Molecular Biology Commons^™

Interaction Of Rhizobium Sp. Strain Irbg74 With A Legume (Sesbania Cannabina) And A Cereal (Oryza Sativa), Shubhajit Mitra

Theses and Dissertations

Rhizobium sp. IRBG74 (IRBG74) develops a classical nitrogen-fixing symbiosis with the legume Sesbania cannabina and also promotes the growth of rice (Oryza sativa), but not much is known about the rhizobial determinants important for these interactions. We hypothesize that Rhizobium sp. IRBG74 utilizes similar mechanisms to endophytically colonize both legume and cereal hosts. In this study, we analyzed the colonization of rice and S. cannabina using a strain of IRBG74 marked with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). IRBG74 infected both of the host plants through crack entry under submerged conditions, but showed root hair mediated infection under aerobic …

Gene Regulatory Pathways Driving Central Nervous System Regeneration In Zebrafish, Ishwariya Venkatesh

Theses and Dissertations

Damage to the central nervous system (CNS) circuitry of adult mammals results in permanent disability. In contrast, the ability to regenerate damaged CNS nerves and achieve functional recovery occurs naturally in fish. The ability of fish to successfully regrow damaged CNS nerves is in part a consequence of their ability to re-express key neuronal growth-associated genes/proteins in response to CNS injury. On such protein is Growth-Associated Protein-43 (Gap43), a protein which is highly enriched in axonal growth cones during CNS development and regeneration. Experiments conducted in mammals have demonstrated that ectopic expression of GAP-43 improves axonal re-growth after injury. Using …

Characterization Of A Putative Phospholipase D ´ Like Gene As A Lipid Signaling Modulator And Its Role In Salicylic Acid Mediated Defense Pathway In Nicotiana Tabacum, Phillip T. Dean

Electronic Theses and Dissertations

Plants are in a perpetual evolutionary arms race with a wide range of pathogens. Their sessile nature has led plants to evolve defense mechanisms that can quickly recognize a unique stressor and deploy a resistance tailored for a specific attack. The salicylic acid (SA) mediated defense pathway has been shown to be one of the major defense tactics plants can initiate to defend themselves against microbial pathogens. Following a pathogen attack high levels of methyl salicylate (MeSA) are produced that can be converted to SA by the enzyme salicylic acid binding protein 2 (SABP2). A yeast two-hybrid screening was performed …

Ribosomes Left In The Dust: Diverse Strategies For Peptide-Mediated Translation Stalling, Benjamin H. Hudson, Hani S. Zaher

Biology Faculty Publications & Presentations

In two recent papers, Arenz et al. (2014a) and Bischoff et al. (2014) provide structural insights into drug-induced, peptide-mediated stalling of the ribosome.

Cross-Disciplinary Sciences At Gettysburg College: Second Annual Poster Presentation, X-Sig

Student Publications

This booklet includes Biology student presentations by: Taylor Bury, Abigail Dworkin-Brodsky, Mary Pearce, Jasper Leavitt, Morgan Panzer, Ellen Petley, Kalli Qutub, Taylor Randell, Samantha Eck, Lana McDowell, Jenn Soroka, Celina Harris, Natalie Tanke, Alexandra Turano, and Caroline Garliss.

This booklet includes Biochemistry & Molecular Biology student presentations by: Matthew Dunworth, Andrew Sydenstricker, Brianne Tomko, Albert Vill, Warren Campbell, David Van Doren, Kevin Mrugalski, Stacey Heaver, Alecia Achimovich, and Katherine Boas.

This booklet includes Chemistry student presentations by: Kristen Baker, Laura Lee, Kathryn Fodale, Daniel Ruff, Michael Counihan, Ida DiMucci, Joshua Sgroi, Celina Harris, and Natalie Tanke.

