Molecular Biology Commons^™

Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion In Protein Lysine Methyltransferase Smyd2, Nicholas Spellmon, Xiaonan Sun, Nualpun Sirinupong, Brian Fp Edwards, Chunying Li, Zhe Yang

Biochemistry and Molecular Biology Faculty Publications

SMYD proteins are an exciting field of study as they are linked to many types of cancer- related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open–closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative cor- related inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to …

Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap

Dartmouth Scholarship

In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift …

A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage

LSU New Orleans Theses and Dissertations

Plants respond to environmental stress by altering their gene expression. Under stress conditions some genes are activated and some genes are repressed. Even though a lot of work has been done to understand mechanisms of gene activation under abiotic stress very little information is available on how stress responsive genes are kept repressed under normal growth conditions. Recent work has revealed that plants use transcriptional repression as common mechanism of gene repression. Transcriptional repression is achieved by recruitment co-repressor complexes to the target genes. Recent studies have revealed that the co-repressor LUH complexes with SLK1 and SLK2 to silence Arabidopsis …

Regulation Of The Transmembrane Mucin Muc4 By Wnt/Β-Catenin In Gastrointestinal Cancers, Priya Pai

Theses & Dissertations

The transmembrane mucin MUC4 is a high molecular weight glycoprotein that is expressed de novo in pancreatic ductal adenocarcinoma (PDAC). MUC4 has been shown to play a tumor-promoting role in malignancies such as PDAC, ovarian cancer and breast cancer. Unlike the normal pancreas, MUC4 is ordinarily expressed by goblet and absorptive cells in the normal colonic epithelium. However, its expression/role in colorectal cancer (CRC) is not well studied.

In this dissertation, the goal was to identify factor(s) that may differentially regulate MUC4 in these two disparate malignancies. Furthermore, in light of its pro-tumorigenic role in other malignancies, we analyzed the …

Control Of The Basal Recycling And Surface Expression Of Epidermal Growth Factor Receptor By The Endocytic Recycling Regulator Ehd1 Utilizing A Pathway Shared By Rusc2, Eric Tom

Theses & Dissertations

The epidermal growth factor receptor (EGFR) is a prototype receptor tyrosine kinase (RTK) and oncogene aberrantly expressed or mutated in solid tumors. Its surface expression is dynamically regulated. Display of an activation-competent pool is essential for response to ligands. Internalization and degradation of EGFR following stimulation has received the most attention, fewer studies have characterized the recycling arm of EGFR transit, basal traffic and surface display are poorly understood. Thus, we evaluated the endocytic recycling of EGFR for its therapeutic potential in EGFR driven cancers. The C-Terminal Eps15 homology (EH) domain-containing proteins have emerged as regulators of surface receptor recycling …

Blackberry Virosome: A Micro And Macro Approach, Archana Khadgi

Graduate Theses and Dissertations

Viruses pose a major concern for blackberry production around the world with more than 40 species known to infect the crop. Virus complexes have been identified recently as the major cause of plant decline with blackberry yellow vein disease (BYVD) being the most important disease of the crop in the Southern United States. The objective of this research was to study the blackberry virosome in both the macro and micro scale. The large scale approach involves identification of the major viruses known to be associated with BYVD in the Southern United States as well as the identification of other viruses …

Preventing Thymus Involution In K5.Cyclin D1 Transgenic Mice Sustains The Naïve T Cell Compartment With Age, Michelle L. Bolner

Dissertations and Theses (Open Access)

The thymus maintains T cell receptor (TCR) repertoire diversity through perpetual release of self-MHC restricted naive T cells. However, thymus involution during the aging process reduces naïve T cell output, leading to defective immune responsiveness to newly encountered antigens. We have found that early thymus involution precipitates the age-associated shift favoring memory T cell dominancy in young control mice. Furthermore, we have shown that age-related thymus involution is prevented in mice expressing a keratin 5 promoter-driven Cyclin D1 (K5.D1) transgene in thymic epithelial cells (TECs). Thymopoiesis occurs normally in K5.D1 transgenic thymi and sustains T cell output to prevent the …

Co-Treatment With Conjugated Linoleic Acid And Nitrite Modulates Mitochondrial Respiration And Electron Transport Chain Activity In Vivo And Attenuates Mitochondrial Dysfunction During Cardiac Injury., Patrick Van Hoose

