Biochemistry, Biophysics, and Structural Biology Commons^™

In Planta Evaluation Of Gene Regulation By Soybean Auxin Response Factors, Pratiksha K C

Electronic Theses and Dissertations

Nitrogen (N) is an important plant nutrient but its abundance in the soil is not sufficient for profitable crop production. N input in the form of chemical fertilizers helps fill this need; however, an alternative for fertilizers is an immediate need due to the environmental pollution resulting from excessive use of fertilizers. Leguminous plants such as soybean (Glycine max) that form root nodules through symbiotic association with N-fixing rhizobia and therefore need little or no chemical N fertilizers. The plant hormone auxin plays a crucial role in determining the number of nodules and their rate of maturity in soybean. Auxin …

Profiling Transcription And Retrotransposition Of Mouse L1 Subfamilies, Lingqi Kong

Electronic Theses and Dissertations

Transposable elements, also called jumping genes, comprise almost 45% of the human genome. In contrast, only 1% of the human genome is protein-coding sequences. The function and advantages of maintaining such massive copies of transposable elements in the human genome are still unclear. Long interspersed element 1 (L1), the most substantial group and the only active autonomous transposable element in the human genome, has revealed its unique roles in many diseases. The insertional mutagenesis induced by L1 retrotransposition events could threaten human genomic stability and generate unexpected mutations. L1 overexpression has been documented in both somatic and germline cells and, …

Scavenger Hunt: The Search For Sulfur Mustard-Neutralizing Compound In 2-Chloroethyl Ethyl Sulfide (Cees) Treated Human Keratinocyte (Hacat) Epithelial Cells, Tanner Diemer

Electronic Theses and Dissertations

Sulfur mustard is a highly toxic and dangerous vesicant that has been utilized as a chemical warfare agent (CWA) since World War I. Despite its extensive history, an effective antidote to sulfur mustard exposure still does not exist. With detectable levels of unreacted sulfur mustard lasting days after initial contact, a window of opportunity exists to administer a “scavenger” to affected individual immediately and in the days following exposure in hopes of reducing harm by neutralizing unreacted sulfur mustard. For this strategy to be effectively implemented, it is essential to identify a candidate compound with excellent affinity towards sulfur mustard …

The Characterization And Reactivity Of Tris(4-Methylpyrazolyl)Methane And Its Tungsten And Molybdenum Metal Complexes, Julia M. Pomeroy

Undergraduate Honors Thesis Collection

The scorpionate ligand tris(pyrazolyl)borate (Tp) has contributed to the understanding of coordination and organometallic chemistry and has proven to be useful in the synthesis of metalloprotein models. Studies focusing on the similar ligand, tris(pyrazolyl)methane (Tpm), have recently been made possible with improved synthetic techniques. Characterization of the Tpm ligand and its metal derivatives, [TpmW(CO)3L]+ and [TpmMo(CO)3L]+, unveiled unexpected activity in the 1H NMR chemical shift of the methane hydrogen after the coordination of a seventh ligand. The more electronegative the seventh ligand was, the more downfield the chemical shift appeared. Various analogs of Tpm have since been synthesized that substitute …

Single-Lipid Sorting And Dynamics At Nanoscale Membrane Curvatures: The Effects Of Fluorescence Labeling, Composition, Phase, And Temperature, Xinxin Woodward

Wayne State University Dissertations

Nanoscale membrane curvature on cell plasma membrane assists in the spatial organization and domain formation that are critical for life of eukaryotic cells. Lipids and proteins can sense, be sorted by, and generate both functional domains and membrane curvature. Reveal the relationship between membrane curvature, phase separation, and single-molecule behavior is a key to understanding fundamental processes, such as phagocytosis initiation, cell signaling, and membrane budding. Single lipid dynamic and sorting on engineered membrane curvature is studied to understand the effects of fluorescence labeling, composition, phase separation, and temperature. Single particle tracking was used to find radial averaged diffusion at …

Vibrational Spectroscopy For In Vitro Monitoring Stem Cell Differentiation, Francesca Ravera, Esen Efeoglu, Hugh Byrne

Other resources

Stem cell technology has attracted considerable attention over recent decades due to its enormous potential in regenerative medicine and disease therapeutics. Studying the underlying mechanisms of stem cell differentiation and tissue generation is critical, and robust methodologies and different technologies are required. Towards establishing improved understanding and optimised triggering and control of differentiation processes, analytical techniques such as flow cytometry, immunohistochemistry, reverse transcription polymerase chain reaction, RNA in situ hybridisation analysis, and fluorescence-activated cell sorting have contributed much. However, progress in the field remains limited because such techniques provide only limited information, as they are only able to address specific, …

