Biochemistry Commons^™

Dysregulation Of Micrornas In Blood As Biomarkers For Diagnosing Prostate Cancer, Rhonda W. Daniel

Theses and Dissertations

Prostate cancer is the most common noncutaneous cancer among men, yet current diagnostic methods are insufficient and more reliable diagnostic markers need to be developed. The answer that can bridge this gap and enable more efficient diagnoses may lie in microRNAs. These small, single stranded RNA molecules impact protein expression at the translational level and regulate important cellular pathways. Dysregulation of these small RNA molecules can have tumorigenic effects on cells and lead to many types of cancers.

Currently the Prostate-Stimulating Antigen (PSA) is used as a diagnostic marker for prostate cancer. However, many factors can elevate PSA levels such …

Bacterial Expression Of Plant Pyruvate Kinase, Kristina Fuller

STAR Program Research Presentations

Pyruvate kinases serve an important role in regulating glycolysis pathways. Different pyruvate kinase isozymes can dictate which of several different products will be formed during the final step of glycolysis. Being able to reliably copy active pyruvate kinases (PK) would allow study of the different isozymes, with the goal of eventually creating plants that are more nutritionally beneficial for humans. This study focused on improving the protocol for replicating each of two isolated PK isozymes from the model plant Arabidopsis thaliana. Previous attempts had resulted in the PK denaturing and consequently precipitating out of solution and so we manipulated the …

Primer Efficacy In The Dna Barcoding Of Spiders, Rhennetta Jo Bork

Honors Program Theses

DNA barcoding is the process of amplifying a 650 base pair segment of the sequence of the mitochondrial gene cytochrome c oxidase (COI), and amplifying this gene with a polymerase chain reaction (PCR). It is used to help identify and distinguish animal species and also to help determine genetic differences in species. DNA barcoding can be especially useful when working with spiders since they tend to be very small and hard to distinguish. However, achieving a DNA barcode can be difficult and thus techniques to improve the method of DNA barcoding can be helpful. This research looked into the different …

The Effects Of Hibernation On The Hemostatic Properties Of The American Bullfrog, Rana Catesbeiana, Kiana Cullinan

Honors Program Theses

It is known that hibernating animals display a drastic reduction in metabolic rate, accompanied by reduced heart rate and rate of blood flow through vessels. Sluggish blood flow increases the risk for developing clots, yet it has been observed that hibernators conclusively display elongated clotting times. This observed impairment may be caused by the decrease in body temperature, due to a negative impact on the functioning of the enzymes involved in coagulation. Some hibernating endotherms, or “warm-blooded” animals, employ biological mechanisms as preventative means to prevent clotting during hibernation, such as the down-regulation of certain clotting factors or the production …

Nanoparticle Behavior In Biological Gels And Biofluids: The Impact Of Interactions With Charged Biogels And The Formation Of Protein Coronas On Nanoparticles, Xiaolu Zhang

Theses and Dissertations--Chemistry

With the rapid growth of nanotechnology, situations where nanomaterials will interact with biological systems will unquestionably grow. Therefore, it is increasingly understood that interactions between nanomaterials and biological environments will play an essential role in nanomedicine. Biological polymer networks, including mucus and the extracellular matrix, serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate transport processes through finely tuned particle-network interactions. In chapters 3 and 4, we investigate the role of electrostatics on the basic mechanisms governing the diffusion of charged molecules inside model polymer networks by …

Fors 401: Forensic Biochemistry—A Peer Review Of Teaching Project Inquiry Portfolio, Ashley Hall

UNL Faculty Course Portfolios

Students who participate in active and experiential learning activities develop a better understanding of basic scientific principles and are also more likely to be retained in a STEM discipline. Developing such activities, however, can be difficult. In the present study, we sought to develop classroom activities to engage university students and increase understanding of the theory and practice of forensic science. One common accessory amongst the target audience was the ever-present media, both social and popular (entertainment). In fact, a majority of students report watching at least one of the many popular forensic science shows on TV. Therefore, we hypothesized …

A Comparison Of Whole Body Mercury Concentrations Of Mummichogs (Fundulus Heteroclitus) And Atlantic Silversides (Menidia Menidia), Daniel P. Ferons

Electronic Theses and Dissertations

Few studies have focused on mercury cycling within salt marsh estuaries. Mummichogs (Fundulus heteroclitus) and Atlantic silversides (Menidia menidia) are two species of forage fish that live year round in South Carolina salt marshes. During high tide, mummichogs feed from the water column, sediment, and off of smooth cordgrass while Atlantic silversides prey upon zooplankton. In this study, total and methyl mercury within mummichogs and Atlantic silversides from Dunn Sound, SC were quantified and compared over four seasons throughout 2014. Gut contents were also quantified and compared to determine if there was a dietary impact on the concentrations of total …