Electronic Theses and Dissertations

Cardiovascular disease and subsequent complications, such as myocardial infarction (MI), is the leading cause of death within the United States. Clinical intervention to reduce cardiac damage following myocardial ischemia is limited. Polyunsaturated fatty acids have been linked to an overall beneficial effect on cardiovascular health and function. Conjugated linoleic acid (cLA) is an 18:2 unsaturated fatty acid found within the diet in ruminant meat and dairy products. The cis-9 trans-11 isomer of cLA is the most prominent isomer within the diet and cLA has been linked to favorable outcomes in numerous disease states. The mechanism mediating the effects of cLA …

Molecular Regulation Of Vascular Calcification In Murine Models Of Atherosclerosis, Shanshan Gao

Dissertations and Theses (Open Access)

Background: Calcification occurs often in the atherosclerotic lesions of patients with coronary heart disease and animals with hypercholesterolemia, such as apolipoprotein-E deficient (ApoE-/-) mice. However, the mechanism(s) underlying the development of calcification in atherosclerosis remains unclear. ApoE acts as a lipid transporter, but also has been recognized as a potential regulator of osteogenesis. Little information is available as to whether ApoE has any direct impact on osteogenesis and calcification in vascular smooth muscle cells (VSMC). Several signal transduction pathways play a role in regulation of calcification, including the Wnt/β-catenin system and potentially GTAP, an ubiquitin-conjugating enzyme responsible for protein …

Development And Validation Of A Novel In Vitro Model For The Assessment Of Heterocellular Interactions Mediated By Connexin43, Emily Ongstad

All Dissertations

The injury border zone (IBZ), a region of transitional tissue between intact myocardium and the ischemic area, is often the site of lethal reentrant arrhythmia generation in post-myocardial infarction (MI) patients. Disruption to normal connexin43 (Cx43) localization at the intercalated disc (ID), separation of myocytes by activated fibroblasts and deposited scar tissue are thought to be factors that render the IBZ a pro-arrhythmic substrate, though there is a current need to better understand these changes so directed therapies can be developed. There are no clinically available therapies focused on the mechanistic changes in the IBZ. Additionally, generation of new compounds …

Arsenic Inhibits P19 Stem Cell Differentiation By Altering Microrna Expression And Repressing The Sonic Hedgehog Signaling Pathway, Jui Tung Liu

All Dissertations

Arsenic is a naturally-occurring toxicant that exists in bedrock and can be leached into ground water. Humans can be exposed to arsenic via contaminated drinking water, fruit, rice or crops. Epidemiological studies have shown that arsenic is a developmental toxicant, and in utero exposure reduces IQ scores, verbal learning ability, decreases long term memory, and increases the likelihood of dying from a neurological disorder. Arsenic can also reduce birth weight, weight gain, and muscle function after an in utero exposure. Although the mechanism behind these physiological changes is not known, in vitro studies have shown that arsenic can reduce muscle …

Characterization Of Sbip68: A Putative Tobacco Glucosyltransferase Protein And Its Role In Plant Defense Mechanisms, Abdulkareem O. Odesina

Electronic Theses and Dissertations

Plant secondary metabolites are essential for normal growth and development in plants ultimately affecting crop yield. They play roles ranging from appearance of the plants to defending against pathogen attack and herbivory. They have been used by humans for medicinal and recreational purposes amongst others. Glycosyltransferases catalyze the transfer of sugars from donor substrates to acceptors. Glucosyltransferases are a specific type of glycosyltransferases known to transfer glucose molecules from a glucose donor to a glucose acceptor (aglycone) producing the corresponding glucose secondary metabolite or glycone, in this case glucosides. It was hypothesized that SBIP68, a tobacco putative glucosyltransferase-like protein glucosylated …

Leptin Regulates The Expression Of Autophagy-Related Genes In Chickens, Peter Olawale Ishola

Graduate Theses and Dissertations

Autophagy or cellular self-digestion, a lysosomal degradation pathway that is conserved from yeast to human, plays a key role in recycling cellular constituents, including damaged organelles. It also plays a pivotal role in the adaptation of cells to a plethora of distinct stressors including starvation. Autophagy has been extensively studied in mammals and yeast, but little is known in avian species. Thus, the major objective of the present study was to determine the effects of leptin on autophagy-related genes in chicken hypothalamus, muscle and liver. Leptin is an adipocytokine that is mostly produced by white adipose cells in mammals (as …

