Biology Commons^™

The Arabidopsis Trithorax-Like Factor Atx1 Functions In Dehydration Stress Responses Via Aba-Dependent And Aba-Independent Pathways, Yong Ding, Zoya Avramova, Michael Fromm

School of Biological Sciences: Faculty Publications

Emerging evidence suggests that the molecular mechanisms driving the responses of plants to environmental stresses are associated with specific chromatin modifications. Here, we demonstrate that the Arabidopsis trithorax-like factor ATX1, which trimethylates histone H3 at lysine 4 (H3K4me3), is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. The loss of function of ATX1 results in decreased germination rates, larger stomatal apertures, more rapid transpiration and decreased tolerance to dehydration stress in atx1 plants. This deficiency is caused in part by reduced ABA biosynthesis in atx1 plants resulting from decreased transcript levels from NCED3, which …

Copper Tolerance Of Saccharomyces Cerevisiae Nonsense-Mediated Mrna Decay Mutants, Rafael Deliz-Aguirre, Audrey L. Atkin, Bessie W. Kebaara

School of Biological Sciences: Faculty Publications

The eukaryotic nonsense-mediated mRNA (NMD) is a specialized pathway that leads to the recognition and rapid degradation of mRNAs with premature termination codons, and importantly some natural mRNAs as well. Natural mRNAs with atypically long 3′-untranslated regions (UTRs) are degraded by NMD in Saccharomyces cerevisiae. A number of S. cerevisiae mRNAs undergo alternative 3′-end processing producing mRNA isoforms that differ in their 3′-UTR lengths. Some of these alternatively 3′-end processed mRNA isoforms have atypically long 3′-UTRs and would be likely targets for NMD-mediated degradation. Here, we investigated the role NMD plays in the regulation of expression of CTR2, …

Normalization And Centering Of Array-Based Heterologous Genome Hybridization Based On Divergent Control Probes, Brian J. Darby, Kenneth L. Jones, David Wheeler, Michael A. Herman

School of Biological Sciences: Faculty Publications

Background: Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in nonmodel organisms. However, conventional methods of normalization that assume equivalent distributions (such as quantile normalization) are inappropriate when applied to non-specific (heterologous) hybridization. We propose an algorithm for normalizing and centering intensity data from heterologous hybridization that makes no prior assumptions of distribution, reduces the false appearance of homology, and provides a way for researchers to confirm whether heterologous hybridization is suitable.

Results: Data are normalized by adjusting for Gibbs free energy …

Aphids: A Model For Polyphenism And Epigenetics, Dayalan G. Srinivasan, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions. With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can …

Maize Cellulosic Biofuels: Soil Carbon Loss Can Be A Hidden Cost Of Residue Removal, Amy Kochsiek, Johannes Knops

School of Biological Sciences: Faculty Publications

Second generation biofuels, like cellulosic ethanol, have potential as important energy sources that can lower fossil fuel carbon emissions without affecting global food commodity prices. Agricultural crop residues, especially maize, have been proposed for use as biofuel, but the net greenhouse warming effect of the gained fossil fuel carbon offset needs to account for any ecosystem carbon losses caused by the large-scale maize residue removal. Using differential 13C isotopic ratios between residue and soil in an incubation experiment, we found that removal of residue increased soil organic matter decomposition by an average of 16%, or 540–800 kg carbon ha -1. …

Environmental And Genetic Perturbations Reveal Different Networks Of Metabolic Regulation, Anthony J. Greenberg, Sean R. Hacket, Lawrence G. Harshman, Andrew G. Clark

School of Biological Sciences: Faculty Publications

Progress in systems biology depends on accurate descriptions of biological networks. Connections in a regulatory network are identified as correlations of gene expression across a set of environmental or genetic perturbations. To use this information to predict system behavior, we must test how the nature of perturbations affects topologies of networks they reveal. To probe this question, we focused on metabolism of Drosophila melanogaster. Our source of perturbations is a set of crosses among 92 wild-derived lines from five populations, replicated in a manner permitting separate assessment of the effects of genetic variation and environmental fluctuation. We directly assayed activities …

Survival Rates Of Planidial Larvae Of The Parasitoid Fly Ormia Ochracea (Diptera: Tachinidae), Oliver M. Beckers, Cassandra M. Martin, William E. Wagner Jr.

