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Characterization Of Novel Borrelia Burgdorferi Transcripts Expressed During Tick And Mammalian Infection, Philip Adams

Electronic Theses and Dissertations

The purpose of this dissertation is to characterize the transcriptome of Borrelia (Borreliella) burgdorferi to discover novel transcripts, important for pathogenesis. As a spirochete and the etiological agent of Lyme disease, the foremost vector-borne bacterial infection in the world, B. burgdorferi fulfills a distinctive niche among bacterial pathogens. Persisting in the disparate environments of a tick vector and mammalian reservoirs, it is absolutely dependent on its hosts for transmission and nutrient acquisition. B. burgdorferi harbors a complex fragmented genome which is largely linear, unlike that of most prokaryotes, lacks an array of classically described metabolic genes, and contains an unusually …

Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista

Honors Undergraduate Theses

Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, …

Characterizing The Function Of The N-Terminal Domain Of Omi/Htra2, Christine Nguyen

Honors Undergraduate Theses

The yeast two-hybrid system was used to isolate and characterize protein interactors of the N-terminal domain of the serine protease Omi/HtrA2 (high temperature requirement protein A2) encompassing amino acids 31-133. This large domain of Omi/HtrA2 is usually cleaved and removed through autoproteolysis to produce the mature form of the protein. Whether the N-terminal domain has any function after its removal is unknown. Omi/HtrA2 is involved in a variety of diseases including cancers, neurodegenerative disorders, and metabolic disorders, but thus far, it is assumed that its normal function is the degradation of specific substrates. To characterize any potential function of Omi/HtrA2’s …

A Family Of Genus-Specific Rnas In Tandem With Dna-Binding Proteins Control Expression Of The Bada Major Virulence Factor Gene In Bartonella Henselae, Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson

Molecular Biosciences Faculty Publications

Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9). The Brt family of RNAs is unique to the genus Bartonella and ranges from 194 to 203 nucleotides with high homology and stable predicted secondary structures. Immediately downstream of each …

Transposon-Mediated Stable Suppression Of Gene Expression In The Developing Chick Retina, Masaru Nakamoto, Chizu Nakamoto

Biology Faculty Publications

The embryonic chick has long been a favorite model system for in vivo studies of vertebrate development. However, a major technical limitation of the chick embryo has been the lack of efficient loss-of-function approaches for analyses of gene functions. Here, we describe a methodology in which a transgene encoding artificial microRNA sequences is introduced into embryonic chick retinal cells by in ovo electroporation and integrated into the genome using the Tol2 transposon system. We show that this methodology can induce potent and stable suppression of gene expression. This technique therefore provides a rapid and robust loss-of-function approach for studies of …

Exploring The Physics Of Proteins At Molecular Level By Neutron And X-Ray Scattering, Utsab Raj Shrestha

Wayne State University Dissertations

The protein structures revealed by the crystallographic studies have provided the valuable information over the years regarding their biological functions. However, such snapshots of protein fluctuations averaged over time may not be enough to fully capture the underlying biological phenomena. A deeper understanding of the protein dynamics is crucial for elucidating the structural pathways or the transition mechanism from the initial state to the final state necessary for regulating the physical and chemical processes. Hence, the biological activities and functions are mainly governed by the protein conformational dynamics. However, the direct correlation of a wide range of protein dynamics to …

Real-Time Investigation Of Bulky Lesion Bypass By Y-Family Dna Polymerase, Dpo4, Using Single Molecule Fret, Pramodha Liyanage

Wayne State University Dissertations

DNA is constantly exposed to various DNA damaging agents that are generated by various internal and external sources. Some of this damage may not be able to be repaired by cellular machineries causing DNA replication to be blocked. Once the replication fork is blocked by a DNA adduct, damage tolerance DNA polymerases, mainly Y-family, are able to restore the DNA replication by synthesizing past the DNA adduct. Benzo[a]pyrene (B[a]P) is one of the most studied environmental carcinogens. It is known to make covalent DNA adducts after metabolic activation and the bulkiness of the B[a]P adducts impose a strong barrier to …

Frnk Regulatory Complex Formation With Fak Is Regulated By Erk Mediated Serine 217 Phosphorylation, Taylor J. Zak

Dissertations

Focal adhesion kinase related non-kinase (FRNK) is an endogenous inhibitor of focal adhesion kinase (FAK) that has traditionally been used to inhibit FAK signaling in a variety of experiments and is also an important endogenous regulator of FAK signaling. More recently, FRNK has been shown to be of increasing importance in some pathologic conditions. Despite the increasing importance of FRNK, the molecular mechanism by which it functions remains unclear. In addition, FRNK contains several phosphorylation sites with unknown importance and function. Here I hypothesize that FRNK can inhibit FAK by binding directly to FAK within focal adhesions. Furthermore, I propose …

