Digital Commons Network^™

Development And Application Of Mass Spectrometry-Based Biophysical Approaches, Ying Zhang

Arts & Sciences Graduate Student Theses and Dissertations

Mass spectrometry (MS)-based biophysical approaches are new "tools" for protein characterization owing to its capability to analyze proteins and protein complexes that range in molecular weight from kDa to MDa. Protein characterization requires more than identifying the primary structure. More importantly, protein high order structures (i.e., secondary, tertiary and quaternary structures) are needed for biological studies. MS has become the major tool in studies of protein primary structure and post translational modifications (PTMs) over the past two decades. Because MS has high sensitivity and fast turnaround, more and more biophysical approaches rely on MS to generate information for protein higher …

The Roles Of Mist1 And Rab26 In Zymogenic (Chief) Cell Differentiation And Subcellular Organization, Ramon Jin

Arts & Sciences Graduate Student Theses and Dissertations

Little is known about how differentiating cells reorganize their cellular structure to perform specialized physiological functions. Specifically, exocrine cells like pancreatic acinar and zymogenic chief cells have a highly developed secretory architecture that is rapidly established upon differentiation. What is known in these cells is that the evolutionarily conserved transcription factor MIST1 is required for final maturation. We hypothesized that MIST1 directly regulates specific subcellular components that facilitate functional maturation of secretory cells.We show that MIST1 binds to conserved CATATG E-boxes to activate transcription of 6 genes, including the small GTPases RAB26 and RAB3D. We next demonstrate that RAB26 and …

Metabolic Engineering Of Cyanobacteria For Photosynthetic Production Of Drop-In Liquid Fuels, Bertram Michael Berla

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cyanobacteria are oxygenic phototrophs with great potential as hosts for renewable fuel and chemical production. They grow very quickly (compared with plants) and can use sunlight for energy and CO2 as a carbon source (unlike yeast or E. coli). While cyanobacteria have been engineered to make many chemicals that are native and non-native parts of their metabolism, this work is concerned with the production of heptadecane in Synechocystis sp. PCC 6803. Heptadecane is in a class of natural products produced by all cyanobacteria, but in quantities insufficient for industrialization. Towards this future goal, we have built enabling systems for the …

Functional Roles Of Nucleases In Dna Metabolism And Genome Stability, Justin Lee Sparks

All Theses and Dissertations (ETDs)

The work outlined in this dissertation focuses on two distinct areas that are important for genome stability. Both areas focus on DNA repair pathways that require the action of nucleases, specifically Exonuclease 5 and Ribonuclease H2. First, I describe the biochemical and molecular characterization of the novel Exonuclease 5 family of enzymes from S. cerevisiae, S. pombe, and humans. The Exo5 family consists of bi-directional single-strand DNA specific exonucleases that all contain an iron-sulfur cluster as a structural motif and all have various roles in DNA metabolism. In the Saccharomycetales order that includes the budding yeast, S. cerevisiae, Exo5 is …

Discovery And Characterization Of Novel Polyomaviruses In Humans, Erica Anne Siebrasse

All Theses and Dissertations (ETDs)

The family Polyomaviridae is comprised of small, double-stranded DNA viruses of approximately 5,000 base pairs. Two polyomaviruses are well-established human pathogens and cause significant morbidity and mortality in immunocompromised patients. These viruses were discovered in the 1970s, but the last seven years have seen an explosion of novel human polyomavirus discoveries. The work described here seeks to address two questions: "Are there additional, novel polyomaviruses infecting humans?" and "Do these polyomaviruses cause disease in their human hosts?" The discovery of an additional novel polyomavirus, MW polyomavirus (MWPyV), is described. MWPyV was discovered in the stool of a healthy child from …

Engineering Biosensors For Short-Chain Alcohols, Yu Xia

McKelvey School of Engineering Graduate Student Theses & Dissertations

Biofuel is a promising substitute for fossil fuel and the research of biofuel production has been extensively conducted during the recent years. Great efforts have been made to create many types of the fuel production hosts. However, effective approaches for high specificity and high throughput screening of the fuel production strains are still lacking. The cellular stress response is one universal defense mechanism when a microbial cell is exposed to an unfavorable substance or environment. It triggers a series of downstream responses when a cell senses certain chemicals. Transcriptional factors are widely used in living organisms to regulate gene expression. …

