Biochemistry, Biophysics, and Structural Biology Commons^™

Mechanisms Of Dna Synthesis And Fidelity By Y-Family Translesion And C-Family Replicative Polymerases, Purba Mukherjee

Legacy Theses & Dissertations (2009 - 2024)

Since the discovery of the DNA polymerase by Arthur Kornberg nearly 60 years ago, there have been great advances in understanding the involvement of polymerases in replication and repair. Years of genetic, biochemical and structural studies have lead to the classification of DNA-dependent DNA polymerases into six families: A, B, C, D, X and Y. In this work, I have focussed on two different families, C and Y. Hence this work is divided into two parts. Part one discusses the studies on Y-family polymerases. All Y-family polymerases are involved in replicating past DNA lesions. The ability to tolerate unnatural nucleotides …

Modeling The Early, Aging-Related Changes In Human Recombinant Gammas-Crystallin In Vitro, Christiana Oluwaseun Salami

Legacy Theses & Dissertations (2009 - 2024)

Cataract is the leading cause of blindness in the world. Cataractous lenses scatter a significant part of the light entering the eye. Cataract can be of several types: Age-related cataract, secondary cataract, traumatic cataract, congenital cataract, and radiation cataract. Age-related cataract is the most common type of cataract. Several factors contribute to age-onset cataract; among them are the Post-Translational Modifications (PTMs) to the major lens proteins or crystallins, which constitute about 80-90% of the protein content of the lens. Predominant PTMs of the crystallins are oxidation, deamidation, phosphorylation, glycation, and disulfide crosslinking, which tend to increase as the lens ages.

Molecular Actions Of The Novel Histone Deacetylase Inhibitor Cg-1521 In Models Of Inflammatory Breast Cancer, Namita Chatterjee

Legacy Theses & Dissertations (2009 - 2024)

Inflammatory breast cancer (IBC) is a rare and particularly lethal form of breast cancer. Despite aggressive therapeutic approaches, the 5-year survival rate is only 34%. As this disease is severely understudied, we have investigated the therapeutic potential of the novel hydroxamic acid-derived histone deacetylase inhibitor (HDACi), CG-1521 in comparison to a structurally similar compound, Trichostatin A (TSA) in two IBC cell lines: SUM149PT and SUM190PT. In these cells, CG-1521 and TSA induce dose- and time-dependent induction of cell cycle arrest and apoptosis regardless of the presence of 17β-estradiol (E2). Interestingly, the cell lines have considerably different sensitivities to these treatments …

Mechanisms Of Age-Related Inflammation And Cancer : The Synergistic Effect Of Oxidants And Calcium, Donald A. Mccarthy

Legacy Theses & Dissertations (2009 - 2024)

The accumulation of senescent cells during the process of aging has been implicated as causal in numerous age-related pathologies. Senescent cells adopt a secretory phenotype consisting of many factors including matrix remodeling enzymes, growth factors, cytokines, and chemokines. Their secretory nature is the primary reason that they are associated with disease, but it remains unclear why they become so inflammatory. Using primary human fibroblasts cultured to senescence, we mechanistically determined why senescent cells are such potent inducers of inflammation. Our findings indicate that the early production of the cytokine Interleukin 1-α (IL-1α) is central to this transition. We found that …

Mediation Of Recurrent Hypoglycemia's Physiological And Behavioral Effects In The Hippocampus By Glucocorticoids, Danielle Osborne

Legacy Theses & Dissertations (2009 - 2024)

Recurrent hypoglycemia (RH) occurs with the over administration of insulin resulting in severe hypoglycemia on a repetitive basis. This occurs most commonly among Type I Diabetics who rely on exogenous insulin replacement for management of their disease; however it is becoming increasingly common among Type II Diabetics. Although cognitive deficits are reported during hypoglycemia, the period following restoration of euglycemia has been denoted by improved hippocampally-mediated short-term and working memory in humans and rodents, respectively. RH is also associated with an altered glucocorticoid secretion profile in response to hypoglycemia. In vitro and in vivo approaches were utilized with the goal …

Probing Secondary And Tertiary Rna Folding Using Force And Temperature, William Stephenson

Legacy Theses & Dissertations (2009 - 2024)

RNA folding is the process whereby a single stranded RNA molecule assumes its three-dimensional functional conformation. Along with the protein folding problem, the RNA folding problem remains as one of the great unsolved problems in biophysics. Generally RNA folding occurs in a hierarchical manner whereby the sequence of an RNA (primary structure) determines which regions will form helical segments (secondary structure) before further rearrangement and base pairing of secondary structure motifs (tertiary structure). Due to the intimate connection between structure and function within molecular biology, increased familiarity with the thermodynamic and kinetic factors that govern RNA folding will permit the …

Crosstalk Between Vitamin D₃- And Testosterone-Mediated Signaling In Prostate Cancer Cells, Wei-Lin Winnie Wang

Legacy Theses & Dissertations (2009 - 2024)

