Evolution And Divergence Of The Structural And Physical Properties Of Dna Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3,
2014
Virginia Commonwealth University
Evolution And Divergence Of The Structural And Physical Properties Of Dna Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3, Jason Cramer
Theses and Dissertations
The studies presented in this dissertation, Evolution And Divergence Of The Structural And Physical Properties Of DNA Binding By Methyl-Cytosine Binding Domain Family Members 2 And 3, pertain primarily to two key epigenetic regulators involved with the biological interpretation of methylated DNA marks. We provide insights into the emergence and evolution of the MBD2 and MBD3 and how those molecular entities influence heritable changes in gene activity. We further provide details regarding the mystery surrounding MBD3 function and the MBD2-mediated capacity of primitive animals to carry out methylation-specific epigenetic mechanisms. In chapter two, we describe the DNA binding properties of …
A Summary Of Three Antibiotic Resistant Bacteria Studies Of Plaster Creek,
2014
Calvin University
A Summary Of Three Antibiotic Resistant Bacteria Studies Of Plaster Creek, Yeaeun Lee, David P. Warners
Faculty and Professional Research
No abstract provided.
Nine Year Assessment Of Soil Treatment On Aguacatillo (Nectandontisii And Ocotea Austinii, Lauraceae) Seedling Success In The Restoration Of A Costa Rican Cloud Forestra Cufo,
2014
Calvin University
Nine Year Assessment Of Soil Treatment On Aguacatillo (Nectandontisii And Ocotea Austinii, Lauraceae) Seedling Success In The Restoration Of A Costa Rican Cloud Forestra Cufo, Sheila Devries, David Warners
Faculty and Professional Research
We tracked seedling growth of two species of aguacatillo (Nectandra cufodontisii (O. C. Schmidt) C. K. Allen and Ocotea austinii C. K. Allen) that were planted into an early successional cloud forest hillside in San Gerardo de Dota, Costa Rica over nine years. Seedlings were collected from underneath nearby mother trees and transplanted into one of three soil treatments: indigenous soil; a 50:50 mixture of horse manure and indigenous soil; and a 50:50 mixture of kitchen compost and indigenous soil. After seedlings were transplanted they were measured and each specific location was evaluated for light exposure. Two months later seedlings …
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features,
2014
Old Dominion University
Template-Based C8-Scorpion: A Protein 8 State Secondary Structure Prediction Method Using Structural Information And Context-Based Features, Ashraf Yaseen, Yaohang Li
Computer Science Faculty Publications
Background: Secondary structures prediction of proteins is important to many protein structure modeling applications. Correct prediction of secondary structures can significantly reduce the degrees of freedom in protein tertiary structure modeling and therefore reduces the difficulty of obtaining high resolution 3D models.
Methods: In this work, we investigate a template-based approach to enhance 8-state secondary structure prediction accuracy. We construct structural templates from known protein structures with certain sequence similarity. The structural templates are then incorporated as features with sequence and evolutionary information to train two-stage neural networks. In case of structural templates absence, heuristic structural information is incorporated instead. …
Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions,
2014
Old Dominion University
Tracing Beta Strands Using Strandtwister From Cryo-Em Density Maps At Medium Resolutions, Dong Si, Jing He
Computer Science Faculty Publications
Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5–10 A˚ . However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM …
Characterization Of The Transporter Protein Sodium-Potassium Adenosine Triphosphatase In The Myelin Membrane,
2014
Wilfrid Laurier University
Characterization Of The Transporter Protein Sodium-Potassium Adenosine Triphosphatase In The Myelin Membrane, Dara E C Schaefer
Theses and Dissertations (Comprehensive)
Sodium-potassium adenosine triphosphatase (Na+/K+-ATPase) is an integral membrane protein with known involvement in the maintenance of resting membrane potentials, nutrient uptake, cellular signal transduction, and cell-cell adhesion. The functional enzyme contains a catalytic alpha subunit and a glycosylated beta subunit, of which three isoforms of each are known to exist in the central nervous system (CNS). Altered expression and/or activity of Na+/K+-ATPase subunit isoforms has been previously implicated in the pathophysiology of several neurological disorders. This study characterized Na+/K+-ATPase expression and distribution in the myelin membrane, identified its …
Distribution And Elimination Of 3-Trifluoromethyl-4-Nitrophenol (Tfm) By Sea Lamprey (Petromyzon Marinus) And Non-Target, Rainbow Trout (Oncorhynchus Mykiss) And Lake Sturgeon (Acipenser Fulvescens),