Constitutive Activity In Orphan G Protein Coupled Receptors, Adam Lee Martin

Doctoral Dissertations

"The goal of this research was to use a distal signaling pathway analysis to evaluate the extent of agonist independent constitutive signaling among orphan class-A G protein coupled receptors (GPCRs). These receptors translate extracellular signals via conformational change into intracellular activation of different G proteins and subsequent second messenger synthesis. These small molecules regulate cellular biochemistry, eventually leading to nuclear signaling that results in changes in gene expression. Some GPCRs are capable of signaling in the absence of an activating ligand, a phenomenon called constitutive activity that is inhibited via an "inverse-agonist". The use of cAMP dependent Luciferase expression is …

Effects Of N-Acetylcysteine Amide In Preventing/Treating Cataracts, Sri Krishna Yasaswi Maddirala

Doctoral Dissertations

"Cataract, the opacification of an eye lens, is a common pathological abnormality of the lens accounting for approximately 50% of all blindness. The only effective treatment currently available for a cataract is the surgical removal of the affected lens and replacement with an artificial lens for the restoration of vision. Although, cataract surgery is considered to be a very successful procedure in terms of visual outcome, the cost of surgery, need for trained personnel and surgeons, and postsurgical complications, limit the worldwide availability and accessibility of this procedure. Hence, alternative preventive and treatment procedures are worthy of investigation. The lens …

Characterization Of The Sufc Atpase During Fe-S Cluster Assembly By The Suf Pathway In Escherichia Coli, Khaleh Mykel Thomas

Theses and Dissertations

The gram-negative bacterium E. coli encodes the Suf pathway to assemble iron-sulfur (Fe-S) clusters under iron starvation and oxidative stress conditions. The ATPase activity of SufC is critical for in vivo Fe-S cluster assembly by the Suf pathway. SufC shares homology with the nucleotide binding domain (NBD) of ATP-binding cassette (ABC) transporters and belongs to the AAA+ (ATPases Associated with diverse cellular Activities) ATPase superfamily, a family of proteins that utilizes energy from ATP hydrolysis to perform a variety of cellular functions. SufC forms a stable SufBC2D complex with partner proteins SufB and SufD. The SufBC2D complex serves as a …

Study Of Escherichia Coli Adp-Glucose Pyrophosphorylase Catalysis: Investigating Critical Roles Of Conserved Arg32 And Lys42 Residues, Angela Lynn Mahaffey

Dissertations

Carbohydrates have been most notable as energy sources for mammals, bacteria (glycogen) and plants (starch) – and in many other species. As such the biosynthesis of carbohydrates is essential to the sustainability of many forms of life, on earth. Adenosine-‘5-diphosphate glucose pyrophosphate (ADP-Glc pyrophosphorylase; ADP-Glc PPase) is the allosterically controlled “first committed step” in both the biosynthetic pathways of starch (~25% amylose and ~75% amylopectin, in plants and algae) and glycogen (in bacteria), preceding the starch/glycogen synthase reaction. By catalyzing the following reaction, ATP + α –D-Glc-1P ADP-Glc + PPi , ADP-Glc PPase functions as the primary enzyme in the …

Structure And Molecular Mechanism Of A Plp/Gaba Dependent Transcription Regulator Gabr, Rui Wu

Dissertations

GabR is a member of the MocR/GabR subfamily of the GntR family of bacterial transcription regulators. It regulates the metabolism of γ-aminobutyric acid (GABA), an important nitrogen and carbon source in many bacteria. The crystal structures reported here show that this protein has evolved from the fusion of a type I aminotransferase and a winged helix-turn-helix (wHTH) DNA binding protein to form a chimeric protein that adopts a dimeric head-to-tail configuration. The pyridoxal 5′-phosphate (PLP)-binding regulatory domain of GabR is therefore an example of a coenzyme playing a role in transcription regulation rather than in enzymatic catalysis. Our structural and …

The Role Of Srsf3 In Control Of Alternative Splicing Of Cpeb2 In Triple Negative Breast Cancer, Brian P. Griffin

Theses and Dissertations

In the presented study, we identified that SRSF3 controls the alternative splicing of CPEB2 and consequently promotes a metastatic phenotype in triple negative breast cancer (TNBC). TNBC causes thousands of deaths annually, frequently due to a lack of effective treatments and a high rate of metastasis in patients. Alternative splicing has been found to be dysregulated in numerous cancers, while splicing factors such as SRSF3 are variably expressed. In this study we performed a siRNA panel to screen potential splicing factors, then used specific siRNA to study the effect of its knockdown on cellular function. These results showed that SRSF3 …

Pemetrexed, A Modulator Of Amp-Activated Kinase Signaling And An Inhibitor Of Wild Type And Mutant P53, Stuti Agarwal

