Molecular Biology Commons^™

P53 Drives A Transcriptional Program That Elicits A Non-Cell-Autonomous Response And Alters Cell State In Vivo, Sydney Moyer

Dissertations and Theses (Open Access)

Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene which encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 ChIP-sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes which included Mdm2 but not p21. Global p53 activation …

Genetic Polymorphism Of Bitter Taste Perception In Tempe, Arizona And Its Association With Nutritional Status, Daniel Woodley, Benjamin Cabrera

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Defining Relictual Biodiversity: Conservation Units In Speckled Dace (Leuciscidae: Rhinichthys Osculus) Of The Greater Death Valley Ecosystem, Steven M. Mussmann, Marlis R. Douglas, David D. Oakey, Michael E. Douglas

Biological Sciences Faculty Publications and Presentations

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species–population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

LSU New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Artificial Intron Technology To Generate Conditional Knock-Out Mice, Amber N. Thomas-Gordon

Dissertations and Theses (Open Access)

Genetic engineering has been re-shaped by the invention of new tools in modern biotechnology in a way that offers precision and efficiency in modifying the genome at a single nucleotide level and/or allowing precise control of gene expression. Such gene manipulation brings about significant findings and revelations in comprehending more about embryonic development, cellular and physiological functions, and disease pathology. Current methods used to produce conditional knockouts have limitations on conditional allele placement and modification varies among genes in different organisms. Thus, a system for generating conditional alleles with fidelity remains a challenge. My goal was to examine an approach …

A Novel Serpinb1 Single-Nucleotide Polymorphism Associated With Glycemic Control And Β-Cell Function In Egyptian Type 2 Diabetic Patients, Dina H. Kassem, Aya Adel, Ghada H. Sayed, Mohamed M. Kamal

Pharmacy

Aims: Serine protease inhibitor B1 (SerpinB1) is a neutrophil elastase inhibitor that has been proved to be associated with type 2 diabetes mellitus and pancreatic β-cell proliferation. In this study, we investigated 2 SERPINB1 SNPs, rs114597282 and rs15286, regarding their association with diabetes risk and various anthropometric and biochemical parameters in Egyptian type 2 diabetic patients.

Materials and Methods: A total of 160 subjects (62 control and 98 type 2 diabetic patients) participated in this study. Various anthropometric and biochemical parameters were assessed. Genotyping assay for the two SNPs was done using TaqMan genotyping assays. The association of rs15286 variants …

Characterization Of The Overexpression Of The Native H+-Pumping Pyrophosphatase In The Microalga Picochlorum Soloecismus, Kimberly T. Wright

Biology ETDs

Microalgae are of interest for the creation of sustainable and cost competitive alternatives to petroleum-based fuels and chemicals. However, cultivation, extraction and processing of algal biomass requires improved yields to achieve economic feasibility. The advancement of microalgal biotechnology and various genetic engineering techniques allow the improvement of microalgae biomass for this purpose. Here, the characterization of the overexpression of the native vacuolar H+ pumping pyrophosphate (AVP1) in Picochlorum soloecismus was examined. AVP1 overexpression causes biomass increase in relevant plant crops. When overexpressed in this microalga it increases carbon storage in the form of starch in a closed laboratory photobioreactor. However, …

Novel Long Non-Coding Rna Cdlinc Promotes Nsclc Progression, Christina J. Moss

USF Tampa Graduate Theses and Dissertations

Non-small cell lung cancer (NSCLC) is the leading cause of cancer death worldwide with a low 5-year survival rate of only around 21%. This low 5-year survival rate is due to two main reasons. First, NSCLC is often diagnosed at the later stages when it has already metastasized. Second, NSCLC is an incredibly diverse, heterogenous disease making it very hard to target the true molecular oncogenic drivers. New targets for personalized therapeutics are needed based on the expression status of each individual lung cancer tumor.

One way of looking for these new therapeutics is to begin by identifying the oncogenotype …

Secretion Of Proteins And Antibody Fragments From Transiently Transfected Endothelial Progenitor Cells, Loree Heller, Reynald Thinard, Melanie Chevalier, Sezgi Arpag, Yu Jing, Ruth Greferath, Richard Heller, Claude Nicolau

Bioelectrics Publications

In neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, multiple sclerosis and amyotrophic lateral sclerosis, neuroinflammation can lead to blood-brain barrier (BBB) breakdown. After intravenous or intra-arterial injection into mice, endothelial progenitor cells (EPCs) home to the damaged BBB to promote neurovascular repair. Autologous EPCs transfected to express specific therapeutic proteins offer an innovative therapeutic option. Here, we demonstrate that EPC transfection by electroporation with plasmids encoding the reporter protein GFP or an anti-beta-amyloid antibody fragment (Fab) leads to secretion of each protein. We also demonstrate the secreted anti-beta-amyloid Fab protein functions in beta-amyloid aggregate solubilization.

