Biology Commons^™

Comparison Of Measures Of Marker Informativeness For Ancestry And Admixture Mapping, Lili Ding, Howard Wiener, Tilahun Abebe, Mekbib Altaye, Rodney Cp Go, Carolyn Kercsmar, Greg Grabowski, Lisa J. Martin, Gurjit K. Khurana Hershey, Ranajit Chakorborty, Tesfaye M. Baye

Faculty Work

Background: Admixture mapping is a powerful gene mapping approach for an admixed population formed from ancestral populations with different allele frequencies. The power of this method relies on the ability of ancestry informative markers (AIMs) to infer ancestry along the chromosomes of admixed individuals. In this study, more than one million SNPs from HapMap databases and simulated data have been interrogated in admixed populations using various measures of ancestry informativeness: Fisher Information Content (FIC), Shannon Information Content (SIC), F statistics (F_ST), Informativeness for Assignment Measure (I_n), and the Absolute Allele Frequency Differences (delta, δ). …

The Effects Of Hypergravity On Xenopus Embryo Growth And Cardiac Hypertrophy, Bryce Joseph Duchman

Honors Program Theses

All life on earth has developed and evolved in a 1 G environment. Therefore, any deviation below or above unit gravity will likely have an effect on the development of organisms, including the migration of cells and the dispersion of nutrients. The purpose of this research project is to analyze the effects of hypergravity on the overall body length and cardiac growth of Xenopus laevis embryos. I predict that cardiac hypertrophy will occur in embryos subjected to hypergravity because of the increased force required from the heart to adequately circulate blood and, thus, disperse nutrients. Upon reaching early gastrulation, embryos …

A Phylogenetic Assessment Of Breeding Systems And Floral Morphology Of North American Ipomoea (Convolvulaceae), J. Andrew Mcdonald, Joshua R. Mcdill, Debra R. Hansen, Beryl B. Simpson

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

A phylogenetic investigation of 68 species and two varieties of tropical and temperate North American Ipomoea (Convolvulaceae) using sequence data from the internal transcribed spacer region (ITS) with parsimony and Bayesian analyses revealed multiple origins of autogamy. By assessing breeding systems and floral morphological characters in the context of this phylogeny, we estimate 16 independent origins of autogamy and 4 subsequent reversions to xenogamy. Transitions to autogamy are associated with reduced pollen-ovule ratios, decreased anther-stigma distance, and small flower size. Although the relationship between floral traits and breeding systems has been described in previous studies, this is the first investigation …

Factors Affecting Growth And Condition Of Stocked Rainbow Trout In Eastern Washington Lakes, Tamara Knudson

EWU Masters Thesis Collection

"Rainbow trout growth and condition were examined in 17 ecologically diverse lakes from which physical, limnological, and biological parameters were sampled. Parameters were correlated with rainbow trout growth and condition to identify factor(s) that predict rainbow trout growth and condition across eastern Washington lakes stocked annually with rainbow trout fry. We tested the hypothesis Ho: the environmental variables examined do not predict rainbow trout growth and condition. Data were natural log transformed for better fit, and were analyzed by season. Several models were identified using stepwise multiple regression analysis and general linear modeling which significantly predicted trout growth or condition …

Linear Methods For Analysis And Quality Control Of Relative Expression Ratios From Quantitative Real-Time Polymerase Chain Reaction Experiments, Robert B. Page, A. J. Stromberg

Biology Faculty Publications (Archived)

Relative expression quantitative real-time polymerase chain reaction (RT-qPCR) experiments are a common means of estimating transcript abundances across biological groups and experimental treatments. One of the most frequently used expression measures that results from such experiments is the relative expression ratio (RE), which describes expression in experimental samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to one or more experimental or nonbaseline condition) in terms of fold change relative to calibrator samples (i.e., RNA isolated from organisms, tissues, and/or cells that were exposed to a control or baseline condition). Over the past decade, several models of …

Development Of A Semi-Field System For Contained Field Trials With Aedes Aegypti In Southern Mexico, L. Facchinelli, L. Valerio, J. G. Bond, Megan R. Wise De Valdez, L. C. Harrington, J. M. Ramsey, M. Casas-Martinez, T. W. Scott

Biology Faculty Publications (Archived)

