Biochemistry Commons^™

The Effects Of Jasmonic Acid And Chemicals In The Ja Pathway On The Defense Systems And Gene Expression In Moss, Physcomitrella Patens And Amblystegium Serpens, Allison Shanks

Undergraduate Honors Thesis Collection

Systemic acquired resistance (SAR) is a defense system used by plants that results in increased resistance to future pathogen infection following an initial pathogen exposure. SAR in vascular plants has been well documented; however, a similar defense system has only recently been documented in non-vascular plants. It is believed that chemicals in the jasmonic acid (JA) pathway are able to activate the SAR response in vascular plants. The non-vascular plant, Amb/ystegium serpens, will be used as a model to test if SAR is triggered by JA and two other molecules in the JA pathway, 12-oxo-phytodieonic acid, and methyl jasmonate. To …

2-Acylamido Analogues Of N-Acetylglucosamine Prime Formation Of Chitin Oligosaccharides By Yeast Chitin Synthase 2, Jacob Gyore, Archana Parameswar, Carleigh Hebbard, Younghoon Oh, Erfei Bi, Alexei Demchenko, Neil Price, Peter Orlean

Chemistry & Biochemistry Faculty Works

Chitin, a homopolymer of β1,4-linked N-acetylglucosamine (GlcNAc) residues, is a key component of the cell walls of fungi and the exoskeletons of arthropods. Chitin synthases transfer GlcNAc from UDP-GlcNAc to preexisting chitin chains in reactions that are typically stimulated by free GlcNAc. The effect of GlcNAc was probed by using a yeast strain expressing a single chitin synthase, Chs2, by examining formation of chitin oligosaccharides (COs) and insoluble chitin, and by replacing GlcNAc with 2-acylamido analogues of GlcNAc. Synthesis of COs was strongly dependent on inclusion of GlcNAc in chitin synthase incubations, and N,N′-diacetylchitobiose (GlcNAc2) was the major reaction product. …

Defining The Sites Of Interaction Of The Fancd2, Fance, And Fancl Proteins, Joseph Mcclanaghan

Senior Honors Projects

Fanconi anemia (FA) is a rare genetic disease characterized by congenital defects, bone marrow failure and increased cancer susceptibility. FA is caused by mutations in any one of 16 genes. These genes encode for proteins that function in the FA-BRCA pathway to repair damaged DNA. Because of its important r­­­ole in DNA repair, this pathway is considered a major cellular tumor suppressor pathway, i.e. is critical for the prevention of cancer. Underscoring this fact, several of the FA genes - including BRCA2, BRIP1, PALB2, and RAD51C - are bona fide breast and ovarian cancer susceptibility genes.

My …

Characterization Of Ftsa-Ftsn Interaction During Escherichia Coli Cell Division, [email protected] K. Busiek

Dissertations and Theses (Open Access)

Division of a bacterial cell into two equal daughter cells requires precise assembly and constriction of the division machinery, or divisome. The Escherichia coli divisome includes nearly a dozen essential cell division proteins that assemble at midcell between segregating sister chromosomes. FtsZ, a homolog of eukaryotic tubulin, is the first essential cell division protein to localize at midcell where it polymerizes into a ring-shaped scaffold (Z ring). Establishment of the Z ring is required for recruitment of downstream cell division proteins including FtsA, a cytoplasmic protein that tethers the Z ring to the inner membrane. Following localization of FtsA and …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

All Faculty Scholarship for the College of the Sciences

Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Structural Insights Into The Interaction Between A Potent Anti-Inflammatory Protein, Viral Cc Chemokine Inhibitor (Vcci), And The Human Cc Chemokine, Eotaxin-1, Nai-Wei Kuo, Yong-Guang Gao, Megan Schill, Nancy Isern, Cynthia Dupureur, Patricia Liwang