School of Biological Sciences: Faculty Publications

The tachinid fly, Ormia ochracea Bigot 1889, is a major parasitoid of field crickets in North America. The fly ranges from Florida to California, and it has also been introduced to Hawaii. Across this range, O. ochracea uses at least 6 different Gryllus species as hosts for its larvae (Cade, 1975; Walker, 1986; Walker and Wineriter, 1991; Zuk et al., 1993; Wagner, 1996; Hedrick and Kortet, 2006). O. ochracea finds it hosts by eavesdropping on male mating songs (Cade, 1975). The fly deposits up to 3 planidial larvae (Adamo et al., 1995a) directly on the male and these …

Dtorsin, The Drosophila Ortholog Of The Early-Onset Dystonia Tor1a (Dyt1), Plays A Novel Role In Dopamine Metabolism, Noriko Wakabayashi-Ito, Olugbenga M. Doherty, Hideaki Moriyama, Xandra O. Breakefield, James F. Gusella, Janis M. O’Donnell, Naoto Ito

School of Biological Sciences: Faculty Publications

Dystonia represents the third most common movement disorder in humans. At least 15 genetic loci (DYT1-15) have been identified and some of these genes have been cloned. TOR1A (formally DYT1), the gene responsible for the most common primary hereditary dystonia, encodes torsinA, an AAA ATPase family protein. However, the function of torsinA has yet to be fully understood. Here, we have generated and characterized a complete loss-of-function mutant for dtorsin, the only Drosophila ortholog of TOR1A. Null mutation of the X-linked dtorsin was semi-lethal with most male flies dying by the prepupal stage and the few surviving …

Vapc6, A Ribonucleolytic Toxin Regulates Thermophilicity In The Crenarchaeote Sulfolobus Solfataricus, Yukari Maezato, Amanda Daugherty, Karl Dana, Edith Soo, Charlotte Cooper, Sabrina Tachdjian, Robert M. Kelly, Paul H. Blum

School of Biological Sciences: Faculty Publications

The phylum Crenarchaeota includes hyperthermophilic micro-organisms subjected to dynamic thermal conditions. Previous transcriptomic studies of Sulfolobus solfataricus identified vapBC6 as a heat-shock (HS)-inducible member of the Vap toxin– antitoxin gene family. In this study, the inactivation of the vapBC6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, HS sensitivity and a heat-dependent reduction in the rate of growth. In-frame vapBC6 deletion mutants were analyzed to examine the respective roles of each protein. Since vapB6 transcript abundance was elevated in the vapC6 deletion, the VapC6 toxin appears to regulate abundance of its cognate antitoxin. In contrast, vapC6 …

Identification Of Fabrics Likely To Collect And Disperse Fel D 1, Mary Janice Jones

Electronic Theses and Dissertations

Individuals sensitive to domestic cat allergen Fel d 1 experience a variety of symptoms including eye irritation, respiratory irritation, asthma, and severe respiratory distress. Fel d 1 is a protein produced in the saliva and on the skin of domestic cats. Previous studies have demonstrated that Fel d 1 adheres to clothing, upholstery, and human hair and has been found in non-cat environments in levels high enough to cause allergic reactions in sensitive individuals. In a general sense, two very different approaches have been adopted to study Fel d 1. One area of the literature focuses on the molecular biology …

Analysis Of Biological Features Associated With Meiotic Recombination Hot And Cold Spots In Saccharomyces Cerevisiae, Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman

Mathematics & Statistics Faculty Publications

Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; …

Investigating The Role Of Calcineurin In Axon Growth And Development Of Retinal Neurons, Jesus Iniguez

Undergraduate Honors Theses

This research project entails the characterization of Calcineurin (CaN) in neuron development. CaN is an intracellular protein that has been implicated in different systems as a mediator between cells and their surroundings to promote normal, healthy function (Lee & Park; 2006). Receptors on the surface of cells are known to stimulate intracellular changes, CaN is thought to mediate some of these changes, including during neurodevelopment. As a neuron develops, it extends a process (axon) in search of a specific target with which to form a synapse. Initial embryonic axon growth is directly related to axon growth and regeneration in adults. …

A Survey Of The Chemical Content And Medicinal Activity Of Shrub-Steppe Plants Of The Pacific Northwest, Aaron M. John

Undergraduate Honors Theses

A need for new modes of antibiotic therapy has resulted from the increasing incidence of bacterial resistance to drugs. One approach to this problem involves the search for plant compounds that may help to overcome multi-drug resistance. Many plant genera have been utilized in Native American traditional medicine for their beneficial properties. Such plants include the shrub-steppe genera, Eriogonun and Collomia, which have been used as cold remedies, pain relievers, and for antibiotic-related uses. Limited chemical studies of these genera have revealed medicinally useful compounds such as flavonoids and terpenoids, and further research may result in the identification of …

The Mayfly Newsletter, Peter M. Grant

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Two Notes On Nabokov, Victor Fet

Biological Sciences Faculty Research

No abstract provided.