Development of new genetic approaches to either interfere with the ability of mosquitoes to transmit dengue virus or to reduce vector population density requires progressive evaluation from the laboratory to contained field trials, before open field release. Trials in contained outdoor facilities are an important part of this process because they can be used to evaluate the effectiveness and reliability of modified strains in settings that include natural environmental variations without releasing mosquitoes into the open field. We describe a simple and cost-effective semi-field system designed to study Aedes aegypti carrying a dominant lethal gene (fsRIDL) in semi-field conditions. We …

Genetic Elimination Of Dengue Vector Mosquitoes, Megan R. Wise De Valdez, D. Nimmo, J. Betz, H.-F. Gong, A. A. James, L. Alphey, W. C. Black Iv

Biology Faculty Publications (Archived)

An approach based on mosquitoes carrying a conditional dominant lethal gene (release of insects carrying a dominant lethal, RIDL) is being developed to control the transmission of dengue viruses by vector population suppression. A transgenic strain, designated OX3604C, of the major dengue vector, Aedes aegypti, was engineered to have a repressible female-specific flightless phenotype. This strain circumvents the need for radiation-induced sterilization, allows genetic sexing resulting in male-only releases, and permits the release of eggs instead of adult mosquitoes. OX3604C males introduced weekly into large laboratory cages containing stable target mosquito populations at initial ratios of 8.5-10:1 OX3604C:target eliminated the …

Simulation Of Spatial Movement That Potentially Maximizes Assessment, Presence, And Defence In Territorial And Home-Ranging Animals, With Special Reference To Territorial Sex-Changing Fishes, Thomas R. Brown, Joshua Jowers, Marvin M.F. Lutnesky

Biology Faculty Publications (Archived)

Question: Are there territory sizes, shapes, and movement rules that animals can use to maximize their presence for territorial and reproductive purposes? Features of the model: Individual-oriented simulation model of a focal male, a female (his mate), and six other males in adjacent territories. Simulation variables were territory size and aspect (length-to-width ratio), velocity, step size, and potential movement angle. Each simulation represented 10,000 s of real time, and simulations were repeated until convergence on maximum mean encounter rates (MER) of a focal male with the female and other males was reached. Ranges of variables: Simulations consisted of three velocities …

Altered Calcium Handling In Cerebellar Purkinje Neurons With The Malignant Hyperthermia Mutation, Ryr1-Y522s/+, George C. Talbott

Electronic Theses and Dissertations

To investigate the etiology of malignant hyperthermia and central core disease, mouse models have recently been generated and characterized (Chelu et al., 2006). These RyRY522S/+ knock-in mutant mice provide an excellent tool to investigate calcium dysregulation, its pathological consequences, and potential therapeutic approaches. Skeletal muscle harboring this mutation exhibits calcium leak from internal stores and an increased sensitivity to activation by caffeine, voltage, and temperature (Durham et al., 2008). Although alterations in RyR1 channel function and resultant changes in cellular function have been characterized in skeletal muscle, the effects of MH mutations in RyR1 on central nervous system function have …

Quantifying Agonist Activity At G Protein-Coupled Receptors, Frederick J. Ehlert, Hinako Suga, Michael T. Griffin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

When an agonist activates a population of G protein-coupled receptors (GPCRs), it elicits a signaling pathway that culminates in the response of the cell or tissue. This process can be analyzed at the level of a single receptor, a population of receptors, or a downstream response. Here we describe how to analyze the downstream response to obtain an estimate of the agonist affinity constant for the active state of single receptors.

Receptors behave as quantal switches that alternate between active and inactive states (Figure 1). The active state interacts with specific G proteins or other signaling partners. In the absence …

Society For The Advancement Of Biology Education Research (Saber), Erika G. Offerdahl, Teri Balser, Clarissa Dirks, Kathryn Miller, Jennifer L. Momsen, Lisa Montplaisir, Marcy Osgood, Karen Sirum, Mary Pat Wenderoth, Brian White, William B. Wood, Michelle Withers, Robin Wright

Biology Faculty Research

No abstract provided.