Characterization Of Quorum-Quenching Lactonases And Plp-Dependent Aminotransferases: Structure, Mechanism And Alternative Turnover, Romila Nina Mascarenhas

Dissertations

Cell-to-cell communication by bacteria is essential for the regulation of gene expression important in colonization, biofilm formation, virulence and other processes. This communication is called "quorum-sensing" and is mediated by small molecules called autoinducers. One major class of autoinducers used by gram-negative bacteria is N-acyl homoserine lactones (AHL's). Enzymes capable of disrupting this communication are called "quorum-quenching" catalysts and have proven to be invaluable biochemical tools for understanding quorum-sensing pathways. Quorum-quenching enzymes hold promise for application in anti-biofouling, agriculture, aquaculture, bioremediation and other synthetic biology settings. However, the mechanisms that these enzymes use to recognize and process their substrates are …

Isolation And Spectroscopic Characterization Of Zn(Ii), Cu(Ii), And Pd(Ii) Complexes Of 1,3,4-Thiadiazole-Derived Ligand, Dariusz Karcz, Arkadiusz Matwijczuk, Bozena Boron, Bernadette Creaven, Leszek Fiedor, Andrzej Niewiadomy, Mariusz Gagos

Articles

A series of complexes incorporating Zn(II), Cu(II), and Pd(II) ions, and 4-(5-heptyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (L1) as model ligand, was synthesized in order to examine the nature of potential interactions between biologically active ligands, 1,3,4-thiadiazoles and metal ions with proven biological relevance. The structures of the compounds isolated were characterized using a number of spectroscopic methods including IR, Uv–vis, AAS, steady state and time-resolved fluorescence (TRF). The results obtained suggest that the L1-Zn(II) and L1-Pd(II) complexes consist of one molecule of L1 and one acetate ion acting as ligands, while the L1-Cu(II) complex adapts a 2:1 (L1: metal) stoichiometry. The coordination of L1 …

Towards The Complete Proteinaceous Regulome Of Acinetobacter Baumannii, Leila G. Casella, Andy Weiss, Ernesto Pérez-Rueda, J Antonio Ibarra, Lindsey N. Shaw

Molecular Biosciences Faculty Publications

The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so …

The Role Of Oxidation-Sensitive Nociception And Epigenetics In Endometriosis-Associated Pain, Kristeena Ray Wright

Theses, Dissertations and Capstones

Endometriosis is an enigmatic disease that is associated with severe symptoms and consequences such as total hysterectomy. Upwards of 10% of women of reproductive age have endometriosis, most of whom are afflicted with chronic pelvic pain and/or infertility. Despite many treatment options available to endometriosis patients, there is no cure for this condition and recurrence of symptoms is extremely common. In CHAPTER 1, we describe the mechanisms involved in endometriotic pain and the currently available treatment strategies. Our laboratory has provided evidence for the role of oxidative stress in the etiology of endometriosis and its associated pain. In this dissertation …

Erk3 As A Braf-Regulated Tumor Suppressor Is A New Potential Cancer Target In Melanoma, Minyi Chen

Browse all Theses and Dissertations

Melanoma is the highest mortality rate skin cancer and the sixth most common cancer in the U.S..[1, 2] Arising from melanocytes, melanoma is known for frequent mutation of BRAF to its constitutive activation state BRAFV600E, thus over-activating its downstream MAPK targets ERK1/2 and contributing to melanoma progression.[3, 4, 5] ERK3, a less studied MAPK family protein which contributes to promoting lung, breast, cervical, head and neck (HNC) cancer metastasis, has also shown a correlation with upregulation of BRAF.[6, 7, 8, 9] However, the BRAF-ERK3 regulatory mechanism and the function of ERK3 in melanoma are still unclear. Here, we first elucidate …

Urinary Metabolomics To Detect Polycystic Kidney Disease At Early Stage, Amnah Mahmoud Obidan

Browse all Theses and Dissertations

Urinary metabolomics abilities in detection of biological effects (i.e., toxicity, disease) is compounded by high background variability. Previously, we showed mild kidney dysfunction was detectable under the stress imposed by furosemide (diuretic). Here we tested whether furosemide (FUR) can enhance the sensitivity to detect autosomal dominant polycystic kidney disease (ADPKD) at an early stage. ADPKD is one of the most common inherited renal disorders and is characterized by the growth of numerous cysts in the kidneys. Urinary metabolomics analyses, using nuclear magnetic resonance (NMR) spectroscopy, were conducted in control (WT) and diseased mice (RC) at 7 and 24 weeks of …

