Molecular Biology Commons^™

Molecular Genetic Analysis Of Drought Resistance And Productivity Traits Of Rice Genotypes, Yheni Dwiningsih

Graduate Theses and Dissertations

Rice (Oryza sativa L.) is the staple food for a majority of the world’s population, and uses 30% of the global fresh water during its life cycle. Drought at the reproductive stage is the most important abiotic stress factor limiting grain yield. The United States is the third largest exporter of rice, and Arkansas is the top rice-producing state. The Arkansas rice-growing region in the Lower Mississippi belt is among the 10 areas with the highest risk of water scarcity. Adapted U.S. rice cultivars were screened for drought resistant (DR) traits to find sources for breeding U.S. rice cultivars for …

Population Structure Of A Federally Endangered Plant (Astragalus Jaegerianus Munz, Fabaceae) With Limited Range Using Microsatellites, Sueann Neal

Electronic Theses, Projects, and Dissertations

Studies on population genetics examine the relationship and effects of population structure, migration, gene flow and demographic history, and are therefore important in the conservation of endangered species. Astragalus jaegerianus, a critically federally endangered species found in a geographically restricted range is investigated to determine population structure and genetic variation. Previous research on A. jaegerianus focused on DNA sequence data for cpDNA and nrDNA showed no variation. Further research on A. jaegerianus utilizing AFLP’s on the whole genome indicated substantial gene diversity and population structure consistent with geographically widespread species. AFLP research is a cost-effective process to identify levels …

Regulation Of In Vitro And In Vivo Hepatic Stellate Cell Activation By The Ayrl Hydrocarbon Receptor, Shivakumar Rayavara Veerabhadraiah

Boise State University Theses and Dissertations

Liver fibrosis is a pathological condition characterized by the excessive deposition of extracellular matrix material by activated hepatic stellate cells (HSCs). We recently reported that activation of the aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor, with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) increases HSC activation in vitro and in mouse models of experimental liver fibrosis. The goal of this project was to determine the mechanism by which AhR activation impacts HSC activation and the subsequent development of liver fibrosis. It is possible that HSCs are direct cellular targets for TCDD. Alternatively, TCDD could increase HSC activation indirectly by exacerbating hepatocyte damage …

The Impact Of Microbial Experience On The Murine Innate Immune Response, Cody Thomas Morrison

Masters Theses

The hygiene hypothesis predicts that certain environmental factors shape overall immune system function in animals and humans. While current specific pathogen free (SPF) mouse models are invaluable for studying the immune system, they have limitations for comparison with humans who have microbial exposures throughout their lifetimes. Several studies have shown that the composition of the immune system of SPF mice more closely resembles that of newborns, whereas the immune system from mice exposed to microbial pathogens more closely reflect adult immunity. In this study we have established a model using traditional SPF mice (“clean mice”) and SPF mice that were …

Comprehensive Survey Of The Litter Bacterial Communities In Commercial Turkey Farms, Bishnu Adhikari, Guillermo Tellez-Isaias, Tieshan Jiang, Brian Wooming, Young Min Kwon

Poultry Science Faculty Publications and Presentations

The importance of microbiota in the health and diseases of farm animals has been well-documented for diverse animal species. However, studies on microbiotas in turkey and turkey farms are relatively limited as compared to other farm animal species. In this study, we performed a comprehensive survey of the litter microbiotas in 5 commercial turkey farms in the Northwest Arkansas (H, M, V, K, and R farms) including one farm with positive incidence of cellulitis (R farm). Altogether 246 boot swabs were used for 16S rRNA gene profiling of bacterial communities. At phylum level, 11 major bacterial phyla (≥0.01%) were recovered. …

A Context-Forward In Vivo Functional Genomics Platform For Target Discovery And Establishing Vulnerability Context In Pancreatic Cancer, Johnathon Rose, Johnathon Lynn Rose

Dissertations and Theses (Open Access)

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a very poor patient prognosis (5-year survival of ≤ 7%). While transcriptional profiling has aided in the classification of this disease into at least two broader subtypes, this alone has so far been insufficient to inform on more nuanced patterns of oncogenic dependency. We hypothesized that a more comprehensive and granular characterization of PDAC disease diversity is required to establish relevant context for targeted therapy. To this end, we sought to establish an integrated platform to: i) more comprehensively characterize differential oncogenic signaling across our tumor models, and ii) establish …

