Molecular Biology Commons^™

Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia

Boise State University Theses and Dissertations

VPEvolve is a free and open source application that utilizes a Visual Programming Environment (VPE) for the setup of the Genetic Algorithm (GA), for optimization of computational models. Specifically, the User Interface uses connected glyphs to represent the genetic operators of mutation, reproduction, fitness and selection. These glyphs give the user an intuitive way to set the parameters for the GA, and better visualization of the population's flow through these operators.

VPEvolve is currently being developed alongside research being done in Biocomputing to create models of cellular regeneration based on the regenerative properties of Planaria or flatworms. Since these models …

Phenotypic And Functional Genomics Analyses Of Salmonella For Food Safety Applications, Turki Dawoud

Graduate Theses and Dissertations

Non-typhoidal Salmonella species have been major foodborne zoonotic pathogens causing serious problems in public health and food industry for several decades. Numerous Salmonella species have frequently been associated with different food commodities mainly poultry meat, eggs, and their products. This dissertation begins with a literature reviews discussing many aspects of Salmonella generally; and subsequently focused on two serotypes, Salmonella Enteritidis and S. Typhimurium as they are at the top of all other serovars responsible for most illness cases and outbreaks. In addition, some Salmonella strains have exhibited their ability to tolerate and survive many food processing treatments. We can divide …

The Effect Of Activation Induced Cytidine Deaminase Phosphorylation And Herpes Virus Uracil Dna Glycosylase On Antibody Diversification, Marc Macaluso

Dissertations and Theses (Open Access)

Activation-induced cytidine deaminase (AID) is a mutagenic enzyme that is expressed in mammalian B-cells and initiates the antibody diversification processes of somatic hypermuntation (SHM) and isotype class switch recombination (CSR). AID is targeted to the immunoglobulin gene locus where it deaminates cytosines to generate uracil residues in DNA. This generates guanine-uracil (U:G) mismatch lesion which are recognized by uracil DNA glycosylase (UNG), a DNA repair enzyme that removes uracil from DNA and triggers downstream repair of the lesion. While UNG is a ubiquitously expressed DNA repair enzyme, its recognition and removal of AID introduced uracils is essential in both SHM …

Dna Polymerase Θ (Polq) And The Cellular Defense Against Dna Damage, Matthew J. Yousefzadeh

Dissertations and Theses (Open Access)

In mammalian cells, DNA polymerase θ (POLQ) is an unusual specialized DNA polymerase whose in vivo function is under active investigation. The protein is comprised of an N-terminal helicase-like domain, a C-terminal DNA polymerase domain, and a large central domain that spans between the two. This arrangement is also found in the Drosophila Mus308 protein, which helps confer resistance to DNA interstrand crosslinking agents. Homologs of POLQ and Mus308 are found in eukaryotes, including plants, but a comparison of phenotypes suggests that not all of these genes are functional orthologs. Flies with defective Mus308 are sensitive to DNA interstrand crosslinking …

Investigating The Roles Of P63 And P73 Isoforms To Therapeutically Treat P53-Altered Cancers, Avinashnarayan Venkatanarayan

Dissertations and Theses (Open Access)

Investigating the roles of p63 & p73 isoforms to therapeutically treat

p53-altered cancers

Avinashnarayan Venkatanarayan, M.S.

Supervisory Professor: Elsa R. Flores, Ph.D.

The TP53 tumor suppressor is mutated in approximately 50% of human cancers rendering cancer therapies ineffective. p53 reactivation suppresses tumor formation in mice. However, this strategy has proven difficult to implement therapeutically. An alternate approach to overcome p53 loss is to manipulate the p53-family members, p63 and p73, which interact and share structural similarities to p53. p63 and p73, unlike p53 are less frequently mutated and have two major isoforms with distinct functions …

Measuring Single Cell Responses To Lapatinib In A Heterogeneous Population, Preety Priya

Dissertations and Theses (Open Access)

Cancer is notonedisease butasaga of diseases and is the outcome of disturbed homeostasis in the normal cells due to the deregulation of its genetic makeup. With advent of technologies thatallowdetailed molecular characterizationoftumors, targeted therapies have emerged as a more promising and specific mode of treatment. However, a major challenge with targeted therapy is the acquired resistance in the cancer cells to these therapies, quite often very rapidly in the course of a few months. One of the major targets in cancer has been the EGFR/ErbB2 network in breast and other cancer types. Prior work from our lab and others have …

Regulation Of Cell Adhesion By The Ferm Proteins, Ptpn14 And Merlin, Patty Dimarco Hewitt

Dissertations and Theses (Open Access)