Identification Of Expression And Function Of The Glucagon-Like Peptide-1 Receptor In Gastrointestinal Smooth Muscle, Alexander T. May

Theses and Dissertations

In response to ingestion of nutrients, enteroendocrine L cells secrete the incretin hormone, glucagon-like peptide-1 (GLP-1), to enhance glucose-dependent insulin release. Therapies related to GLP-1 are approved for type 2 diabetes. The GLP-1 receptor (GLP-1R) is expressed in cells of the gastrointestinal tract and elsewhere. In pancreatic beta cells, GLP-1R are coupled to the Gs/cAMP/PKA pathway. The expression and function of GLP-1R in gastrointestinal smooth muscle are not known. Aim. To test the hypothesis that GLP-1 regulates smooth muscle function by acting on GLP-1R expressed on smooth muscle. Methods. Smooth muscle cells (SMC) were isolated and cultured. Expression of GLP-1R …

Novel Role Of The Nociceptin System As A Regulator Of Glutamate Transporter Expression In Developing Astrocytes, Logan Meyer

Theses and Dissertations

Our previous results showed that oligodendrocyte development is regulated by both nociceptin and its G-protein coupled receptor, the nociceptin/orphanin FQ receptor (NOPR). The present in vitro and in vivo findings show that nociceptin plays a crucial conserved role in both human and rodent brain astrocytes, regulating the levels of the glutamate/aspartate transporter GLAST/EAAT1. This nociceptin-mediated response takes place during a critical developmental window that coincides with astrocyte maturation and synapse formation. GLAST/EAAT1 upregulation by nociceptin is mediated by NOPR and the downstream participation of a complex signaling cascade that involves the interaction of several kinase systems, including PI-3K/AKT, mTOR and …

N-Alkyl 4-Methylamphetamine Enantiomers And The Implication For Potential Modulation Of Abuse Liability And Enhancement Of Psychoactive Drug Targeting., Ramsey Sitta

Theses and Dissertations

Drugs of abuse have a long history in humanity. Currently however, a subject of great interest is the phenylalkylamine family of drugs. Not only is the abuse liability of interest but also the potential therapeutic expansion of the capabilities of this family of drugs by utilizing the unique stereospecific effects of the newly discovered hybrid compounds. Based upon prior data of N-Alkyl 4-MA the enantiomers of N-Methyl, N-Ethyl, and N-Propyl were analyzed in hDAT, hNET, and hSERT. It was found that there was a negative correlation between chain length and potency and dopaminergic component. In agreement with the currently established …

Design, Synthesis And Biological Screening Of Novel Cucsinspired Estrone Analogues Towards Treatment Of Hepatocellular Carcinoma, Mater Hussen Mahnashi

Electronic Theses and Dissertations

Cucurbitacins (CUCS) are natural products with highly oxygenated tetracyclic triterpenes produced mostly by Cucurbitaceae family plant. They are known for their therapeutic efficiency with different biological activities, such as anti-inflammatory, hepatoprotective and anti-cancer. Hepatocellular carcinoma (HCC) is the third leading cause of death worldwide. Previous reports have shown the ability of CUCS to inhibit the growth of hepatocellular carcinoma cell lines (HepG-2) significantly. Structural activity relationship studies suggested the potential of the 23, 24 enone side chain of CUCS to bind to the Epidermal Growth Factor Receptor (EGFR). Due to the limited quantities of CUCS upon isolation and the challenges …

The Assembly Factor Pet117 Couples Heme A Synthase Activity To Cytochrome Oxidase Assembly, Nicholas G. Taylor, Samantha Swenson, Nicholas J. Harris, Edward M. Germany, Jennifer L. Fox, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme a is an essential metalloporphyrin cofactor of the mitochondrial respiratory enzyme cytochrome c oxidase (CcO). Its synthesis from heme b requires several enzymes, including the evolutionarily conserved heme a synthase (Cox15). Oligomerization of Cox15 appears to be important for the process of heme a biosynthesis and transfer to maturing CcO. However, the details of this process remain elusive, and the roles of any additional CcO assembly factors that may be involved remain unclear. Here we report the systematic analysis of one such uncharacterized assembly factor, Pet117, and demonstrate in Saccharomyces cerevisiae that this evolutionarily conserved protein is necessary for …