Contrary to the common belief that prostate cancer is a hormone dependent disease, the incidence of prostate cancer and associated mortality actually increases significantly after serum androgen levels decline. This led us to hypothesize that androgen depletion in elder men is an underlying cause for the development and progression of prostate cancer. In addition, serum vitamin D₃ levels also decline in older men. Epidemiological and experimental data support an anti-neoplastic activity of vitamin D₃ in colorectal and breast cancers through regulation of cell proliferation, apoptosis, cell differentiation and metastasis. The effects of vitamin D₃ on prostate cancer …

Improving The Microbial Source Tracking Toolbox : Evaluating The Use Of Selective Enrichments And Artificial Sweeteners In A Multi-Tiered Approach, Stacey A. Helming

Legacy Theses & Dissertations (2009 - 2024)

Microbial contamination of surface waters is a public health concern world-wide, with non-point source fecal input contributing to millions of cases of waterborne illness annually. Numerous techniques have been proposed to monitor for non-point source fecal contamination, but few studies have explored the correlation of multiple chemical and microbial fecal source tracking markers in ambient waters. Therefore, the purpose of these studies was to evaluate the use of multiple "ideal" markers of fecal contamination and improve upon any analytical techniques required to identify species-specific fecal contamination in surface waters. The use of selective enrichments to improve the sensitivity of end-point …

Mechanistic Studies Of C- And Y-Family Dna Polymerases, Indrajit Lahiri

Legacy Theses & Dissertations (2009 - 2024)

DISSERTATION ABSTRACT

Raman Spectroscopy Of Blood Serum And Cerebrospinal Fluid And Multivariate Data Analysis For Alzheimer's Disease Diagnostics, Elena Ryzhikova

Legacy Theses & Dissertations (2009 - 2024)

The efficient and accurate diagnosis at the early stages of dementia is a key moment for effective treatment and productive research to find a new ways to combat the disease. It is especially true for Alzheimer's disease (AD) for which there is no effective cure, but several treatments are known to allow slowing down the degenerative processes. Alzheimer's disease (AD) displays only non-specific clinical symptoms of mental decline for decades after the initiation and is very challenging to differentiate even at the later stages when it becomes very aggressive. Despite the great need, current diagnostic tests are unable to diagnose …

Molecular Actions Of The Vitamin D Receptor In Breast Cancer, Erika Laporta

Legacy Theses & Dissertations (2009 - 2024)

1,25-Dihydroxyvitamin D (1,25D) exerts anti-cancer actions through the vitamin D receptor (VDR) but the specific targets that mediate these effects remain to be defined. In these studies, growth and genomic responses to 1,25D were evaluated in a cellular model system derived from mammary tumors generated in VDR knockout (KO) and wildtype (WT) mice. WT145 cells (derived from WT tumors) expressed VDR and were growth inhibited by 1,25D, whereas KO240 cells (derived from VDRKO tumors) lacked VDR and were not growth inhibited by 1,25D. KO240 cell clones stably expressing VDR (KOhVDR cells) were sensitized to 1,25D mediated growth arrest. Genomic profiling …

A Structural And Functional Comparison Of Human Immunodeficiency Virus Type 1 Nucleocapsid Protein (Ncp7) And Other Retroviral Nucleocapsid Proteins, Christopher Richard Cavender

Legacy Theses & Dissertations (2009 - 2024)

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus belonging to the lentivirus genus of the orthoretrovirinae family. HIV-1 is widely known for causing acquired immunodeficiency syndrome (AIDS) in humans and being responsible for 1.8 million deaths due to AIDS associated illnesses in 201016.

Quantification Of Free Sialic Acid In Human Plasma Through A Robust Quinoxalinone Derivatization And Lc–Ms/Ms Using Isotope-Labeled Standard Calibration, Dan Wang, Xiang Zhou, Lin Wang, Sihe Wang, Xue-Long Sun

Chemistry Faculty Publications

We report an accurate quantification of free sialic acid (SA) in human plasma using LC–MS/MS method with isotope-labeled standard calibration (ILSC) and robust derivatization. Specifically, derivatization of SA with a stable and inexpensive 3,4-diaminotoluene (DAT) provides a stable product of SA with high MS response, proving a convenient and cost-effective LC–MS/MS analysis of free SA. In addition, the use of ¹³C₃-SA as calibration standard ensured the accuracy for the measurement. This assay used ultra high performance liquid chromatography (UHPLC) for separation of native/labeled SA and IS from matrix interference, and employed mass spectrometry in multiple reaction monitoring …

Novel Gammaherpesvirus Functions 1 Encoded By Bovine Herpesvirus (Bovine Lymphotropic Virus), J. Jia, G. Delhon, E. R. Tulman, D. G. Diel, Fernando A. Osorio, X. Wen, G. F. Kutish, D. L. Rock

