Digital Commons Network^™

The E. Coli Protein Ybgl: A Novel Dna Repair Enzyme?, Mason H. Conen, Brooke D. Martin, Kent Sugden, Savannah Whitfield

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Cr(V) is a carcinogen that oxidizes guanine aggressively to form spiroiminodihydantion (Sp) and guanidinohydantoin (Gh), both of which contain an unusual hydantoin moiety that cause G→T transversion mutations at a high rate. Endonuclease VIII (nei) can recognize and excise these oxidation products from DNA and is translated as one of five protein products of the Nei operon in Escherichia coli (E. coli). However, the functions of the other four proteins remain unknown. To address this gap in knowledge, we focused on one of the four that immediately precedes nei, the ybgL protein. Previous work by our group has suggested a …

Investigation Of The Mechanism Of Action For Mithramycin And The Biosynthesis Of L-Rednose In Saquayamycins, Stevi Weidenbach

Theses and Dissertations--Pharmacy

Natural products continue to be a major chemical lead matter for drug discovery due to their diverse chemical structures and bioactivities. Clinically significant natural products include anti-cancer and anti-infective compounds and while many more of these compounds show promising bioactivity, their clinical relevance is often limited by toxicity or poor solubility. Combinatorial biosynthesis can be employed to modify existing chemical scaffolds towards reducing these limitations. To fully take advantage of these biochemical tools, it is important to understand the biosynthesis and mechanism of action of the molecules.

Saccharides in glycosylated natural products provide specific interactions with cellular targets and are …

Evolution Of Equine Arteritis Virus During Persistent Infection In The Reproductive Tract Of The Stallion And The Male Donkey, Bora Nam

Theses and Dissertations--Veterinary Science

Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 …

Manipulating Lipid Spreading Domain Formation With Compositional Gradients And Plasmonic Nanoparticles, Chen-Min Hung

CMC Senior Theses

After colliding two solid-supported spreading bilayers of different compositions, we produce a dynamic gradient as the newly-healed bilayer equilibrates. We apply this approach to study the formation of galactosyl ceramide (GalCer) domains. With a single experiment, we are able to explore the effects of varying cholesterol concentration on GalCer domains. To further control domain formation, we aimed to locally heat membranes with embedded plasmonic nanoparticles. However, we discovered a percolation threshold of spreading lipids over the array of nanoparticles. We found that surfaces with gold nanoparticles deposited at an average inter-particle distance of 40 nm inhibited lipid bilayer spreading, but …

Phage Display To Identify Functional Resistance Mutations To Rigosertib, Nedim Filipovic

CMC Senior Theses

In vitro protein selection has had major impacts in the field of protein engineering. Traditional screens assay individual proteins for specific function. Selection, however, analyzes a pool of mutants and yields the best variants. Phage display, a successful selection technique, also provides a reliable link between variant phenotype and genotype. It can also be coupled with high throughput sequencing to map protein mutations; potentially highlighting vital mutations in variants. We propose to apply this technique to cancer therapy. RAF, a serine/threonine kinase, is critical for cell regulation in mammals. RAF can be activated by oncogenic RAS, found in over 30% …

Steroidogenesis In The Green Anole Lizard Brain And Gonad, Christine Peek

All Graduate Theses, Dissertations, and Other Capstone Projects

Seasonally breeding animals reproduce during certain times of the year and, subsequently, behaviors, steroid hormone levels, and brain morphology change. The green anole lizard (Anolis carolinensis) is an excellent model to study the regulation of steroid hormone production because they have distinct hormonal and behavioral differences between sexes and seasons. As in other vertebrates, steroidogenesis in anoles is under the control of the hypothalamus-pituitary-gonadal (HPG) axis. We tested the hypothesis that natural variations in steroid hormone levels between sexes and seasons are mediated within the brain and gonad by examining four genes involved in steroidogenesis: StAR, Cyp17α1, HSD17β3, and Cyp19α1. …