Examining Interactions Between Opsins And Carotenoid Biosynthetic Proteins In Halophilic Archaea, Alexandru M. Plesa

Honors Theses

Organisms have evolved numerous specialized molecules for constantly responding to environmental changes. Examples of such molecules are the light-driven proton-pump rhodopsins, such as bacteriorhodopsin (BR) and cruxrhodopsin (cR), and the carotenoid pigments, such as retinal and bacterioruberin. In halophilic Archaea, retinal can covalently bind bacterioopsin (BO) and cruxopsin (CO) to form the corresponding protein complexes, and its biosynthesis is indirectly controlled by the activity of the lycopene elongase (Lye) enzyme, which converts lycopene, a retinal precursor, to a form of bacterioruberin. Interestingly, opsins were shown to inhibit the activity of Lye, thereby promoting retinal biosynthesis and indirectly regulating the apoprotein-cofactor …

Expression, Purification, And Characterization Of An Intrinsically Disordered Late Embryogenesis Abundant (Lea) Protein From Artemia Franciscana Utilizing Escherichia Coli And Nicotiana Tabacum, Md Fazlul Karim

Masters Theses

Anhydrobiosis is an astounding strategy that allows certain species (both animals and plants) to survive severe environmental conditions such as desiccation, extreme cold, or heat in the habitat. Despite the occurrence of several different molecular strategies, expression of highly hydrophilic polypeptides termed LEA proteins has been most conclusive identified as a requirement for the survival of plants and animals during periods of water stress such as freezing and drying. Several classification schemes for LEA proteins have been proposed and the brine shrimp, Artemia franciscana, is the only known animal that naturally expresses LEA proteins from three different classification groups …

Effects Of Asiatic Acid On Neurite Outgrowth In Neuro-2a Cells, Aishah Asiri

Masters Theses

Recently, medicinal plants from ancient Ayurvedic medicine have provided clues to the discovery of novel therapeutics for various diseases. In Ayurvedic medicine, a common Indian plant, Centella asiatica is highly regarded as a "rasayana" or nerve tonic. The Centella extract is used to ward off age-related dementia and to increase memory and intelligence. The mechanism by which Centella improves memory and learning and reduces the risk of dementia is unclear.

We recently tested the effects of asiatic acid, the main active component of Centella, on neuronal growth. We hypothesized that asiatic acid will promote neuronal growth and neurite network …

Enhancement Of The Physicochemical Properties Of Pt(Dien)(Nucleobase) (2+) For Hivncp7 Targeting, S. D. Tsotsoros, P. B. Lutz, A. G. Daniel, E. J. Peterson, R. E. F. De Paiva, E. Rivera, Y. Qu, C. A. Bayse, N. P. Farrell

Chemistry & Biochemistry Faculty Publications

Physicochemical properties of coordination compounds can be exploited for molecular recognition of biomolecules. The inherent π-π stacking properties of [Pt(chelate)(N-donor)]²⁺([PtN₄]) complexes were modulated by systematic variation of the chelate (diethylenetriamine and substituted derivatives) and N-donor (nucleobase or nucleoside) in the formally substitution-inert PtN₄ coordination sphere. Approaches to target the HIV nucleocapsid protein HIVNCp7 are summarized building on (i) assessment of stacking interactions with simple tryptophan or tryptophan derivatives to (ii) the tryptophan-containing C-terminal zinc finger and (iii) to the full two-zinc finger peptide and its interactions with RNA and DNA. The xanthosine nucleoside was identified …

Optimization Of In Vitro Transcription/Translation Conditions For In Vitro Compartmentalization Studies And Synthesis Of 4-Fluorohistidine, Christine Ring

Theses and Dissertations

Genetic code expansion allows the incorporation of non-canonical amino acids with a variety of new functional groups: fluorescent amino acids,^1-3 azides,^4-6 alkynes,^5-10 and photocrosslinkers.^4,11,12 This incorporation requires the evolution of new tRNA/aminoacyl tRNA sythetase pairs. Traditionally screenings of novel tRNA/aminoacyl tRNA synthetase pairs have been done in vivo. While these in vivo screenings have proven robust, they are limited in multiple ways: non-canonical amino acids (ncAAs) must be nontoxic and bioavailable. Furthermore, library size is limited by transformation efficiency. Lastly, in vivo screenings require substantial amounts of the target ncAA, which is often not available …

Nickel Reduces Calcium Dependent Dimerization In Neural Cadherin, Matthew Paul Dukes

