Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders,
2017
Virginia Commonwealth University
Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders, Robin F. Chan
Theses and Dissertations
DNA methylation is necessary for learning, memory consolidation and has been implicated in a number of neuropsychiatric disorders. Obtaining high quality and comprehensive data for the three common forms of methylation in brain is challenging for methylome-wide association studies (MWAS). To address this we optimized a panel of enrichment methods for screening the brain methylome. Results show that these enrichment techniques approach the coverage and fidelity of the current gold standard bisulfite based techniques. Our MBD-based method can also be used with low amounts of genomic material from limited human biomaterials. Psychiatric disorders have high prevalence and are often chronic …
Relb Acts As A Molecular Switch To Drive Chronic Inflammation In Glioblastoma Multiforme (Gbm).,
2017
Virginia Commonwealth University
Relb Acts As A Molecular Switch To Drive Chronic Inflammation In Glioblastoma Multiforme (Gbm)., Michael R. Waters
Theses and Dissertations
Inflammation is a homeostatic response to tissue injury or infection, which is normally short- lived and quickly resolves to limit tissue damage. In contrast, chronic inflammation has been linked to a variety of human diseases, including cancers such as glioblastoma multiforme (GBM). GBMs are very aggressive tumors with very low patient survival rates, which have not improved in several decades. GBM tumors are characterized by necrosis and profound inflammation; with cytokines secreted by both GBM cells and the tumor microenvironment. The mechanisms by which chronic inflammation develops and persists in GBM regardless of multiple anti-inflammatory feedback loops remain elusive. This …
Plaster Creek Bacterial Monitoring And Source Tracking Project - Final Report,
2017
Calvin University
Plaster Creek Bacterial Monitoring And Source Tracking Project - Final Report, Randall J. Dejong
Faculty and Professional Research
The objective of this project was to identify important sources of bacterial loading in Plaster Creek (Kent County). The following goals were set to reach this objective: 1) the relative contributions of bacterial loading for 10 major tributaries will be assessed and the five most egregious contributors will be prioritized; 2) molecular markers will be used to try to identify the primary taxonomic sources, and 3) to pinpoint bacterial loading locations using molecular markers and scent-trained canines in sub-watersheds.
The Role Of Gln146 To The Stability And Activity Of Manganese Superoxide Dismutase,
2017
University of Kentucky
The Role Of Gln146 To The Stability And Activity Of Manganese Superoxide Dismutase, Ting Wang
Theses and Dissertations--Chemistry
Gln146 is a highly conserved outer-sphere amino acid residue at the active site of MnSOD. It serves as a hydrogen bond donor to both the solvent molecules at the active site and Tyr 34, the conserved “gateway” amino acid residue. This dissertation develops our understanding of the effect of amino acid Gln146 at the second shell of the active site of metalloprotein MnSOD in facilitating metal binding, the modulation of redox potential, and the optimization of catalytic activity and structure stability. Different from the wild-type MnSOD, Q146E is always purified as a completely apo-protein with zero active metal ion and …
Illuminate The Pathway Of Membrane Protein Association And Degradation,
2017
University of Kentucky
Illuminate The Pathway Of Membrane Protein Association And Degradation, Zhaoshuai Wang
Theses and Dissertations--Chemistry
Escherichia coli transporter protein AcrB and its homologues are the inner membrane components of the Resistance-Nodulation-Division (RND) family efflux pumps in Gram-negative bacteria. It is well accepted that soluble proteins are only marginally stable, but such insight is missing for membrane proteins. The lack of stability data, including thermodynamic stability and oligomer association affinity is a result of intrinsic difficulties in working with membrane proteins. In addition, the degradation of soluble proteins in E. coli has been extensively studied whereas the degradation process of membrane proteins remains unclear. A focus of my thesis is the validation and development of methods …
Synthesis And Development Of Zwitterionic Pei (Zpei) For Optimized Delivery Of Nucleic Acids,
2017
University of Kentucky
Synthesis And Development Of Zwitterionic Pei (Zpei) For Optimized Delivery Of Nucleic Acids, Joseph Raleigh Duke Iii
