Biochemistry, Biophysics, and Structural Biology Commons^™

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Abcb11 Functions With B1 And B19 To Regulate Rootward Auxin Transport, Jesica Elyse Reemmer

Open Access Theses

Auxin transport is essential for the architecture and development of erect plants. In a network of transporters directing auxin flows, ATP-Binding Cassette (ABC) transporters are a ubiquitous family of proteins that actively transport important substrates, including auxins, across the plasma membrane. ABCB1 and ABCB19 have been shown to account for the majority of rootward auxin transport, but residual fluxes to the root tip in Arabidopsis b1b19 double mutants implies the involvement of at least one additional auxin transporter in this process. Of specific interest, the severe dwarfism seen in abcb1abcb19 is strikingly reminiscent of that seen in mutants defective in …

Efficacy Of Cleaning Method For Removal Of Exogenous Welding Fume Contamination From Nail Tissue Prior To Use As A Biomarker For Welding Fume Manganese Exposure, Jeffrey Corral Bainter

Open Access Theses

Nail tissue has been proposed as a biomarker for body burden of occupational exposure to manganese from welding fumes. Though recent studies have shown correlation between manganese exposure and both nail tissue concentration as well as concentrations in dopaminergic regions of the brain, concerns of the validity of nail tissue as a biomarker have arisen due to the potential for exogenous contamination of Mn to undermine the quantization of endogenous Mn in nail. Previous studies have used a cleaning method of 1% Triton X-100 surfactant plus sonication in order to attempt to remove exogenous welding fume contamination. Determination of the …

1,25-Dihydroxyvitamin D Alters Lipid Metabolism And Epithelialto- Mesenchymal Transition In Metastatic Epithelial Breast Cancer Cells, Alle Nicole Barnard

Open Access Theses

Evidence suggests that high vitamin D status (marked by serum 25-hydroxyvitamin D, 25(OH)2 D) is associated with a decreased risk of breast cancer. It has been established that 1,25-dihydroxyvitamin D (1,25(OH) 2 D) can alter glycolysis and the Krebs cycle of breast cancer cells (Jiang et al., 2010; Zheng et al., 2013) but little information is available on 1,25(OH) 2 D's alterations of lipid metabolism in breast cancer cells. Thus, the current research investigates if there was an effect of 1,25(OH) 2 D on proteins that regulate lipid metabolism in MCF10A, MCF10A-ras, MCF10CA1h, and MCF10CA1a epithelial breast cancer cells. While …

Using The Microsoft Kinect To Assess Human Bimanual Coordination, Joshua James Liddy

Open Access Theses

Optical marker-based systems are the gold-standard for capturing three-dimensional (3D) human kinematics. However, these systems have various drawbacks including time consuming marker placement, soft tissue movement artifact, and are prohibitively expensive and non-portable. The Microsoft Kinect is an inexpensive, portable, depth camera that can be used to capture 3D human movement kinematics. Numerous investigations have assessed the Kinect's ability to capture postural control and gait, but to date, no study has evaluated it's capabilities for measuring spatiotemporal coordination. In order to investigate human coordination and coordination stability with the Kinect, a well-studied bimanual coordination paradigm (Kelso, 1984, Kelso; Scholz, & …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.

Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park

Open Access Theses

Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …

Developing An Unstructured Model To Investigate The Effect Of Ethanol On Product Yields For Glucose And Xylose Cofermentation In Saccharomyces Cerevisiae 424a (Lnh-St), Shane D. Clingenpeel

Open Access Theses

Production of bio-ethanol from lignocellulose requires the efficient fermentation of glucose and xylose, even in the presence of inhibitors. The desired product, ethanol itself, will inhibit the fermentation. A further understanding of how ethanol affects the organism is critical to overcoming its inhibition.

This thesis evaluated the effect of ethanol on the cofermentation of glucose and xylose in two different cases. The first case had an unstructured model created for Saccharomyces cerevisiae 424A (LNH-ST), a genetically modified strain of yeast capable of cofermenting glucose and xylose. The differential equations were based around sugar consumption, and the product yields were investigated …

Neurotrophins And Their Effects On Breast Cancer Cell Proliferation And Migration, Kayla Elise Minser

Open Access Theses

Cancer is a large health issue in all parts of the world. In the United States alone, approximately 1 in 4 deaths are cancer related. Breast cancer is a particularly prevalent form, accounting for a little over 14 percent of all cancer incidence. The largest obstacle to overcome for breast cancer morbidity is metastasis. Over 90 percent of all breast cancer related deaths are due to metastasis. Because metastasis is a complex, multi-step process, it is difficult to treat. A recent observation in the Kirshner lab has revealed a type of phenotypic plasticity, where migratory cancer cells have a neuronal-like …

Pharmaceuticals And Personal Care Products: Emerging Contaminants In Aquatic Ecosystems, Jenny E. Zenobio

Open Access Theses

In recent years, the presence of pharmaceuticals and personal care products (PPCPs) in aquatic systems has led to research on their fate and effects. PPCPs have been found in mixture in wastewater effluents, surface, ground, and drinking water at low concentrations from areas of intense urbanization. Although adverse effects to human health from the current environmental concentrations are unlikely, the impacts to ecological receptors are not clear. We performed field and laboratory studies to quantify and evaluate effects of PPCPs on fish. First, a field study was conducted at the Baca National Wildlife Refuge, Colorado (2010-2012) because a portion of …