Submicron-Resolution Photoacoustic Microscopy Of Endogenous Light-Absorbing Biomolecules, Chi Zhang

All Theses and Dissertations (ETDs)

Photoacoustic imaging in biomedicine has the unique advantage of probing endogenous light absorbers at various length scales with a 100% relative sensitivity. Among the several modalities of photoacoustic imaging, optical-resolution photoacoustic microscopy (OR-PAM) can achieve high spatial resolution, on the order of optical wavelength, at <1 mm depth in biological tissue (the optical ballistic regime). OR-PAM has been applied successfully to structural and functional imaging of blood vasculature and red blood cells in vivo. Any molecules which absorb sufficient light at certain wavelengths can potentially be imaged by PAM. Compared with pure optical imaging, which typically targets fluorescent markers, label-free PAM avoids the major concerns that the fluorescent labeling probes may disturb the function of biomolecules and may have an insufficient density. This dissertation aims to advance label-free OR-PAM to the subcellular scale.

The first part of this dissertation describes the technological advancement of PAM yielding high spatial resolution in 3D. The lateral resolution was improved by using optical objectives with high numerical apertures for optical focusing. The axial resolution was improved by using broadband ultrasonic transducers for ultrasound detection. We achieved 220 nm lateral resolution in transmission …

The Processing Of Amyloid Precursor Protein In The Central Nervous System Of Humans And Rhesus Macaques, Justyna Anna Dobrowolska

All Theses and Dissertations (ETDs)

Alzheimer's disease: AD) is the most common dementia, currently afflicting 30 million people worldwide, with prevalence steadily increasing. Over 99% of AD cases are classified as sporadic, in which the major risk factors are age: greater than 65 years) and the ApoE-ε4 allele: in a gene dose dependent manner). The minority of AD cases: less than 1%) are caused by autosomal dominant inheritance of a genetic mutation in one of three genes: Amyloid Precursor Protein: APP), Presenilin-1: PSEN1), or Presenilin-2: PSEN2). Mutation carriers will generally notice cognitive decline starting at a relatively young age, anytime between their 30s-50s, and eventually …

Dissecting The Mechanisms And The Nutritional Requirements Of The Expansion Of Normal And Tumorigenic Intestinal Stem Cell Lineages In Drosophila Melanogaster, Wen-Chih Lee

All Theses and Dissertations (ETDs)

Organisms are constantly challenged by injury and senescence. To replenish lost cells, adult tissue must contain a cellular reserve to maintain homeostasis. For example, adult stem cells exhibit two unique properties, self-renewal and potency, that make them well suited for this role. Tight regulatory control of stem cell properties is critical to maintain homeostatic balance; misregulation often leads to tumors or diseases. Recently, homeostasis of the intestinal epithelium has been shown to depend on a population of molecular defined intestinal stem cells: ISCs) in both Drosophila and mammals. However, the regulatory mechanisms controlling ISC behaviors remain poorly defined. We took …

Joint Entropy Of Continuously Differentiable Ultrasonic Waveforms, M S. Hughes, John E. Mccarthy, J N. Marsh, S A. Wickline

Mathematics Faculty Research

This study is based on an extension of the concept of joint entropy of two random variables to continuous functions, such as backscattered ultrasound. For two continuous random variables, X and Y, the joint probability density p(x,y) is ordinarily a continuous function of x and y that takes on values in a two dimensional region of the real plane. However, in the case where X=f(t) and Y=g(t) are both continuously differentiable functions, X and Y are concentrated exclusively on a curve, γ(t)=(f(t),g(t)), in the x,y plane. This concentration can only be represented using a mathematically "singular" object such as a …

Development Of Patterned Self-Assembled Monolayers Toward The Study Of Axonal Differentiation, Dawn Marie Johnson

All Theses and Dissertations (ETDs)

The following work discusses the development of several techniques and new methods for the production of patterned surfaces for protein and cell confinement. These well-defined substrates allow us to study the mechanism of axonal differentiation in neurons confined to a two-dimensional starburst pattern. We utilize self-assembled monolayer: SAM) chemistry in conjunction with microcontact printing to create stable patterned substrates for cell culture. Photolithography is employed in the fabrication of patterned masters, which are used to create elastomeric stamps for microcontact printing.