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 …

Sine Oculis Homeobox Homolog 1 (Six1) Plays A Critical Role In The Progression Of Pulmonary Fibrosis., Cory Wilson

Dissertations and Theses (Open Access)

Idiopathic pulmonary fibrosis (IPF) is the most common idiopathic interstitial pneumonia with a median survival time of 2-4 years after diagnosis. The alarming mortality rate is due to the lack of effective treatments. IPF is a chronic disease that is characterized by alveolar destruction due to increasing extracellular matrix deposition that leads to poor lung compliance, impaired gas exchange, and ultimately respiratory failure. Repetitive alveolar epithelial injury is a central process to the underlying pathology with injury to the type II alveolar epithelial cells (AT2) specifically being a key player in the pathogenesis of IPF. Recent studies have shown that …

Ionic Mechanism Of Lysosomal Function And Cell Metabolism, Jian Xiong

Dissertations and Theses (Open Access)

Two Pore Channels (TPCs) are endolysosomal ion channels that are permeable to sodium and calcium. Defects in TPCs have been implicated to impair vesicle trafficking, autophagy and cell metabolism control; however, the detailed mechanism remains largely unknown. In this study, I show that TPCs are critical for appropriate cargo delivery to the lysosomes and deletion of either TPC1 or TPC2 leads to delayed clearance of autophagosomes, resulting in enlarged lysosomes and accumulated contents inside the lysosomes. Cells with both TPC deleted also exhibit 50% reduction in lysosomal amino acids under normal culture conditions, leading to reduced homeostatic mTORC1 activation.

Glutamine …

Functional And Physiological Role Of Extra-Hypothalamic Corticotropin Releasing Hormone Neurons In The Nucleus Of The Hippocampal Commissure In Regulation Of Stress Response, Hakeem Kadhim

Graduate Theses and Dissertations

Corticotropin releasing hormone (CRH) neurons located within the paraventricular nucleus (PVN) are known to be involved in regulation of stress responses. Recently, CRH neurons were identified above the PVN within the nucleus of the hippocampal commissure (NHpC) that located in the septum. We hypothesized that CRH neurons in the NHpC play a critical role in the stress response due to their rapid activation and could be a part of the traditional hypothalamo-pituitary-adrenal (HPA) axis. The dissertation addresses the role of 1) CRH expressing neurons in the NHpC compared with those within the PVN utilizing two different stressors, food deprivation (FD) …

The Effect Of Epa And Dha On Skeletal Muscle Physiology And Energy Balance, Saeed Jebor Ghnaimawi

Graduate Theses and Dissertations

Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) supplementation commonly suggested during pregnancy confers many health benefits on offspring and more recently improves fetal BAT development and induces myoblast trans-differentiation into adiopocytes through activating PPARs expression. Embryonic myoblast is a highly flexible cell showing great capacity to change its phenotype into adipocyte in response to EPA and DHA supplementation in many in vitro models. However, a little is known about the identity of derived adipocytes, whether, they change into brown or white adipocyte, and in vivo evidence is still missing. Given that the myogeneis process is initiated at the mid of …

Prevention Of Chronic Inflammation By Targeting Macrophage Integrin Adb2, Cady Forgey

Electronic Theses and Dissertations

Macrophage integrin a_Db₂ promotes macrophage retention and accumulation within inflamed tissue, a key event in development of chronic inflammation. Recently, the P5 peptide was identified as a specific inhibitor for integrin a_Db₂ interaction with 2-(ω-carboxyethyl) pyrole (CEP), a ligand at inflammatory sites. This thesis aims to identify integrin a_D I-domain amino acids involved in binding P5 peptide and likewise to CEP. We propose that non-conserved, basic amino acids of the integrin a_Db₂ I-domain are responsible for binding to P5 peptide and likewise to CEP. Eight amino acids were analyzed by …

Degree Of Conservation Of Methionines Found To Be Oxidized In The Human Urinary Proteome, Alexis Hall