This booklet include Health …

Host Cell Death In Legionella Pneumophila Pathogenesis And Immunity, Wenhan Zhu

Open Access Dissertations

Legionella pneumophila is an intracellular pathogen that causes a severe, atypical pneumonia termed Legionnaires' disease. Upon entering the host cell, L. pneumophila resides in a membrane-bound vacuole, in which the bacterium evades lysosomal fusion and replicates. The establishment of the vacuole requires the Dot/Icm (Defect in organelle trafficking/ intracellular multiplication) transport system, which translocates a large number of substrates into host cells to re-orchestrate various cellular processes, such as intracellular trafficking, protein synthesis and host cell death pathways. Therefore, a key step in understanding the biology of Legionella is to dissect the mechanisms of action of the Dot/Icm substrates. By …

Associated Behavioral, Genetic, And Gene Expression Variation With Alternative Life History Tactics In Salmonid Fishes, Ashley Chin-Baarstad

Open Access Dissertations

Individual differences in behavior can have potential fitness consequences and often reflect underlying genetic variation. My research focuses on three objectives related to individual level variation: 1) evaluating the innate behavioral variation within and between individuals, families, and progeny of different life-history types across time; 2) testing for differences in gene expression within the brain associated with this behavioral variation; and 3) using genetic polymorphisms to test for associations with ecotype, as well as population structure, in polymorphic populations. First, we evaluated the variation in a suite of ecologically relevant behaviors across time in juvenile progeny produced from crosses within …

Dietary Carbohydrates Influence The Structure And Function Of The Intestinal Alpha-Glucosidases, Mohammad Chegeni

Open Access Dissertations

As the primary products of starch digestion by pancreatic α-amylase, maltooligosaccharides (including maltose) are the main substrates for the α-glucosidases at the intestinal brush border. Here, maltose was shown to induce the formation of a higher molecular weight (HMW) sucrase-isomaltase (SI) species in Caco-2 cells that sorts more quickly to the enterocyte surface to act as a digestive enzyme. As this finding suggested a maltose sensing ability of small intestinal enterocytes, molecular mechanisms associated with the maturation and trafficking of HMW SI were further investigated. A pulse-chase experiment using [ ³⁵S]-methionine revealed a higher rate of early trafficking and …

Determining The Binding Between Saga Subunits And Spliceosomal Components, Peyton J. Spreacker, Rachel L. Stegeman, Vikki M. Weake

The Summer Undergraduate Research Fellowship (SURF) Symposium

Proper gene regulation is vital to the health and development of an organism. Determining the relationship between splicing, transcription, and chromatin structure is vital for understanding gene regulation as a whole. There have been previous studies linking these elements pairwise; however, no evidence exists for a direct link between all three. Recent data shows that splicing components of the U2 small nuclear ribonucleic protein (snRNP) co-purify with Spt-Ada-Gcn5-acetyltransferase (SAGA), a highly conserved transcriptional co-activator and chromatin modifier. We hypothesize that SAGA binds with splicing components through a multi-protein binding surface with certain core components based on preliminary yeast two-hybrid data. …

Characterizing Populations Of Non-Coding Rnas In Karenia Brevis At Different Times Of The Diel Cycle, Scott Boyd Anglin

Master's Theses

Karenia brevis is a mixotrophic, marine dinoflagellate found in the Gulf of Mexico that generates periodic, if not annual, harmful algal blooms (also known as “red tides”) in certain coastal areas. In an effort to better understand the biology of this organism, a functional genomics project has been initiated. As part of that project, it has been determined that a significant number of natural antisense transcripts (NATs) as well as double-stranded RNA (dsRNA) molecules exist within the transcriptome of K. brevis. I hypothesize that the non-coding NATs, similar to microRNAs (miRNAs) in other organisms play a role in regulating …

Key Residues Of Human Cytoplasmic Protein Tyrosine Phosphatase-A And -B For Substrate Binding And Specificity, Byunghyun Park

Open Access Theses

Reversible tyrosine phosphorylation plays an important role in signaling pathways that are essential for regulating cellular growth, differentiation and metabolism. Moreover, several human diseases such as diabetes, obesity and cancers are associated with the deregulation of protein tyrosine phosphatases (PTPs). Several studies provide evidence that PTPs not only contribute to cellular differentiation, but over-expression of these molecules also leads to transformation of non-transfomed cells as well. Based on these results, designing specific PTP inhibitors may ultimately function as potential therapeutic agents to treat various diseases including cancer, diabetes, and autoimmune diseases. EphA2 is a receptor tyrosine kinase which is hypo-phosphorylated …

Rna Detection Technology For Applications In Marine Science: Microbes To Fish, Robert Michael Ulrich