Theses and Dissertations

New drug discoveries and new approaches towards diagnosis and treatment have improved cancer therapeutics remarkably. One of the most influential and effective discoveries in the field of cancer therapeutics was antimetabolites, such as the antifolates. The interest in antifolates increased as some of the antifolates showed responses in cancers, such as mesothelioma, leukemia, and breast cancers. When pemetrexed (PTX) was discovered, our laboratory had established that the primary mechanism of action of pemetrexed is to inhibit thymidylate 22 synthase (TS) (E. Taylor et al., 1992). Preclinical studies have shown that PTX has a broad range of antitumor activity in human …

Interaction Between Atm Kinase And P53 In Determining Glioma Radiosensitivity, Syed F. Ahmad

Theses and Dissertations

Glioblastoma multiforme (GBM) is the most common primary brain tumor. Studies have shown that targeting the DNA damage response can sensitize cancer cells to DNA damaging agents. Ataxia telangiectasia mutated (ATM) is involved in signaling DNA double strand breaks. Our group has previously shown that ATM inhibitors (ATMi) sensitize GBM cells and tumors to ionizing radiation. This effect is greater when the tumor suppressor p53 is mutated.

The goals of this work include validation of a new ATM inhibitor, AZ32, and elucidation of how ATMi and p53 status interact to promote cell death after radiation. We propose that ATMi and …

Nitric Oxide Synthase Activity And Its Modulation In The Treatment Of Colorectal Cancer, Asim Alam

Theses and Dissertations

The American Cancer Society estimates more than 141,000 new cases of and about 50,000 deaths from colorectal cancer every year. Treatment options include surgery, radiation therapy and targeted therapies such as anti-angiogenics. However, no therapies address the key driving factor of colorectal cancer: inflammation. It is well known that chronic inflammatory conditions such as Crohn’s Disease, ulcerative colitis, diabetes, obesity and cigarette smoking all elevate the risk of developing colorectal cancer. One of the hallmarks of chronic inflammation is the elevated levels of reactive oxygen/nitrogen species (ROS/RNS). A primary source of these ROS/RNS is uncoupled Nitric Oxide Synthase (NOS). Under …

Biophysical Characterization Of The Folding, Membrane Topology And Ion Transport Activity Of Ucp2 Using Selective Trp Mutants, Tyler C. Auld

Theses and Dissertations (Comprehensive)

Human Uncoupling Protein 2 (hUCP2) is one of five known human UCPs which are found in the inner mitochondrial membrane and have been shown to facilitate the translocation of protons from the intermembrane space to the mitochondrial matrix. The detailed physiological role of UCP2 proton transport, the mechanism by which it mediates this proton transport, as well as its structure has also yet to be elucidated. In order to help determine the topology of UCP2 embedded in the membrane as well as its mechanism of proton transport, the intrinsic fluorescence properties of the two tryptophan residues (Trp) present in its …

Regulation And Targeting Of The Fancd2 Activation In Dna Repair, Valentina Celeste Caceres

USF Tampa Graduate Theses and Dissertations

Fanconi anemia (FA) is a genome instability syndrome that is clinically manifested by bone marrow failure, congenital defects, and elevated cancer susceptibility. The FA pathway is known to regulate the repair of DNA interstrand crosslinks in part through DNA homologous recombination (HR) repair. Up to today 16 FA proteins have been discovered that may participate in the common pathway. Cells that have mutations in the FA genes are hypersensitive to DNA damaging agents and display chromosome instability. A key regulatory event in the FA pathway is monoubiquitination of FANCD2-FANCI heterodimer that is mediated by a multi-component E3 ubiquitin ligase complex …

Biosynthesis Of Long-Chain Fatty Acid Amides, Kristen A. Jeffries

USF Tampa Graduate Theses and Dissertations

The vast variety of long-chain fatty acid amides identified in biological systems is intriguing. The general structure of a fatty acid amide is R-CO-NH-X, where R is an alkyl group and X is derived from an immense variety of biogenic amines. Although structurally simple, the bioactivities of these molecules as signaling lipids are very diverse and have just recently begun to emerge in the literature. Interest in the long-chain fatty acid amides dramatically increased following the identification and characterization of one specific N-acylethanolamine, N-arachidonoylethanolamine (anandamide), as the endogenous ligand for the cannabinoid receptors in the mammalian brain. Since …

Characterization Of The Trans-Plasma Membrane Electron Transport System In The Myelin Membrane, Afshan Sohail

Theses and Dissertations (Comprehensive)

Myelination is the key feature of evolution in the nervous system of vertebrates. Myelin is the protrusion of glial cells. More specifically, "oligodendrocytes" in the central nervous system (CNS), and "Schwann" cells in the peripheral nervous system (PNS) form myelin membranes. Myelin remarkably, enhances the propagation of nerve impulses. However, myelin restricts the access of extracellular metabolites to the axons. A pathology called "demyelination" is associated with myelin. The myelin sheath is not only an insulator, but it is itself metabolically active. In this study it is hypothesized that the ratio of NAD(P)⁺/NAD(P)H and the glycolytic pathway of …