2014
Wilfrid Laurier University
Distribution And Elimination Of 3-Trifluoromethyl-4-Nitrophenol (Tfm) By Sea Lamprey (Petromyzon Marinus) And Non-Target, Rainbow Trout (Oncorhynchus Mykiss) And Lake Sturgeon (Acipenser Fulvescens), Michael W. Le Clair
Theses and Dissertations (Comprehensive)
The pesticide, 3-trifluoromethyl-4-nitrophenol (TFM), has been highly successful in the control of sea lamprey (Petromyzon marinus) populations in the Great Lakes. Treatments with TFM involve applying it to streams, where it targets larval sea lamprey which live burrowed in the stream substrate. While the toxic mechanism of TFM has been elucidated, and its effects on sea lamprey described, its effects on non-target fish species such as rainbow trout (Oncorhynchus mykiss) and lake sturgeon (Acipenser fulvescens) are not as well understood. The present work demonstrated that rainbow trout show a great capacity to detoxify the lampricide using glucuronidation, when exposed to …
Partitioning The Fitness Components Of Rna Populations Evolving In Vitro,
2013
Portland State University
Partitioning The Fitness Components Of Rna Populations Evolving In Vitro, Carolina Diaz Arenas, Niles Lehman
Chemistry Faculty Publications and Presentations
All individuals in an evolving population compete for resources, and their performance is measured by a fitness metric. The performance of the individuals is relative to their abilities and to the biotic surroundings – the conditions under which they are competing – and involves many components. Molecules evolving in a test tube can also face complex environments and dynamics, and their fitnessmeasurements should reflect the complexity of various contributing factors as well. Here, the fitnesses of a set of ligase ribozymes evolved by the continuous in vitroevolution system were measured. During these evolution cycles there are three different catalytic …
Novel And Predominant Pathogen Responsible For The Enterovirus-Associated Encephalitis In Eastern China,
2013
Zhejiang Provincial Center for Disease Control and Prevention
Novel And Predominant Pathogen Responsible For The Enterovirus-Associated Encephalitis In Eastern China, Lei Zhang, Jie Yan, David M. Ojcius, Huakun Lv, Ziping Miao, Yin Chen, Yanjun Zhang, Jvying Yan
All Dugoni School of Dentistry Faculty Articles
Enteroviruses (EV) have been increasingly identified as the causative agent for unknown etiological encephalitis in many parts of the world, but the long period surveillance for enterovirus-associated encephalitis (EAE) was not reported in China. From 2002-2012 in Zhejiang, Coxsackieviruses A9, B1, B2, B3, B4, B5; and echoviruses 3, 4, 6, 9, 14, 25, 30 were detected from the unknown etiological encephalitis cases, with coxsackievirus B4 been identified here for the first time. From 2002-2004 and 2010-2012, echovirus 30 was found to be the periodically predominant serotype for in the EAE. The molecular typing results showed that all the EV isolates …
Using Expression Profiling To Understand The Effects Of Chronic Cadmium Exposure On Mcf-7 Breast Cancer Cells,
2013
Systems Biology Research Centre – Bioinformatics, School of Bioscience, University of Skövde
Using Expression Profiling To Understand The Effects Of Chronic Cadmium Exposure On Mcf-7 Breast Cancer Cells, Zelmina Lubovac-Pilav, Daniel M. Borras, Esmeralda Ponce, Maggie Louie
Collected Faculty Scholarship
Cadmium is a metalloestrogen known to activate the estrogen receptor and promote breast cancer cell growth. Previous studies have implicated cadmium in the development of more malignant tumors; however the molecular mechanisms behind this cadmium-induced malignancy remain elusive. Using clonal cell lines derived from exposing breast cancer cells to cadmium for over 6 months (MCF-7-Cd4, -Cd6, -Cd7, -Cd8 and -Cd12), this study aims to identify gene expression signatures associated with chronic cadmium exposure. Our results demonstrate that prolonged cadmium exposure does not merely result in the deregulation of genes but actually leads to a distinctive expression profile. The genes deregulated …
Purifying The Human Rna-Lariat Debranching Enzyme,
2013
St. Mary's University
Purifying The Human Rna-Lariat Debranching Enzyme, Ammar Saigal
Honors Program Theses and Research Projects
This project is my first official research endeavor and it involved becoming acquainted with a large variety of biochemistry and molecular biology techniques. The goal is to elucidate the structure of a protein common to most if not all cells of organisms within the Domain Eukarya, which is one of the three taxonomic domains into which all life is categorized. This is the domain most relevant to human beings as it includes plants, fungi, and animals (from a strictly biologically-taxonomic perspective, the species Homo sapiens to which you and I belong is considered belonging to the Kingdom Animalia [Animal]).
