Biochemistry, Biophysics, and Structural Biology Commons^™

Developing C. Elegans As A Model To Study Type 2 Diabetes Mellitus, Jheesoo Ahn

Theses and Dissertations

Caenorhabditis elegans has been studied as a model organism in various areas of biomedical research because it shares many conserved functions at molecular and genetic levels with humans. Specifically, it is an ideal organism to study heterogeneous metabolic syndromes such as Type 2 Diabetes Mellitus (T2DM) as C. elegans can be used to delineate molecular pathways that are at the core of its problems. A growing number of populations worldwide are faced with chronic T2DM, which also manifests several complications, such as blindness, neuropathy and cardiovascular diseases. Currently, metformin is the first-line drug of choice administered to treat T2DM. While …

A Conservative Isoleucine To Leucine Mutation Of Klentaq1 Dna Polymerase 1 Induces Conformational Change For Cold-Sensitive Phenotype, Emma Caroline Materne

Honors Theses

Polymerase Chain Reaction (PCR) typically employs the Taq or Klentaq1 DNA polymerase from Thermus aquaticus to elongate short sequences of DNA during DNA amplification. Both Taq and Klentaq1 retain activity at room temperature. During assembly of PCR at room temperature, the activity of Taq and Klentaq1 can result in spurious products due to elongation of primers bound to non-target sequences. A mutation of isoleucine to leucine at position 707 of Klentaq1 results in slowing of the enzyme at room temperature without compromising the fidelity of the enzyme. To understand how a mutation over 20Å from the active site can affect …

Transmural Heterogeneity Of Cellular Level Cardiac Contractile Properties In Aging And Heart Failure, Premi Haynes

Theses and Dissertations--Physiology

The left ventricle of the heart relaxes when it fills with blood and contracts to eject blood into circulation to meet the body’s metabolic demands. Dysfunction in either relaxation or contraction of the left ventricle can lead to heart failure. Transmural heterogeneity is thought to contribute to normal ventricular wall motion but it is not well understood how transmural modifications affect the failing left ventricle. The overall hypothesis of this dissertation is that normal left ventricles exhibit transmural heterogeneity in cellular level contractile properties and with aging and heart failure there are region-specific changes in cellular level contractile mechanisms.

Age …

Population Analysis And Protein Stability Assays Illustrate Xenobiotic Metabolizing Enzymes Have No Detectable Effect On Breast Cancer Development And Progression, Thomas Daniel Crowder

Theses and Dissertations

Xenobiotic Metabolizing Pathway works to detoxify the cell from numerous carcinogenic, mutagenic, and toxic hydrophobic compounds. As a member of the phase I enzymes (the first phase in the Xenobiotic Metabolizing Pathway) the Cytochrome P-450 Family 1 Sub-family B Protein 1 (Cyp1B1) works to attach an oxygen molecule to its hydrophobic substrate. In performing this reaction, Cyp1B1 often increases the reactivity of the xenobiotic compound. If these reactive Cyp1B1 products migrate into the nucleus and they can cause damage by reacting with DNA. However, the Glutathione S-Transferase Theta 1 (GSTT1) and Glutathione S-Transferase Mu 1 (GSTM1), members of the phase …

The Effects Of Snmp-2 Gene Expression On Mating Discrimination In Male Drosophila Melanogaster, Kristen Taylor Ashourian

Theses and Dissertations

In order to distinguish between relevant and extraneous stimuli, insects have adapted specialized processes to perceive cues that are beneficial for survival and proliferation. Volatile molecules in the environment can stimulate olfactory receptors (ORs) and gustatory receptors (GRs) in chemosensory organs called sensilla. Specialized proteins located within these sensilla guide and assist chemosensory molecules to the receptors, which then trigger a transduction pathway that elicits behavioral responses. Sensory Neuron Membrane Proteins (SNMPs) are transmembrane proteins found on both gustatory and olfactory sensory organs in insects. There are two forms of these proteins, SNMP-1 and SNMP-2. InDrosophila melanogaster, the function of …

Il-2rβ T450 Phosphorylation Is A Positive Regulator For Receptor Complex Stability And Activation Of Signaling Molecules, Blanca Estela Ruiz-Medina