Probing The Limits Of Singular Gene Expression Through The Activity Of High Representation Odorant Receptor Transgenes, Eugene Lempert

Dissertations, Theses, and Capstone Projects

Singular gene expression is a common phenomenon in biology, making its appearance in immunoglobulin selection, protocadherin expression, X chromosome-inactivation, random monoallelic expression, and olfactory receptor choice. Singularity involves an activation and a feedback step. The mechanisms of singular gene choice have some capacity to integrate additional member genes while still maintaining singularity, but will activate an additional member if an earlier choice was incapable of triggering the feedback step. Odorant Receptor (OR) genes are substantially divergent from each other in terms of coding sequence, promoter structure, and genomic locus, all of which plays a role in how many Olfactory Sensory …

A Study On The Regulation Of Mitochondrial Biogenesis And Gluconeogenesis In S. Cerevisiae, Manika Bhondeley

LSU New Orleans Theses and Dissertations

Budding yeast has been used as a powerful model organism to study the network that communicate functions of nucleus, cytoplasm and mitochondria. Depending upon environmental cues, yeast cells regulate their metabolic programming, for example, presence of glucose repress utilization of alternate carbon source to produce energy. This phenomenon is called carbon catabolite repression, which is relieved when glucose is limiting, and alternate carbon source utilization is achieved by an increase in mitochondrial biogenesis (oxidative catabolism) and the upregulation of TCA cycle and gluconeogenesis. Most of genes involved in alternate carbon source utilization are encoded in the nucleus and undergo tight …

Investigating The Redox Sensitivity Of Mitf Splice Variants, Rachel Berryman

Senior Theses

Within pigment-producing cells known as melanocytes, the transcription factor MITF is intimately involved in regulating genes associated with cell cycle maintenance and melanocyte differentiation. Research, however, has provided conflicting results on the relationship between the expression levels of MITF and melanocyte cell fate. To complicate matters, two splice variants of MITF exist, differing by only 18 base pairs. These variants have been observed at variable levels of expression in melanocyte and melanoma cells, raising the question as to their functional purpose. Building upon previous research by the Leachman/Cassidy lab that identified the redox sensitivity of MITF while additionally establishing a …

Subcellular Localization Of Tobacco Sabp2 Under Normal And Stress Conditions, Sanjeev Das

Undergraduate Honors Theses

Subcellular Localization of Tobacco SABP2 under Normal and Stress Conditions

Salicylic acid (SA), a phytohormone, plays an important role in plant physiology. SA mediated innate immune pathway is an important pathway for plant immunity against pathogens. Plants resisting pathogen infection synthesize higher levels of Methyl Salicylate (MeSA), which is then converted to SA by the esterase activity of Salicylic Acid Binding Protein 2 (SABP2). The high level of the converted SA leads to enhanced pathogen resistance. The study of subcellular localization of a protein is critical in explaining its potential biochemical functions. SABP2 tagged with eGFP was expressed transiently in …

Discrimination Of Monozygotic Twins Using Dna Methylation Levels Of One Cpg Site At Chromosome 3, Dino O. Robinson

Student Theses

Conventional STR typing, commonly used in forensics for human identification, poses a problem in criminal cases and paternity disputes involving monozygotic (MZ) twins because they share identical DNA sequences. To date, no routine method is available in forensics to differentiate between individuals of MZ pairs. Recently, epigenetic methods measuring differential DNA methylation patterns have been applied to MZ twin differentiation. In this study, we investigated the potential to identify MZ twins using a previously identified DNA methylation site in chromosome 3, cg18562578, in a sample of 129 MZ and 37 dizygotic (DZ) twin pairs. We used bisulfite converted saliva DNA …

Loss Of Caspase-8 Function In Combination With Smac Mimetic Treatment Sensitizes Head And Neck Squamous Carcinoma To Radiation Through Induction Of Necroptosis., Burak Uzunparmak

Dissertations and Theses (Open Access)

Caspase-8 (CASP8) is one of the most frequently mutated genes in Head and Neck Squamous Carcinomas (HNSCC), and mutations of CASP8 are associated with poor overall survival. The distribution of these mutations in HNSCC suggests that they are likely to be inactivating. Inhibition of CASP8 has been reported to sensitize cancer cells to necroptosis, a unique cell death mechanism. Here, we evaluated how CASP8 regulates necroptosis in HSNCC using cell line models and syngeneic mouse xenografts. In vitro, knockdown of CASP8 rendered HNSCCs susceptible to necroptosis induced by a second mitochondria-derived activator of caspase (SMAC) mimetic, Birinapant, when combined …

