Biology Commons^™

The Role Of Sigirr In Innate And Adaptive Immunity, Muhammet Fatih Gulen

ETD Archive

Single immunoglobulin IL-1R-related receptor (SIGIRR) is a transmembrane protein, which belongs to interleukin 1 receptor (IL-1R)/Toll like receptor (TLR) superfamily (Toll-IL-1R superfamily). SIGIRR has been identified as a negative modulator for IL-1R/TLR signaling. Recently, detailed structural and functional analysis of SIGIRR has been published, however physiological function of SIGIRR has not been studied. To asses the physiological function of SIGIRR, the expression of SIGIRR mRNA in different mouse tissues was analyzed. Although SIGIRR is expressed in many tissues, its expression in different cell types was more restricted, with extremely high expression in primary kidney, colon epithelial cells and T cells, …

Characterization Of A Microrna Harboring Intron For Pre-Mrna Splicing And Microrna Processing, Neha Aggarwal

ETD Archive

Nuclear pre-mRNA splicing is an important step in eukaryotic RNA processing and can yield a variety of transcripts. Further, it is known that nuclear pre-mRNA introns are of two types, U2-dependent and U12-dependent. Recently discovered, microRNAs (miRNA) are short, endogenous, 20-22 nucleotide long, non-coding RNA molecules that base pair with target mRNAs to modulate translation. Current evidence suggests that processing of intronic miRNA does not affect the splicing. Since, intronic miRNAs are involved in essential cellular processes, we surmised if splice sites of miRNA coding introns are flexible to support productive precursor and mature miRNA processing. We constructed a minigene …

Targets Of Hsa-Mir-488* In Human Prostate Carcinoma Cells, Jinani E. Slaibi

ETD Archive

Prostate cancer (PCa) is one of the most prevalent forms of cancer among men in America and is second only to lung cancer as a cause of cancer-related deaths in men. Recent epidemiological study shows that one in every six men over the age of forty five is at risk of PCa. Androgen receptor (AR) plays a causative role in the development of PCa. Hormonal blockade therapy which inhibits the expression of AR eventually fails and disease progresses to fatal androgen-refractory stage from androgen-dependent stage. Therefore, novel molecular approaches which can target and block the expression of AR are required. …

Characterization And Evolution Of The Serh Immobilization Antigen Genes In Tetrahymena Thermophila, Christopher Thomas Mcginness

ETD Archive

Tetrahymena thermophila express a major cell surface protein known as the immobilization (i-) antigen which coats the entire cell surface including the cilia. T. thermophila has several different i-antigens which are expressed in a mutually exclusive manner under varying environmental conditions. When the genes for these i-antigens were sequenced it was found that they encode proteins consisting of imperfect repeats with cysteine periodicity. The best characterized of these i-antigens are those specified by alleles at the SerH i-antigen locus. The H proteins all contain a section of 8-cysteine containing imperfect repeats. The presence of repeats allows for the possibility that …

Dc Expressing Transgene Foxp3 Are Regulatory Apc, Michael Lipscomb

Department of Biology Faculty Publications

Tolerogenic DC and suppressive Foxp3(+) Treg play important roles in preventing autoimmunity and allograft rejection. We report that (adenovirus mediated) ectopic expression of Foxp3 in human DC (i.e. DC.Foxp3) yields an APC that severely limits T-cell proliferation and type-1 immune responses from the naïve, but not memory, pool of responder T cells in vitro. In marked contrast, the frequencies of type-2 and Treg responses were dramatically increased after stimulation of naïve T cells with DC.Foxp3 versus control DC. DC.Foxp3-induced CD4(+)CD25(+) Treg cells potently suppressed the proliferation of, and IFN-gamma production from, CD4(+) and CD8(+) responder T cells. Notably, the immunosuppressive …

Linking Snake Behavior To Nest Predation In A Midwestern Bird Community, Patrick J. Weatherhead, Gerardo L.F. Carfagno, Jinelle H. Sperry, Jeffrey D. Brawn, Scott K. Robinson