Iron Metabolism Genes In Browsing And Grazing Rhinoceroses: Implications For Iron Overload Disorder, Lorien Salyer

Undergraduate Honors Thesis Projects

Iron overload disorder is a serious condition that affects many animals of conservation interest, including rhinoceroses. Iron overload disorder is only found in browsing rhinos (African black, Diceros bicornis, and Sumatran, Dicerorhinus sumatrensis) but not in grazing species (African white, Ceratotherium simum, and greater one-horned, Rhinoceros unicornis). Iron overload is connected with many of the other health issues seen in captive browsing rhinoceroses, so it is vitally important that the iron metabolism process is studied to improve the existing husbandry procedures of these critically endangered animals. The objective of this study was to characterize genes related to …

Ligands Of Therapeutic Utility For The Liver X Receptors., Rajesh Komati, Dominick Spadoni, Shilong Zheng, Jayalakshmi Sridhar

Faculty and Staff Publications

Liver X receptors (LXRs) have been increasingly recognized as a potential therapeutic target to treat pathological conditions ranging from vascular and metabolic diseases, neurological degeneration, to cancers that are driven by lipid metabolism. Amidst intensifying efforts to discover ligands that act through LXRs to achieve the sought-after pharmacological outcomes, several lead compounds are already being tested in clinical trials for a variety of disease interventions. While more potent and selective LXR ligands continue to emerge from screening of small molecule libraries, rational design, and empirical medicinal chemistry approaches, challenges remain in minimizing undesirable effects of LXR activation on lipid metabolism. …

Methane Fluxes And Porewater Dissolved Organic Carbon Dynamics From Different Peatlands Types In The Pastaza-Marañon Basin Of The Peruvian Amazon., Jhon Del Aguila-Pasquel

Dissertations, Master's Theses and Master's Reports

Relevant components of the carbon budget such as methane fluxes and porewater dissolved organic carbon (DOC) are poorly characterized in the Peruvian Pastaza Marañon basin (PMB). PMB is associated with a tropospheric hotspot for methane and therefore it may represent a significant methane source. We aimed to quantify the magnitude of CH₄ fluxes and porewater DOC; and to determine their predictors across different peatland types in the PMB (open peatland, palm swamp, and pole forest). The study was conducted in two peatland sites covering the three main vegetation types in PMB. We collected gas and water samples using chamber-based …

Disrupted Superior Collicular Activity May Reveal Cervical Dystonia Disease Pathomechanisms, Eavan M. Mcgovern, Owen Killian, Shruti Narashimham, Brendan Quinlivan, John Butler, Rebecca Beck, Ines Beiser, Laura W. Williams, Ronan P. Killeen, Michael Farrell, Sean O'Riordan, Richard B. Reilly, Michael Hutchinson

Articles

Cervical dystonia is a common neurological movement disorder characterised by muscle contractions causing abnormal movements and postures affecting the head and neck. The neural networks underpinning this condition are incompletely understood. While animal models suggest a role for the superior colliculus in its pathophysiology, this link has yet to be established in humans. The present experiment was designed to test the hypothesis that disrupted superior collicular processing is evident in affected patients and in relatives harbouring a disease-specific endophenotype (abnormal temporal discrimination). The study participants were 16 cervical dystonia patients, 16 unaffected first-degree relatives with abnormal temporal discrimination, 16 unaffected …

Chemical Profiling And Chemical Standardization Of Vitex Negundo Using 13c Nmr, Fabian M. Dayrit, Lolita G. Lagurin, John Daniel J. Magsalin, Anthony R. Zosa

Chemistry Faculty Publications

Chemical profiling and standardization of the defatted methanol extract of the leaves of Vitex negundo L. were carried out using 13C nuclear magnetic resonance (NMR) analysis followed by chemometric analysis of the chemical shift data. Chemical profile was obtained using a k-means cluster profile and chemical standardization which was achieved using a multivariate control chart. The V. negundo samples were made up of four groups: the training set, submitted samples from production farms, commercial samples, such as tablets, capsules and teas, and experimental samples (samples which were allowed to degrade). Four groups were generated in k-means cluster, which generally corresponded …