Chemistry & Biochemistry Faculty Works

Chemokines play important roles in the immune system, not only recruiting leukocytes to the site of infection and inflammation but also guiding cell homing and cell development. The soluble poxvirus-encoded protein viral CC chemokine inhibitor (vCCI), a CC chemokine inhibitor, can bind to human CC chemokines tightly to impair the host immune defense. This protein has no known homologs in eukaryotes and may represent a potent method to stop inflammation. Previously, our structure of the vCCI·MIP-1β (macrophage inflammatory protein-1β) complex indicated that vCCI uses negatively charged residues in β-sheet II to interact with positively charged residues in the MIP-1β N …

Lipid Dependence In Ras-Driven Tumors, Darin Salloum

Dissertations, Theses, and Capstone Projects

Over past decade, metabolic alterations in cancer cells have received a substantial amount of interest. It had been established that cancer cells undergo a significant amount of metabolic alterations, and some of these alterations are similar to those in normal highly proliferative cells. However, it is becoming more apparent that many of the metabolic alterations are specific to particular oncogenic signaling pathways. Although altered metabolic machinery makes cancer cells more efficient at promoting growth when nutrients are supplied at the sufficient amounts, the dependency of cancer cells on particular metabolic reprogramming deems cancer cells susceptible to disruptions within metabolic network. …

Metabolic Checkpoints In Cancer Cell Cycle, Mahesh Saqcena

Dissertations, Theses, and Capstone Projects

Growth factors (GFs) as well as nutrient sufficiency regulate cell division in metazoans. The vast majority of mutations that contribute to cancer are in genes that regulate progression through the G1 phase of the cell cycle. A key regulatory site in G1 is the growth factor-dependent Restriction Point (R), where cells get permissive signals to divide. In the absence of GF instructions, cells enter the quiescent G0 state. Despite fundamental differences between GF signaling and nutrient sensing, they both have been confusingly referred to as R and therefore by definition considered to be a singular event in G1. Autonomy from …

Identification And Characterization Of Protein Phopshatases Regulating The Sma/Mab Pathway In C. Elegans, Sheng Xiong

Dissertations, Theses, and Capstone Projects

TGF-beta signaling is a conserved signaling pathway among eukaryotes, which controls various normal cellular responses from cell proliferation to cell death. The mutations in its components are found in developmental disorders and cancer. Therefore, this signaling pathway is extensively investigated so that new therapeutic targets could be discovered and novel drugs could be developed. Previous studies suggested the involvement of phosphatases in regulation of TGF-beta signaling, but these studies were performed in cell culture rather than intact organisms. C. elegans is a tractable organism in which to study signaling in vivo. In C. elegans, growth is controled by a conserved …

Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, Juan Pan

Theses and Dissertations--Plant Pathology

Loline alkaloids, found in many grass-Epichloë symbiota, are toxic or feeding deterrent to invertebrates. The loline alkaloids all share a saturated pyrrolizidine ring with a 1-amine group and an ether bridge linking C2 and C7. The steps in biosynthesis of loline alkaloids are catalyzed by enzymes encoded by a gene cluster, designated LOL, in the Epichloë genome. This dissertation addresses the enzymatic, genetic and evolutionary basis for diversification of these alkaloids, focusing on ether bridge formation and the subsequent modifications of the 1-amine to form different loline alkaloids.

Through gene complementation of a natural lolO mutant and comparison …

Disassembly Of Actin Structures By Nanosecond Pulsed Electric Field Is A Downstream Effect Of Cell Swelling, Andrei G. Pakhomov, Shu Xiao, Olga N. Pakhomova, Iurii Semenov, Marjorie A. Kuipers, Bennett L. Ibey

Bioelectrics Publications

Disruption of the actin cytoskeleton structures was reported as one of the characteristic effects of nanosecond-duration pulsed electric field (nsPEF) in both mammalian and plant cells. We utilized CHO cells that expressed the monomeric fluorescent protein (mApple) tagged to actin to test if nsPEF modifies the cell actin directly or as a consequence of cell membrane permeabilization. A train of four 600-ns pulses at 19.2 kV/cm (2 Hz) caused immediate cell membrane poration manifested by YO-PRO-1 dye uptake, gradual cell rounding and swelling. Concurrently, bright actin features were replaced by dimmer and uniform fluorescence of diffuse actin. To block the …

The Role Of Angiotensinogen In Atherosclerosis And Obesity, Congqing Wu

Theses and Dissertations--Nutritional Sciences

Angiotensinogen is the only known precursor in the renin-angiotensin system, a hormonal system best known as an essential regulator of blood pressure and fluid homeostasis. Angiotensinogen is sequentially cleaved by renin and angiotensin- converting enzyme to generate angiotensin II. As the major effector peptide, angiotensin II mainly function through angiotensin type 1 receptor.

Angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, and more recently renin inhibitors are widely known as the 3 classic renin-angiotensin system inhibitory drugs against hypertension and atherosclerosis. Here, we developed an array of regents to explore the effects of angiotensinogen inhibition. First, we demonstrated that genetic deficiency of …

Ph Regulation And The Assessment Of Renal Injury Biomarkers In A Warm Perfusion Renal Allograft Preservation System, Aaron Meyer

Legacy Theses & Dissertations (2009 - 2024)

A shortage of viable kidneys available for transplantation exists today, as the number of individuals waiting for a kidney transplant continues to grow while the number of kidneys available each year for transplantation has remained stagnant. The development of technology that will allow for transplantation of organs that currently may be considered too damaged for transplant will provide access to a large number of donors who have experienced traumatic injury deaths resulting in loss of cardiac function. These potential donors account for the majority of all traumatic injury deaths in intensive care units, however their organs have experienced a degree …

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 …

Molecular Mechanisms Of Neuropilin-Ligand Binding, Matthew W. Parker

Theses and Dissertations--Molecular and Cellular Biochemistry

Neuropilin (Nrp) is an essential cell surface receptor with dual functionality in the cardiovascular and nervous systems. The first identified Nrp-ligand family was the Semaphorin-3 (Sema3) family of axon repulsion molecules. Subsequently, Nrp was found to serve as a receptor for the vascular endothelial growth factor (VEGF) family of pro-angiogenic cytokines. In addition to its physiological role, VEGF signaling via Nrp directly contributes to cancer stemness, growth, and metastasis. Thus, the Nrp/VEGF signaling axis is a promising anti-cancer therapeutic target. Interestingly, it has recently been shown that Sema3 and VEGF are functionally opposed to one another, with Sema3 possessing potent …

Bipolar Nanosecond Electric Pulses Are Less Efficient At Electropermeabilization And Killing Cells Than Monopolar Pulses, Bennett L. Ibey, Olga N. Pakhomova, Caleb C. Roth, Shu Xiao, Karl Schoenbach, Andrei G. Pakhomov

Bioelectrics Publications

Multiple studies have shown that bipolar (BP) electric pulses in the microsecond range are more effective at permeabilizing cells while maintaining similar cell survival rates as compared to monopolar (MP) pulse equivalents. In this paper, we investigated whether the same advantage existed for BP nanosecond-pulsed electric fields (nsPEF) as compared to MP nsPEF. To study permeabilization effectiveness, MP or BP pulses were delivered to single Chinese hamster ovary (CHO) cells and the response of three dyes, Calcium Green-1, propidium iodide (PI), and FM1-43, was measured by confocal microscopy. Results show that BP pulses were less effective at increasing intracellular calcium …

Bioc 435: Advanced Topics In Biochemistry—A Peer Review Of Teaching Project Benchmark Portfolio, Edward N. Harris

UNL Faculty Course Portfolios

BIOC 435 or Advanced Topics in Biochemistry is an ACE 10 (Achievement centered education)course for students in their senior year. This is a capstone course for Biochemistry majors and is the last of several biochemistry courses that they will take in their undergraduate enrollment. The course is also open to non-majors in a related science such as Biology and Biological Sciences, although these students typically do not do as well as the majors. Students who take this course should be well-prepared in the basic concepts of biochemistry with regards to nucleic acids and proteins as well as some familiarity with …

A Summary Of Three Antibiotic Resistant Bacteria Studies Of Plaster Creek, Yeaeun Lee, David P. Warners

Faculty and Professional Research

No abstract provided.

