Molecular Biology Commons^™

Ph-Induced Folding Of The Caspase-Cleaved Par-4 Tumor Suppressor: Evidence Of Structure Outside Of The Coiled Coil Domain, Andrea M. Clark, Komala Ponniah, Meghan S. Warden, Emily M. Raitt, Andrea C. Yawn, Stephen M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) is a 38 kDa largely intrinsically disordered tumor suppressor protein that functions in cancer cell apoptosis. Par-4 down-regulation is often observed in cancer while up-regulation is characteristic of neurodegenerative conditions such as Alzheimer’s disease. Cleavage of Par-4 by caspase-3 activates tumor suppression via formation of an approximately 25 kDa fragment (cl-Par-4) that enters the nucleus and inhibits Bcl-2 and NF-ƙB, which function in pro-survival pathways. Here, we have investigated the structure of cl-Par-4 using biophysical techniques including circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and intrinsic tyrosine fluorescence. The results demonstrate pH-dependent folding of cl-Par-4, …

Localization Of Sip470, A Plant Lipid Transfer Protein In Nicotiana Tabacum, Shantaya Andrews

Electronic Theses and Dissertations

SABP2-interacting protein 470 (SIP470), a non-specific lipid transfer protein (nsLTP), was discovered in a yeast two-hybrid screening using SABP2 as bait and tobacco leaf proteins as prey. SABP2 is an important enzyme in systemic acquired resistance that converts salicylic acid to methyl salicylate. Localization studies are an important aspect to understanding the biological function of proteins. nsLTPs are generally considered apoplastic proteins and has been localized intracellularly and extracellularly. Transient expression shows highest expression of SIP470-eGFP at 2 days post infiltration into Nicotiana benthamiana. Confocal microscopy showed localization near the periphery of the cell. Subcellular localization using differential centrifugation showed …

Functional Consequence Of Psat1 Association On Pkm2'S Inherent Enzymatic Activity., Alexis Avidan Vega

Electronic Theses and Dissertations

Pyruvate kinase M2 (PKM2) is predominantly found in tumors, where it allows the cancer cell to adapt to metabolic conditions through allosteric regulation of its activity. We recently discovered that phosphoserine aminotransferase 1 (PSAT1) associates with and activates PKM2. Here, I sought to affirm PSAT1's ability to increase PKM2 activity through kinetic and association studies of wild-type or mutant PKM2 enzymes. I demonstrate that His-tagged WT and mutant PKM2 enzymes are active, exhibit different kinetics, yet cannot be activated by PSAT1. Comparison studies using untagged WT PKM2 suggest that inclusion of the His-tag disrupts PSAT1 association. In support, pull-down strategies …

Role Of P300 Zz Domain In Chromatin Association And Histone Acetylation, Yongming Xue

Dissertations and Theses (Open Access)

Transcription is strictly regulated by numerous factors including transcription coactivators. The p300 protein and its close paralogue CREB-binding protein (CREBBP, aka CBP) are well-known transcriptional coactivators that have intrinsic lysine acetyltransferase activity. The functions of p300/CBP largely rely on their capabilities to bind to chromatin and to acetylate the histone substrates. However, the molecular mechanisms underlying the regulation of these processes are not fully understood.

Through combination of various biochemical, biophysical and molecular approaches, we show that the ZZ-type zinc finger (ZZ) domain of p300 functions as a histone reader that specifically binds the N-terminal tail of histone H3. Crystal …

Sip-428, A Sir2 Deacetylase Enzyme And Its Role In Biotic Stress Signaling Pathway, Bal Krishna Chand Thakuri

Electronic Theses and Dissertations

SABP2 (Salicylic Acid Binding Protein 2) plays a vital role in the salicylic acid signaling pathway of plants both regarding basal resistance and systemic acquired resistance against pathogen infection. SIP-428 (SABP2 Interacting Protein-428) is a Silent information regulator 2 (SIR2) like deacetylase enzyme that physically interacts with SABP2 in a yeast two-hybrid interaction and confirmed independently by a GST pull-down assay. We demonstrated that SIP- 428 is an NAD+ dependent SIR2 deacetylase enzyme. Transgenic tobacco plants silenced in SIP- 428 expression via RNAi showed enhanced basal resistance to microbial pathogens. Moreover, these SIP-428-silenced lines also exhibited a robust induction of …

Characterization Of Acyltransferases And Wrinkled Orthologs Involved In Tag Biosynthesis In Avocado, Md Mahbubur Rahman

Electronic Theses and Dissertations

Triacylglycerols (TAG) or storage oils in plants are utilized by humans for nutrition, production of biomaterials and fuels. Since nonseed tissues comprise the bulk biomass, it is pertinent to understand how to improve their TAG content. Typically, the final step in TAG biosynthesis is catalyzed by diacylglycerol (DAG) acyltransferases (DGAT) and/or phospholipid: diacylglycerol acyltransferases (PDAT), which also determine the content and composition of TAG. Besides enzymatic regulation of TAG synthesis, transcription factors such as WRINKLED1 (WRI1) play a critical role during fatty acid synthesis. In this study, mesocarp of Persea americana, with > 60% TAG by dry weight and oleic …