“C1orf150”: A Novel Regulator Of Jak2 Kinase, And Candidate Tumor Suppressor In Human Blood Cell Progenitors, Tyler M. Wade

Honors Theses and Capstones

Erythropoietin (EPO) is an essential growth factor for red blood cell (RBC) production. In response to anemia, hypoxia-sensing cells in the kidney express and release EPO. EPO then acts in bone marrow to drive RBC formation from erythroid progenitors. Upon binding to its cell surface receptor, EPO triggers a JAK2 kinase signaling cascade for progenitor cell growth. Our lab has discovered a novel regulator of JAK2, “C1ORF150” (“150”). “150” is conserved in H sapiens and primates and is a new orthologue of the B-cell receptor adaptor protein and tumor marker, HGAL. Using a shRNA knockdown approach, I investigated the actions …

Understanding The Rage Signaling Pathway And Its Contribution To Diabetic Complications, Leon Vegas Ho

Legacy Theses & Dissertations (2009 - 2024)

The binding of advanced glycation end products (AGEs) to the receptor for advanced glycation end products (RAGE) is an important feature of the RAGE signaling pathway that plays a role in the pathogenesis of diabetes. Under high glucose concentration, RAGE expression increases immensely from the formation of a Schiff base by glucose bounded to lysine. This triggers an inflammatory and immune response and upregulates the expression of RAGE and causes an accumulation of AGEs in the body. As a result, this leads to the development of diabetes and other complications such as, atherosclerosis, nephrothapy, and retinopathy. To remedy AGE accumulation, …

Adaptation Of Vibrio Cholerae O1 To Protective, Lipopolysaccharide-Specific Antibodies In The Intestinal Lumen, Danielle Elizabeth Baranova

Legacy Theses & Dissertations (2009 - 2024)

The outer membrane (OM) of Gram-negative enteric pathogens like Vibrio cholerae is a barrier against host defense factors, as well as a sensor of physical and chemical stimuli that the bacteria encounter in the gastrointestinal tract. The OM is also the primary target of the mucosal immune response, which consists of secretory antibodies primarily directed against lipopolysaccharide (LPS). ZAC-3 is a monoclonal antibody (MAb) that targets the conserved core/lipid A region of LPS of the pandemic V. cholerae O1 serotype. In a neonatal mouse model, passively administered ZAC-3 IgG has been shown to reduce the ability of V. cholerae to …

Novel Substrate-Free Cholinesterase Based Sensing Of Organophosphorus Compounds, Hailey J. Marini

Legacy Theses & Dissertations (2009 - 2024)

The increasing concerns of chemical weapons used by terrorists is growing, creating a need for infield detection methods that can rapidly detect these compounds that are a major health concern for civilians and military personnel. Displacement is a novel concept for the detection of cholinesterase inhibitors, including organophosphorus compounds, that could replace the classical instrumentation methods currently being used for diagnostics.

The Stromal Response In Salivary Gland Injury, Kevin O'Keefe

Legacy Theses & Dissertations (2009 - 2024)

Abstract

Launching The Next Generation : Transcriptional Regulation During Oogenesis, Alicia K. Mccarthy

Legacy Theses & Dissertations (2009 - 2024)

Germ cells give rise to gametes and link generations by passing genetic information from parent to offspring. Gametes arise from, in many sexually reproducing organisms, germline stem cells (GSCs) which are set aside early during development. GSCs have an amazing capacity to undergo self-renewal to give rise to a pool of undifferentiated cells, while also differentiating to generate specialized germ cells such as haploid gametes. Upon female GSC differentiation, mitotically dividing germ cells can initiate meiosis, and mature within a follicle. During maturation, the specified oocyte is provided with a trust fund of RNAs and proteins for the next generation …

Targeting The Rage Signaling Pathway To Ameliorate The Complications Of Diabetes, Stephen James Dansereau

Legacy Theses & Dissertations (2009 - 2024)

Diabetes is a global health epidemic that can be devastating to those afflicted,

Biochemical And Chemical Methods Of Key Derivation For Cryptographic Ciphers, Leif K. Mcgoldrick