Magnetic Scanometric Dna Microarray Detection Of Methyl Tertiary Butyl Ether Degrading Bacteria For Environmental Monitoring, Mei-Lin Chan, Gerardo Jaramillo, Krassimira R. Hristova, David A. Horsley

Biological Sciences Faculty Research and Publications

A magnetoresistive biosensing platform based on a single magnetic tunnel junction (MTJ) scanning probe and DNA microarrays labeled with magnetic particles has been developed to provide an inexpensive, sensitive and reliable detection of DNA. The biosensing platform was demonstrated on a DNA microarray assay for quantifying bacteria capable of degrading methyl tertiary butyl ether (MTBE), where concentrations as low as 10 pM were detectable. Synthetic probe bacterial DNA was immobilized on a microarray glass slide surface, hybridized with the 48 base pair long biotinylated target DNA and subsequently incubated with streptavidin-coated 2.8 μm diameter magnetic particles. The biosensing platform then …

Novel Insights Into The Biotin Carboxylase Domain Reactions Of Pyruvate Carboxylase From Rhizobium Etli, Tonya N. Zeczycki, Ann L. Menefee, Abdussalam Adina-Zada, Sarawut Jitrapakdee, Kathy H. Surinya, John C. Wallace, Paul V. Attwood, Martin St. Maurice, W Wallace Cleland

Biological Sciences Faculty Research and Publications

The catalytic mechanism of the MgATP-dependent carboxylation of biotin in the biotin carboxylase domain of pyruvate carboxylase from R. etli (RePC) is common to the biotin-dependent carboxylases. The current site-directed mutagenesis study has clarified the catalytic functions of several residues proposed to be pivotal in MgATP-binding and cleavage (Glu218 and Lys245), HCO3 − deprotonation (Glu305 and Arg301), and biotin enolization (Arg353). The E218A mutant was inactive for any reaction involving the BC domain and the E218Q mutant exhibited a 75-fold decrease in kcat for both pyruvate carboxylation and the full reverse reaction. The E305A mutant also showed a 75- and …

Techniques To Facilitate The Acquisition Of Accurate Spectral Measurements And Multispectral Imagery Of Plant Foliage Under Artificial Lighting Conditions, Yuridia Patricia Gandy, Ashish Mamachen, Adarsh Mamachen, Jonathan Lieman, Michael W. Persans, Jason Parsons, Elamin E. Ibrahim, James H. Everitt, Christopher R. Little, Kenneth R. Summy

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Spectral measurements obtained in the laboratory under artificial lighting sources have been used for many years to develop spectral ‘libraries’ for various soil types, rocks and minerals, and other inanimate features occurring on or near the earth’s surface. Quartz halogen lamps have been shown to emit all of the electromagnetic (EMR) wavelengths required for the acquisition of quality multispectral imagery, and various techniques have been developed to facilitate the acquisition of accurate spectral measurements using such artificial lighting sources. Our objectives in this study were to evaluate the several factors of critical importance in obtaining accurate spectral measurements for plant …

Effects Of Leaf Excision And Sample Storage Methods On Spectral Reflectance By Foliage Of Giant Reed, Arundo Donax, Kenneth R. Summy, Jonathan Lieman, Yuridia Patricia Gandy, Adarsh Mamachen, Ashish Mamachen, John A. Goolsby, Patricia J. Moran

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Research was conducted to evaluate the effects of leaf excision and sample storage methods on spectral reflectance by foliage of giant reed, Arundo donax, an invasive weed which has caused extensive damage in many areas of the Rio Grande Basin in Texas and Mexico. Within 24 hours of excision, A. donax leaves exposed to ambient laboratory conditions (room temperature under natural lighting conditions) exhibited two trends indicative of physiological stress: 1) small but significant increases in reflectance of blue and red wavelengths (400-500 nm and 600-700 nm, respectively) and 2) a substantial reduction in reflectance of near-infrared (NIR) wavelengths (700-1,100 …

Two Mechanosensitive Channel Homologs Influence Division Ring Placement In Arabidopsis Chloroplasts, Margaret E. Wilson, Gregory S. Jensen, Elizabeth S. Haswell

Biology Faculty Research

Chloroplasts must divide repeatedly to maintain their population during plant growth and development. A number of proteins required for chloroplast division have been identified, and the functional relationships between them are beginning to be elucidated. In both chloroplasts and bacteria, the future site of division is specified by placement of the Filamentous temperature sensitive Z (FtsZ) ring, and the Min system serves to restrict FtsZ ring formation to mid-chloroplast or mid-cell. How the Min system is regulated in response to environmental and developmental factors is largely unstudied. Here, we investigated the role in chloroplast division played by two Arabidopsis thaliana …