Open Access Theses & Dissertations

Homeostasis of the immune system is required for proper defense against pathogenic insult. Cells of the innate and adaptive compartments provide a strictly regulated response to clear infections while allowing for self-tolerance. Dysregulation of the components of the immune system can lead to immunodeficiency, autoimmunity, and cancer. Key players of the immune response are T, B, and NK cells, which become strongly activated by IL2 through its receptor. The β subunit of the receptor becomes tyrosine, serine, and threonine phosphorylated upon induction with IL2. Phosphorylation of tyrosine residues has been extensively studied, however, the putative regulatory role of serine and …

The Benefits Of Breastfeeding, Avery Kordus

Senior Honors Theses

Breastfeeding research is plentiful, and the majority of the literature shows that breast milk is the superior form of infant nutrition except in the rare circumstances of infant metabolic disorders, maternal drug use, or positive HIV status. In comparison to formula, breast milk provides improved cognition, development, behavior, bonding, nutrition, digestion, immunity, and long-term health with fewer diseases and conditions in infants. Mothers are benefited by breastfeeding through bonding, faster weight loss, and reduction in certain cancers and conditions. Breast milk contains the proper amount of carbohydrates, fats, proteins, vitamins, and minerals, and is also specialized for each infant and …

One-Pot Heteroconjugate Addition-Diels-Alder Reactions And Acetate-Catalyzed Aldol Reactions Of Α-Silyl Nitriles, Carly Mueller

Honors Theses

1. A one-pot three-step Diels–Alder reaction sequence of ethyl propiolate and thiols can be performed to produce high yields of complex bicyclic products. A KOt-Bu-catalyzed thioconjugate addition of thiols to enoates, oxidation of the generated thioenoate by mCPBA, and Li-catalyzed Diels–Alder addition of cyclopentadiene occur in situ, without any purification of intermediates.
2. Stereoselectivity of the Diels–Alder product was examined by utilizing a chiral sulfone substrate. It was determined that these substrates were unable to provide significant stereochemical control.
3. Silylation of 3-phenylpropionitrile is achieved at the α-position with trimethylsilyl trifluoromethanesulfonate and trialkylamine base. Catalyzed by tetrabutylammonium acetate (2.5 mol%), …

Do The Inter-Nucleotide Domain Loops Act As An Entropic Sink In The Catalytic Activity Of 3-Phosphoglycerate Dehydrogenase (3pgdh)?, Cristina Adelia Meeham

Honors Theses

In protein science the relationship between protein dynamics and catalytic activity are the subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Currently, the field of protein science is trying to uncover the deeper role that dynamics plays in the catalytic activity and allosteric regulation of proteins and to better understand how to more effectively and efficiently target proteins in cancer therapeutics and other metabolic pathways.

Dephosphorylation Of Iqg1 By Cdc14 Temporally Regulates Actin Ring Formation, Daniel Patrick Miller

Masters Theses

"Cytokinesis is the final step in cell division when the cell separates the cytoplasm by contracting a ring composed of filamentous actin (F-actin) and type II myosin. Iqg1, an IQGAP family member, is an essential scaffolding protein in budding yeast (S. cerevisiae) required for actin recruitment to, and contraction of, the actomyosin ring. Actin is recruited by the calponin homology domain (CHD) in anaphase after Iqg1 is localized to the bud neck. Consensus sites for the cyclin-dependent kinase (CDK) Cdc28 were identified flanking the CHD. This led us to the hypothesis that phosphorylation of Iqg1 by Cdc28 negatively regulates actin …

Comparative Analyses Of Three Chlorella Species In Response To Light And Sugar Reveal Distinctive Lipid Accumulation Patterns In The Microalga C. Sorokiniana, Julian N. Rosenberg, Naoko Kobayashi, Austin Barnes, Eric A. Noel, Michael J. Betenbaugh, George A. Oyler

Department of Biochemistry: Faculty Publications

While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold’s basal medium (BBM) and heterotrophy in BBM supplemented …

Evaluating The Clinical And Physiological Effects Of Long Term Ultraviolet B Radiation On Guinea Pigs (Cavia Porcellus), Megan K. Watson, Adam W. Stern, Amber L. Labelle, Stephen Joslyn, Timonthy M. Fan, Katie Leister, Micah Kohles, Kemba Marshall, Mark A. Mitchell

