Integrative Biology Commons^™

Novel Applications Of Biolayer Interferometry To Investigate Molecular Interactions, Mareena M. Pitts

Master of Science in Integrative Biology Theses

In this study, BLI is used to explore various molecular interactions to demonstrate molecular binding and to provide quantitative characterization of binding kinetics and affinities of phage-protein and DNA-protein interactions. The results of this study demonstrate novel use of biolayer interferometry to immobilize whole Sf6 bacteriophage onto the biosensor to measure the binding to its outer membrane host receptor protein OmpA. The use of BLI also demonstrates the technology as a probe to predict and verify binding interactions at the molecular level to assign the role of protein function in both Vibrio fischeri and Pseudomonas aeruginosa. Each aim of this …

Sperm-Mediated Effects Of Predation Risk On Reproduction In Male Threespined Sticklebacks, Shayne Kempfer, Erika Carlson, Jennifer Hellmann, Jason Keagy, Alison Bell

PRECS student projects

Threespined sticklebacks, Gasterosteus aculeatus, exhibit male-only parental care, but will decrease paternal care if exposed to predators while given care or if their mate has had prior experiences with predators. The offspring will experience lasting effects based on the experience of their parents (behavior-mediated transgenerational plasticity). While other studies have concluded that male exposure to predators prior to fertilization (sperm-mediated transgenerational plasticity) impacts offspring, whether sperm-mediated effects exist in sticklebacks, and for how many generations the effects persist is unknown. Courtship trials with both predator exposed and predator unexposed females with six male treatment groups shows significant impact of maternal …

The Influence Of Landscape And Environmental Factors On Ranavirus Epidemiology In A California Amphibian Assemblage, Brian J. Tornabene, Andrew R. Blausten, Cheryl J. Briggs, Dana M. Calhoun, Pieter T. J. Johnson, Travis Mcdevitt-Galles, Jason R. Rohr, Jason T. Hoverman

Integrative Biology Faculty and Staff Publications

1. A fundamental goal of disease ecology is to determine the landscape and environmental processes that drive disease dynamics at different biological levels to guide management and conservation. Although ranaviruses (family Iridoviridae) are emerging amphibian pathogens, few studies have conducted comprehensive field surveys to assess potential drivers of ranavirus disease dynamics.
2. We examined the factors underlying patterns in site‐level ranavirus presence and individual‐level ranavirus infection in 76 ponds and 1,088 individuals representing five amphibian species within the East Bay region of California.
3. Based on a competing‐model approach followed by variance partitioning, landscape and biotic variables explained the most variation in …

Selective Muscle Degeneration In A Drosophila Model Of Cachexia; A Role For The Transcriptional Regulator Cabut, Matthew Giedd

Master of Science in Integrative Biology Theses

Cachexia is a systemic metabolic syndrome characterized by progressive muscle wasting. Cachectic muscle wasting presents as a comorbidity with pathological illnesses like cancer, chronic inflammation, and type 2 diabetes. The development of cachexia complicates treatment of these diseases and worsens clinical outcomes. Thus, it has become the focus of intense investigation. While many of the upstream mechanisms that propagate cachectic muscle wasting have been brought to light, little is known of the downstream mechanisms which would be more clinically relevant. Here, we have adopted a Drosophila model of cachectic muscle wasting to elucidate a novel role of the transcriptional regulator, …

Sources And Fates Of Carbamyl Phosphate: A Labile Energy-Rich Molecule With Multiple Facets., Dashuang Shi, Ljubica Caldovic, Mendel Tuchman

Genomics and Precision Medicine Faculty Publications

Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether

The Influence Of Dose Of A Plant-Derived Volatile Cue On Arabidopsis Thaliana Resistance Against Insect Herbivores, Sarah Bissmeyer, Grace Freundlich, Christopher Frost

Kentucky Journal of Undergraduate Scholarship

Green leaf volatiles (GLVs) are plant-derived volatile organic compounds (VOCs) known to affect plant-plant communication. Specifically, GLVs can facilitate “priming”, whereby plants initiate a faster and stronger defensive response to a subsequent stress. The stress-induced GLV cis-3-hexenyl acetate (z3HAC) is a known priming cue, yet whether the concentration of the z3HAC affects plant defenses is unknown. Here, we tested the hypothesis that z3HAC concentration of would influence Arabidopsis thaliana resistance against a specialist (Trichoplusia ni) and generalist (Spodoptera exigua) herbivore. Our z3HAC treatments ranged from 0-100 ng/hr, which spanned the …