Graduate Theses and Dissertations

In previous work from this laboratory, methionine containing peptides from the human urinary proteome were examined by mass spectrometry for the degree of methionine oxidation to the sulfoxide form. While this demonstrated that many of the methionines detected were capable of being oxidized, the question of whether these methionines are important in the structure and/or function of the parent proteins came about. In some proteins, methionine oxidation has been linked to conformational changes and alteration of function and thus can serve as a mechanism for reversible regulation of activity. It is hypothesized that methionines which might serve a regulatory purpose …

Copper And Cobalt Metal Conjugation Enhances Flaviviral Replication, And Denv/Zikv Caused Thrombocytopenia Suppresses Integrin Signaling, Shovan Dutta

Biomedical Sciences Theses & Dissertations

Vector control is a global concern, and effective strategies have been on the way. Among the many different strategies, insect repellents to protect us from blood-feeding arthropods are very common. Food processing or preservatives in food expose us to several chemicals associated with insect repellents, insecticides, and pesticides. Using metallic conjugation with plant extracts or essential oils has become a widespread strategy to increase their efficacy. But it is worth it to be aware that some of those metallic compounds like Cobalt or Copper upon conjugation with thiosemicarbazone ligands derived from Citral and 2-acetylethiazole at the center coordination enhance both …

Dna Aptamer‑Based Rolling Circle Amplification Product As A Novel Immunological Adjuvant, Adil Sabr Al-Ogaili, Rohana Liyanage, Jack O. Lay Jr., Tieshan Jiang, Christine N. Vuong, Shilpi Agrawal, Thallapuranam Krishnaswamy Suresh Kumar, Luc R. Berghman, Billy M. Hargis, Young Min Kwon

Chemistry & Biochemistry Faculty Publications and Presentations

Several agonists to CD40 have shown to induce acquired immune responses. Here, we developed and evaluated the rolling circle amplification (RCA) products that are based on anti-CD40 DNA aptamers as a novel vaccine adjuvant. First, we developed DNA aptamers with specific binding affinity to chicken CD40 extra domain (chCD40ED). Next, we prepared the RCA products that consist of these aptamers to increase the spanning space and overall binding affinity to chCD40ED. Using 8 DNA aptamer candidates, 4 aptamer-based RCA products (aptamer RCAs) were generated, each consisting of two distinct aptamers. We demonstrated that all 4 aptamer RCAs significantly induced the …

Interactions Of The Nlrp3 Inflammasome Complex, Nyasha Makoni

Dissertations

The innate immune system is the first line of defense in response to invasion by pathogens. One of the major pathways in the innate immune system involves a three-protein complex known as the NLRP3 inflammasome. This complex comprises of NLRP3, ASC, and procaspase-1. In response to stimuli, the inflammasome assembles to activate caspase-1 which subsequently facilitates production of interleukin-1β (IL-1β), an inflammatory cytokine. The NLRP3 inflammasome has been implicated in a variety of inflammatory disorders including Alzheimer’s disease (AD). Amyloid beta (Aβ) is the protein that causes AD and Aβ deposits in the brain activate microglia resulting in chronic inflammation. …

An Investigation Into The Adverse Effects Of Oxidative Stress From Exposure To Bisphenol A And Its Analogues, Rachel Nas

Senior Honors Theses

Oxidative stress is a physiological event caused by an overaccumulation of reactive oxygen species (ROS) within the body. While ROS are a natural by-product of oxygen metabolism, too many can lead to cell and tissue damage and contribute to many etiologies. Bisphenol A (BPA), a component of many plastic products, has been shown to induce oxidative stress. While the industrial usage of BPA usage has lessened, the safety of its replacements is unknown. This paper will primarily discuss ROS and mechanisms of oxidative stress, the usage of BPA and its analogues, etiologies associated with oxidative stress resulting from exposure to …

Dna Aptamer-Drug Targeting Chemotherapy: Investigation Of Cell Cycle Inhibition Via S15 Aptamer – Norcantharidin Complex, Shannon Fehr

Senior Honors Theses

Lung Cancer is the leading cause of cancer related death in both men and women in the United States (Bray et al., 2018). Cancer treatments are often non-specific and kill many dividing cells within a patient causing unwanted side effects. Norcantharidin (NCTD) is a synthetic FDA approved treatment for cancers including non-small cell lung cancers (NSCLC). NCTD suppresses cell proliferation by inhibiting cells from exiting the G2 phase of the cell cycle. Aptamers are short single-stranded DNA or RNA molecules with ligand directed self-annealing capabilities allowing selective binding to specific targets. This paper will discuss the hypothesized effects of using …

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.

