muscles cells and the uptake of modified LDL by monocyte/macrophages in foam cell formation. In the presence …

Utah Lotus: North American Legume For Possible Use In Rangeland Revegetation In The Southern Great Basin Of The Western United States, Jason M. Stettler

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This thesis project explored the production and forage quality characteristics of Utah lotus (Lotus utahensis Ottley) and scrub lotus (L. wrightii (A. Gray) Greene) seed collections during a two-year period. The variation of 14 Utah lotus and five scrub lotus seed collections was evaluated by measuring important plant characteristics at three common garden sites in northern Utah. In addition, the genetic structure of the collections was determined by molecular biological techniques. Large variation was observed among collections for all phenotypic traits measured, with Utah lotus and scrub lotus being phenotypically quite different. Two collections of Utah lotus (LU-5 …

Arthropods Infesting Small Mammals (Insectivora And Rodentia) Near Cedar Point Biological Station In Southwestern Nebraska, Lindsey Howell, Katelyn Jelden, S. Elizabeth Rácz, Scott L. Gardner, Donald D. Gettinger

Insecta Mundi

Cedar Point Biological Station (CPBS) is located in the mixed grass prairie of the central Great Plains, at the transition between the subregions known as the “tall grass” and “short grass” prairies. Adding to the habitat diversity, there are wetlands and riparian habitats associated with the North Platte River and the edge of the Sandhills region of north central Nebraska. This concurrence of habitats supports a diverse small mammal community. The purpose of this paper is to assemble all published information on ectoparasites associated with small mammals (Insectivora, Rodentia) of southwestern Nebraska, and to report the results of an intensive …

Integrated Systems Biology Analysis Of Transcriptomes Reveals Candidate Genes For Acidity Control In Developing Fruits Of Sweet Orange (Citrus Sinensis L. Osbeck), Dingquang Huang, Yihong Zhao, Minghao Cao, Liang Qiao, Zhi-Liang Zheng

Publications and Research

Organic acids, such as citrate and malate, are important contributors for the sensory traits of fleshy fruits. Although their biosynthesis has been illustrated, regulatory mechanisms of acid accumulation remain to be dissected. To provide transcriptional architecture and identify candidate genes for citrate accumulation in fruits, we have selected for transcriptome analysis four varieties of sweet orange (Citrus sinensis L. Osbeck) with varying fruit acidity, Succari (acidless), Bingtang (low acid), and Newhall and Xinhui (normal acid). Fruits of these varieties at 45 days post anthesis (DPA), which corresponds to Stage I (cell division), had similar acidity, but they displayed differential acid …

Tidal Hydrodynamics Under Future Sea Level Rise And Coastal Morphology In The Northern Gulf Of Mexico, Davina L. Passeri, Scott C. Hagen, Nathaniel G. Plant, Matthew V. Bilskie, Stephen C. Medeiros, Karim Alizad

Faculty Publications

This study examines the integrated influence of sea level rise (SLR) and future morphology on tidal hydrodynamics along the Northern Gulf of Mexico (NGOM) coast including seven embayments and three ecologically and economically significant estuaries. A large-domain hydrodynamic model was used to simulate astronomic tides for present and future conditions (circa 2050 and 2100). Future conditions were simulated by imposing four SLR scenarios to alter hydrodynamic boundary conditions and updating shoreline position and dune heights using a probabilistic model that is coupled to SLR. Under the highest SLR scenario, tidal amplitudes within the bays increased as much as 67% (10.0 …

Section Abstracts: Biology

Virginia Journal of Science

Abstracts of the Biology Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

The Effects Of Low Dam Removal And Kayak Run Installation On The Biodiversity Of Fish And Macroinvertebrates In The Great Miami River In Downtown Dayton, Ohio, Sarah Anne Stalder

Honors Theses

Five Rivers Metroparks and the Miami Conservancy District have made plans to remove the upper portion of the Monument Avenue low-head dam in downtown Dayton due to the hazard it poses for recreation on the river and its negative impact on water quality and biodiversity. The plans also include modifying the dam with “kayak drops” and the construction of a second kayak drop slightly upstream of the location of the current low dam to enhance recreational opportunities on the river. Typically, low dam removal alter the flow and depth of a river, especially above the dam in the impounded area …

Synthesis And Mechanistic Investigations Of Transition Metal Complexes And Ligands For Chemotherapeutic Applications, Jimmie Lee Bullock Jr.

Chemistry & Biochemistry Theses & Dissertations

Transition metal complexes have played a critical role in antitumor therapy with many complexes incorporating platinum, ruthenium, and lanthanum having been investigated in preclinical and clinical trials. The best known transition metal therapeutic is cisplatin, which is utilized in nearly 50% of all cancer therapies, despite its significant toxic side effects. The toxic side effects of current FDA approved platinum-based chemotherapeutics are often overlooked due to the “special status” granted to these drugs due to their ability to fight, what is often considered an incurable disease with life expectancies often measured in months. Oncology drug development has therefore now focused …

Integrative Analyses Reveal Signaling Pathways Underlying Familial Breast Cancer Susceptibility, Stephen R. Piccolo, Laura M. Hoffman, Thomas Conner, Gajendra Shrestha, Adam L. Cohen, Jeffrey R. Marks, Leigh A. Neumayer, Cori A. Agarwal, Mary C. Beckerle, Irene L. Andrulis, Avrum E. Spira, Philip J. Moos, Saundra S. Buys, William Evan Johnson, Andrea H. Bild

Faculty Publications

The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple genes may influence FBC risk, we hypothesized that a pathway‐based strategy examining different data types from multiple tissues could elucidate the biological basis for FBC. In this study, we performed integrated analyses of gene expression and exome‐sequencing data from peripheral blood mononuclear cells and showed that cell adhesion pathways are significantly and consistently dysregulated in women who develop FBC. The dysregulation …