Legacy Theses & Dissertations (2009 - 2024)

Cryptography is a vital component of digital communication and digital data in general. The use of cryptography is necessary to support the veracity of data and to protect it from outside parties with malicious intent. Cryptography focuses on two main facets that are vital for this goal: data encryption and user authentication. Encryption protects the data by transforming it into an encrypted text that would not allow someone access without having or breaking the encryption method that was used to make it. User authentication is a multiple part process that allows for one to be able to identify oneself to …

The Guardian Of The Genome : Regulation Of The Enhancer Networks Governing The P53-Mediated Stress Response, Allison Catizone

Legacy Theses & Dissertations (2009 - 2024)

After fertilization in vertebrates, cells work to build organs, tissues and begin to rapidly differentiate and proliferate. This process is the orchestration of finely tuned signals and perfectly timed gene expression patterns. The first step in gene expression, transcription, is governed by proteins known as transcription factors (TF). TFs are responsible for binding to DNA, altering chromatin structure, and driving activation of other genes based on the organism’s needs. Once the process of development is complete, organisms shift their resources to maintaining homeostasis. Humans regularly encounter outside stressors such as UV radiation, pollution, allergens, and drugs. Cells also accumulate mutations …

Development Of Small Molecule Antibiotics Against A Conserved Rna Gene Regulatory Element In Gram-Positive Bacteria, Ville Yrjö Petteri Väre

Legacy Theses & Dissertations (2009 - 2024)

Bacterial infections and the rise of antibiotic resistance, especially multidrug resistant strains, have generated a clear need for discovery of novel therapeutics. Most antibiotics in use today are derivatives of previous antibiotics to which resistance mechanisms already exist, and traditionally they have a single target: either a protein or rRNA. Gram-positive bacteria regulate the expression of several essential genes or operons using a mechanism called the T-box. The T-box is a structurally conserved riboswitch-like gene regulator in the 5’-untranslated region (UTR) of numerous essential genes of Gram-positive bacteria. T-boxes are stabilized by cognate, unacylated tRNA ligands, allowing the formation of …

Development Of Dual Functional Dna/Rna Nanostructures For Drug Delivery, Vibhav Amit Valsangkar

Legacy Theses & Dissertations (2009 - 2024)

In addition to the traditional biochemical functions, DNA and RNA have been increasingly studied as building blocks for the formation of various 2D and 3D nanostructures. DNA has emerged as a versatile building block for programmable self-assembly. DNA-based nanostructures have been widely applied in biosensing, bioimaging, drug delivery, molecular computation and macromolecular scaffolding. A variety of strategies have been developed to functionalize these nanostructures. The major advantage is that DNA is a very stable molecule and its base-pairing properties can be easily utilized to control and program the formation of desired nanostructures. In addition, some of these DNA/RNA nanostructures have …

Regulation Of Gene Expression Through Ribosome-Associated Proteins, Clare Margaret Miller

Legacy Theses & Dissertations (2009 - 2024)

Translation is a crucial mechanism for generating proteins to carry out cellular processes and for ensuring proper cell functions. Ribosomes are at the center of translation and are complex pieces of machinery. They consist of at least 80 core eukaryotic ribosomal proteins, which are conserved from prokaryotes, and four ribosomal RNAs (rRNAs): 18S, 28S, 5,8A 5S. In addition, numerous translation factors aid the ribosome in protein production. While ribosomes are typically described by these core features, they are known to exist in a heterogenous pool with variations in protein composition, modifications of rRNA, and an assortment of non-ribosomal proteins that …

Role Of Microrna-483 In Pancreatic Β-Cells, Jackson Waugh

Dissertations, Master's Theses and Master's Reports

Insulin is an essential hormone produced by β-cells in the pancreas. The release of insulin is tightly regulated in healthy people in order to control blood sugar level in our body. However, people with Type 2 Diabetes have insufficient insulin secretion from pancreatic β-cells, leaving to high blood sugar (hyperglycemia) and β-cell failure. microRNAs (miRNAs or miR) are newly discovered small regulatory molecules and have emerged as important regulator of cell growth, differentiation, and organ function. Altered miRNA function has been implicated in the pathogenesis of a variety of human disease, including diabetes. In this report, we focus on dissecting …

First Records Of Established Populations Of Ixodes Scapularis (Acari: Ixodidae) Collected From Three Nebraska Counties, Lindsey E. Nielsen, Roberto Cortinas, Paul D. Fey, Peter C. Iwen, David H. Nielsen