The Effects Of Chronic Simvastatin Treatment On The Expression Of Behavioral Symptoms In A Transgenic Mouse Model Of Huntington’S Disease,
2013
University of New Orleans
The Effects Of Chronic Simvastatin Treatment On The Expression Of Behavioral Symptoms In A Transgenic Mouse Model Of Huntington’S Disease, Ashley Whitmarsh
LSU New Orleans Theses and Dissertations
Huntington’s disease (HD) is a heritable, neurodegenerative disorder characterized by motor, cognitive, and psychiatric disturbances. An unstable CAG expansion within the gene normally encoding for the Huntingtin protein is responsible. The expanded mutant form of Huntingtin and the putative protein co-factor Rhes interact and cause cell death within the striatum. We hypothesized chronic treatment with simvastatin, a cholesterol lowering drug, would disrupt the biosynthetical pathway which gives both Rhes and its target cells binding sites and render Rhes inactive. Healthy and HD mice were treated with simvastatin or a vehicle. Animals’ motor behavior was assessed with three separate tests over …
The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage,
2013
Coastal Carolina University
The Effects Of Salinity, Ph, Temperature, And Dissolved Oxygen On Sensitivity Of Pcr Identification Of T4 Bacteriophage, Joesph F. Cannon, Nicholas A. Thurn, Paul E. Richardson
Journal of the South Carolina Academy of Science
Bacteriophages are used as indicators of pathogenic bacteria in drinking, and wastewaters. They also show potential in limiting aquatic bacterial populations through their lytic properties. The effect of different water characteristics (salinity, pH, dissolved oxygen, and temperature) on the sensitivity of the PCR identification of virus particles were analyzed to determine at what levels bacteriophage can be detected in environmental samples. Results from this preliminary study indicate that a PCR bacteriophage detection technique has potential as a relatively efficient and economical indicator of coliform contamination in multiple aquatic environments. While further evaluation is needed, the protocol appears to function in …
Molecular Evolution Of Protein-Rna Mimicry As A Mechanism For Translational Control,
2013
The Ohio State University
Molecular Evolution Of Protein-Rna Mimicry As A Mechanism For Translational Control, Assaf Katz, Lindsey Solden, S. Betty Zou, William Wiley Navarre, Michael Ibba
Biology, Chemistry, and Environmental Sciences Faculty Articles and Research
Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the …
Biochemical Assay Optimization And Computational Screening Efforts To Identify Potential Luxs Inhibitors,
2013
University of San Francisco
Biochemical Assay Optimization And Computational Screening Efforts To Identify Potential Luxs Inhibitors, Keeshia Q. Wang
Master's Theses
Quorum sensing (QS) is a process of coordination of bacterial gene expression in response to cell population. System two QS is regulated by the small signaling molecule autoinducer-2 (AI-2) and is implicated in the infectious behaviors of various bacterial species. AI-2 is biosynthesized from S-ribosylhomocysteine (SRH) by the enzyme LuxS and induces interspecies cell-to-cell communication. Inhibition of LuxS would therefore inhibit interspecies QS. Herein, a search for novel molecular species that will competitively bind with SRH in the LuxS binding site is performed in silico. Computational screening results are then validated in vitro using an optimized LuxS inhibition …
Synthesis, Characterization, And Application Of High Surface Area, Mesoporous, Stabilized Anatase Tio2 Catalyst Supports,
2013
Brigham Young University - Provo
Synthesis, Characterization, And Application Of High Surface Area, Mesoporous, Stabilized Anatase Tio2 Catalyst Supports, Rebecca Elizabeth Olsen
Theses and Dissertations
Nanomaterials have attracted substantial attention in the area of catalysis due to the unique properties they exhibit such as high surface areas, intricate pore networks and unique morphologies. TiO2 has attracted attention as a catalyst since the discovery of its high photocatalytic activity by Fuishima and Honda in 1972. Given its high thermal stability, low cost, low environmental impact, and versatility, TiO2 is a widely used commercial catalyst and catalyst support. TiO2 is used in many applications such as photocatalysis is also an excellent support material for noble metals in a number of oxidative synthesis and pollution-control reactions. Though TiO2 …