Optimizing A Luciferase-Based Tool For Studying The Effects Of Fatty Acid Desaturase 7 On Singlet Oxygen Accumulation In Arabidopsis Thaliana, Abeer Muhammedali Alnasrawi

Graduate Theses and Dissertations

In plants, reactive oxygen species (ROS) are generated as a byproduct of normal metabolism, as well as in response to adverse conditions such as light stress, extreme temperatures, and exposure to pests and pathogens. Singlet oxygen (1O2) is a ROS that is formed during photosynthesis in photosystem II (PSII) of the chloroplasts. Levels of 1O2 and other ROS are tightly controlled in healthy plants, but some studies suggest that levels of fatty acid desaturase (FAD) activity in Arabidopsis thaliana can influence constitutive and/or stress-responsive ROS accumulation. In this study, a luciferase-based reporter gene that is selectively stimulated by 1O2 (AAA-ATPase: …

Analysis Of Ac/Ds Activation Tagged Mutants In Tomato (Solanum Lycopersicum), Ipeleng Randome

Graduate Theses and Dissertations

Tomato (Solanum lycopersicum) is a crop of immense economic and nutritional importance worldwide and also a good model organism for genomic studies of other dicot species. The recent completion of the tomato genome sequence is a great milestone towards learning about the tomato genome. Elucidation of the function of the different genes using different functional genomic tools is therefore important in adding to this resource. To this end, we have developed an Ac-Ds transposon ‘activation tagging’ (ATag) system to be able to transpose transposon inserts, bearing a strong 35S-enhancer element, all around the genome. An Ac-Ds ATag construct was used …

Transcriptomics Of Chicken Primordial Germ Cells, Nhung Thi Nguyen

Graduate Theses and Dissertations

Chicken primordial germ cells (PGCs) are derived from extraembryonic tissue of the embryo and first appear at stage X of development. They enter the bloodstream and migrate to the genital ridge, unite with somatic tissue to form a developing gonad, and then differentiate to sperm or ova (Fujimoto et al., 1976). Understanding molecular features of both male and female PGCs not only clarify the differentiation mechanism of such cells toward different germ lines, but will also help in selecting for highly productive types of commercial chicken. Most previous studies focused on the location of PGCs (Eyal-Giladi et al., 1981; Swift …

Autophagy And Its Potential Role In Stress And Feed Efficiency Using Avian Lines, Alissa Laura Piekarski

Graduate Theses and Dissertations

Autophagy is a highly conserved cellular mechanism that is responsible for the degradation and recycling of damaged organelles. Recently, autophagy has been involved in critical roles during overall development of the organism and degradation of damaged cellular components. This pathway has witnessed dramatic growth in the last few years and has been extensively studied in yeast and mammals, however, there is a paucity of information in avian (non-mammalian) species. First, we characterized genes involved in the autophagy pathway in male and female Jungle Fowl to determine gender and tissue specific differences. Secondly, tissue and genotype differences in Japanese quail selected …

In Vivo Periodical Monitoring Of Immune Cell Infiltration In Response To Feathers And Intramuscular Injection Of Ionps Using The Pulp (Dermis) Of Growing Feathers As Test Site Tissue In Chickens, Olfat Taleb Alaamri

Graduate Theses and Dissertations

The applications of nanoparticles are growing, but little is known about their interactions with the immune system as most studies did not use suitable in vivo test systems. The purpose of these studies was to investigate the utility of chicken growing feathers as an in vivo test site for iron oxide nanoparticle (IONP) interactions with the immune system. The first objective of this study was to monitor leukocyte infiltration into the growing feather pulp upon the administration of IONP and IO-mIgG preparations. The second objective was to test the utility of IONPs as vaccine adjuvants by monitoring primary and memory …

Understanding The Causal Agent Of Rose Rosette Disease, Patrick Louis Di Bello

Graduate Theses and Dissertations

A number viruses are known to infect roses, ranging from those in the genera Nepovirus, and Ilarvirus, which have been reported since the inception of rose virology, to recently discovered viruses in the genera Carmovirus, Closterovirus, Emaravirus, Luteovirus, Rosadnavirus, and Potyvirus. Of the viral diseases in rose, arguably the most damaging is Rose rosette (RRD), which is associated with the Emaravirus, Rose rosette virus (RRV). The objective of this thesis is to fill in the gaps in knowledge on the epidemiological aspects of RRD and RRV. There has been significant progress in the epidemiology of the RRD agent prior to …