Cell-cell adhesion is critical for the control of tissue organization and homeostasis. A family of proteins that regulate cell-cell adhesions is the FERM (4.1 protein, Ezrin, Radixin, Moesin) domain-containing proteins.One FERM domain protein, the non-receptor tyrosine phosphatase PTPN14, is mutated or deleted in several human cancers suggesting that it may be involved in tumor development and/or progression. Additionally, the loss of the FERM domain protein Merlin is associated with tumor development and metastasis.Both PTPN14 and Merlin have been shown to localize and possibly regulate adherens junction (AJ) functions. This work sought to determine if …

Molecular Mechanisms Of Tandem Cbd Of Clostridium Histolyticum, Dawn Weir

Chemistry & Biochemistry Undergraduate Honors Theses

In order to spread infections, bacterial collagenases methodically unravel collagen fibril in tissues. Collagen is the most abundant protein in the body, and can be found in the skin, bone and cartilage [1]. Two collagenases, ColG and ColH, synergistically dismantle collagen fibrils by seeking different weak links in the collagen structure. The collagen-binding domain (CBD) of these collagenases binds to most vulnerable regions in collagen [8]. Without CBDs, collagen fibril cannot be degraded. Cells express collagen receptors in order to anchor themselves, which is a critical step in cell proliferation. Binding sites for some collagen receptors, such as integrin and …

The Cancer Genome Atlas (Tcga): Breast And Ovarian Cancers, Laura Ann Riccio

Senior Honors Projects

The field of genomics originated in the 1970’s starting with the sequencing of small organisms’ genomes such as the bacterium, Haemophilus influenzae, and the yeast, Saccharomyces cerevisiae. A genome is the complete ordered sequence of DNA bases (A, C, G, and T) comprising all of the protein- and RNA-coding genes, as well as all of the regulatory sequences necessary for the construction of an organism. Over time, scientists sequenced the genomes of larger and more complex organisms, eventually leading to the sequencing of the human genome. The Human Genome Project (HGP) was initiated in 1990 and took over ten …

Local Modulation And Measurement Of Macrophage-Derived Bioactive Proteins From Implanted Biomaterials In Rat, Geetika Bajpai

Graduate Theses and Dissertations

Fibrosis around the implanted medical devices is a severe problem that can plague long-term device reliability. Activation of macrophage phenotype (macrophage polarization) has emerged as a new and possible means for reducing fibrosis in the fields of biomaterials and regenerative medicine. Macrophages are phagocytic cells that respond to microenvironmental cues that direct their phenotype. Macrophage activation has been widely studied in mouse and human in the context of tumor biology, yet little information is available regarding how macrophage activation could be used in a biomaterials context. Further, rats rather than mice are the common subjects in biomaterials experiments. A significant …

Venom Peptide Induced Inhibition Of Escherichia Coli Atp Synthase, Sofiya Azim

Undergraduate Honors Theses

ATP is the main cellular energy generated by the enzyme ATP synthase in almost all organisms from bacteria to vertebrates. While malfunction of the ATP synthase complex is responsible for several disease conditions, the enzyme itself can be used as a potent molecular drug target to combat many diseases including microbial infections, cancer, tuberculosis, and obesity. Recent widespread escalation of antibiotic resistant microbes in general and E. coli in particular demands novel alternative approaches to combat microbial infections. Inhibition of ATP synthase by inhibitors such as peptides is known to deprive microbes of required energy, resulting in microbial cell death. …

Functional Significance Of Gill Claudin Proteins In Rainbow Trout (Oncorhynchus Mykiss) Osmoregulation, Joanna Katarzyna Bujak

Graduate Theses and Dissertations

Claudin proteins, a key element of tight junction complexes, are known to control paracellular permeability. In euryhaline fish, changes in claudin abundance and localization are critical during salinity acclimation. In seawater, a leaky paracellular pathway that facilitates sodium extrusion is hypothesized to be controlled by claudin proteins. The aim of this study was to evaluate the role of Claudin-10c, -10d -10e and Claudin-30 in gill function in freshwater (FW) and seawater (SW) rainbow trout (Oncorhynchus mykiss). I examined mRNA and protein abundance along with cellular localization. A tissue distribution survey showed that all of the claudins studied were predominantly expressed …

Impacts Of Micrornas On Skeletal Muscle Protein Synthesis And Mitochondrial Quality, David Lee

Graduate Theses and Dissertations

microRNA (miRNA) post-transcriptional modification is becoming a well-established mechanism for controlling mRNA translation. microRNAs -1, -133, and -206 are under the control of skeletal muscle promoters and affect muscle plasticity and metabolic health. A detailed review on the generation and processing of miRNAs with a view to skeletal muscle brings up intriguing connections in the transcriptional connections between multiple miRNAs. Additionally, exciting new research has defined a role of miRNAs in skeletal muscle mitochondria showing an additional, direct link to metabolic function. Multiple investigations in models of exercise, aging, hypertrophy, and injury have shown how these interventions can affect miRNA …