Posttranslational Modification And Protein Disorder Regulate Protein-Protein Interactions And Dna Binding Specificity Of P53, Robin Levy

USF Tampa Graduate Theses and Dissertations

p53 is an intrinsically disordered transcription factor that suppresses tumor development by arresting the cell cycle and promoting DNA repair. p53 deletions or mutations can lead to cancer due to the inability of cells to respond to stress. The protein levels and post-translational modification state of p53 changes in response to cellular stress like DNA damage. Previous studies have shown that p53 can undergo coupled folding and binding with the E3 ubiquitin ligase, Mdm2, and the histone deacetylase, p300. In normal cells, p53 is kept at a low level by Mdm2, which marks it with ubiquitin, targeting p53 for proteasome …

New Mechanisms That Control Fact Histone Chaperone And Transcription-Mediated Genome Stability, Angelo Vincenzo De Vivo Diaz

USF Tampa Graduate Theses and Dissertations

The Role of deubiquitinating enzymes (DUBs) in transcription, replication and genome integrity is not one that has been extensively researched. OTU DUBs are a particular class of enzyme with very little known about them.OTUD5 is a cysteine protease in the OTU family responsible to processing lysine 48 and lysine 63 ubiquitin chains. Recently, it has been implicated in to play a role in transcription through its binding partner UBR5. OTUD5 has also been shown to interact with proteins such as PDCD5 and p53, potentially have great importance in cell fate. In this study, I describe new discovered functions for OTUD5 …

White Matter Plasticity In Anxiety: Disruption Of Neural Network Synchronization During Threat-Safety Discrimination, Jia Liu, Ekaterina Likhti, A. Duke Shereen, Tracy A. Dennis-Tiwary, Patricia Casaccia

Advanced Science Research Center

Recent evidence highlighted the importance of white matter tracts in typical and atypical behaviors. White matter dynamically changes in response to learning, stress, and social experiences. Several lines of evidence have reported white matter dysfunction in psychiatric conditions, including depression, stress- and anxiety-related disorders. The mechanistic underpinnings of these associations, however, remain poorly understood. Here, we outline an integrative perspective positing a link between aberrant myelin plasticity and anxiety. Drawing on extant literature and emerging new findings, we suggest that in anxiety, unique changes may occur in response to threat and to safety learning and the ability to discriminate between …

Prevalence Of Brca1 And Brca2 Mutations Among Breast And Ovarian Cancer Patients In Northern Emirates, Zahra Ahmed Mohammed Saeed

Theses

Breast Cancer (BC) is the most common cancer and the second most cause of death among women. Mutations in BRCA1 and BRCA2 genes confer high susceptibility to both breast and ovarian cancer. However, data on the prevalence of the BRCA1/2 mutations among breast and ovarian cancer patients is limited. The genetic component of breast cancer in the UAE is largely unknown and no study has evaluated the BRCA mutations status in breast and ovarian cancer patients in the UAE population. This retrospective study aimed to establish mutation frequencies of the BRCA genes in breast and ovarian cancer patients from the …

In Vitro Invistigation Of The Heterodimerization Between Angiotensin Ii And Thrombin Receptors, Isra Mansur Al Zamel

Biology Theses

The renin angiotensin system (RAS) through its hormone angiotensin (AngII) and the protease thrombin are two major physiological regulators of vascular and renal functions. RAS is involved in the regulation of blood pressure and water-electrolytes hemostasis, while thrombin has a crucial role in platelets activation and thrombosis. The interplay between these two systems at the physiological and the pathophysiological levels has been documented in many studies. However, such an interplay at the pharmacological level between the AngII and thrombin receptors still has not been explored. Our study aimed to explore the interplay between the AngII type 1 receptor (AT1R) and …