Initially, trichlorosilanes were employed in our patterned SAMs because they react rapidly with glass. These patterned surfaces confined protein …

New Methods For The Construction And Characterization Of Molecules On An Addressable Array, Bo Bi

All Theses and Dissertations (ETDs)

Microelectrode array has great potential as a platform for building "addressable" molecular libraries and being utilized to probe the ligand-receptor binding events in "real-time". To achieve this objective, a complete study would generally include three phases: 1) to enable and expand site-selective chemistry on the array; 2) to understand structural information of the molecules loaded; and 3) to develop research protocols of electrochemical analysis on the device to monitor those molecular interactions. While 2), quality-control analysis, is a core task of this thesis, the studies in other phases that drove this work or derived from it, are also discussed in …

The Psycho-Economic Model Of Ecstasy Consumption And Related Consequences: A Multi-Site Study With Community Samples, Arbi Ben Abdallah

All Theses and Dissertations (ETDs)

A Psycho-Economic Model of Ecstasy Consumption and Related Consequences: A Multi-Site Study with Community Samples By Arbi Ben Abdallah The consumption of mind-altering drugs is well recognized as a complex behavior entailing many different etiological precursors. To understand its complexity, drug use has to be considered from multiple perspectives. Over time, numerous theories have been advanced to explain drug use, the pattern of its use, and its related consequences. Because they approach such a behavior from slightly different vantage points, these theories offer unique explanations with different take on its genetic, physiological, psychological, and environment risk factors. A substantial body …

Development And Study Of Inhibitors Of Heat Shock Protein 70 Induction, Rongsheng Wang

All Theses and Dissertations (ETDs)

Tumor and cancer cells that over express heat shock protein 70: HSP70) are found to be multidrug resistant and thermo tolerant, creating a hurdle to existing therapy. Although HSP70 is recognized as an increasingly important drug target, the protein structure of this highly conserved chaperone remains challenging for direct targeting. An alternative strategy is to inhibit the transcription of HSP70. Among known small molecule inhibitors of HSP70 induction, quercetin has very low toxicity and has the advantage of being easily modified for structure-activity studies. One part of the dissertation focuses on the identification of quercetin derivatives with improved specificity and …

Microbial Diversity And Geochemical Energy Sources Of Tutum Bay, Ambitle Island, Papua New Guinea, An Arsenic-Rich, Shallow-Sea Hydrothermal System, Nancy Akerman

All Theses and Dissertations (ETDs)

I investigate the hydrothermal system located in Tutum Bay, Ambitle Island, Papua New Guinea, a shallow-sea system ~5 - 10 meters below sea level that is arsenic-rich. Hydrothermal vents in the bay expel fluids with arsenite: AsIII) concentrations as high as 950 μg/L. To determine the role that Tutum Bay microorganisms might play in mediating As-redox reactions, three approaches were used: analyzing the geochemical environment for energy sources, characterizing the archaeal community composition of the sediments, and conducting culture-dependent As-cycling experiments. The second chapter of this dissertation discusses an energetic study of potential chemolithotrophic metabolic reactions, including As-redox reactions. Results …

Discovering Weak Community Structures In Large Biological Networks , Jianhua Ruan, Weixiong Zhang

All Computer Science and Engineering Research

Identifying intrinsic structures in large networks is a fundamental problem in many fields, such as biology, engineering and social sciences. Motivated by biology applications, in this paper we are concerned with identifying community structures, which are densely connected sub-graphs, in large biological networks. We address several critical issues for finding community structures. First, biological networks directly constructed from experimental data often contain spurious edges and may also miss genuine connections. As a result, community structures in biological networks are often weak. We introduce simple operations to capture local neighborhood structures for identifying weak communities. Second, we consider the issue of …

Productive Engagement Of Older Adults: Effects On Well-Being, Nancy Morrow-Howell

Center for Social Development Research

Productive Engagement of Older Adults: Effects on Well-Being