Exosomes Serve As Novel Modes Of Tick-Borne Flavivirus Transmission From Arthropod To Human Cells And Facilitates Dissemination Of Viral Rna And Proteins To The Vertebrate Neuronal Cells, Wenshuo Zhou, Michael Woodson, Biswas Neupane, Fengwei Bai, Michael B. Sherman, Kyung H. Choi, Girish Neelakanta, Hameeda Sultana

Biological Sciences Faculty Publications

Molecular determinants and mechanisms of arthropod-borne flavivirus transmission to the vertebrate host are poorly understood. In this study, we show for the first time that a cell line from medically important arthropods, such as ticks, secretes extracellular vesicles (EVs) including exosomes that mediate transmission of flavivirus RNA and proteins to the human cells. Our study shows that tick-borne Langat virus (LGTV), a model pathogen closely related to tick-borne encephalitis virus (TBEV), profusely uses arthropod exosomes for transmission of viral RNA and proteins to the human- skin keratinocytes and blood endothelial cells. Cryo-electron microscopy showed the presence of purified arthropod/neuronal exosomes …

Investigating The Relationship Between Instructors’ Use Of Active Learning Strategies And Students’ Conceptual Understanding And Affective Changes In Introductory Biology: A Comparison Of Two Active-Learning Environments, Lacy M. Cleveland, Jeffrey T. Olimpo, Sue Dechenne-Peters

Biology: Faculty Publications

In response to calls for reform in undergraduate biology education, we conducted research examining how varying active-learning strategies impacted students’ conceptual understanding, attitudes, and motivation in two sections of a large-lecture introductory cell and molecular biology course. Using a quasi-experimental design, we collected quantitative data to compare participants’ conceptual understanding, attitudes, and motivation in the biological sciences across two contexts that employed different active-learning strategies and that were facilitated by unique instructors. Students participated in either graphic organizer/worksheet activities or clicker-based case studies. After controlling for demographic and presemester affective differences, we found that students in both active-learning environments displayed …

Do Elevated Levels Of Glutathione Decrease The Toxicity Of Plasticizers In Mouse Liver Cells?, Khatoon Albahrani

All Master's Theses

Phthalates are esters of phthalic acid that play a crucial role in the manufacturing industries for enhancing the properties of plastic materials. Di-(2-ethylhexyl) phthalate (DEHP) is one of the most common phthalates used in a variety of products including food packaging and medical equipment. Their use has caused public health concerns because of their toxic effects on reproductive and developmental processes. This study aims to investigate the response of two mouse hepatoma cell lines to the effects of DEHP and its bioactive metabolite mono (2-ethylhexyl) phthalate (MEHP). Cells were exposed to four concentrations (10, 50, 100, and 300 µM) of …

End-To-End Molecular Communication Channels In Cell Metabolism: An Information Theoretic Study, Zahmeeth Sayed Sakkaff, Jennie L. Catlett, Mikaela Cashman, Massimiliano Pierobon, Nicole R. Buan, Myra B. Cohen, Christine A. Kelley

Department of Biochemistry: Faculty Publications

The opportunity to control and fine-tune the behavior of biological cells is a fascinating possibility for many diverse disciplines, ranging from medicine and ecology, to chemical industry and space exploration. While synthetic biology is providing novel tools to reprogram cell behavior from their genetic code, many challenges need to be solved before it can become a true engineering discipline, such as reliability, safety assurance, reproducibility and stability. This paper aims to understand the limits in the controllability of the behavior of a natural (non-engineered) biological cell. In particular, the focus is on cell metabolism, and its natural regulation mechanisms, and …

Cytolytic Toxin Production By Staphylococcus Aureus Is Dependent Upon The Activity Of The Protoheme Ix Farnesyltransferase, Emily Stevens, Maisem Laabei, Stewart Gardner, Greg A. Somerville, Ruth C. Massey