Genetic And Epigenetic Investigations On Pulmonary Hypertension Syndrome In Meat Type- Chickens, Khaloud Alzahrani

Graduate Theses and Dissertations

This dissertation presents a collection of studies that investigate the genetic and epigenetic associations to ascites phenotype in broiler chickens. Ascites is a significant metabolic disease associated with fast-growing meat-type chickens (broilers) and is a terminal result of pulmonary hypertension syndrome PHS. It is a multi-factorial syndrome caused by interactions between genetic, physiological, environmental, and managemental factors. It was estimated that ascites accounts for losses of about US$1 billion annually worldwide and for over 25% of broilers mortality. Although traditional and molecular genetic methods in the selection and in performance improvements, has greatly reduced ascites frequency, yet it has not …

Genetic And Genomic Analyses Of Bacterial Responses To Different Stress Environments, Sakshi Rampal

Graduate Theses and Dissertations

Bacteria encounter a plethora of environmental stresses and have evolved different mechanisms to recognize and respond to various harmful conditions. Understanding and elucidating common themes as well as unique aspects of the molecular mechanisms underlying stress adaptation is important and can provide valuable strategies for applications. This study focuses on stress responses in three different bacteria, namely, Acidothermus cellulolyticus, Mycobacterium smegmatis and Escherichia coli. The thermophilic and acidophilic organism A. cellulolyticus was used as a model system to understand the effects of lignin phenolic acids on cellulolytic bacteria. Lignin phenolic acids pose a significant challenge to microbial deconstruction of lignocellulosic …

Developing Ultra-High Throughput Sequencing Based Assay For Ligase Ribozymes For The Study Of Evolutionary Innovations, James Collet

Boise State University Theses and Dissertations

The study of evolutionary innovations, or novel traits, is integral to understanding evolution yet is poorly understood. By studying the regions between genotype networks that produce the same phenotype, we can better characterize the process by which innovation occurs. The overarching goal of this study is to assign fitness values to the overlapping genotype network of two catalytic RNA molecules, or ribozymes. Properly characterizing this region requires the study of thousands of individual sequences, which is achievable through the use of high-throughput sequencing analysis. This thesis focuses on developing assays for one of the ribozymes, the ligase ribozyme. Due to …

Investigating Autophagy Dysfunction Induced By A Parkinson's Disease-Causing Mutation In Vps35, Abir Ashfakur Rahman

Boise State University Theses and Dissertations

Parkinson’s Disease (PD) is an idiopathic disorder with no known cure. With number of cases steadily rising around the world, it is imperative to turn to the underlying cellular and molecular mechanisms of the disease manifestation and neurodegeneration to craft novel modes of therapy. VPS35 is one of the few genes that have identified and definitively linked to familial PD. The particular mutation that has been associated is known to cause dysfunction of a key cellular process known as autophagy. This process is primarily responsible for clearance of unwanted, damaged or misfolded proteins, among other things. Our study reveals an …

A Simple Metabolic Switch May Activate Apomixis In Arabidopsis Thaliana, David Alan Sherwood

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Apomixis, asexual or clonal seed production in plants, can decrease the cost of producing hybrid seed and enable currently open pollinated crops to be converted to more vigorous and higher yielding hybrids that can reproduce themselves through their own seed. Sexual reproduction may be triggered by a programmed stress signaling event that occurs in both the meiocyte, just prior to meiosis, and later in the egg just prior to embryo sac maturation. The prevention of stress signaling and the activation of a pro-growth signal prior to meiosis triggered apomeiosis, the first half of apomixis. The same approach was used prior …

Differentiation Of Oligodendrocytes For Myelination In The Nervous System, Krishna Deo Sharma

Student Theses and Dissertations

Differentiation of neural stem cells (NSCs) into large a number of oligodendrocytes (ODCs) for transplantation therapy has been a challenge. Evidence indicates that NSC differentiation is influenced by the interaction of the stem cells and their extracellular environment such as extracellular matrix (ECM), and soluble factors, such as growth factors and hormones. We tested if (1) well planned sequential addition of a combination of soluble factors increase the population of NSCs differentiating into ODCs and (2) a natural ECM (e.g, matrigel) promotes ODC differentiation better than poly-D-lysine (PDL). Embryonic rat NSCs were propagated in the presence of basic fibroblast growth …

Metformin, Oxidative Stress, And Infertility: A Way Forward, Rehana Rehman, Syed Hani Abidi, Faiza Alam

Department of Biological & Biomedical Sciences

No abstract provided.