Nonlinear Spectroscopic Investigation Of Adsorption To C-18 Model Stationary Phase,
2013
Brigham Young University - Provo
Nonlinear Spectroscopic Investigation Of Adsorption To C-18 Model Stationary Phase, Anthony D. Peterson
Theses and Dissertations
Reversed-phase liquid chromatography (RPLC) is a commonly used separation technique in chemistry. Nevertheless, the mechanistic interactions at the molecular level among the eluent, analyte, and the stationary phase are not fully understood. Because of this limited understanding, optimization of the separation must be done experimentally. Learning more about molecular interactions should aid in improving separations. We are currently using second-harmonic generation (SHG) spectroscopy to investigate how analytes adsorb to the surface. SHG is a spectroscopic technique that produces signal only at places of non-isotropic symmetry; this typically occurs at surfaces. SHG can be used to produce surface isotherms of test …
Making Chlamydomonas Reinhardtii A Better Model Organism: Tackling The Inefficiency Of Nuclear Transgene Expression And Improving Methods For The Generation And Characterization Of Insertional Mutant Libraries,
2013
University of Nebraska-Lincoln
Making Chlamydomonas Reinhardtii A Better Model Organism: Tackling The Inefficiency Of Nuclear Transgene Expression And Improving Methods For The Generation And Characterization Of Insertional Mutant Libraries, Thomas M. Plucinak
Department of Biochemistry: Dissertations, Theses, and Student Research
The green algal species Chlamydomonas reinhardtii possesses many beneficial features that have made it a useful model organism for many decades. Many types of experimentation however are difficult to conduct with this organism due to the relative under-development of genetic tools available for use. Tasks such as transgene expression, overexpression of proteins of interest (POIs) or site specific genomic modification that are routine in other more facile microbial model organisms such as Escherichia coli and yeast are difficult to accomplish in C. reinhardtii. The second chapter of this thesis describes the development of a novel nuclear transgene expression system …
Functional Analysis Of The Acetic Acid Resistance (Aar) Gene Cluster In Acetobacter Aceti Strain 1023,
2013
Purdue University
Functional Analysis Of The Acetic Acid Resistance (Aar) Gene Cluster In Acetobacter Aceti Strain 1023, Elwood Mullins, T Joseph Kappock
Department of Biochemistry Faculty Publications
Vinegar production requires acetic acid bacteria that produce, tolerate, and conserve high levels of acetic acid. When ethanol is depleted, aerobic acetate overoxidation to carbon dioxide ensues. The resulting diauxic growth pattern has two logarithmic growth phases, the first associated with ethanol oxidation and the second associated with acetate overoxidation. The vinegar factory isolate Acetobacter aceti strain 1023 has a long intermediate stationary phase that persists at elevated acetic acid levels. Strain 1023 conserves acetic acid despite possessing a complete set of citric acid cycle (CAC) enzymes, including succinyl-CoA:acetate CoA-transferase (SCACT), the product of the acetic acid resistance (aar …
Formation And Analysis Of Zinc Oxide Nanoparticles And Zinc Oxide Hexagonal Prisms And Optical Analysis Of Cadmium Selenide Nanoparticles,
2013
Brigham Young University - Provo
Formation And Analysis Of Zinc Oxide Nanoparticles And Zinc Oxide Hexagonal Prisms And Optical Analysis Of Cadmium Selenide Nanoparticles, Jared M. Hancock
Theses and Dissertations
In this dissertation, methods to synthesize ZnO are reported. First, zinc oxide nanoparticles were synthesized with small amounts of transition metal ions to create materials called dilute magnetic semiconductors (DMS). We employed a low temperature sol-gel method that produces ZnO nanoparticles of reproducible size and incorporates cobalt, nickel, and manganese ions into the nanoparticles. Conditions were controlled such that a range of amounts of Co, Ni, and Mn were incorporated. The incorporation was tracked by color changes in the white ZnO powder to blue for Co, green for Ni and yellow for Mn. XRD measurements showed the nanoparticles were on …