Theses and Dissertations--Chemistry
Gene therapy holds promise for the treatment a wide range of diseases ranging from cystic fibrosis to cardiovascular disease to cancer. The need for safe and efficient gene delivery methods remains the primary barrier to human gene therapy. Non-viral vector materials, including polymers, can be designed to be biocompatible and non-immunogenic, but lack the efficiency to be clinically relevant. Gene therapy awaits the development of new materials that are both safe and efficient. Here, we have synthesized a series of modified zwitterionic polymers based on the common transfecting agent polyethylenimine (PEI). Using a variety of biochemical and biophysical methods we …
Engineering An Alkane-Hydroxylating Bacterial Monooxygenase: A Tale Of Two Chemistries,
2017
Pomona College
Engineering An Alkane-Hydroxylating Bacterial Monooxygenase: A Tale Of Two Chemistries, Arjun Nanda
Pomona Senior Theses
Toluene / o-xylene monooxyenase (ToMO) from Pseudomonas sp. OX1 is a multimeric metalloenzyme enzyme that efficiently catalyzes the hydroxylation of aromatic hydrocarbons with high specificity. Though included in a larger group of conserved bacterial multicomponent monooxygenases (BMMs) studied as potential biocatalysts for industrial hydrocarbon chemistry, the substrate specificity and oxygenated intermediates of ToMO differ greatly from its well-characterized, alkane-hydroxylating analog sMMO. Despite a shared global topology and near identical active sites, sMMO can cleave inert C-H bonds in alkanes while ToMO cannot - two seemingly similar structures give rise to vastly different chemistries. This work seeks to determine a structural …
High-Throughput Single-Molecule Mapping Links Subtelomeric Variants And Long-Range Haplotypes With Specific Telomeres,
2017
Old Dominion University
High-Throughput Single-Molecule Mapping Links Subtelomeric Variants And Long-Range Haplotypes With Specific Telomeres, Eleanor Young, Steven Pastor, Ramakrishnan Rajagopalan, Jennifer Mccaffrey, Justin Sibert, Angel C. Y. Mak, Pui-Yan Kwok, Harold Riethman, Ming Xiao
School of Medical Diagnostics & Translational Sciences Publications
Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomereterminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG) n repeat tracts. We establish detailed maps for subtelomere gap regions in the human reference sequence, detect many new large subtelomeric variants and demonstrate the feasibility of long-range haplotyping through segmentally duplicated subtelomere regions. …
Tissue Specific Microenvironments: A Key Tool For Tissue Engineering And Regenerative Medicine,
2017
Old Dominion University
Tissue Specific Microenvironments: A Key Tool For Tissue Engineering And Regenerative Medicine, Patrick C. Sachs, Peter A. Mollica, Robert D. Bruno
School of Medical Diagnostics & Translational Sciences Publications
The accumulated evidence points to the microenvironment as the primary mediator of cellular fate determination. Comprised of parenchymal cells, stromal cells, structural extracellular matrix proteins, and signaling molecules, the microenvironment is a complex and synergistic edifice that varies tissue to tissue. Furthermore, it has become increasingly clear that the microenvironment plays crucial roles in the establishment and progression of diseases such as cardiovascular disease, neurodegeneration, cancer, and ageing. Here we review the historical perspectives on the microenvironment, and how it has directed current explorations in tissue engineering. By thoroughly understanding the role of the microenvironment, we can begin to correctly …
Characterization Of A Putative Hemolysin Expressed By Sneathia Amnii, A Preterm Birth-Associated Pathogen,
2017
Virginia Commonwealth University
Characterization Of A Putative Hemolysin Expressed By Sneathia Amnii, A Preterm Birth-Associated Pathogen, Lizette Carrasco, Kimberly Jefferson
UROP Posters
The gram-negative bacteria Sneathia amnii is a poorly-characterized commensal of the female urogenital tract frequently associated with adverse clinical outcomes such as bacterial vaginosis (BV), amnionitis, and preterm labor. To investigate its potential role in virulence, we sought to identify and characterize virulence determinants produced by S. amnii in an effort to better understand the pathogenesis of infectious preterm birth. Through sequencing of the Sn35 genome (type strain of S. amnii), we identified two genes with amino acid sequence similarity and structural similarity to the filamentous hemagglutinin (FHA) protein of Bordetella pertussis and its Type Vb transporter. Because S. amnii …