Electronic Theses and Dissertations

Cadherins are the primary transmembrane component in adherens junctions, structures that link the actin cytoskeleton in adjacent cells within solid tissues including neurological synapses, epithelium and endothelium. Cell-cell adhesion by cadherins requires the binding of calcium ions to specific sites in the extracellular region. Given the complexity of the cell adhesion microenvironment, we are investigating whether other divalent cations might affect calciumdependent dimerization of neural-(N-) cadherin. The first chapter focuses on studies to characterize the impact of binding physiological magnesium (II) or neurotoxic nickel (II) on calcium-dependent N-cadherin function. Physiological levels of magnesium have only a small effect on the …

Pretreatment, Enzymatic Hydrolysis, And Fermentation To Ethanol Using A Lignocellulosic Feedstock And Subsequent Recovery Of A Value Added Co-Product: Pure Crystalline Cellulose, Ryan J. Bouza

Electronic Theses and Dissertations

As more demand for alternatives to petroleum and the industrial world’s love of cars increase, cellulosic ethanol will become more important. The ethanol can, of course, be used in the transportation fuel sector, but there is also a potential for co-products to be developed out of the cellulose to ethanol process. Some of these co-products have the potential to replace current petrol products. These co-products may provide the extra revenue generation needed for further investment and development of this industry. This would not only provide better energy independence, but in the United States, it would better satisfy the cellulosic ethanol …

Cbl And Cbl-B Dictate Csf-1r Endocytic Traffic And Signaling In Macrophages, Lu Huang

Electronic Theses and Dissertations

Macrophage colony stimulating factor receptor (CSF-1R or MCSFR) is a receptor tyrosine kinase essential for the growth and function of macrophages. Understanding the mechanisms that regulate CSF-1R activation and deactivation will provide insights to clinical treatment of macrophage related diseases including chronic inflammation and cancer. Previously, our laboratory showed that CSF-1R undergoes a novel membrane trafficking route that involves macropinocytosis to deactivate CSF-1R signaling. This thesis makes the discovery that the ubiquitin ligases Cbl and Cbl-b cooperate to regulate CSF-1R endocytosis and traffic to macropinosome in macrophages. Macrophages were derived from mice knocked out for Cbl, Cbl-b or the double …

Regulation Of Arf16-2 By Microrna160 During Soybean Root Nodule Development, Spencer Schreier

Electronic Theses and Dissertations

Soybean is an excellent candidate for sustainable agriculture due to its production of nutritious, versatile beans and the ability to form symbiotic organs called root nodules that perform nitrogen fixation. As demand for both yield and sustainable agriculture continue to increase, root nodules offer an attractive alternative to expensive and environmentally harmful nitrogen fertilizers. Understanding root nodule formation may open genetic engineering avenues for optimizing nitrogen fixation performance and transferring the nodule-formation ability to other plants. A major determinant of nodule numbers and quality in soybean is microRNA 160 (miR160), which dictates developmental stage-specific auxin sensitivity by targeting repressor auxin …

The Synthetic Biology Of N2-Fixing Cyanobacteria For Photosynthetic Terpenoid Production, Charles T. Halfmann

Electronic Theses and Dissertations

In the last few decades, concerns over global climate change, energy security, and environmental pollution have been rising. To overcome these challenges, the concept of “-n^th generation” biofuels has emerged as a strategy to convert solar radiation into fuels and bulk industrial chemicals for societal use, while decreasing our consumption of nonrenewable energy sources. Nitrogen-fixing cyanobacteria hold a distinct advantage in biofuel production over plants, given their ability to convert sunlight, air (CO₂ and N₂), and mineralized water to energy-dense carbon molecules, as well as fix atmospheric nitrogen gas into ammonia for metabolism. Engineered cyanobacteria with …

Determining The Effects Of Methanol, Ethanol, Isopropanol, And Glycerol On Both Thermal Stability And Catalytic Activity Of Rv0045c, An Enzyme From M. Tuberculosis, Katelyn Baumer

Undergraduate Honors Thesis Collection

Tuberculosis (TB) is a highly infectious respiratory disease contracted through the inhalation of Mycobacterium tuberculosis. Serine hydrolases are abundant in M. tuberculosis and serve as a model for studying the inhibition of TB. Rv0045c is an example of such with little known regarding its biological function. Rv0045c was exposed to methanol, ethanol, isopropanol, or glycerol and the effects of varying concentration of these alcohols on the catalytic efficiency and thermal stability of the enzyme was determined. The thermal stability of Rv0045c was found to decrease with concentration of methanol, ethanol, or isopropanol. The opposite was true of the thermal stability …