School of Veterinary and Biomedical Sciences: Faculty Publications

Vitamin D is an important hormone in vertebrates. Most animals acquire this hormone through their diet, secondary to exposure to ultraviolet B (UVB) radiation, or a combination thereof. The objectives for this research were to evaluate the clinical and physiologic effects of artificial UVB light supplementation on guinea pigs (Cavia porcellus) and to evaluate the long-term safety of artificial UVB light supplementation over the course of six months. Twelve juvenile acromelanic Hartley guinea pigs were randomly assigned to one of two treatment groups: Group A was exposed to 12 hours of artificial UVB radiation daily and Group B …

Virus Purification, Detection And Removal, Khrupa Saagar Vijayaragavan

Dissertations, Master's Theses and Master's Reports - Open

The biopharmaceutical industry has a growing demand and an increasing need to improve the current virus purification technologies, especially as more and more vaccines are produced from cell-culture derived virus particles. Downstream purification strategies can be expensive and account for 70% of the overall manufacturing costs. The economic pressure and purification processes can be particularly challenging when the virus to be purified is small, as in our model virus, porcine parvovirus (PPV). Our efforts are focused on designing an easy, economical, scalable and efficient system for virus purification, and we focused on aqueous two-phase systems. Industry acceptable standards for virus …

Role Of Microrna Let-7 In Pancreatic Beta Cells, Shungang Zhang

Dissertations, Master's Theses and Master's Reports - Open

MicroRNAs (miRNAs) are small non-coding RNAs that inhibit gene expression at transcriptional or post-transcriptional level. Let-7 family is among the first identified human miRNAs and regulates multiple cellular processes including glucose metabolism in multiple organs. It has been reported that overexpression of let-7 resulted in insulin resistance and impaired glucose tolerance through repressing insulin signaling pathway in both muscle and liver. However, the role and mechanism underlying let-7 function in pancreatic beta-cells have yet to be elucidated.

Let-7 family contains nine members, which poses a significant challenge in complete deletion of this miRNA family. To study the function of let-7 …

Spatial Gaussian Markov Random Fields: Modelling, Applications And Efficient Computations, Yu Ryan Yue, Xiao-Feng Wang

Publications and Research

A powerful modelling tool for spatial data is the framework of Gaussian Markov random fields (GMRFs), which are discrete domain Gaussian random fields equipped with a Markov property. GMRFs allow us to combine the analytical results for the Gaussian distribution as well as Markov properties, thus allow for the development of computationally efficient algorithms. Here we briefly review popular spatial GMRFs, show how to construct them, and outline their recent developments and possible future work.

Evaluation Of Effects Of Epigenetic Modifications, Macromolecular Crowding, Degree Of Hydration, And Transcription Factor Binding On The Thermodynamic Stability Of Dna I-Motif Structures, Yogini Bhavsar

Electronic Theses and Dissertations

No abstract provided.

Evaluation Of Wild Yam (Dioscorea Villosa) As A Demethylating Agent And Its Anti Metastatic Activity In Human Breast Cancer Cells, Pranapda Aumsuwan

Electronic Theses and Dissertations

No abstract provided.

Sumoylation Affects Ns1'S Ability To Neutralize The Interferon Response, Jeanette Cecilia Gonzalez

Open Access Theses & Dissertations

It is of huge concern the possibility that at some point in the future we may face a new pandemic involving a highly pathogenic virus due to our current preventive and treatment options to fight this viral disease. The main reason for such limitations is the ability of the virus to go over constant antigenic shifts and drifts on its viral surface proteins HA and NA. The constant mutations that affect this virus cause the need of developing new vaccines for each influenza season. Periodically, the World Health Organization (WHO) reports that around 10% of the world population gets infected …

Global Sphingolipid Profile Of Giardia Lamblia During Stage Differentiation: The Influence Of Sphingomyelin Abundance On Viable Cyst Production, Trevor Thomas Duarte

Open Access Theses & Dissertations

Giardia lamblia is a protozoan parasite and a major cause of the waterborne-illness, giardiasis, worldwide. Giardiasis is endemic in developing countries and is a leading cause of non-viral- and non-bacterial-associated intestinal disorders. Acute symptoms of giardiasis include diarrhea, cramps, and malabsorption. The disease is often self-limiting, although the infection can result in long-term disorders such as chronic fatigue, stunted cognitive skills, and failure to thrive even after the parasite has been cleared.