The Extension Of Rbc Longevity And Functionality In The Prevention Of Graft Versus Host Disease,
2017
Virginia Commonwealth University
The Extension Of Rbc Longevity And Functionality In The Prevention Of Graft Versus Host Disease, Shanmuka Gadiraju, Megh Kumar
UROP Posters
Given today’s current scientific method of preservation, red blood cells (RBCs) donated or drawn from live humans have a storage life of approximately 42 days, after which the blood will be discarded due to of degradation of the RBCs. The mechanism that drives said degradation is known as oxidative stress, in which the cells’ inability to balance out the creation and excretion of free radicals causes a conformational change in the shape and efficacy of RBCs. In order to counteract the oxidative actions upon the cells, it has been thought that the addition of reducing agents, specifically ascorbic acid, the …
Separation Of Blood Mixtures Using Fluorescently Labeled Antibodies,
2017
Virginia Commonwealth University
Separation Of Blood Mixtures Using Fluorescently Labeled Antibodies, Dani Jabado
UROP Posters
Identifying and analyzing biological mixture samples at a crime scene are of paramount concern for forensic scientists, especially if that type of evidence contains only one cell type. The presence of multiple contributors in a biological evidence sample reduces the probative value of DNA evidence and can sometimes lead to its eventual loss of value. As such, this study was performed in an attempt to examine and evaluate flow cytometry analysis as a means to separate blood mixture samples labeled with fluorescent antibodies. Fluorescein Isothiocyanate (FITC) antibodies were specifically targeted and bound to HLA (Human Leukocyte Antigens) markers present on …
Characterization Of Multi-Albumin Pegylated Complexes Synthesized Using "Click" Chemistry As Drug Delivery Systems,
2017
Loyola University Chicago
Characterization Of Multi-Albumin Pegylated Complexes Synthesized Using "Click" Chemistry As Drug Delivery Systems, Jonathan Alejandro Hill
Dissertations
Due to its ability to transport hydrophobic materials through the bloodstream, human serum albumin has become an intriguing component for drug delivery systems. The most pressing concerns with current albumin-based systems are the risk of pathogenic transfer associated with human-sourced blood proteins, the negative effect on osmotic pressure due to administration of a large dose of albumins, the potential immune response and loss of biological activity due to heavy modification of these albumins, and the need for organic solvents for preparation of these products. Key residues in the two main drug binding sites, DS1 and DS2, are conserved in bovine …
Utilizing Single-Molecule Fret Methods To Study Conformational Changes In Trim5Α,
2017
Loyola University Chicago
Utilizing Single-Molecule Fret Methods To Study Conformational Changes In Trim5Α, Margret Suzanne Bradley
Master's Theses
Single-molecule FRET (smFRET) is a method by which dynamic conformational changes can be monitored in a protein microscopically and in real time. smFRET relies on the creation of FRET (Förster Resonance Energy Transfer) between small molecule fluorophores conjugated to the biomolecules of interest. FRET efficiency allows calculation of interfluorophore distances. Changes in FRET efficiency represent changes in protein conformation which can inform further structural and molecular studies of the protein of interest. For example, in the Campbell Lab, we study the protein TRIM5α, an antiretroviral cellular protein which can cause premature dissociation of the HIV capsid core by an unknown …
Potential Efficacy Of Targeting Mll1 In Breast Cancer,
2017
Loyola University Chicago
Potential Efficacy Of Targeting Mll1 In Breast Cancer, Austin Gable Holmes
Master's Theses
In 2017, it is estimated that breast cancer will be the most prevalent newly diagnosed cancer in females, at 30% in the U.S. alone1. From the early 1990s to 2014 the death rate in females from breast cancer has dropped by 10% but still stands as the second highest cancer related death in females in the U.S.2. One of the biggest hurdles in breast cancer research is disease heterogeneity. New mechanisms of disease development and progression are encountered frequently. One mechanism studied in the past decades is epigenetics. It has been theorized that the cancer epigenome can maintain an abnormal …
Evidence Of A Perilipin 5 Splice Variant,
2017
Otterbein University
Evidence Of A Perilipin 5 Splice Variant, Brodie Ranzau
Undergraduate Honors Thesis Projects