School of Veterinary and Biomedical Sciences: Faculty Publications

Reported cases of Lyme disease in Nebraska have been assumed to be imported from other endemic areas. Previous surveillance efforts provided no evidence of established populations as only individual specimens of Ixodes scapularis (Say) had been collected. In the winter of 2018, adult I. scapularis were found on a dog at Two Rivers State Recreation Area, Douglas County, prompting tick collection at the site and nearby natural areas. In May 2019, all life stages of host-seeking I. scapularis were collected using dragging and flagging techniques in sites located near the Platte River in Douglas, Sarpy, and Saunders counties. This is …

Intimate Attachment Of Escherichia Coli O157:H7 To Urinary Bladder Epithelium In The Gnotobiotic Piglet Model, Rodney A. Moxley, Tom W. Bargar, Stephen D. Kachman, Diane R. Baker, David H. Francis

School of Veterinary and Biomedical Sciences: Faculty Publications

Enterohemorrhagic Escherichia coli (EHEC), a pathogenic subset of Shiga toxin-producing E. coli (STEC), is an important cause of hemorrhagic colitis and hemolytic–uremic syndrome (HUS), and a rare cause of urinary tract infections (UTIs) with associated HUS. EHEC strains attach intimately to intestinal epithelium with formation of actin pedestals (attaching-effacing (A/E) lesions); however, the mechanism of EHEC attachment to the uroepithelium is unknown. We conducted a retrospective study on archived urinary bladder specimens from gnotobiotic piglets that naturally developed cystitis associated with EHEC O157:H7 infection following oral inoculation and fecal shedding. Paraffin-embedded bladder tissues from three piglets with cystitis and immunohistochemical …

Triggers Of Inflammatory Heart Disease, Ninaad Lasrado, Bharathi Yalaka, Jay Reddy

School of Veterinary and Biomedical Sciences: Faculty Publications

Inflammatory heart disease (IHD) is a group of diseases that includes pericarditis, myocarditis, and endocarditis. Although males appear to be more commonly affected than females, IHD can be seen in any age group. While the disease can be self-limiting leading to full recovery, affected individuals can develop chronic disease, suggesting that identification of primary triggers is critical for successful therapies. Adding to this complexity, however, is the fact that IHD can be triggered by a variety of infectious and non-infectious causes that can also occur as secondary events to primary insults. In this review, we discuss the immunological insights into …

Current Status Of Zika Virus Vaccines: Successes And Challenges, Aryamav Pattnaik, Bikash R. Sahoo, Asit K. Pattnaik

School of Veterinary and Biomedical Sciences: Faculty Publications

The recently emerged Zika virus (ZIKV) spread to the Americas, causing a spectrum of congenital diseases including microcephaly in newborn and Guillain-Barré syndrome (GBS) in adults. The unprecedented nature of the epidemic and serious diseases associated with the viral infections prompted the global research community to understand the immunopathogenic mechanisms of the virus and rapidly develop safe and efficacious vaccines. This has led to a number of ZIKV vaccine candidates that have shown significant promise in human clinical trials. These candidates include nucleic acid vaccines, inactivated vaccines, viral-vectored vaccines, and attenuated vaccines. Additionally, a number of vaccine candidates have been …

Rapid Differentiation Of Moraxella Bovoculi Genotypes 1 And 2 Using Maldi-Tof Mass Spectrometry Profiles, Matthew M. Hille, Aaron M. Dickey, Kara Robbins, Michael L. Clawson, John Dustin Loy

School of Veterinary and Biomedical Sciences: Faculty Publications

Moraxella bovoculi is the most frequently isolated bacteria from the eyes of cattle with Infectious Bovine Keratoconjunctivitis (IBK), also known as bovine pinkeye. Two distinct genotypes of M. bovoculi, genotype 1 and genotype 2, were characterized after whole genome sequencing showed a large degree of single nucleotide polymorphism (SNP) diversity within the species. To date, both genotypes have been isolated from the eyes of cattle without clinical signs of IBK while only genotype 1 strains have been isolated from the eyes of cattle with clinical signs of IBK. We used 38 known genotype 1 strains and 26 known genotype …

Life In A Rural Emergency Department: Patients Speak To Underlying, Fundamental Disparities In Physician And Resource Allocation, Jessica Gustad