Dancing Through Life: Molecular Dynamics Simulations And Network-Centric Modeling Of Allosteric Mechanisms In Hsp70 And Hsp110 Chaperone Proteins, Gabrielle Stetz, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that …

Characterization Of Two Novel Gene Regulatory Systems In The Zoonotic Bacterium Bartonella Henselae, Nhan Tu

USF Tampa Graduate Theses and Dissertations

The genus Bartonella contains Gram-negative arthropod-borne bacteria that are found in many small animal reservoirs and are capable of causing human disease. Bacteria utilize a general stress response system to combat stresses from their surrounding environments. In α-proteobacteria, the general stress response system uses an alternate σ factor as the main regulator and incorporates it with a two-component system into a unique system. Our study identifies the general stress response system in the α-proteobacterium, Bartonella henselae, where the gene synteny is conserved and both the PhyR and alternate σ factor have similar sequence and domain structures with other α-proteobacteria. …

Mass Spectrometry-Based Investigation Of App-Dependent Mechanisms In Neurodegeneration, Dale Chaput

USF Tampa Graduate Theses and Dissertations

Alzheimer’s disease (AD) is the most prevalent form of dementia affecting the elderly, and as the aging population increases the social and economic burden of AD grows substantially. Pathological hallmarks of AD include the accumulation of extracellular amyloid plaques and intracellular neurofibrillary tangles (NFTs), as well as significant neuron loss. Amyloid plaques consist of aggregated amyloid beta (Aβ) peptide, which is generated from the proteolytic processing of amyloid precursor protein (APP) in addition to several other peptides. While the processing of APP has been characterized, its primary physiological function and its involvement in AD pathology are poorly understood. Developing a …

Targeting Autopalmitoylation To Modulate Protein S-Palmitoylation, Laura Dawn Hamel

USF Tampa Graduate Theses and Dissertations

Palmitoylation refers to the covalent attachment of fatty acids, such as palmitate, onto the cysteine residues of proteins. This process may subsequently alter their localization and function. Nearly all of the enzymes that catalyze palmitoylation, zDHHC protein acyl transferases (PATs), are implicated in neurological disorders, infectious diseases, and cancer in humans. Of particular interest to those who study palmitoylation are Ras family GTPas and zDHHC9-GCP16, the zDHHC PAT that palmitoylates Ras proteins. Erf2-Erf4 is the zDHHC PAT that palmitoylates Ras proteins in Saccharomyces cerevisiae. Currently, there are no methods to therapeutically target palmitoylation for the treatment of disease. One …

Ion Trap Mass Analyzer Apparatus, Methods, And Systems Utilizing One Or More Multiple Potential Ion Guide (Mpig) Electrodes, Curtiss Dwight Hanson

Patents (University of Northern Iowa)

In one aspect of the invention, an ion trap mass analyzer includes a variable- or multi-potential type ion guide (MPIG) assembly which has been pre-configured to produce a parabolic-type potential field. Each MPIG electrode has a resistive coating of designed characteristics. In one example the coating varies in thickness along the length of an underlying uniform substrate. The MPIG assembly can be a single MPIG electrode or an array of a plurality of MPIG electrodes. An array can facilitate delocalization for improved performance. This chemical modification of a uniform underlying substrate promotes cheaper and flexible instruments. The modified MPIG electrodes …

Molecular And Phenotypic Studies Validating The Role Of The Ecdysone Receptor In The Human Parasite Brugia Malayi, Amruta Mhashilkar

USF Tampa Graduate Theses and Dissertations

Filariasis and onchocerciasis are debilitating diseases affecting 120 million people globally. The massive socio-economic impact of these diseases energized the international community to declare a goal of eliminating filariasis 2020. This resulted in a dramatic increase in the efforts to eliminate filariasis and onchocerciasis, employing a strategy of mass drug administration (MDA). However, these programs rely upon the small arsenal of drugs. This leaves these programs vulnerable to failure in the face of developing resistance and local intolerance to the current drug regimens. Thus, new drugs against these infections are critically needed. A homologue of the ecdysone receptor (EcR), a …