Cryptic Diversity In The Mexican Highlands: Thousands Of Uce Loci Help Illuminate Phylogenetic Relationships, Species Limits And Divergence Times Of Montane Rattlesnakes (Viperidae: Crotalus ), Christopher Blair, Robert W. Bryson Jr, Charles W. Linkem, David Lazcano, John Klicka, John E. Mccormack

Publications and Research

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum …

Puf Proteins: Regulation Of Condition-Specific Mrna Decay And Contributions To Ribosome Biogenesis In Yeast, Anthony Fischer

Dissertations

Regulation of protein expression is critical to organism survival. Multiple disease states arise from aberrant accumulation/aggregation of proteins or reduced production of key enzymes. Cells have many ways to manipulate protein levels, including transcription factors, chromatin modification, modification of messenger RNA (mRNA), and manipulation of proteolytic protein decay. Cells can indirectly control protein volume by controlling mRNA lifespan, which is directly correlated with protein output. Often, sequence-specific elements in mRNA contribute to this lifespan. The Puf family of RNA-binding proteins is ubiquitous throughout eukarya, and plays important cellular and developmental roles through mRNA lifespan regulation. Puf proteins contain a C-terminal …

Cyclophilin 40 As A Novel Disaggregase, Jeremy Dustin Baker

USF Tampa Graduate Theses and Dissertations

The negative health and economic impacts of neurodegenerative diseases on Americans is astounding and accelerating with an aging population. The Alzheimer’s Association reports that 5.7 million Americans suffer from Alzheimer’s disease (AD), a number which is expected to increase to 14 million by 2050. In economic terms, AD and other neurodegenerative disorders will cost the US over $275 billion in 2018, rising to over $1 trillion annually by 2050. AD causes gross brain atrophy and is most damaging throughout the cortex and the hippocampus, regions required for higher cognitive function and memory. AD presents as tangles within neurons composed of …

Actinomycin D And Telmisartan Combination Therapy Targets Lung Cancer Stem Cells, Ryan Green

USF Tampa Graduate Theses and Dissertations

The failure of lung cancer treatments has been attributed partly to the development of drug resistance, however the underlying cellular and molecular mechanisms are poorly understood. It has been suggested that a very small group of specific cells within the heterogeneous tumors, cancer initiating stem cells (CSC), develop resistance to treatment, survive and later initiate the growth of new tumors. Due to their pivotal role in maintenance and relapse of tumors following the acquisition of drug resistance, we reasoned that novel drugs targeting cancer cells and CSC might provide the most effective treatments, if not a cure. To this end, …

Investigating The Roles Of Fucosylation And Calcium Signaling In Melanoma Invasion, Tyler S. Keeley

USF Tampa Graduate Theses and Dissertations

Melanoma is the deadliest form of skin cancer. Prognosis for early stage melanoma patients is excellent, and surgery is often curative for these patients. However, once patients have presented with invasive disease, the average 5-year survival rate drops significantly from over 90% to between 10 and 15%. Several therapies have been developed to target a commonly mutated oncogene BRAF, or its downstream effectors. Unfortunately, while these treatments show robust initial response, most patients relapse within a year. Moreover, therapy-resistant tumors are often more invasive and metastatic. Therefore, it is important to investigate the molecular mechanisms underlying melanoma invasion and metastasis, …

Investigating The Role Of The Rna Binding Protein Lin28 In The Human Placenta: Implications For Preeclampsia, John Canfield

USF Tampa Graduate Theses and Dissertations

An essential event during early pregnancy is the invasion of trophoblasts into the maternal decidua, which is necessary for proper implantation and establishment of maternal-fetal interface and ultimately allows for proper nutrient exchange and immunological tolerance of the growing fetus. For this invasion to occur, cells originating from the trophectoderm undergo an epithelial to mesenchymal transition to become invasive extravillous trophoblasts and begin invading the uterine decidual tissue. Through the secretion of matrix metalloproteinases and through interactions with many cytokines and cell-adhesion molecules, this well-orchestrated process of trophoblast invasion results in extensive remodeling of the maternal spiral vasculature by the …

Development Of A Pd-L1 Pet Imaging Biomarker, Caleb Jack Bridgwater

Posters-at-the-Capitol

Immunotherapy strategies are very promising treatments for cancer patients. Specifically, Immune checkpoint inhibitor therapy focusing on the PD-1/PD-L1 pathway shows long-lasting positive results in many cancer patients. Unfortunately, not all the patients can benefit from this highly effective treatment. Hence, there is a great need for predictive biomarkers. Immunohistochemical (IHC) staining has been used as a way of predicting patient response, yet shows many problems. For example, IHC utilizes an invasive biopsy and sample fixing, which creates an incomplete and delayed picture of the patient’s biochemistry and the tumor microenvironment, consequently ignoring metastases.

The purpose of this study is to …