Honors Projects

In the Journal of Health Services Research and Policy, access to health care was defined as, “The availability of an adequate supply of health care services and the individual’s opportunity to obtain health care when it is wanted or needed” (MacKinney, 2014). Current trends in rural emergency departments are trying to communicate a critical message about the fundamental problems with the distribution of health care services in America today and the inability to properly meet the definition above. In rural communities, patient complaints and behaviors demonstrate the pressing concerns of inadequate access to primary care, limited specialty care, insufficient mental …

Molecular Facet Of Host-Pathogen Interactions In Fusarium Head Blight In Wheat ( Triticum Aestivum L.), Bimal Paudel

Electronic Theses and Dissertations

Fusarium head blight (FHB) is a severe disease of wheat (Triticum aestivum L.). It not only reduces the quantity of the harvested grains but also decreases the grain quality due to mycotoxins contamination, especially Deoxynivalenol (DON). Qfhb1 (or simply called Fhb1) is the most important quantitative trait locus (QTL) for FHB resistance. Our lab has previously identified wheat gene WFhb1-1 (aka. Wfhb1_c1) as a candidate for FHB resistance gene. Here we report that WFhb1-1 has been cloned. The gene (GenBank # KU304333.1) consists of a single exon, encoding a putative membrane protein of 127 amino acids. WFhb1-1 protein produced in …

Genetic Study Of Alkane Production And Oxic Nitrogen Fixation In Anabaena Sp. Pcc 7120, Jaimie L. Gibbons

Electronic Theses and Dissertations

Anabaena sp. PCC 7120 is a filamentous, nitrogen-fixing cyanobacterium that uses spatial separation to perform photosynthesis and nitrogen fixation simultaneously. Under fixed nitrogen limiting conditions, Anabaena 7120 forms specialized cells, called heterocysts, to fix nitrogen. In this research, I sought to add to the knowledge surrounding the process of heterocystous nitrogen fixation in Anabaena 7120. Cyanobacteria universally produce alkanes, which have been suggested to play a role in helping the organism adapt to abiotic stress, such as diazotrophic conditions. In my first study, I sought to identify the genes required for production of the hydrocarbon heptadecane (C17H36). Through using a …

Synthesis And The Genetic Encoding Of Novel Lysine Post-Translational Modifications, Sahan A. Galbada Liyanage

Theses and Dissertations

Post-translational modifications (PTMs) play a significant role in regulating cell signaling and regulating the inner cellular environment. The study of PTMs and their primary biological functions is critical for the development of new medicines targeting the pathways and biomolecules responsible for the PTMs.

Previous studies revealed the direct coupling of the β -hydroxybutyryl lysine (K_BHB) modification with the gene expression. K_BHB in histone proteins links metabolism to epigenetics and gene expression and enables to study in-depth, how cell metabolism controls the gene expression and vice versa. Similar novel histone modification, K_Lac, attracts a special interest …

Hormonal Regulation Of Glycine Decarboxylase And Its Metabolic Outcomes, Ruta Milind Jog

Wayne State University Dissertations

The amino acid glycine is involved in generation of multiple critical metabolites including glutathione, heme, and creatinine. Interestingly, in both humans and rodents, circulating glycine levels are significantly reduced in obesity, glucose intolerance, type II diabetes and non-alcoholic fatty liver disease. The glycine cleavage system is the predominant glycine degradation pathway in humans. The rate-limiting enzyme of glycine cleavage system is glycine decarboxylase (GLDC), and loss-of-function mutations of GLDC cause hyperglycinemia. Here, we show that GLDC gene expression is upregulated in livers of mouse models of diabetes and diet-induced obesity as well as in the fasted state in normal animals. …

A Review Of Small Molecule Inhibitors And Functional Probes Of Human Cathepsin L, Dibyendu Dana, Sanjai Kumar

Publications and Research

Human cathepsin L belongs to the cathepsin family of proteolytic enzymes with primarily an endopeptidase activity. Although its primary functions were originally thought to be only of a housekeeping enzyme that degraded intracellular and endocytosed proteins in lysosome, numerous recent studies suggest that it plays many critical and specific roles in diverse cellular settings. Not surprisingly, the dysregulated function of cathepsin L has manifested itself in several human diseases, making it an attractive target for drug development. Unfortunately, several redundant and isoform-specific functions have recently emerged, adding complexities to the drug discovery process. To address this, a series of chemical …