Heterogeneous Dynamics In Dna Site Discrimination By The Structurally Homologous Dna-Binding Domains Of Ets-Family Transcription Factors, Gaofei He, Ana Tolic, James Bashkin, Gregory Poon

Chemistry & Biochemistry Faculty Works

The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only …

Repsa-Directed Identification Of Dna-Binding Specificity For Orphan Transcription Factors, Kamir Hiam

Symposium of Student Scholars

The function of many genes and the biological roles of their encoded products are still not well characterized. Given the sequence-specific DNA-binding properties of transcription factor proteins, it is possible to purify them, identify the responsible polypeptide(s), determine their consensus binding sequences, and identify their genomic binding sites. Thus, one can go from cellular extract to proposed biological regulatory roles in relatively short order. Our goal is to identify and characterize orphan DNA-binding proteins in the model organism E. coli K12 using the novel combinatorial technique, REPSA (Restriction Endonuclease Protection Selection Amplification), as well as further develop the REPSA to …

Determining Lung Cancer Subtypes, Classifications, And Potential Gene Markers, Daniel L. Johnson

Student Theses and Dissertations

Lung Cancer is the leading cause of cancer-related deaths in the United States. The key to surviving this disease is early discovery and treatment. Precise diagnosis is critical when selecting the treatment for the patient. Diagnosis of the patient will depend upon the location of the tumor, the stage of the tumor, and the class of the tumor. Clinically, lung cancer is divided into two classes: small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). Non small-cell lung cancer accounts for 85% of all lung cancer. NSCLC can be separated into three major subtypes: adenocarcinoma, squamous-cell, and large-cell …

The Effect Of Red Maple Leaf Toxicosis On Reduced Glutathione Levels In Equine Erythrocytes In Vitro, Madeline A. Rohl

Undergraduate Honors Thesis Projects

Red maple leaf toxicosis is an equine blood disorder resulting from the consumption of wilted red maple (Acer rubrum L.) leaves by horses. Compounds within the leaves of red maple have oxidative effects on equine erythrocytes and can cause hemolysis of erythrocytes, the conversion of hemoglobin to methemoglobin, and the production of Heinz bodies. Reduced glutathione is important in the protection of equine erythrocytes from these oxidative events; however, in the presence of red maple toxin, glutathione is rapidly oxidized and is unavailable. The objective of this study is to determine whether the presence of vitamin C alters levels …

Consumption Of Oral Nicotine: Its Effects On The Reproductive System And Nicotine Metabolism Of Female Sprague-Dawley Rats, Swapnali Halder

Student Theses and Dissertations

Smoking is a major preventable cause of death throughout the world and the need for cessation is unanimously supported by clinicians and scientists. Nicotine in cigarettes is believed to cause tobacco dependence and addiction and low doses of nicotine are found in nicotine replacement therapies (NRT) to mitigate withdrawal symptoms and improve cessation efforts. In addition to smoking associated health risks that are common for men and women, women smokers are more likely to suffer from pregnancy or other reproductive health related complications than non-smokers. Studies show that female smokers are more vulnerable to smoking, and find it harder to …

Characterization Of Hessian Fly From Israel, Alisha J Johnson

Open Access Dissertations

Mayetiola destructor Say, the Hessian fly, is a gall midge and a member of the Dipteran family Cecidomyiidae. It is a common pest of wheat found throughout all of the major wheat growing areas of the world and poses a serious economic threat to the United States (US), particularly in the Southeast winter wheat region. Damage to wheat is done solely by feeding first and second in-star larvae. Hessian fly (Hf) infestations result in a loss in grain yield by the stunting and/or killing of seedling wheat plants in the winter and by causing breakage at the nodes of the …

Analysis Of Chd Remodelers During Development: A Tale In Two Organisms, Brett Bishop

Open Access Dissertations

The correct development of different organisms requires the precise timing of genes important for development transitions. Organisms have recruited ATP-dependent chromatin remodelers to ensure the correct timing of gene expression during developmental transitions. Here I show how different CHD ATP-dependent chromatin remodelers regulate developmental transitions of different organisms. I show that PICKLE not only promotes H3K27me3 during development to repress developmental genes but also is targeted to these genes. The association of PICKLE to these genes suggests that both repression and H3K27me3 levels is a direct action of PICKLE on these loci. Using zebrafish as a model system, I show …