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Biochemistry, Biophysics, and Structural Biology Commons™
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Articles 1 - 21 of 21
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson
Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson
Electronic Theses and Dissertations
Epigenetics is the study of molecular modification of a genome without changing its base pairs. The most studied type of epigenetic mechanism is DNA methylation, which is capable of turning a gene “on” or “off.” Epigenetic potential is the capacity to which an individual can have methylation on its genome. The more CpGs available, the greater the epigenetic potential. In invasive species, genetic variation has been observed to be paradoxical: not much of it exists on a genomic level, but epigenetically, phenotypic variation can occur. The focus on shift in gene expression in this study is on Toll-Like Receptor 4 …
Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler
Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler
Electronic Theses and Dissertations
Microbial communities contain densely packed cells where competition for space and resources are fierce. These communities are generally referred to as biofilms and provide advantages to individual cells against immunological and antimicrobial intervention, dehydration, and predation. High intracellular pools of cyclic diguanylate monophosphate (c-di-GMP) cause cells to aggregate during biofilm formation through the production of diverse extracellular polymers. Genes that encode c-di-GMP catalytic enzymes are commonly mutated during chronic infections where opportunists display enhanced resistance to phagocytosis and antibiotics. Our lab uses an emergent multicellular trait in the model organism Pseudomonas fluorescens Pf0-1 to study the emergence of c-di-GMP mutations …
A Review Of Current Methods In Avian Dietary Analysis And Their Integrated Application To Characterize The Trophic Niche Of Louisiana Waterthrush (Parkesia Motacilla)., Brandon Hoenig
Electronic Theses and Dissertations
Characterizing a species’ dietary composition presents an avenue to understand many facets of its ecological niche and can provide essential information for the species’ long-term conservation. To date, the vast majority of diet studies have relied on direct identification of prey during foraging observations or from diet samples to characterize the dietary habits of birds. However, advancements in laboratory-based approaches have revolutionized the field of trophic ecology by allowing researchers to indirectly infer dietary habits with higher resolution across greater time scales. Here, I apply two of these laboratory-based techniques, namely DNA metabarcoding and stable isotope analysis, to characterize the …
Understanding The Impact Of Human Germline Single-Nucleotide Variants, Samuel Adjei
Understanding The Impact Of Human Germline Single-Nucleotide Variants, Samuel Adjei
Electronic Theses and Dissertations
No abstract provided.
Deciphering The Perpetual Fight Between Virus And Host: Utilizing Bioinformatics To Elucidate The Host's Genetic Mechanisms That Influence Jc Polyomavirus Infection, Michael P. Wilczek
Deciphering The Perpetual Fight Between Virus And Host: Utilizing Bioinformatics To Elucidate The Host's Genetic Mechanisms That Influence Jc Polyomavirus Infection, Michael P. Wilczek
Electronic Theses and Dissertations
JC polyomavirus (JCPyV) is a human-specific pathogen that infects 50-80% of the population, and can cause a deadly, demyelinating disease, known as progressive multifocal leukoencephalopathy (PML). In most of the population, JCPyV persistently infects the kidneys but during immunosuppression, it can reactivate and spread to the central nervous system (CNS), causing PML. In the CNS, JCPyV targets two cell types, astrocytes, and oligodendrocytes. Due to the hallmark pathology of oligodendrocyte lysis observed in disease, oligodendrocytes were thought to be the main cell type involved during JCPyV infection. However, recent evidence suggests that astrocytes are targeted by the virus and act …
Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer
Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer
Electronic Theses and Dissertations
The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional …
Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri
Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri
Electronic Theses and Dissertations
SABP2 (Salicylic Acid Binding Protein 2) plays a vital role in the salicylic acid signaling pathway of plants both regarding basal resistance and systemic acquired resistance against pathogen infection. SIP-428 (SABP2 Interacting Protein-428) is a Silent information regulator 2 (SIR2) like deacetylase enzyme that physically interacts with SABP2 in a yeast two-hybrid interaction and confirmed independently by a GST pull-down assay. We demonstrated that SIP- 428 is an NAD+ dependent SIR2 deacetylase enzyme. Transgenic tobacco plants silenced in SIP- 428 expression via RNAi showed enhanced basal resistance to microbial pathogens. Moreover, these SIP-428-silenced lines also exhibited a robust induction of …
Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright
Temperature And Polyunsaturated Fatty Acid’S Effect On Daphnia Magna Reproduction, Mark Albright
Electronic Theses and Dissertations