Alternative splicing occurs throughout the human genome, leading to multiple proteins from a single gene. The resulting proteins can be nearly identical or vastly different in how they function. Alternative splicing within the perilipin family has been observed in perilipins 1 and 3, giving rise to proteins with varying functions. In the course of our studies on perilipin 5, an immunoblot signal was observed that corresponded to an approximately 35 kDa protein. Western blot analysis of this protein has revealed its expression in C2C12 cultured myoblasts and in heart and liver mouse tissue. Further analysis of perilipin 5 cDNA through …
Cloning And Characterisation Of Alternansucrase From Leuconostoc Citreum Abk-1 And Role Of Surface Aromatic Acids On Product Size,
2017
Faculty of Science
Cloning And Characterisation Of Alternansucrase From Leuconostoc Citreum Abk-1 And Role Of Surface Aromatic Acids On Product Size, Karan Wangpaiboon
Chulalongkorn University Theses and Dissertations (Chula ETD)
The alternansucrase (ALT, EC 2.4.1.140) catalyses transferring of glucose from sucrose to produce a polymer with α-1,6 and α- 1,3 linkages, so-called "alternan". The ALT-encoding gene from Leuconostoc citreum ABK-1 (WTalt) was successfully cloned and expressed in Escherichia coli BL21 (DE3). The two versions of truncated SH3-like domains, ∆3SHALT and ∆7SHALT, were successfully constructed. The WTALT, ∆3SHALT and ∆7SHALT possessed optimum temperature of 40 °C, while optimum pH of WTALT was at 5.0 but ∆3SHALT's and ∆7SHALT's were shifted to pH 4.0. Their activities could be enhanced by Mn²⁺. Kinetic studies of all ALTs were mainly responsible for transglycosylation activity …
Expression And Characterization Of Α-Glucosidase From Weissella Confusa Bbk-1,
2017
Faculty of Science
Expression And Characterization Of Α-Glucosidase From Weissella Confusa Bbk-1, Lalita Silapasom
Chulalongkorn University Theses and Dissertations (Chula ETD)
Alpha-glucosidase [EC 3.2.1.20; α-D-glucoside glucohydrolase] is an exohydrolase which catalyzes non-reducing end of substrates to release D-glucose. In addition, alpha-glucosidase also displays a transferase activity, which bring about the formation of α-glucosylated compounds such as soluble starch and glycogen. This research aims to express and characterize α-glucosidase from Weissella confusa BBK-1 (WcAG). WcAG gene was expressed in modified pET28b vector. This gene contained an open reading frame of 1,775 bps. Optimum expression condition of WcAG was cultured in LB medium containing 1% (w/v) glucose and induced with 0.4 mM IPTG at 20°C for 20 h. The recombinant WcAG containing his-tag …
Synthesis Of Fisetin Glycosides By Cyclodextrin Glycosyltransferase From Paenibacillus Sp. Rb01,
2017
Faculty of Science
Synthesis Of Fisetin Glycosides By Cyclodextrin Glycosyltransferase From Paenibacillus Sp. Rb01, Nattawadee Lorthongpanich
Chulalongkorn University Theses and Dissertations (Chula ETD)
Fisetin is a flavonoid which was widely exerted in pharmacological industries. However, fisetin has low water solubility and unstable in aqueous solution. So the uses of fisetin have been limited. The purpose of this study was to increase water solubility of fisetin by transglycosylation reaction using cyclodextrin glycosyltransferase (CGTase) from Paenibacillus sp. RB01. The reaction had to perform in co-organic solvent system and DMSO at 40% (v/v) was proved to be the most suitable co-organic solvent since it provided the high enzyme stability and high production yield. Moreover, the types of glycosyl donor were also determined and β-cyclodextrin was found …
Oxidative Responses In Transgenic 'Kdml105' Rice Oryza Sativa L. Overexpressing Oscam1-1 Against Drought Stress,
2017
Faculty of Science
Oxidative Responses In Transgenic 'Kdml105' Rice Oryza Sativa L. Overexpressing Oscam1-1 Against Drought Stress, Pun Sangchai
Chulalongkorn University Theses and Dissertations (Chula ETD)
The OsCaM1-1 is a rice calmodulin protein which transduces Ca2+ signals to their target protein that is important to regulate cellular and physiological responses. Drought stress is the one of essential environmental stresses that affected the crop by changing in morphological, physiological, and biochemical direction tactics of plants. In this study, the effect of drought stress on growth and antioxidant system in the transgenic rice overexpressing OsCaM1-1 gene was investigated and compared to the control and wild type KDML 105. The overexpression of OsCaM1-1 in transgenic rice could increase plant tolerance to drought stress, the results showed the greater increase …