Intra-Specific Variation Across A Small Temperature Difference In The Spider Rabidosa Rabida (Araneae: Lycosidae) From The Mountains In Arkansas, Ryan Joseph Stork

Biology Dissertations - Archive

Temperature affects all levels of biological organization and ultimately affects multiple aspects of ecological performance and fitness. Generalist arthropod predators are ectothermic and are strongly affected by temperature in ways that are not fully understood. Descriptions of thermal ecology of important generalist arthropod predators are, therefore, essential pieces of information for studying ecology in changing thermal environments. Rabidosa rabida is a wolf spider that inhabits much of the eastern United States and plays an important role as a generalist predator of large herbivorous arthropods. This study makes the first description of the thermal ecology of R. rabida. A description of …

Targeting Of Site-Specific Non-Ltr Retrotransposons: Role Of Amino-Terminal Domains, Haridha Shivram

Biology Theses - Archive

Restriction-like endonuclease (RLE) bearing non-LTR retrotransposons are site-specificelements that integrate into the genome through target primed reverse transcription (TPRT). RLE-bearing elements have been used as a model system for investigating non-LTR retrotransposon integration. R2 elements target a specific site in the 28S rDNA gene. We previously demonstrated that the two major sub-classes of R2 (R2-A and R2-D) target the R2 insertion site in an opposing manner with regard to the pairing of known DNA binding domains and bound sequences―indicating that the A- and D-clades represent independently derived modes of targeting that site. Elements have been discovered that group phylogenetically with …

A Biochemical Approach To Determine The Target Site Recognition Mechanism Of The R2 Retrotransposable Elements, Blaine K. Thompson

Biology Theses - Archive

Non-LTR Retrotransposons (NLRs) are selfish mobile genetic elements which parasitize the genomes of many organisms including humans. These elements transpose through an RNA intermediate and integrate directly into their genomic site using reverse transcription, a process called Target Primed Reverse Transcription (TPRT). Members of this family of transposons are abundant in the genomes of many eukaryotes including mammals, reptiles, fish, and insects. Several NLR family members such as R2 and NeSL-1 avoid causing deleterious mutations by specifically targeting repetitive genomic loci such as the 28S ribosomal DNA gene and the Spliced leader-1 exon respectively. This literature review focuses on the …

A Comparative Study Of The Expression Of Line, Mys And Sine Retrotransposon Loci In Somatic And Germ-Line Tissues In Peromyscus Maniculatus, Saedeh J. Sepehri

Master's Theses and Doctoral Dissertations

This study was to determine if one or more loci are serving as a master gene for the amplification of LINE, ID, and mys elements, which mobilize via RNA, in Peromyscus maniculatus tissues, by the use of the RT-PCR technique. It was concluded that potentially more than one master gene is responsible for the amplification of LINE and mys in P.maniculatus. RT-PCR products of testes and brain for ID matched that of the BC1 gene, known to be the master gene for ID elements. However, none of the cloned products detected from ovary matched any gene available in the …

The Decline Of Soft Inheritance, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Evolution Of The Actin Gene Family In Testate Lobose Amoebae (Arcellinida) Is Characterized By Two Distinct Clades Of Paralogs And Recent Independent Expansions, Daniel J.G. Lahr, Truc B. Nguyen, Erika Barbero, Laura A. Katz

Biological Sciences: Faculty Publications

The evolution of actin gene families is characterized by independent expansions and contractions across the eukaryotic tree of life. Here, we assess diversity of actin gene sequences within three lineages of the genus Arcella, a free-living testate (shelled) amoeba in the Arcellinida. We established four clonal lines of two morphospecies, Arcella hemisphaerica and A. vulgaris, and assessed their phylogenetic relationship within the "Amoebozoa" using small subunit ribosomal DNA (SSU-rDNA) genealogy. We determined that the two lines of A. hemisphaerica are identical in SSU-rDNA, while the two A. vulgaris are independent genetic lineages. Furthermore, we characterized multiple actin gene copies from …

Hemorrhagic Stroke, Kelsey Bigham

Natural Sciences Student Research Presentations

No abstract provided.

Taking Care Of Pressure Ulcers, Christina Madura

Natural Sciences Student Research Presentations

No abstract provided.

Effects Of Xs® Energy Drink On Aerobic Exercise Capacity Of Athletes, Kevin M. Sheehan, Lynn K. Hartzler

Biological Sciences Faculty Publications

A small increase in performance is often the difference between winning and losing for athletes, and energy supplements are marketed to give them a competitive edge. One such supplement is XS® Energy Drink which contains B vitamins, caffeine, taurine, and an herbal adaptogen blend. XS® Energy Drink is primarily designed and marketed as an alertness stimulus; however, it is also marketed to athletes as a performance enhancing supplement. The hypothesis of this investigation was that the consumption of XS® Energy Drink before exercise would increase aerobic capacity (an increase in Vo2max) and time to fatigue, and would decrease time for …