Organisms adapt to their environments by adjusting their biochemistry and physiology; such adaptation is limited by resource availability and physiological constraints. The freshwater crustacean Daphnia magna inhabits a wide range of environments and must survive and reproduce within a range of temperatures. One limit to low-temperature adaptation is thought to be the availability of unsaturated fatty acids necessary to maintain proper fluidity of cellular membranes. D. magna maintained at 10 ºC on a diet poor in unsaturated fatty acids have been observed to produce clutches that fail to develop. However, this has not been observed on a diet rich in …
Thermal And Microbial Effects On Brown Macroalgae: Heat Acclimation And The Biodiversity Of The Microbiome, Charlotte Tc Quigley
Thermal And Microbial Effects On Brown Macroalgae: Heat Acclimation And The Biodiversity Of The Microbiome, Charlotte Tc Quigley
Electronic Theses and Dissertations
This dissertation examines effects of stress on brown algal biology from a macroscopic scale by examining the whole aquaculture crops, and at a microscopic level by examining the macroalgal microbiome, across the vertical stress gradient of the intertidal zone and across the latitudes of their biogeographic ranges. Thermal stress negatively affected seedstock gametophytes of the kelp Alaria esculenta isolated from northern and southern locations in Maine. However, previous thermal stress had a positive effect on growth of the next-generation sporophytes. Alaria esculenta has potential as a kelp crop in Maine’s sea vegetable aquaculture sector and implementing this protocol may allow …
Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle
Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle
Electronic Theses and Dissertations
Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences …
Quantitative Studies Of Amyloidogenic Protein Residue Interaction Networks And Abnormal Ammonia Metabolism In Neurotoxicity And Disease, Jeddidiah Griffin
Quantitative Studies Of Amyloidogenic Protein Residue Interaction Networks And Abnormal Ammonia Metabolism In Neurotoxicity And Disease, Jeddidiah Griffin
Electronic Theses and Dissertations
Investigating similarities among neurological diseases can provide insight into disease processes. Two prominent commonalities of neurological diseases are the formation of amyloid deposits and altered ammonia and glutamate metabolism. Computational techniques were used to explore these processes in several neurological diseases. Residue interaction networks (RINs) abstract protein structure into a series of nodes (representing residues) and edges (representing connections between residues likely to interact). Analyzing the RINs of monomeric forms of amyloidogenic proteins for common network features revealed similarities not previously known. First, amyloidogenic variants of lysozyme were used to demonstrate the usefulness of RINs to the study of amyloidogenic …
Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor
Electronic Theses and Dissertations
Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics, …
The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn
The N-Terminal Methyltransferase Homologs Nrmt1 And Nrmt2 Exhibit Novel Regulation Of Activity Through Heterotrimer Formation., Jon David Faughn
Electronic Theses and Dissertations
Protein, DNA, and RNA methyltransferases have an ever-expanding list of novel substrates and catalytic activities. Even within families and between homologs, it is becoming clear the intricacies of methyltransferase specificity and regulation are far more diverse than originally thought. In addition to specific substrates and distinct methylation levels, methyltransferase activity can be altered through formation of complexes with close homologs. This work involves the N-terminal methyltransferase homologs NRMT1 and NRMT2. NRMT1 is a ubiquitously expressed distributive trimethylase. NRMT2 is a monomethylase expressed at low levels and in a tissue-specific manner. They are both nuclear methyltransferases with overlapping target consensus sequences …
Functional And Structural Impact Of The Loss Of The Leucine-Rich Repeat Protein Lrit1 In The Mouse Retina., Catherine Ann Cobb
Functional And Structural Impact Of The Loss Of The Leucine-Rich Repeat Protein Lrit1 In The Mouse Retina., Catherine Ann Cobb
Electronic Theses and Dissertations
Mutations in genes encoding the leucine-rich repeat (LRR) proteins nyctalopin and LRIT3 lead to complete congenital stationary night blindness because they are critical to depolarizing bipolar cell function in the retina. LRIT3 has two closely related family members, LRIT1 and LRIT2. In silico analyses of publicly available RNA-Seq data showed that Lrit1 was highly expressed in the retina. Here I describe the expression pattern and impact of loss of LRIT1 on retinal function. To enable these studies, we used CRISPR/Cas9 technology to create an Lrit1-/- mouse line. Retinal morphology and morphometry analyses showed no gross changes in retinal structure …
The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers
The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers
Electronic Theses and Dissertations
Primordial germ cells (PGCs) are hypothesized to deposit hematopoietic stem cells (HSCs) along their migration route through the embryo during the early stages of embryogenesis. PGCs also undergo global chromatin remodeling, including the erasure and reestablishment of genomic imprints, during this migration. While PGCs do not spontaneously form teratomas, their malignant development into germ cell tumors (GCTs) in vivo is often accompanied by the retention of hypomethylation at the IGF2-H19 imprinting control differentially methylated region (DMR). Previous studies in bimaternal embryos determined that proper genomic imprinting at two paternally imprinted loci was necessary for their growth and development: Igf2-H19 and …