School of Veterinary and Biomedical Sciences: Faculty Publications

Staphylococcus aureus is a medically important pathogen with an abundance of virulence factors that are necessary for survival within a host, including the production of cytolytic toxins. The regulation of toxin production is mediated by the Agr quorum sensing system, and a poorly defined post-exponential growth phase signal independent of Agr. As part of a recent genome wide association study (GWAS) to identify novel loci that alter the expression of cytolytic toxins, a polymorphism in the cyoE gene, which encodes a protoheme IX farnesyltransferase, was identified. This enzyme is essential for processing heme into the electron transport chain for use …

Portulaca Oleracea Extract Can Inhibit Nodule Formation Of Colon Cancer Stem Cells By Regulating Gene Expression Of Notch Signal Transduction Pathway, Li Chen

Dissertations, Master's Theses and Master's Reports

The main aim of this study was to investigate the effects of Portulaca oleracea extract on tumor formation in colon cancer stem cells and chemotherapy sensitivity. In addition, this study analyzed the genetic changes within the Notch signal transduction pathway associated with the effects of the extracts. Serum-free cultures of colon cancer cells (HT-29) and HT-29 stem cells were treated with the chemotherapeutic drug 5-FU to assess sensitivity. Injections of the stem cells were also given to BALB/c mice to confirm tumor growth and characteristics. In addition, the effect of different concentrations of P. oleracea extract was tested on the …

Heterologous Expression And Purification Of Full-Length Human Polybromo-1 Protein, Sarah Hopson

Dissertations, Master's Theses and Master's Reports

Over the past decade, it has become apparent that the human polybromo-1 protein (BAF180) has a critical role in cancer. BAF180 is known to be a driver mutation in clear cell renal cell carcinoma, where it has been found to be mutated in approximately 40% of cases. Mutations have also been found in several other cancers, including intrahepatic cholangiocarcinomas and epithelioid sarcomas. BAF180 is the chromatin targeting subunit of the PBAF (Polybromo-associated BRG1-associated factor) chromatin remodeling complex, a role facilitated by its nine domains: six bromodomains, which recognize and bind to acetylated lysines on histones; two BAH (bromo-adjacent homology) domains, …

Hyper-Activation Of Pp60(Src) Limits Nitric Oxide Signaling By Increasing Asymmetric Dimethylarginine Levels During Acute Lung Injury, Sanjiv Kumar, Xutong Sun, Satish Kumar Noonepalle, Qing Lu, Evgeny Zemskov, Ting Wang, Saurabh Aggarwal, Christine Gross, Shruti Sharma, Ankit A. Sesai, John D. Catravas

Bioelectrics Publications

The molecular mechanisms by which the endothelial barrier becomes compromised during lipopolysaccharide (LPS) mediated acute lung injury (ALI) are still unresolved. We have previously reported that the disruption of the endothelial barrier is due, at least in part, to the uncoupling of endothelial nitric oxide synthase (eNOS) and increased peroxynitrite-mediated nitration of RhoA. The purpose of this study was to elucidate the molecular mechanisms by which LPS induces eNOS uncoupling during ALI. Exposure of pulmonary endothelial cells (PAEC) to LPS increased pp60^Src activity and this correlated with an increase in nitric oxide (NO) production, but also an increase in …

The Role Of Alternative Polyadenylation Mediated By Cpsf30 In Arabidopsis Thaliana, Guijie Hao

Theses and Dissertations--Plant and Soil Sciences

Drought stress is considered one of the most devastating abiotic stress factors that limit crop productivity for modern agriculture worldwide. There is a large range of physiological and biochemical responses induced by drought stress. The responses range from physiological and biochemical to regulation at transcription and posttranscriptional levels. Post-transcription, the products encoded by eukaryotic genes must undergo a series of modifications to become a mature mRNA. Polyadenylation is an important one in terms of regulation. Polyadenylation impacts gene expression through determining the coding and regulation potential of the mRNA, especially when different mRNAs from the same gene may be polyadenylated …