This parasite exists in two morphologic forms--infective trophozoites and transmissible, water-resistant cyst, which is passed by the fecal-oral route and is likely to be spread by contaminated drinking …

A Comparative Approach To Assessing The Functional And Structural Characteristics Of Human Fkbp52 In The Regulation Of Steroid Hormone Receptor Signaling Pathway, Diondra Crystal Harris

Open Access Theses & Dissertations

The 52 kDa FK506 binding protein (h52) is a key positive regulator of Androgen Receptor (AR) in cellular and animal models and is an attractive target for the treatment of prostate cancer. Human FKBP52 is a known regulatory protein and co-chaperone that has been shown to play an important role in the regulation of the AR signaling pathway, and in the development of the male sexual phenotype. Cellular studies in mammalian and yeast cells reveal that FKBP52 is a positive regulator of AR, glucocorticoid receptor (GR), and progesterone receptor (PR), potentiating receptor-mediated gene expression up to 60-fold in some systems. …

Furthering Our Understanding And Assessing The Effectiveness Of Scaling Patterns And Controls Of Land-Atmosphere Carbon Exchange In A Shrubland Of The Chihuahuan Desert With Novel Cyberinfrastructure, Aline Jaimes

Open Access Theses & Dissertations

Over the last century, arid and semiarid regions have undergone intense desertification and in many regions, vegetation has shifted from grassland to shrubland dominated ecosystems. This land cover change has important implications for how desert ecosystems function - especially with regards to land-atmosphere exchange of carbon, water, and energy. Although the extent of desertified landscapes is expected to expand over the next 30 to 40 years, there is a relatively poor understanding of how this state transition will impact ecosystem function and feedbacks to other components of the earth system. Key to addressing this challenge is an improved understanding of …

Mechanisms To Mitigate Neurodegeneration By Maintaining Mitochondrial Health, Parijat Kabiraj

Open Access Theses & Dissertations

Cerebral accumulation of amyloidogenic protein aggregates is most frequently observed in the pathogenesis of neurodegenerative diseases. Recent studies showed prion like spreading of beta amyloid (A beta) in Alzheimer's disease (AD) and alpha synuclein protein in Parkinson's disease (PD) brain. Failure or compromise to the chaperone activity of protein disulfide isomerase (PDI) is also been reported as a major factor of aggregate formation. Nitrosative stress mediated S-nitrosylation (SNO) of protein disulfide isomerase (PDI), a housekeeping oxidoreductase, has been implicated in the pathogenesis of sporadic PD and AD. Mitochondrial dysfunction, leading to elevated levels of reactive oxygen species (ROS), is associated …

The Role Of Surface Chemistry In The Toxicity Of Manufactured Cerium Dioxide Nanomaterials To Caenorhabditis Elegans, Emily Kay Oostveen

Theses and Dissertations--Plant and Soil Sciences

Manufactured CeO₂ nanomaterials (CeO₂-MNMs) are used for a wide variety of applications including diesel fuel additives and chemical/mechanical planarization media. To test the effects of CeO₂-MNM surface coating charge on to model organism Caenorhabditis elegans, we synthesized 4 nm CeO₂ with cationic (DEAE-), anionic (CM-), and neutral (DEX) coatings. In L3 nematodes exposed for 24 hours, DEAE-CeO₂ induced lethality at lower concentrations than CM- or DEX-CeO₂. Feeding slightly decreased CeO₂ toxicity, regardless of coating. In L2 nematodes exposed for 48 hours with feeding, DEAE-CeO₂ caused lethality at the …

Understanding The Chemical Gymnastics Of Enzyme-Catalyzed 1’-1 And 1’-3 Triterpene Linkages, Stephen A. Bell

Theses and Dissertations--Plant and Soil Sciences

Squalene synthase (SS) is an essential enzyme in eukaryotic systems responsible for an important branch point in isoprenoid metabolism that leads to sterol formation. The mechanistic complexity of SS has made it a difficult enzyme to study. The green alga Botryococcus braunii race B possesses several squalene synthase-like (SSL) enzymes that afford a unique opportunity to study the complex mechanism of triterpene biosynthesis. SSL-1 catalyzes presqualene diphosphate (PSPP) formation, which can either be converted to squalene by SSL-2 or botryococcene by SSL-3. A rationally designed mutant study of B. braunii squalene synthase (BbSS) and SSL-3 was conducted to understand structure-function …