Liver Transcriptomic Analysis After Short- And Long-Term Feeding Of Soy Protein Isolate And Its Ability To Reduce Liver Steatosis In Obese Zucker Rats, Melisa Kozaczek

Graduate Theses and Dissertations

According to the Centers for Disease Control and Prevention (CDC) the prevalence of obesity in adults in the United States during 2017-2018 was a 42.4%, a high number considering all the risks factors associated with this disorder, such as cardiovascular disease, insulin resistance, diabetes type 2, and fatty liver disease, among others. Fatty liver disease is the accumulation of lipids in the liver that can account for more than 5 to 10% of the liver’s weight. There are two types of fatty liver disease, alcoholic fatty liver disease (AFLD), and non-alcoholic fatty liver disease (NAFLD). AFLD is the detrimental accumulation …

An Analysis Of Crispr-Cas Gene Editing In Agriculture, Ashley Laliberte

Honors Scholar Theses

The CRISPR-Cas system is a promising form of gene editing, especially for the agriculture industry. The ability to make single-nucleotide edits within a gene of interest, without the need to introduce foreign DNA, is a powerful tool for designing healthier and more efficient crops and food animals. This system provides opportunity for increased nutritional value, decreased food waste, and more economically and environmentally sustainable food production. Though this biotechnology is facing mechanistic limitations due to off-target effects and inefficient homology-directed repair, vast improvements have already been made to improve its efficacy. The CRISPR-Cas system is already the most advanced form …

Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore …

Diversity Of The Major Histocompatibility Complex In African Penguins (Spheniscus Demersus) In Situ, Athena Schalk

Undergraduate Honors Thesis Projects

The Major Histocompatibility Complex (MHC) is responsible for the immune response in all jawed vertebrates and protects individuals against a variety of pathogens and diseases. Maintaining genetic diversity within the MHC exons is critical to protecting endangered species. African penguins (Spheniscus demersus) are in danger of losing their MHC diversity in isolated populations due to reductions in population size associated with environmental changes and human activity. This study analyzes the diversity within the exons in the DNA encoding the MHC by amplifying the exons through polymerase chain reaction and identifying alleles through denaturing gradient gel electrophoresis. Wild populations of …

Tip60 Regulation Of Δnp63Α Is Associated With Cisplatin Resistance, Akshay Hira, Andrew Stacy, Jin Zhang, Michael P. Craig, Madhavi Kadakia

Celebration of Undergraduate & Graduate Research, Scholarship, and Creative Activities Materials

About 5.4 million basal and squamous cell skin cancers are diagnosed every year in the US. ΔNp63a, a member of the p53 transcription factor family, is overexpressed in non-melanoma skin cancer and regulates cell survival, migration and invasion. TIP60 is histone acetyltransferase (HAT) which mediates cellular processes such as transcription and the DNA damage response (DDR). Previous studies in our lab have shown that overexpression of TIP60 induces ΔNp63a protein stabilization in a catalytic-dependent manner. Since ΔNp63a is known to transcriptionally regulate several DDR genes and promote cisplatin resistance, its stabilization by TIP60 may contribute to the failure of platinum-based …

Cellulolytic Enzymes From The Maize Seed Production System—Characterization, Inhibition, And Novel Activities, Hong Fang

Student Theses and Dissertations

Enzymatic saccharification of ligno-cellulosic material is a key process in advanced biofuel production. Different enzymes are required in the enzymatic saccharification. To meet the large demand of these enzymes for industrial purposes, a transgenic maize seed expression system had been utilized in our laboratory to acquire adequate and cost-effective pure enzymes including β-1,4-endoglucanase, cellobiohydrolase I, cellobiohydrolase II and expansin. In this dissertation, the possibility of utilizing maize-produced recombinant cellulases in promoting the saccharification of ligno-cellulosic material was investigated. From the purification and basic characterization of these target enzymes to the identification of different inhibitors, this project has partially addressed the …

Functions Of Cdk/Cyclin Complexes In Endoreplication Regulation By The Cdk Inhibitor Siamese, Kai Wang