School of Veterinary and Biomedical Sciences: Faculty Publications

The genus Macavirus of the subfamily Gammaherpesvirinae includes viruses that infect lymphoid cells of domestic and wild ruminants and swine, causing asymptomatic latent infections in reservoir hosts. Here, we describe the genome of bovine herpesvirus 6 (BoHV-6), a

macavirus ubiquitous in healthy cattle populations. The BoHV-6 genome exhibited architecture conserved in macaviruses, including a repetitive H-DNA region and unique, 141 kilobase pair L

DNA region predicted to encode 77 genes. BoHV-6 encoded in variable genomic regions a novel complement of genes relative to other characterized macaviruses, likely contributing to distinctive aspects of BoHV-6 infection biology and host range. Most notably, …

Identification And Characterization Of Human Plasma Prekallikrein-Prolylcarboxypeptidase Interaction Sites, Jingjing Wang

Electronic Theses and Dissertations

Prolylcarboxypeptidase isoform1 (PRCP1, also known as angiotensinase C, PCP, PRCP, PrCP) is a widely distributed serine protease found throughout the human body. PRCP1 removes the C-terminal amino acid which is next to a proline residue of a peptide. Through this activity, PRCP1 is postulated to play distinct biological roles including the regulation of vascular homeostasis, the induction of inflammation and the adjustment of metabolism. Compelling evidence indicates that human PRCP1 activates plasma prekallikrein (PK) to kallikrein on endothelial cells. However, the mechanism of this activation is yet unknown. The formation of kallikrein leads to the generation of proinflammatory factors and …

Comparative Phenolic Content And Antioxidant Activities Of Blueberry (Vaccinium Corymbosum) Afected By In Vitro Digestion, Sonia Gharbi

Wayne State University Theses

Abstract

COMPARATIVE PHENOLIC CONTENT AND ANTIOXIDANT ACTIVITIES OF BLUEBERRY (VACCINIUM CORYMBOSUM) AFECTED BY IN VITRO DIGESTION

By

SONIA GHARBI

May 2014

Adviser: Dr. Kevin Zhou

Major: Nutrition and Food Science

Degree: Master of Science

The biological properties of antioxidants depend on their release from the food matrix during the digestion process. Blueberry contains a wide range of phenolic compounds which are of great significance due to their antioxidant activity. In vitro digestion is a rapid and inexpensive method used to determine the availability of nutrients involved in the absorption studies with humans. Total phenolic content and antioxidant activity of Vaccinium …

Rates And Modes Of Sequence Evolution In Various Lineages Within Chenopodiaceae, James Andrew Naeger

Wayne State University Theses

Sexual dimorphism in domesticated spinach, Spinacia oleracea, is thought to be determined by differential expression of floral organ identity genes. We examined the floral organ morphologies of seven species in the Chenopodiaceae, including two wild species of spinach, in order to gain insight into the evolution of floral reproductive strategy in this clade. The species within the Anserineae demonstrate extensive evolution in floral morphology and reproductive strategy, and Spinacia is unique for having been domesticated rather recently and for being dioecious. We found C. album to be hermaphroditic, C. foliosum and M. nuttalliana to be gynomonoecious, while C. bonus-henricus …

In Vitro Characterization Of Serine 47 Phosphorylated Cytochrome C, Ashwathy Mary Varughese

Wayne State University Theses

Cytochrome c is a 12.4kDa ubiquitously expressed protein known to be involved in many physiological processes of the cell such as respiration and apoptosis. The goal of our lab is to increase our knowledge of the regulation of cytochrome c in these opposite activities, and our working model posits that cytochrome c is decisively regulated by phosphorylation. When phosphorylated, cytochrome c leads to an "optimal" functioning in the electron transport chain by lowering electron flux, preventing harmful high mitochondrial membrane potentials and thus ROS production under healthy conditions. However, under cellular stress cytochrome c might be dephosphorylated favoring high mitochondrial …

Biophysical Studies Of Mutant H69 Rna Constructs, Daya Nidhi Kharel

Wayne State University Theses

The importance of helix 69 (H69) of the large ribosomal subunit is emphasized by its location in the ribosome and key contacts with protein factors and tRNAs during different steps of protein synthesis. The presence of three highly conserved pseudouridine modifications in H69 has a significant impact on modulation of the ribosome conformations. Specific nucleotides of H69 may be necessary for the function of this helix-loop RNA, as some mutations are deleterious to bacterial growth. In this study, we investigated the effects of single nucleotide mutations in a 19-nucleotide H69 construct with and without pseudouridines on the RNA stability and …

Effect Of Long Term Rapamycin Treatment On Mtor Signalling Network In Colon And Liver Of C57bl/6 Mice, John Sorge

Wayne State University Theses

Many studies have investigated the effects of rapamycin on aging and cancer. However, the effects of long-term rapamycin supplementation on a cancer model have not been performed. This is the first study that investigates the effects of long-term supplementation of rapamycin in a cancer model. ACF analysis of colon tissues in mice showed no significant difference between controls and those supplemented with rapamycin. Factors such as energy balance, cellular environment, PI3K/Akt/mTOR pathway, and more have been assessed in this study. The duration of rapamycin supplementation seems to play an important role in the protection against cancer. Ultimately, this study suggests …