USF Tampa Graduate Theses and Dissertations

The accurate identification of taxa from mixed assemblages using genetic analysis remains an important field of molecular biology research. The common principle behind the development of numerous documented genetic detection technologies is to exploit specific nucleotide sequences inherent to each taxon. This body of work focuses on practical applications of real-time nucleic acid sequence-based amplification (RT-NASBA) in marine science, and is presented in four case studies. Each study represents novel work in the genetic identification of respective taxa of interest using RT-NASBA. Two case studies documented the development of an assay targeting mitochondrial 16S rRNA to discern legally salable grouper …

Characterizing The Response Of Multidrug-Resistant Klebsiella Pneumoniae Species To The Application Of A Phage Cocktail, Steven Liu

Symposium

Project Summary: The application of bacteriophages to treat bacterial infections is known as phage therapy, which takes advantage of bacteriophage’s natural ability to infect and lyse bacterial hosts. Phages have been shaped by billions of years of evolution to be highly specialized deliverers of bactericidal agents to the cytoplasm of their target bacteria. Ever since discovery of bacteriophages in 1915, phage therapy was recognized as a potentially powerful tool for eliminating bacterial infections. The effectiveness of phage therapy can be increased by creating a mixture of multiple phages to target a wider variety of bacterial strains. Furthermore, phage therapy has …

Investigation Of Fshr-L Protein Function In Regulating Synaptic Transmission At The Neuromuscular Junction In C. Elegans, Julie Christine Kolnik

Undergraduate Honors Thesis Collection

euronal communication (synaptic transmission) is critical for nervous system function. This communication occurs at specialized junctions called synapses where chemical neurotransmitters signal from presynaptic to postsynaptic cells. Additional signaling via neuropeptide activated G protein-coupled receptors (GPCRs) fine-tunes synaptic communication. GPCRs are a large family of transmembrane receptor proteins that bind extracellular neurotransmitters and neuropeptides to activate intracellular signaling pathways. My project investigated the function of FSHR-l, a GPCR and potential neuropeptide receptor, in regulating synaptic transmission at the neuromuscular junction (NMJ) in Caenorhabditis elegans roundworms, which share conservation of nervous system structure and function with humans. Worms lacking the fshr-I …

The Mechanism Of Small Rna Biogenesis, Degradation, And Function In Arabidopsis, Meng Xie

School of Biological Sciences: Dissertations, Theses, and Student Research

Eukaryotic small RNAs play important roles in many biological processes through sequence-specific RNA silencing. In plants, there are mainly two small RNAs triggering gene silencing: microRNAs (miRNAs) and small interfering RNAs (siRNAs). The biogenesis and precise regulation of small RNA abundance are crucial for plant growth, development, genomic stability, and the resistance to both abiotic and biotic stresses. In this study, we used Arabidopsis thaliana, the model plant, to study the mechanism of RNA-directed DNA methylation (RdDM), in which siRNAs can trigger DNA methylation and gene silencing. In addition, we investigated the mechanism of miRNA biogenesis and degradation. For …

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. …

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

Alexei Demchenko

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, Kimberly.Busiek@Gmail.Com K. Busiek

Dissertations & 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 …

Sirna Targeting Of Thymidylate Synthase, Thymidine Kinase 1 And Thymidine Kinase 2 As An Anticancer Therapy: A Combinatorial Rnai Approach, Christine Di Cresce

Electronic Thesis and Dissertation Repository

Thymidylate synthase (TS) is the only de novo source of thymidylate (dTMP) for DNA synthesis and repair. Drugs targeting TS protein are a mainstay in cancer treatment but off-target effects and toxicity limit their use. Cytosolic thymidine kinase (TK1) and mitochondrial thymidine kinase (TK2) contribute to an alternative dTMP-producing pathway, by salvaging thymidine from the tumour milieu, and may modulate resistance to TS-targeting drugs. We have previously shown that TS antisense molecules (oligodeoxynucleotides, ODNs, and small interfering siRNA, siRNA) sensitize tumour cells, both in vitro and in vivo, to TS targeting drugs. As both TS and TKs contribute to cellular …

Investigating Mitochondrial Protein Trafficking In Crithidia Fasciculata, Jeremiah Arnold

Georgia State Undergraduate Research Conference

No abstract provided.