LSU Doctoral Dissertations

Arabidopsis trichome (leaf hair) is a specialized single cell extended from epidermal cell on the leaves, which is a typical endoreplication and is also known as endoreduplication. Several D-type cyclins were tested to check the cell division in trichome, and the trichome expressing either CYCB1;2 or CDKB2;2 cannot trigger cell division, even if simultaneous expression of CYCB1;2 and CDKB2;2 failed to produce mitosis in trichome. Only CYCD3;1 specifically promotes multicellular trichome. cdkb1;1cdbk1;2 double mutants and sim cdkb1;1cdkb1;2 triple mutants exhibit the phenotype similar to the wild type and very limited cell division respectively. Overexpression of a CDKB1;1 dominant-negative construct that …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

Identification Of Uncommon Antibiotic-Producing Illinois Soil Isolates, Lesly Muniz, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from the soil. We researched tester strains B. subtilis and E. coli from the soil isolates obtained. We further verified if the isolates were common antibiotic bacteria. Unfortunately, this project heavily relied on biochemical tests, colony morphology, and Gram stains to reject or fail to reject our hypothesis. Our goal was to discover new antibiotic-producing bacteria that could be beneficial in combating ESKAPE strains. A proper PCR and DNA extraction would be required …

Screening For Antibiotic-Producers In Soil From A Garden, Long Tran, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

Multidrug-resistant pathogens are the leading cause of nosocomial infection, which killed more than 30,000 people in the United States every year. Among these, ESKAPE strains bugs, which comprise six highly drug-resistant bacteria, pose the greatest challenge to the healthcare system. In order to fight the antibiotic-resistant crises, novel antibiotic-producers must be discovered. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on student sourcing antibiotic discovery from the soil. Pseudomonas was revealed to produce a zone of inhibition against Bacillus subtilis on LB media. The next step …

Pseudomonas And Bacillus Soil Isolates Produce Antibiotics, Chelsea Brandt, Dr. Lori Scott

Identifying and Characterizing Novel Antibiotic Producing Microbes From the Soil

The recent emergence of antibiotic resistance bacterial strains presents a significant challenge and threat to human healthcare. While new methods of treatment such as bacteriophage therapy and combinations of existing antibiotics are being researched, the human population is in dire need of new antibiotics to replace those that are ineffective. This research addresses this need by identifying antibiotic producing bacteria in a soil sample from Davenport, IA. This project is a collaboration with the Tiny Earth Project Initiative (TEPI), which is a global network of educators and students focused on studentsourcing antibiotic discovery from soil. Microbiology lab techniques and 16S …

The Role Of Manganese In Streptococcus Sanguinis, Tanya M. Puccio

Theses and Dissertations

Streptococcus sanguinis is primarily associated with oral health as a commensal bacterium. As an opportunistic pathogen, S. sanguinis is capable of colonizing heart valve vegetations, leading to the disease infective endocarditis. Previous studies from our lab have identified the high-affinity manganese transporter SsaACB as important for endocarditis virulence. The impact that manganese depletion has on S. sanguinis had never been evaluated and a secondary manganese transporter has not been identified. Thus, we employed the use of a fermentor to control large-scale growth over time and depleted manganese in an ΔssaACB mutant using a metal chelator, EDTA. The changes in …

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 …

Investigation Of The Phenotypic Effect Of Mutating A Highly-Conserved Cysteine Residue In The Rna Polymerase Beta Prime Subunit Of E. Coli Rna Polymerase, Meg Dillingham

Mahurin Honors College Capstone Experience/Thesis Projects

All bacteria contain a multi-subunit RNA polymerase (RNAPs) that is essential for gene expression. Because of the centrality of these enzymes in cellular life, the structure and function of the various subunits is intensely studied. The primary sequence of the RNAP β’ subunit contains five cysteine residues that are highly conserved. Four of the cysteines coordinate a zinc atom and form the beta prime subunit zinc binding domain (ZBD). Mutation of any one of the ZBD cysteines is lethal to the cell. However, the role of the fifth residue (C58), which is located upstream of the ZBD cysteines, has not …

Epigenetic Implications In Inorganic Arsenic-Mediated Carcinogenesis, Meredith Eckstein

Theses and Dissertations--Molecular and Cellular Biochemistry

Chronic, low dose exposure to inorganic arsenic (iAs) is a public health concern throughout the world, contributing to the development of many diseases, including lung cancer. Several mechanisms for iAs-mediated carcinogenesis have been proposed, of which the production of reactive oxygen species and formation of chromosomal aberrations are the most studied. Another equally important, yet less studied mechanism is dysregulation of epigenetic marks. “Epigenetics” refers to changes that occur on the DNA and chromatin that do not alter base pair identity, but alter compaction, expression, and regulation of specific DNA sequences. There are several types of epigenetic marks including histone …