Natural Variation In Life History And Aging Phenotypes Is Associated With Mitochondrial Dna Deletion Frequency In Caenorhabditis Briggsae, Suzanne Estes, Anna Luella Coleman-Hulbert, Kiley Ann Hicks, Gene De Haan, Sarah R. Martha, Jeremiah B. Knapp, Samson William Smith, Kevin C. Stein, Dee R. Denver

Biology Faculty Publications and Presentations

Background: Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the …

Escherichia Coli Fpg Glycosylase Is Nonrendundant And Required For The Rapid Global Repair Of Oxidized Purine And Pyrimidine Damage In Vivo, Brandy J. Schalow, Charmain T. Courcelle, Justin Courcelle

Biology Faculty Publications and Presentations

Endonuclease (Endo) III and formamidopyrimidine-N-glycosylase (Fpg) are two of the predominant DNA glycosylases in Escherichia coli that remove oxidative base damage. In cell extracts and purified form, Endo III is generally more active toward oxidized pyrimidines, while Fpg is more active towards oxidized purines. However, the substrate specificities of these enzymes partially overlap in vitro. Less is known about the relative contribution of these enzymes in restoring the genomic template following oxidative damage. In this study, we examined how efficiently Endo III and Fpg repair their oxidative substrates in vivo following treatment with hydrogen peroxide. We found …

Comparison Of The Anticoagulant Response Of A Novel Fluorogenic Anti-Fxa Assay Wth Two Commercial Anti-Fxa Chromogenic Assays, Leanne F. Harris, Aoife O'Brien, Vanessa Castro-Lopez, James S. O'Donnell, Anthony J. Killard

Articles

Introduction: Fast and accurate monitoring is crucial in the successful regulation of coagulation therapy. For the treatment of venous thromboembolism, both unfractionated heparin (UFH) and low molecular weight heparins (LMWH) are commonly administered. The chromogenic anti-factor Xa (FXa) assay is currently considered the ‘gold standard’ assay for monitoring LMWH. However different commercial chromogenic methods often differ when tested with the same samples. Fluorogenic anti-FXa assays have the potential to offer greater benefits over chromogenic assays in terms of greater specificity, sensitivity and they are not so influenced by sample opacity or turbidity. Materials and Methods: Commercial plasmas were spiked with …

Phytosociology, History And Diversity In Farmer-Managed Landscapes On The Tonle Sap Floodplain, Cambodia, Andrew S. Roberts

Dissertations, Theses, and Capstone Projects

Driven by the annual flood pulse of the Tonle Sap Lake, the Tonle Sap floodplain in central Cambodia is a landscape characterized by dynamism, both ecological and social. Annual floods and rainfall vary in timing, duration and intensity from year to year. Patterns of burning, grazing, and agricultural expansion and contraction all leave their imprint on the landscape. While in the social domain, the region is likewise as complex. The genocidal, Maoist regime of Pol Pot darkened the 1970s. However, this was both preceded by, and followed by, years of civil war and social unrest. In recent years, Cambodia has …

Influenza A And Flavivirus Manipulation Of Cell Death, Jeffrey E. Mclean

Dissertations, Theses, and Capstone Projects

Viruses employ a variety of strategies to manipulate cell fate and maximize their replication potential during infection. Interacting specifically with cell death pathways allows viruses direct control over the cellular decision to survive or die during infection.

Influenza A virus, of the family Orthomyxoviridae, encodes proteins that interact with the cell at several points along the apoptosis pathway to induce apoptosis. We demonstrate that caspase activation through pro-apoptotic Bax, a downstream target of Bcl-2, is a critical determinant of the nature of cell death induced by Influenza A infection. Influenza A virus cannot establish an apoptotic response without functional Bax, …

Myth4 And Ferm Have Overlapping And Distinct Roles In The Function Of Myo1, A Class Xiv Myosin In Tetrahymena Thermophila, Michael Gotesman

Dissertations, Theses, and Capstone Projects

MyTH4 and FERM are conserved tail domains in myosin classes VII, X, XII, XIV, XV and in MyoG. Myo1, a class XIV myosin in Tetrahymena thermophila, contains MyTH4 and FERM. Previous studies have shown that Myo1 localizes to phagosomes, the cytoskeleton, and the macronucleus, and that phagosome trafficking and division of the macronucleus are affected in a MYO1 knockout. To investigate the roles for MyTH4 and FERM in the function of Myo1, GFP-tagged MyTH4, FERM, and truncated FERM were separately overexpressed in Tetrahymena. Actin antibody coprecipitated tubulin, GFP-MyTH4, and GFP-FERM. GFP-MyTH4 and GFP-FERM cosedimented with either exogenous microtubules or exogenous …

Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman

Biology Faculty Publications and Presentations

The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein …

Average Adult Size In Female Lizards, Eric Charnov, Robin Warne

Biology Faculty & Staff Publications

No abstract provided.