Nine Year Assessment Of Soil Treatment On Aguacatillo (Nectandontisii And Ocotea Austinii, Lauraceae) Seedling Success In The Restoration Of A Costa Rican Cloud Forestra Cufo, Sheila Devries, David Warners

Faculty and Professional Research

We tracked seedling growth of two species of aguacatillo (Nectandra cufodontisii (O. C. Schmidt) C. K. Allen and Ocotea austinii C. K. Allen) that were planted into an early successional cloud forest hillside in San Gerardo de Dota, Costa Rica over nine years. Seedlings were collected from underneath nearby mother trees and transplanted into one of three soil treatments: indigenous soil; a 50:50 mixture of horse manure and indigenous soil; and a 50:50 mixture of kitchen compost and indigenous soil. After seedlings were transplanted they were measured and each specific location was evaluated for light exposure. Two months later seedlings …

Distribution And Elimination Of 3-Trifluoromethyl-4-Nitrophenol (Tfm) By Sea Lamprey (Petromyzon Marinus) And Non-Target, Rainbow Trout (Oncorhynchus Mykiss) And Lake Sturgeon (Acipenser Fulvescens), Michael W. Le Clair

Theses and Dissertations (Comprehensive)

The pesticide, 3-trifluoromethyl-4-nitrophenol (TFM), has been highly successful in the control of sea lamprey (Petromyzon marinus) populations in the Great Lakes. Treatments with TFM involve applying it to streams, where it targets larval sea lamprey which live burrowed in the stream substrate. While the toxic mechanism of TFM has been elucidated, and its effects on sea lamprey described, its effects on non-target fish species such as rainbow trout (Oncorhynchus mykiss) and lake sturgeon (Acipenser fulvescens) are not as well understood. The present work demonstrated that rainbow trout show a great capacity to detoxify the lampricide using glucuronidation, when exposed to …

The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, Joesph F. Cannon, Nicholas A. Thurn, Paul E. Richardson

Journal of the South Carolina Academy of Science

Bacteriophages are used as indicators of pathogenic bacteria in drinking, and wastewaters. They also show potential in limiting aquatic bacterial populations through their lytic properties. The effect of different water characteristics (salinity, pH, dissolved oxygen, and temperature) on the sensitivity of the PCR identification of virus particles were analyzed to determine at what levels bacteriophage can be detected in environmental samples. Results from this preliminary study indicate that a PCR bacteriophage detection technique has potential as a relatively efficient and economical indicator of coliform contamination in multiple aquatic environments. While further evaluation is needed, the protocol appears to function in …

Identification Of Disulfide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1, Morgan E. Roberts, Jacquelyn P. Crail, Megan M. Laffoon, William G. Fernandez, Michael A. Menze, Mary E. Konkle

Faculty Research & Creative Activity

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

Identification Of Disufide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1, Morgan E. Roberts, Jacquelyn P. Crail, Megan M. Laffoon, William G. Fernandez, Michael A. Menze, Mary E. Konkle

Faculty Research & Creative Activity

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

Mechanisms For Regulation Of Plant Kinesins, Anindya Ganguly, Ram Dixit

Biology Faculty Research

Throughout the eukaryotic world, kinesins serve as molecular motors for the directional transport of cellular cargo along microtubule tracks. Plants contain a large number of kinesins that have conserved as well as specialized functions. These functions depend on mechanisms that regulate when, where and what kinesins transport. In this review, we highlight recent studies that have revealed conserved modes of regulation between plant kinesins and their non-photosynthetic counterparts. These findings lay the groundwork for understanding how plant kinesins are differentially engaged in various cellular processes that underlie plant growth and development.