Evolution Of The Kinetics And Dynamics Of Heme-Crevice Loop Regulating Chemistry In Human Cytochrome C, Shiloh M. Nold

Graduate Student Theses, Dissertations, & Professional Papers

Cytochrome c, cytc, is a metalloprotein that plays primary roles in electron transport and intrinsic apoptotic pathways. Much of the chemistry that cytc is involved with is regulated by a highly conserved region known as the heme crevice loop, consisting of residues 70-85. Only three of these residues (those at positions 81, 83 and 85) are not universally conserved within the evolutionary timeline. Here I look to elucidate possible evolutionary roles for several of the key residues known to be important in regulating heme chemistry of cytc.

I first address the role that lysine …

Analysis Of Microbial Diversity In Disturbed Soil, Tyler G. Sanda

Williams Honors College, Honors Research Projects

This paper uses the composition and abundance of microbial species to analyze soil recovery in disturbed land. Surface mining disturbs ecological communities throughout the world. As organizations seek to reclaim these disturbed lands, a proper analysis of recovery is needed. In previous studies, recovery of disturbed land was limited to surface examinations, which do not characterize the possible unseen devastating effects of the subsoil. Soil microorganisms are extremely sensitive to environmental changes such as strip mining. It is proposed that these microorganisms may serve as better indicators of recovery post disturbance. Our analysis indicates microbial recovery, however it may not …

Effects Of Novel Fragment-Warhead Adducts In Situ And In Vitro With Glutaredoxin Orthologs., Andrew J. Caras

Williams Honors College, Honors Research Projects

Fragment-based drug design (FBDD) is a method of pharmaceutical research involving characterization of small “fragment” molecule interactions with a target protein. These fragments are optimized with the addition of a nucleophilic “warhead” moiety. Several novel fragment-warhead adducts have been synthesized in house by group member Ram Khattri Ph.D. The experiment investigates reactivity of these adducts with glutaredoxin protein (Grx) orthologs from Homo sapiens, Pseudomonas aeruginosa and Brucella melitensis. Three novel fragment-warhead adducts have been identified to cause weakly bacteriostatic and bacteriocidal effects, most with minimum inhibitory concentration values near 1.28 mg/mL. Discussed herein are molecular effects of these fragment-warhead …

Regulation Of The Kras Promoter In Pancreatic Cancer By Proteins And Small Molecules, Harshul Batra

Electronic Theses and Dissertations

DNA-binding proteins play a pivotal role in cell biology. The major class of DNA-binding proteins are transcription factors (TFs). TFs are central to almost every fundamental cellular process such as cell development, differentiation, cell growth, and gene expression. They account for 10% of the genes in eukaryotes. In mammals, more than 700 TFs are identified to be DNA-binding TFs. They bind to the TF binding sites (TFBSs) in the genome and regulate the expression of their target genes. kRAS is a proto-oncogene with intrinsic GTPase activity, that contributes to cell proliferation, division, and apoptosis. kRAS mutations are observed in >95% …

Structural Basis Of Membrane Protein Scaffolding And Signaling In Human Disease, Joshua Holcomb

Wayne State University Dissertations

Protein structural elucidation by means of X-ray crystallography is a powerful approach for both insight into a proteins biophysical properties and function. To date X-ray crystallography remains the gold standard in high resolution structural determination and serves as the basis for rational drug design for the purpose of combating a number of human diseases. Such an approach also allows for the exploitation of how various proteins interact with their substrates providing a molecular basis for their physiological function. In this dissertation, using X-ray crystallographic analysis along with other biophysical characterization methods, we seek to understand the mechanistic foundation for which …

Role Of Alström Syndrome 1 (Alms1) In Nkcc2 Endocytosis, Thick Ascending Limb Function, Blood Pressure Regulation And Metabolic Function, Ankita Bachhawat Jaykumar