Biology Faculty Publications

Nest predators can adversely affect the viability of songbird populations, and their impact is exacerbated in fragmented habitats. Despite substantial research on this predator-prey interaction, however, almost all of the focus has been on the birds rather than their nest predators, thereby limiting our understanding of the factors that bring predators and nests into contact. We used radiotelemetry to document the activity of two snake species (rat snakes, Elaphe obsoleta; racers, Coluber constrictor) known to prey on nests in Midwestern bird communities and simultaneously monitored 300 songbird nests and tested the hypothesis that predation risk should increase for nests when …

Adaptive Evolution And Inherent Tolerance To Extreme Thermal Environments, Jennifer Cox, Alyxandria Schubert, Michael Travisano, Catherine Putonti

Bioinformatics Faculty Publications

Background

When introduced to novel environments, the ability for a species to survive and rapidly proliferate corresponds with its adaptive potential. Of the many factors that can yield an environment inhospitable to foreign species, phenotypic response to variation in the thermal climate has been observed within a wide variety of species. Experimental evolution studies using bacteriophage model systems have been able to elucidate mutations, which may correspond with the ability of phage to survive modest increases/decreases in the temperature of their environment.

Results

Phage ΦX174 was subjected to both elevated (50°C) and extreme (70°C+) temperatures for anywhere from a few …

Mechanisms Responsible For A Φx174 Mutant's Ability To Infect Escherichia Coli By Phosphorylation, Jennifer Cox, Catherine Putonti

Bioinformatics Faculty Publications

The ability for a virus to expand its host range is dependent upon a successful mode of viral entry. As such, the host range of the well-studied ΦX174 bacteriophage is dictated by the presence of a particular lipopolysaccharide (LPS) on the bacterial surface. The mutant ΦX174 strain JACS-K, unlike its ancestor, is capable of infecting both its native host Escherichia coli C and E. coli K-12, which does not have the necessary LPS. The conversion of an alanine to a very reactive threonine on its virion surface was found to be responsible for the strain's expanded host range.

Evolution Of The Sequence Composition Of Flaviviruses, Alyxandria M. Schubert, Catherine Putonti

Bioinformatics Faculty Publications

The adaption of pathogens to their host(s) is a major factor in the emergence of infectious disease and the persistent survival of many of the infectious diseases within the population. Since many of the smaller viral pathogens are entirely dependent upon host machinery, it has been postulated that they are under selection for a composition similar to that of their host. Analyses of sequence composition have been conducted for numerous small viral species including the Flavivirus genus. Examination of the species within this particular genus that infect vertebrate hosts revealed that sequence composition proclivities do not correspond with vector transmission …

Grassland Root Communities: Species Distributions And How They Are Linked To Aboveground Abundance., Douglas Frank, Alyssa Pontes, Eleanor M. Maine, Julie Caruana, Ramesh Raina, Surahbi Raina, Jason Fridley

Biology - All Scholarship

There is little comprehensive information on the distribution of root systems among coexisting species, despite the expected importance of those distributions in determining the composition and diversity of plant communities. This gap in knowledge is particularly acute for grasslands, which possess large numbers of species with morphologically indistinguishable roots. In this study we adapted a molecular method, fluorescent fragment length polymorphism, to identify root fragments and determine species root distributions in two grasslands in Yellowstone National Park. Aboveground biomass was measured and soil cores (2 cm diam) were collected to 40 cm and 90 cm in an upland, dry grassland …

A Candidate Subspecies Discrimination System Involving A Vomeronasal Receptor Gene With Different Alleles Fixed In M. M. Domesticus And M. M. Musculus, Robert C. Karn, Janet M. Young, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Assortative mating, a potentially efficient prezygotic reproductive barrier, may prevent loss of genetic potential by avoiding the production of unfit hybrids (i.e., because of hybrid infertility or hybrid breakdown) that occur at regions of secondary contact between incipient species. In the case of the mouse hybrid zone, where two subspecies of Mus musculus (M. m. domesticus and M. m. musculus) meet and exchange genes to a limited extent, assortative mating requires a means of subspecies recognition. We based the work reported here on the hypothesis that, if there is a pheromone sufficiently diverged between M. m. domesticus and …

Combined Effects Of A Parasite, Qpx, And The Harmful-Alga, Prorocentrum Minimum On Northern Quahogs, Mercenaria Mercenaria, Hélène Hégaret, Roxanna Smolowitz, Inke Sunila, Sandra E. Shumway, Jennifer Alix, Mark Dixon, Gary H. Wikfors