Thermoregulatory Dysfunction In Multiple Sclerosis, Dustin R. Allen

Applied Physiology and Wellness Theses and Dissertations

Multiple sclerosis (MS) is a progressive neurological disease of the central nervous system (CNS) affecting an estimated 2.3 million people worldwide. Marked by lesions in the brain and spinal cord, MS leads to conduction abnormalities in the CNS. Evidence suggests ~60% of individuals with MS experience temporary worsening of their symptoms upon exposure to heat. Adding complexity, observational evidence suggests these individuals exhibit reduced thermoregulatory responses in upon increases in core temperature. Consequently, these individuals face a vicious cycle of heat sensitivity and thermoregulatory dysfunction, substantially impacting their quality of life. With this in mind, our lab is dedicated to …

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim …

An Integrative Approach To Evaluating Radiocesium Contamination In Fukushima Prefecture, James Thornhill

Master of Science in Integrative Biology Theses

An earthquake in Japan led to the meltdown of the Fukushima Daiichi Nuclear Power Plant which released radionuclides into the surrounding regions. Of these radionuclides, cesium-137 (¹³⁷Cs⁺) has been shown to be the most abundant. Research has shown that adsorption of K⁺ and Cs⁺ on 2:1 clay minerals can collapse the interlayers, causing the adsorbed ion to become non-exchangeable. This thesis takes an integrative approach to the restoration of radiocesium-contaminated soil in three parts by 1) evaluating the adsorption behavior and mechanisms of Cs⁺ in vermiculite, 2) using plants as bioindicators to elucidate …

Transcending The Cell Fate Stereotype: Cell Penetrating Peptide Technology Helps Induce Pluripotency In Multiple Cell Types, Kelsey Clearman

Master of Science in Integrative Biology Theses

Induced pluripotent stem cells (iPSCs) are one of the most promising new technologies in the field of regenerative medicine. iPSCs can be generated directly from a patient’s own fibroblast cells then converted into any cell type, thus overcoming challenges associated with embryonic stem cells and graft-vs-host disease that result from current methods. Generation of iPSCs from fibroblasts is traditionally accomplished by ectopic expression of four key transcription factors (TFs): Oct4, Sox2, Klf4, and c-Myc also known as OSKM. These TFs have been shown to be involved in maintaining pluripotency and inhibiting embryonic stem (ES) cell differentiation. Reprogramming fibroblasts into iPSCs …

Morpho: Expectations & Mutations, Lynda Bostrom

Masters Theses, 2010-2019

Morpho: Expectations & Mutations is a written document accompanying the culmination of my three years painting at a graduate level. The result of which is an autobiographical body of work navigating the tension of being a human with an invisible disease, while straining to understand Western societal constructs of women. I simultaneously reject these fairy tales as a standard recipe for happiness, yet identify with its visual language that is rooted in the vernacular of my generation. Redefining the elements I reject or embrace helps me to look beyond the boundaries of these constructs, and adopt an attitude of curiosity …

Evolution Of Voltage-Gated Ion Channels, Kevin Gregory Bennett, Kevin Bennett

Master of Science in Integrative Biology Theses

Voltage-gated Ion Channels (VICs) form a superfamily of energy-independent membrane transporters that facilitate the transfer of charged sodium, calcium, and potassium ions across the cell membrane (Hodgkin & Huxley 1952). The channels contain a selective ion-conducting pore along with several other structural and gating features that come together to form a functional hetero- or homotetramer. A comprehensive phylogenetic study of all available proteins aimed at finding unknown distribution and illuminating evolutionary paths would be immensely useful in understanding relationships of structure, function, and organismal distribution. This phylogenetic analysis of VICs will be immensely useful in characterizing functional and structural distribution, …

Evaluating In Situ Grazing Patterns Of Lytechinus Variegatus And Their Effects On Seagrass Beds Of Thalassia Testudinum, Adrianna Parson

Master of Science in Integrative Biology Theses

The sea urchin Lytechinus variegatus is a known grazer of the seagrass Thalassia testudinum, and has been known to denude vast stands of seagrass beds at high densities. Outside of these denudation events, the effects of sea urchins on seagrass are poorly understood. This study examines the effects of L. variegatus on T. testudinum in situ, to understand how sea urchins are affecting seagrasses in situ. Results indicate that urchins were found in the offshore portion of the seagrass bed at densities up to 4 urchins/m². Changes in temperature and sediment size in the bay indicate …

A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian

Dissertations, Theses, and Capstone Projects

Gyroporus (Sclerodermatineae, Boletales, Agaricomycetes, Basidiomycota, Fungi) is a genus of ectomycorrhizal mushroom-forming fungi distributed throughout the world in suitable habitats. Previous attempts to untangle the diversity of this genus proved difficult due to the presence of semi-cryptic species and equivocal results from phylogenetic analysis of ribosomal RNA markers. To overcome these obstacles, a combined taxonomic and phylogenetic (emphasizing protein-coding genes) approach is used here to delimit species and elucidate geographic and evolutionary patterns of Gyroporus. Careful study of relevant literature and herbarium specimens was augmented by field work in North America, Australia, and East Asia for observation and collection …