Section Abstracts: Biology With Microbiology And Molecular Biology

Virginia Journal of Science

Abstracts of the Biology with Microbiology and Molecular Biology Section for the 92nd Annual Meeting of the Virginia Academy of Science, May 13-15, 2014, Virginia Commonwealth University, Richmond, Virginia

Carbon Source-Dependent Alteration Of Puf3p Activity Mediates Rapid Changes In The Stabilities Of Mrnas Involved In Mitochondrial Function, Melanie Miller, Joseph Russo, Anthony Fischer, Florencia Leban, Wendy Olivas

Biology Department Faculty Works

The Puf family of RNA-binding proteins regulates gene expression primarily by interacting with the 3′ untranslated region (3′ UTR) of targeted mRNAs and inhibiting translation and/or stimulating decay. Physical association and computational analyses of yeast Puf3p identified >150 potential mRNA targets involved in mitochondrial function. However, only COX17 has been established as a target of Puf3p-mediated deadenylation and decapping. We have identified 10 new targets that are rapidly degraded in a Puf3p-dependent manner. We also observed changes in Puf3p activity in response to environmental conditions. Puf3p promotes rapid degradation of mRNA targets in the fermentable carbon source dextrose. However, Puf3p-mediated …

Carbon Source-Dependent Alteration Of Puf3p Activity Mediates Rapid Changes In The Stabilities Of Mrnas Involved In Mitochondrial Function, Melanie A. Miller, Joseph Russo, Anthony D. Fischer, Florencia A. Lopez Leban, Wendy M. Olivas

Wendy Olivas

Transcriptional Control Of Toxoplasma Development, Joshua Byran Radke

USF Tampa Graduate Theses and Dissertations

Toxoplasma gondii is an obligate intracellular protozoan parasite of animals and man. The asexual life cycle of Toxoplasma involves three very distinct, but tightly coordinated developmental stages. In nature, the sporozoite (contained within an oocyst) and bradyzoite (contained within a tissue cyst) initiate infection of the intermediate host, followed by rapid differentiation into the actively replicating tachyzoite. When countered by an effective host response, the tachyzoite differentiates back into the latent bradyzoite and this unique ability of Toxoplasma to interconvert between the replicating tachyzoite and the latent bradyzoite within a single host is the cause of life long infection. The …

Novel Insights Into The Mechanisms Of Regulation Of Tyrosine Kinase Receptors By Ras Interference 1, Adriana Galvis

FIU Electronic Theses and Dissertations

Receptor-tyrosine kinases (RTKs) are membrane bound receptors characterized by their intrinsic kinase activity. RTK activities play an essential role in several human diseases, including cancer, diabetes and neurodegenerative diseases. RTK activities have been regulated by the expression or silencing of several genes as well as by the utilization of small molecules.

Ras Interference 1 (Rin1) is a multifunctional protein that becomes associated with activated RTKs upon ligand stimulation. Rin1 plays a key role in receptor internalization and in signal transduction via activation of Rab5 and association with active form of Ras. This study has two main objectives: (1) It determines …

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 …

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 S. Schill, Nancy Isern, Cynthia M. Dupureur, Patricia J. Liwang

Cynthia Dupureur

Polymerase Alpha Components Associate With Telomeres To Mediate Overhang Processing, Raffaella Diotti

Dissertations, Theses, and Capstone Projects

Telomeres consist of TTAGGG repeats, which end with a 3' G-overhang and are bound by a six-protein complex, known as Shelterin. In humans, telomeres shorten at each cell division, unless telomerase is expressed and able to add telomeric repeats to the 3' G-overhang. However, for effective telomere maintenance, the DNA strand complementary to that made by telomerase must be synthesized. In this study, I focused on the Polα/primase complex, in particular the subunits p68 (POLA2, the regulatory subunit) and p180 (Polα, the catalytic subunit), and their potential roles at telomeres. I was able to detect p180, p68 and OBFC1, a …

Ecdysis Triggering Hormone And Its Role In Juvenile Hormone Synthesis In The Yellow-Fever Mosquito, Aedes Aegypti, Maria Areiza

FIU Electronic Theses and Dissertations

Ecdysis triggering hormone (ETH) is a neuropeptide known for its role in the orchestration of ecdysis. However, its role in the regulation of Juvenile Hormone (JH) synthesis is unknown. In Aedes aegypti, JH is synthesized by the corpora allata (CA) and titers are tightly regulated by allatoregulatory factors. In this study I describe the effect of ETH on JH synthesis during the late pupal stage and in the adult female after blood feeding. Analysis of ETH receptor (ETHRs) expression showed that ETHRs are present in both the CA and the corpora cardiaca (CC), a neurohemal organ. The data suggest …