Divergent Responses Of Larval And Juvenile Blue Mussels To Low Salinity Exposure, Melissa A. May
Divergent Responses Of Larval And Juvenile Blue Mussels To Low Salinity Exposure, Melissa A. May
Electronic Theses and Dissertations
In this study, we compared the osmotic stress response of larval and juvenile blue mussels (Mytilus edulis) at the transcriptomic, metabolomic, and whole organism levels. Blue mussels inhabit coastal areas, where they face climate-induced reductions in nearshore salinity. Despite their ecological and economic importance, scientists do not fully understand the underlying transcriptomic and cellular mechanisms of the osmotic stress response in blue mussels or how the ability to respond to stress changes throughout development. Blue mussels spend the first weeks of life developing through several larval stages in the plankton. These early life history stages are more vulnerable …
The Role Of Artificial Structures In Facilitating Range Expansion Of The Introduced Barnacle Megabalanus Coccopoma In The Southeastern U.S.A., Alicia M. Reigel
The Role Of Artificial Structures In Facilitating Range Expansion Of The Introduced Barnacle Megabalanus Coccopoma In The Southeastern U.S.A., Alicia M. Reigel
Electronic Theses and Dissertations
The barnacle Megabalanus coccopoma is a recent invader of the southeastern U.S.A. from the tropical eastern Pacific. In Georgia, M. coccopoma populations along the immediate coastline often suffer extensive mortality during the winter, but population rebuilding is common after these events suggesting that there may be nearby larval sources. I investigated the hypothesis that artificial structures (i.e., buoys, towers), occurring far enough offshore of Georgia for water temperatures to be moderated by the Gulf Stream, provide refuges for breeding adults of M. coccopoma and can serve as the larval source. I investigated this hypothesis by first developing thirteen microsatellite primer …
Mitochondrial Dna Analysis By Denaturing High-Performance Liquid Chromatography For The Characterization And Separation Of Mixtures In Forensic Samples, Richard Kristinsson
Mitochondrial Dna Analysis By Denaturing High-Performance Liquid Chromatography For The Characterization And Separation Of Mixtures In Forensic Samples, Richard Kristinsson
Electronic Theses and Dissertations
A mixture of different mtDNA molecules in a single sample is a significant obstacle to the successful use of standard methods of mtDNA analysis (i.e., dideoxy dye-terminator sequencing). Forensic analysts often encounter either naturally occurring mixtures (e.g., heteroplasmy) or situational mixtures typically arising from a combination of body fluids from separate individuals. The ability to accurately resolve and interpret these types of samples in a timely and cost efficient manner would substantially increase the power of mtDNA analysis and potentially provide valuable investigative information by allowing its use in cases where the current approach is limited or fails. Therefore, this …
Cloning Of Bovine Placental Lactogen And Production In Vitro, Stephanie A. Doucette
Cloning Of Bovine Placental Lactogen And Production In Vitro, Stephanie A. Doucette
Electronic Theses and Dissertations
Bovine placental lactogen (bPL) is a hormone produced by the fetal portion of the placenta during gestation. Although there is little known about the structure and function of the protein, it is thought to play a role in the growth of the fetus and in mammary growth and differentiation. Attempts have been made to heighten the understanding of bPL through the use of recombinant DNA technology. Thus far, researchers have been able to produce the recombinant molecule in bacteria cells. Bacteria, however, are incapable of carrying out some of the post-translational modifications characteristic of mammalian proteins. For example, unlike native …
A Temperature-Sensitive Mutant Of Escherichia Coli Affected In The Alpha Subunit Of Rna Polymerase, Majid Mehrpouyan
A Temperature-Sensitive Mutant Of Escherichia Coli Affected In The Alpha Subunit Of Rna Polymerase, Majid Mehrpouyan
Electronic Theses and Dissertations
A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min on the bacterial chromosome. The rate of RNA synthesis in vivo and the accumulation of ribosomal RNA were significantly reduced in the mutant at 44$\sp\circ$C. The thermostability at 44$\sp\circ$C of the purified holoenzyme from mutant cells was about 20% of that of the normal enzyme. Assays with T7 DNA as a template showed that the fraction of active enzyme competent for transcription was reduced as a …
Variants And Polymorphisms Of Three Repetitive Dna Families In The Human Genome, Robert M. Roudabush
Variants And Polymorphisms Of Three Repetitive Dna Families In The Human Genome, Robert M. Roudabush
Electronic Theses and Dissertations
A novel 0.6 kb LINE family in human DNA, designated L2Hs, has been described (Musich and Dykes 1986). Studies employing clone N6.4, containing three 0.6 kb segments of this family, indicate that these sequences are interspersed and moderately repetitive. Two additional variant sequences of the L2Hs family, N6.1 and N6.3, have been identified. Restriction mapping of each cloned segment indicates similarities among N6.4, N6.3 and N6.1. When the cloned DNAs were cleaved with restriction enzymes and subjected to cross-hybridization, each cloned insert produced a pattern indicating that the sequences contained in N6.1 and N6.3 are represented in at least one …