Novel Use Of A Cell-Penetrating Peptide-Adaptor System To Characterize Akirin Constructs And Investigate Activity Of Bacterial Effector Proteins, Shaquanna Young

Master of Science in Integrative Biology Theses

In the late 1980s, HIV protein TAT was found to confer the passage of HIV through the plasma membrane of mammalian cells. The McMurry lab developed a CPP-adaptor system which consists of the fusion of TAT to calmodulin to which mediates the delivery of exogenous proteins into cells and prevents endosomal entrapment. Calmodulin (CaM) is capable of binding to the calmodulin binding site (CBS) of cargo only in the presence of calcium. TAT-CaM can be used to characterize Akirin constructs and investigate the activity of bacterial effectors, AopP and AvrA, in the NF-kB pathway. Akirin is a small nuclear protein …

A Basal Laryngeal Cartilage Is Present In Neotropical Túngara Frogs (Engystomops Pustulosus), Amy D. Lagorio, Marcos Gridi-Papp

Pacific Research & Scholarship Day

No abstract provided.

Investigating The Molecular Function Of Akirin During Skeletal Myogenesis In Drosophila Melanogaster, Kristina Rowland

Master of Science in Integrative Biology Theses

The specification and differentiation of muscle precursor cells, or myoblasts, by the action of the mesodermal and muscle transcription regulator Twist is a key event in the formation of the Drosophila larval musculature. Akirin, a highly conserved nuclear protein, appears to play a critical role in the regulation of Twist-dependent gene expression during mesodermal specification and muscle development. Specifically, Akirin serves as a cofactor to promote interactions between regulatory transcription factors and multisubunit Brahma SWI/SNF-class chromatin remodeling complex to impact gene expression across varying targets. Using a genetic interaction screen in Drosophila, we have begun to identify other Akirin …

Skeletal, Cardiac, And Respiratory Muscle Function And Histopathology In The P448lneo- Mouse Model Of Fkrp-Deficient Muscular Dystrophy., Qing Yu, Melissa Morales, Ning Li, Alexander G Fritz, Ren Ruobing, Anthony Blaeser, Ershia Francois, Qi-Long Lu, Kanneboyina Nagaraju, Christopher F Spurney

Genomics and Precision Medicine Faculty Publications

BACKGROUND: Fukutin-related protein (FKRP) mutations are the most common cause of dystroglycanopathies known to cause both limb girdle and congenital muscular dystrophy. The P448Lneo- mouse model has a knock-in mutation in the FKRP gene and develops skeletal, respiratory, and cardiac muscle disease.

METHODS: We studied the natural history of the P448Lneo- mouse model over 9 months and the effects of twice weekly treadmill running. Forelimb and hindlimb grip strength (Columbus Instruments) and overall activity (Omnitech Electronics) assessed skeletal muscle function. Echocardiography was performed using VisualSonics Vevo 770 (FujiFilm VisualSonics). Plethysmography was performed using whole body system (ADInstruments). Histological evaluations included …

Examining The Relationship Between Climate And Seasonal Stream Thermal Regimes In A High Desert Ecosystem, Hannah Moore, Melody Feden

Scholars Week

Climate change is negatively affecting ecosystems around the world, and in the coming years, scientists predict that these changes will only intensify and accelerate. In the western mountains of North America, climate change projections predict elevated temperatures, reduced snowpack, and earlier snowmelt. Elevated air temperatures have the propensity to affect water temperatures in sensitive freshwater ecosystems. Temperature increases may cause streams to reach the upper thermal limit for many aquatic organisms, such as aquatic invertebrates and fish, and result in death or dispersal for these organisms. This makes the availability of cold-water refugia in streams that much more important for …

Can Omnivores Mediate The Effects Of Degradation?, Hannah Moore

Scholars Week

Omnivores feed at multiple trophic levels and have large effects on community structuring and stability. The magnitude and direction of such effects, whether omnivores stabilize or destabilize communities, remains unresolved. Shifts in omnivore diet and trophic position may be of particular importance to community stability in degraded habitats, where resources are sparse. For example, omnivores may reduce the severity and duration of community responses to degradationby dampening the effects of any disturbance-mediated trophic cascade. The relatively simple food webs of freshwater systems are ideal for studying trophic ecology, and in the western U.S., streams are heavily degraded by overgrazing, beaver …