Body Size Is The History Of Life: Growth Confronting Landscapes Of Death, Eric Charnov

Biology Faculty & Staff Publications

No abstract provided.

Human Hunting Mortality Threshold Rules For Extinction In Mammals (And Fish), Eric Charnov, Wenyun Zuo

Biology Faculty & Staff Publications

No abstract provided.

Synthesis And Toxicity Studies Of Imidazolium-Based Ionic Liquids, Ninu Madria

Masters Theses

"There is a considerable recent interest in the applications of room temperature ionic liquids (RTILs) as green solvents in organic synthesis and as nonvolatile electrolytes in lithium ion batteries. A variety of commercially available imidazolium based RTILs have been used for these applications, mainly due to their negligible vapor pressures, high thermal stabilities, wide liquid range, wide electrochemical windows and high anodic stability. The state of the art lithium ion batteries require the use of electrolytes that have relatively low viscosities at temperatures as low as -35°C. This thesis describes the synthesis of novel oxygenated and fluorinated imidazolium based RTILs …

Head-Start Juvenile And Adult Resident Eastern Box Turtles (Terrapene Carolina Carolina): Winter Ecology Including Microhabitat Selection, Temperature Tolerance And Philopatry, Amberly Moon

Theses and Dissertations

The Eastern box turtle (Terrapene carolina carolina) is one of the most common reptiles in North America, but is soon to be threatened due to increased urbanization, disease, and the pet and food trades. In order to assist resource managers in choosing suitable sites for relocation studies, more information on the winter ecology of this species is necessary. We examined the temperature tolerance, microhabitat and degree of philopatry to hibernacula for juvenile and adult E. box turtles for two consecutive winters in Charles City Co, VA. The turtles were tracked via radio telemetry to record point locations during the active …

Molecular Cloning, Characterization, And Homologous Expression Of An Endochitinase Gene From Bacillus Thuringiensis Serovar Morrisoni, Sezer Okay, Gülay Özcengi̇z

Turkish Journal of Biology

The endochitinase gene (chi3023) of Bacillus thuringiensis (Bt) serovar morrisoni strain 3023 was amplified via polymerase chain reaction (PCR) and cloned in Escherichia coli. The ORF of chi3023 (GenBank Accession Number: DQ993175) consists of 2031 nucleotides encoding a 676-residue protein with a calculated molecular mass of 74.5 kDa and a pI value of 6.0. The amino acid sequence of Chi3023 was compared with previously sequenced Bt chitinases and the phylogenetic relationships among them were determined. The deduced N-terminal 34 amino acids of the premature Chi3023 exhibited a typical signal peptide. The E. coli-Bt shuttle vector pHT315 was used for homologous …

Determination And Pathogenicity Of The Bacterial Flora Associated With The Spruce Bark Beetle, Ips Typographus (L.) (Coleoptera: Curculionidae: Scolytinae), Hacer Muratoğlu, Kazim Sezen, Zi̇hni̇ Demi̇rbağ

Turkish Journal of Biology

The Eurasian spruce bark beetle, Ips typographus (L.) (Coleoptera: Curculionidae: Scolytinae), is one of the most serious pests of spruce trees. We identified 8 bacterial isolates from this pest using conventional bacteriological tests (API 20E and API 50CH strips, and VITEK system (bioMerieux) analysis) and 16S rRNA gene sequence analysis. Based on these studies, all isolates could be identified to the genus or species level as Bacillus sphaericus (It1), Acinetobacter sp. (It2), Kluyvera cryocrescens (It3), Acinetobacter sp. (It4), Vagococcus sp. (It5), Acinetobacter sp. (It6), Proteus vulgaris (It7), and Serratia liquefaciens (It8). We also evaluated the pathogenicity of these bacteria on …