Hepatic Nutrient And Hormonal Regulation Of The Pancreatic-Derived Factor (Pander) Promoter, Whitney Ratliff

USF Tampa Graduate Theses and Dissertations

PANcreatic-DERived factor (PANDER, FAM3B) has been shown to regulate glycemic levels via interactions with both pancreatic islets and the liver. Although PANDER is predominantly expressed from the endocrine pancreas, recent work has provided sufficient evidence that the liver may also be an additional tissue source of PANDER production. At physiological levels, PANDER is capable of disrupting insulin signaling and promoting increased hepatic glucose production. As shown in some animal models, strong expression of PANDER, induced by viral delivery within the liver, induces hepatic steatosis. However, no studies to date have explicitly characterized the transcriptional regulation of PANDER from the liver. …

Novel Enzyme Perspectives: Arylalkylamine N-Acyltransferases From Bombyx Mori & 1-Deoxy- D-Xylulose-5-Phosphate Synthase From Plasmodium Falciparum And Plasmodium Vivax, Matthew R. Battistini

USF Tampa Graduate Theses and Dissertations

This dissertation is dedicated to the research and investigation of novel enzymes and the methods used to study them, with physiological roles ranging from isoprenoid biosynthesis to neurotransmitter production. Using a combination of bioinformatics, recombinant cloning, enzymology, and proteomics, we have contributed to the understanding and exploration of several human illnesses, including malaria, cancer, and endocrine dysfunction.

Our first project involved studying the enzymes responsible for N-acylarylalkylamide biosynthesis in Bombyx mori. Very little is known how these potent signaling molecules are produced in vivo, however, one possible pathway is the direct conjugation of an acyl-CoA to a corresponding …

Serum Proteins Enhance Dispersion Stability And Influence The Cytotoxicity And Dosimetry Of Zno Nanoparticles In Suspension And Adherent Cancer Cell Models, Catherine B. Anders, Jordan J. Chess, Denise G. Wingett, Alex Punnoose

Biomedical Research Institute Publications and Presentations

Agglomeration and sedimentation of nanoparticles (NPs) within biological solutions is a major limitation in their use in many downstream applications. It has been proposed that serum proteins associate with the NP surface to form a protein corona that limits agglomeration and sedimentation. Here, we investigate the effect of fetal bovine serum (FBS) proteins on the dispersion stability, dosimetry, and NP-induced cytotoxicity of cationic zinc oxide nanoparticles (nZnO) synthesized via forced hydrolysis with a core size of 10 nm. Two different in vitro cell culture models, suspension and adherent, were evaluated by comparing a phosphate buffered saline (PBS) nZnO dispersion (nZnO/PBS) …

Degradation Of The Cancer Genomic Dna Deaminase Apobec3b By Siv Vif, Allison M. Land, Jiayi Wang, Emily K. Law, Ryan Aberle, Andrea Kirmaier, Annabel Krupp, Welkin E. Johnson, Reuben S. Harris

Biological Sciences Department Publications

APOBEC3B is a newly identified source of mutation in many cancers, including breast, head/neck, lung, bladder, cervical, and ovarian. APOBEC3B is a member of the APOBEC3 family of enzymes that deaminate DNA cytosine to produce the promutagenic lesion, uracil. Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes. HIV-1 counteracts these APOBEC3s with the viral protein Vif, which targets the relevant APOBEC3s for proteasomal degradation. While APOBEC3B does not restrict HIV-1 and is not targeted by HIV-1 Vif in CD4-positive T cells, we asked whether related …

The Generation, Exploitation And Future Of Induced Pluripotent Stem Cells, Jacob Steenwyk

Scholarly Undergraduate Research Journal at Clark (SURJ)

The foundational advancements of John Gurdon and Shinya Yamanaka have improved understanding of dedifferen- tiation of cells to a pluripotent state. The seminal discovery established a novel system to study disease pathogenesis, drug screening, and toxicity, as well as sprouted the new field of regenerative medicine. In this article, the method- ology to obtain dedifferentiated cells, known as induced pluripotent stem (iPS) cells, subsequent validation, and application of which are reviewed. The experiments investigated here aim to demonstrate the capacity of iPS cells to replace the ethically-gray human embryonic cells by developing human livers and viable, healthy animals. It is …