The Staphylococcus Pseudintermedius Adhesin Spsd Contains A Central Fibronectin-Binding Domain, Andrea S. Bordt

Dissertations and Theses (Open Access)

Staphylococcus pseudintermedius is a Gram-positive bacterium significant because of its ability to cause costly and difficult to treat veterinary infections worldwide. It exhibits several similarities to Staphylococcus aureus, however, very little is known about its surface adhesins. Surface adhesins in S. aureus are significant contributors to pathogenesis. S. pseudintermedius encodes the surface protein SpsD, which contains characteristics of the microbial surface components recognizing adhesive matrix molecules family and confers attachment of the heterologous host Lactococcus lactis to fibronectin. This work has identified a centrally-located fibronectin binding domain in SpsD which binds the 30 kDa N-terminal domain of fibronectin with …

Identification Of Disufide Bond Formation Between Mitoneet And Glutamate Dehydrogenase 1., Morgan Roberts, Jacquelyn Crail, Megan Laffoon, William Fernandez, Michael Menze, Mary Konkle

Faculty and Staff Scholarship

MitoNEET is a protein that was identified as a drug target for diabetes, but its cellular function as well as its role in diabetes remains elusive. Protein pull-down experiments identified glutamate dehydrogenase 1 (GDH1) as a potential binding partner. GDH1 is a key metabolic enzyme with emerging roles in insulin regulation. MitoNEET forms a covalent complex with GDH1 through disulfide bond formation and acts as an activator. Proteomic analysis identified the specific cysteine residues that participate in the disulfide bond. This is the first report that effectively links mitoNEET to activation of the insulin regulator GDH1.

Mutational Analysis Of The Rotavirus Nsp4 Enterotoxic Domain That Binds To Caveolin-1, Judith M. Ball, Megan E. Schroeder, Cecelia V. Williams, Friedhelm Schroeder, Rebecca D. Parr

Faculty Publications

Background: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction.

Methods: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed …

Microtubule Severing At Crossover Sites By Katanin Generates Ordered Cortical Microtubule Arrays In Arabidopsis, Quan Zhang, Erica Fishel, Tyler Bertroche, Ram Dixit

Biology Faculty Research

Highlights

• Severing primarily depolymerizes the overlying CMT at crossover sites
• Severing probability increases nonlinearly with crossover time
• Katanin localizes to crossover sites and is required for severing
• Loss of katanin activity prevents the formation of coaligned CMT arrays

Summary
The noncentrosomal cortical microtubules (CMTs) of land plants form highly ordered parallel arrays that mediate cell morphogenesis by orienting cellulose deposition [1, 2 and 3]. Since new CMTs initiate from dispersed cortical sites at random orientations [4], parallel array organization is hypothesized to require selective pruning of CMTs that are not in the dominant orientation. Severing of CMTs at crossover sites …

Identification Of Set1 Target Genes, William Beyer, Scott D. Briggs

The Summer Undergraduate Research Fellowship (SURF) Symposium

The Set1 complex, a histone methyltransferase complex found in S. cerevisiae (budding yeast), is the only histone methyltransferase responsible for catalyzing methylation of histone H3 at Lysine 4. It possesses homologues in other species, humans included. While yeast only have the Set1 complex, the human homologues of the yeast Set1 complex include mixed-lineage leukemia family (MLL1-4), Set1 A, Set1 B, among others. MLL1-4 has been shown to play a role in transcription, cell type specification, and the development of leukemia. One application of characterizing the role of a protein is that the information gained can provide insight into the function …

Characterization Of Caxck31, A Bacterial Calcium/Proton Antiporter, Marc Robert Ridilla

Open Access Dissertations

To better understand a class of transporters known as Calcium/Cation Antiporters (CaCAs), the bacterial calcium/proton antiporter CAXCK31 was purified and characterized. New methods were developed for its heterologous overexpression and purification. These methods help to define stress responses to toxic membrane overproduction in E. coli and may be broadly applicable to studies of membrane proteins. The results from a variety of biochemical and biophysical experiments demonstrated that CAXCK31 exists as a dimer in the membrane and can be purified in the dimeric state. The methods used include chemical cross-linking, FRET, and SEC-MALS. In addition, various transport properties of CAXCK31, including …