Ontogenetic Changes In The Bell Morphology And Kinematics And Swimming Behavior Of Rowing Medusae: The Special Case Of The Limnomedusa Liriope Tetraphylla, Tasia Blough, Sean Colin, John H. Costello, Antonio C. Marques

Arts & Sciences Faculty Publications

Swimming animals may experience significant changes in the Reynolds number (Re) of their surrounding fluid flows throughout ontogeny. Many medusae experience Re environments with significant viscous forces as small juveniles but inertially dominated Re environments as adults. These different environments may affect their propulsive strategies. In particular, rowing, a propulsive strategy with ecological advantages for large adults, may be constrained by viscosity for small juvenile medusae. We examined changes in the bell morphology and swimming kinematics of the limnomedusa Liriope tetraphylla at different stages of development. L. tetraphylla maintained an oblate bell (fineness ratio _ 0.5–0.6), large velar …

Ecogeographical Distribution Of The Herpetofauna Of Indio Mountains Research Station, Hudspeth County, Texas, Ross Owen Couvillon

Open Access Theses & Dissertations

Indio Mountain Research Station (IMRS) in Trans-Pecos, Texas is dominated by Chihuahuan Desert scrub vegetation, but a complexity of plant communities exist relating to elevation, slope, and geologic formations. Surrounding the Indio Mountains are desert grasslands with various desert scrub associations. This mosaic of habitats forms a unique assemblage of amphibians and reptiles. The goal of this study was to determine if the current number of amphibians, turtles, lizards, and snakes (43 species) of IMRS was accurate and identify which biotic and abiotic factors define the distribution of these species. Records from the last approximately 25 years were used to …

Diet, Growth And Bioenergetics Of Northern Pike (Esox Lucius Linnaeus, 1758) In Box Canyon Reservoir, Pend Oreille River, Washington, Shane Joseph Harvey

EWU Masters Thesis Collection

"The objectives of this study were to describe the growth of northern pike, describe the food habits of northern pike and using bioenergetics modeling assess the mass and total numbers of each species of forage fish the northern pike population consumed in Box Canyon Reservoir,Pend Orielle River, Washington. Northern pike (n=328) were collected by boat electrofishing, fyke netting, angling and gillnetting in 2009 and 2010. All northern pike were sacrificed to obtain stomach contents. Stomach contents were examined in the laboratory and identified to the appropriate level; amphibians and mammals to species, insect prey (aquatic/terrestrial) to family and prey fish …

Ecology Of The Rock Rattlesnake, Crotalus Lepidus, In The Northern Chihuahuan Desert, Vicente Mata Silva

Open Access Theses & Dissertations

The Rock Rattlesnake, Crotalus lepidus is a small species that is found from southern Arizona, southern New Mexico, and southern Texas, in the U.S., into northern Mexico. To date, little is known about the ecology of this species. Ecological information is becoming desperately needed for supporting the conservation and protection of species living in fragile environments such as the Chihuahuan Desert amid current local and global threats (e.g., habitat destruction and modification, urban development, and climate change). Although rattlesnakes spend a significant amount of time underground while overwintering, little is known about the physiology and behavior of these organisms during …

Dissimilatory Nitrate Reductionpathways In An Oligotrophic Aquatic Ecosystem: Spatial And Temporal Trends, I. J. Washbourne, C. L. Crenshaw, Michelle A. Baker

Biology Faculty Publications

Elevated nitrate (NO₃⁻) concentrations can cause eutrophication, which may lead to harmful algal blooms, loss of habitat and reduction in biodiversity. Denitrification, a dissimilatory process that removes NO₃⁻ mainly as dinitrogen gas (N₂), is believed to be the dominant NO₃⁻ removal pathway in aquatic ecosystems. Evidence suggests that a less well-studied process, dissimilatory nitrate reduction to ammonium (DNRA), which retains nitrogen (N) in the system, may also be important under favorable conditions. Using stable isotope tracers in sealed microcosms, we measured the potential for NO₃⁻ losses due to DNRA …

On The Use Of Log-Transformation Vs. Nonlinear Regression For Analyzing Biological Power-Laws, Xiao Xiao, Ethan P. White, M. B. Hooten, Susan L. Durham

Biology Faculty Publications

Power-law relationships are among the most well-studied functional relationships in biology. Recently the common practice of fitting power-laws using linear regression on log-transformed data (LR) has been criticized, calling into question the conclusions of hundreds of studies. It has been suggested that nonlinear regression (NLR) is preferable, but no rigorous comparison of these two methods has been conducted. Using Monte Carlo simulations we demonstrate that the error distribution determines which method performs better, with LR better characterizing data with multiplicative lognormal error and NLR better characterizing data with additive, homoscedastic, normal error. Analysis of 471 biological power-laws shows that both …