Molecular And Physiological Assessment Of Salinity Stress Tolerance In Transgenic Arabidopsis Lines Expressing A Solanum Tuberosum Ribosome-Binding Protein, Onoud Rashed Saeed Ali Alyammahi

Biology Theses

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily associated with translation of mRNA leading to protein synthesis. Additionally, some of these proteins are known to play critical role in plants RNA metabolism during stress responses, growth, and development. In this study, transgenic Arabidopsis plants expressing a ribosomal protein S27 (hereafter D26) isolated from Solanum tuberosum was subjected to NaCl-induced salinity stress conditions, to evaluate their putative stress resistance. Transgenic plants were exposed to high salinity stress, induced by 200 mM NaCl and physiological and biochemical assays were performed. The D26 transgenic plants demonstrated improved plant height and …

Identification Of Inherited And De Novo Exomic Variations In An Emirati Family With Neurodevelopmental Disorders, Asmaa Samir Muhammed Abdelaziz Refaey

Biology Theses

Neurodevelopmental disorders (NDDs) are a heterogenous group of disorders that affect children at any point of development and lead to mental and motor function deficits. Often, the underlying cause could be genetic and inherited. This study investigated possible genetic variations that could have led to these neurological abnormalities and other genetic disorders in an Emirati family. Whole exome sequencing (WES) was used to sequence the protein-coding regions of the genome to identify potential de novo and inherited variants that are associated with disorders in this family.

WES of DNA from the parents and ten children were performed. Several variants were …

Evaluation Of The Genetic And Structural Variations Of Camel Hemoglobin, Amanat Ali

Dissertations

The single-humped Arabian camel (Camelus dromedarius) thrives in the hot arid Arabian desert. Many unique adaptations permit it to accomplish this. Camel erythrocytes or red blood cells (RBCs) have a peculiar elliptical shape and are amenable to large variations in physical conditions resulting from dehydration and rehydration cycles. The oxygen transport protein hemoglobin is found abundantly in RBCs and is also believed to behave differently in camels. While several physiological and biochemical studies have been performed on camel hemoglobin, very little is known about genetic and structural adaptions in this protein. The camel genome harbors several unique variations …

Presence Of The Hppd Inhibitor Sensitive 1 Gene And AlsS653n Mutation In Weedy Oryza Sativa Sensitive To Benzobicyclon, Chad Brabham, Jason K. Norsworthy, Fidel Gonzalez-Torralva

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha⁻¹, SC formulation) at 30 days after treatment (DAT). …

Use Of Florpyrauxifen-Benzyl In Non-Flooded Rice Production Systems, Hannah Wright, Jason K. Norsworthy, Trenton L. Roberts, Robert C. Scott, Jarrod T. Hardke, Edward E. Gbur

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The lack of a flood on rice (Oryza sativa) levees and in furrow-irrigated rice creates a favorable environment for terrestrial weeds like Palmer amaranth (Amaranthus palmeri S. Wats) to emerge and quickly overtake the crop for a longer portion of the year than in flooded rice culture. Florpyrauxifen-benzyl is a new auxin herbicide labeled for use in rice that has activity on both grasses and broadleaf weeds, as well as certain sedges. Field experiments were conducted to determine the efficacy of florpyrauxifen-benzyl in a non-flooded environment. Experiments were conducted in 2017 and 2018 at the Lon Mann …

Effect Of Ceratonia Siliqua And Cucurbita Pepo Seeds Extracts On Spermatogenesis In Male Mice, Nour Elakhdar, Roweida Bawab, Jamilah Borjac

BAU Journal - Health and Wellbeing

Worldwide, a percentage close to 50% of infertility cases is due to male-related problems including spermatogenesis defects, the process that determines sperm cells’ number and thus male fertility. Spermatogenesis is controlled by different hormones including the luteinizing hormone (LH), the follicle stimulation hormone (FSH), and testosterone. LH stimulates the Leydig cells to synthesize testosterone. FSH acts synergistically with testosterone. There is no current efficient treatment for spermatogenesis defects and people are reverting to natural remedies among which are the pumpkin and carob seeds. This study aims to evaluate the effects of pumpkin and carob seeds’ aqueous extracts on spermatogenesis and …