Molecular Studies On The Anti-Tumor Effects Of Metal-Based Complexes: Involvement Of The Ubiquitin-Proteasome And Apoptotic Pathways, Sara M. Schmitt

Wayne State University Dissertations

The ubiquitin-proteasome pathway is crucial to normal cellular function, and as such, has been extensively investigated as a potential target for cancer therapeutics. Many compounds have been tested for their proteasome inhibitory ability, including various small peptide aldehydes, and, following the success of cisplatin, several metal-containing complexes. The efficacy of these compounds in preclinical studies ultimately resulted in the development and approval of the first-in-class proteasome inhibitor bortezomib, the use of which, unfortunately, has been hindered by toxicity and resistance. These limitations have led to a massive push toward designing and developing new, less toxic proteasome inhibitors for clinical use. …

Structural Basis Of Epigenetic Regulation And Protein Scaffolding In Development And Diseases, Yuanyuan Jiang

Wayne State University Dissertations

Protein X-ray crystallography is a powerful approach for elucidating protein structure and function. The high-resolution data generated by X-ray allow us to visualize protein structures in a three-dimensional (3D) space, which is vital for our understanding of the protein intra- and intermolecular interactions that explain the mechanisms of various biological events. More importantly, such information can provide a structural basis for developing new methods and strategies of targeted drug discovery. In this dissertation, by using X-ray crystallography as the primary approach, we have performed the structural and functional studies of SMYD2 and NHERF1 and have determined their mechanisms of action …

General Transcription Factors Play Dual Roles In Initiation And Termination, Scott Alan Medler

Wayne State University Dissertations

Gene looping, defined as the interaction of the promoter and the terminator regions of a gene during transcription, is emerging as an important gene regulatory mechanism in eukaryotes. The role of promoter bound general transcription factors during initiation is well established. However, recent studies have revealed that some initiation factors also interact with the 3' end of a gene. The biological role of initiation factors at the 3' end of a gene is unknown. The general transcription factors TFIIB and TFIIH have been found to interact genetically with Ssu72, a component of CPF 3' end processing complex. Accordingly, we found …

Proximate And Evolutionary Insights Into The Epigenetics Of Posttraumatic Stress Disorder, Levent Sipahi

Wayne State University Dissertations

Posttraumatic stress disorder (PTSD) is an important medical and social condition. Although the vast majority of individuals are exposed to traumatic events within their lifetime, a minority subsequently develop diagnosable PTSD. What underlies differential risk and resiliency in the face of trauma is an ongoing research and clinical question with implications for prevention and treatment. Recent work has revealed a putative role of epigenetic variation and modification - most notably DNA methylation - in the etiology of PTSD. That DNA methylation is stable, yet modifiable in response to lived experiences, makes it a strong candidate to mechanistically explain the ontogeny …

Linking Molecular, Electrical And Anatomical Properties Of Human Epileptic Brain, Shruti Bagla

Wayne State University Dissertations

Epilepsy is a common neurological disorder of recurrent unprovoked seizures. It affects almost 1% of the world population. Although there is a wide range of anti-epileptic drugs (AEDs) available, they only treat the seizure symptoms and do not cure the disease itself. The poor role of AEDs can be attributed to the lack of knowledge of exact mechanisms and networks that produce epileptic activities in the neocortex. At present, the best cure for epilepsy is surgical removal of electrically localized epileptic brain tissue. Surgically removed brain tissue presents an excellent opportunity to discover the molecular and cellular basis of human …

Regulation Of Inositol Biosynthesis And Cellular Consequences Of Inositol Depletion: Implications For The Mechanism Of Action Of Valproate, Rania M. Deranieh

Wayne State University Dissertations

Inositol is a six-carbon cyclitol that is ubiquitous in biological systems. It is a precursor for the synthesis of numerous biologically important compounds, including inositol phosphates and phosphoinositides that are essential for cell function and viability. Inositol compounds play a role in membrane formation, gene regulation, signaling, regulation of ion channels, and membrane trafficking. Furthermore, inositol regulates hundreds of genes, including those involved in the biosynthesis of inositol and phospholipids. While transcriptional regulation of inositol biosynthesis has been extensively studied and well characterized, regulation of inositol biosynthesis at the enzymatic level has not been addressed. The current study shows that …