Wayne State University Dissertations

NaCl absorption by the Thick Ascending Limb (TAL) is mediated by the apical Na+/K+/2Cl- co-transporter, NKCC2. Increased NKCC2 activity and apical trafficking are associated to salt sensitive hypertension in rodents and humans. NKCC2 endocytosis is important for maintaining surface NKCC2 such that blocking NKCC2 endocytosis increased NKCC2 surface abundance and NKCC2-mediated NaCl reabsorption. Despite its importance, NKCC2 endocytosis has been poorly studied and a part of the reason may be attributed to the lack of availability of methods with good time resolution. Hence, we developed a method to image apical NKCC2 to monitor its endocytosis in real-time by Total Internal …

Rad Gtpase: Identification Of Novel Regulatory Mechanisms And A New Function In Modulation Of Bone Density And Marrow Adiposity, Catherine Nicole Kaminski Withers

Theses and Dissertations--Molecular and Cellular Biochemistry

The small GTP-binding protein Rad (RRAD, Ras associated with diabetes) is the founding member of the RGK (Rad, Rem, Rem2, and Gem/Kir) family that regulates voltage-dependent calcium channel function. Given its expression in both excitable and non-excitable cell types, the control mechanisms for Rad regulation and the potential for novel functions for Rad beyond calcium channel modulation are open questions. Here we report a novel interaction between Rad and Enigma, a scaffolding protein that also binds to the E3 ubiquitin ligase Smad ubiquitin regulatory factor 1 (Smurf1). Overexpression of Smurf1, but not …

Viral Fusion Protein Tm-Tm Interactions: Modulators Of Protein Function And Potential Antiviral Targets, Stacy Webb

Theses and Dissertations--Molecular and Cellular Biochemistry

Enveloped viruses, such as HIV, influenza, and Ebola, utilize surface glycoproteins to bind and fuse with a target cell membrane. This fusion event is necessary for release of viral genomic material so the virus can ultimately reproduce and spread. The recently emerged Hendra virus (HeV) is a negative-sense, single-stranded RNA paramyxovirus that presents a considerable threat to human health as there are currently no human vaccines or antivirals available. The HeV utilizes two surface glycoproteins, the fusion protein (F) and the attachment protein (G), to drive membrane fusion. Through this process, the F protein undergoes an irreversible conformational change, transitioning …

Platelet Endocytosis: Roles In Hemostasis And Innate Immunity, Meenakshi Banerjee

Theses and Dissertations--Molecular and Cellular Biochemistry

Endocytosis is key to fibrinogen (Fg) uptake, receptor trafficking of integrins (α_IIbβ₃, α_vβ₃) and purinergic receptors (P2Y₁, P2Y₁₂), and thereby for normal platelet function. However, platelet endocytosis could potentially be critical for actively sensing changes in vascular micro-environments and responding accordingly to what is being taken up. This is a more dynamic view of platelets as active surveyors of the vasculature; extending the importance of platelet endocytosis beyond granule biogenesis and perhaps even hemostasis. The mechanistic underpinnings of endocytosis, its importance in platelets, and the molecular machinery required …

Micrornas Modulate Pathogenesis Resulting From Chlamydial Infection In Mice, Laxmi Yeruva, S. Pouncey, Michael R. Eledge, Sudeepa Bhattacharya, Chunqiao Luo, Erin W. Weatherford, David M. Ojcius, Roger G. Rank

All Dugoni School of Dentistry Faculty Articles

Not all women infected with chlamydiae develop upper genital tract disease, but the reason(s) for this remains undefined. Host genetics and hormonal changes associated with the menstrual cycle are possible explanations for variable infection outcomes. It is also possible that disease severity depends on the virulence of the chlamydial inoculum. It is likely that the inoculum contains multiple genetic variants, differing in virulence. If the virulent variants dominate, then the individual is more likely to develop severe disease. Based on our previous studies, we hypothesized that the relative degree of virulence of a chlamydial population dictates the microRNA (miRNA) expression …