Arts & Sciences Faculty Publications

Northern quahogs, Mercenaria mercenaria (L.), frequently are infected with the parasite Quahog Parasite Unknown (QPX, Labyrintohomorpha, Thraustochytriales), which can cause morbidity and mortality of the quahogs. Possible interactions between this parasitic disease and exposure to the harmful dinoflagellate Prorocentrum minimum in M. mercenaria were studied experimentally. Quahogs from Massachusetts with variable intensity of QPX infection were exposed, under controlled laboratory conditions, to cultured P. minimum added to the natural plankton at a cell density equivalent to a natural bloom. After 5 days of exposure, individual clams were diagnosed histologically to assess prevalence and intensity of parasitic infection, as well as …

Two New Species Of Freshwater Crabs From Mt. Elgon, East Africa With A Redescription Of Potamonautes Niloticus And Notes On Their Natural History" , Neil Cumberlidge, Paul F. Clark

Journal Articles

No abstract provided.

Effects Of Flight Speed Upon Muscle Activity In Hummingbirds, Bret W. Tobalske, Andrew A. Biewener, Douglas R. Warrick, Tyson L. Hedrick, Donald R. Powers

Faculty Publications - Department of Biological & Molecular Science

Hummingbirds have the smallest body size and highest wingbeat frequencies of all flying vertebrates, so they represent one endpoint for evaluating the effects of body size on sustained muscle function and flight performance. Other bird species vary neuromuscular recruitment and contractile behavior to accomplish flight over a wide range of speeds, typically exhibiting a Ushaped curve with maxima at the slowest and fastest flight speeds. To test whether the high wingbeat frequencies and aerodynamically active upstroke of hummingbirds lead to different patterns, we flew rufous hummingbirds (Selasphorus rufus, 3��g body mass, 42��Hz wingbeat frequency) in a variable-speed wind tunnel (0–10��m��s–1). …

Erk Activation And Cell Growth Require Cam Kinases In Mcf-7 Breast Cancer Cells, John M. Schmitt, Ellen Abell, Andrea Wagner, Monika A. Davare

Faculty Publications - Department of Biological & Molecular Science

Previous studies on MCF-7 breast cancer cells have shown that the G-protein coupled receptor (GPCR) agonist carbachol increases intracellular calcium levels and the activation of extracellular signal-regulated kinase (ERK). Calcium and calmodulin regulate the calcium/calmodulin- dependent kinase (CaM kinase) family of proteins that have been proposed to regulate ERK and gene transcription. Our results suggest that both estrogen (E2) and carbachol treatment of MCF-7 breast cancer cells trigger phosphorylation of ERK I /2 and the transcription factor Elk-1. Carbachol and estrogen triggered nearly a four- to sixfold increase in MCF-7 cell proliferation by 96 h, respectively. Carbachol-stimulated ERK activation and …

Arthropod Foraging By A Southeastern Arizona Hummingbird Guild, Don Powers, Jessamyn A. Van Hook, Elizabeth A. Sandlin, Todd J. Mcwhorter

Faculty Publications - Department of Biological & Molecular Science

We tested the hypothesis that foraging for arthropods may be a viable source of energy when hummingbirds are competitively excluded from sources of nectar. We hypothesized that the Magnificent Hummingbird (Eugenes fulgens) relies more upon arthropods than the Blue-throated Hummingbird (Lampornis clemenciae) or Blackchinned Hummingbird (Archilochus alexandri) in southeastern Arizona. We were unable to quantify arthropod foraging by A. alexandri, but measured frequent arthropod foraging by both E. fulgens and L. clemenciae. E. fulgens engaged in more aerial flycatching than L. clemenciae, and their rate of flycatching attempts was higher than by L. clemenciae. Analysis of gut contents showed that …

Inhibition Of Nonsense-Mediated Mrna Decay By Antisense Morpholino Oligonucleotides Restores Functional Expression Of Herg Nonsense And Frameshift Mutations In Long-Qt Syndrome, Qiuming Gong, Matthew R. Stump, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

Mutations in the human ether-a-go-go-related gene (hERG) cause long-QT syndrome type 2 (LQT2). We previously described a homozygous LQT2 nonsense mutation Q1070X in which the mutant mRNA is degraded by nonsense-mediated mRNA decay (NMD) leading to a severe clinical phenotype. The degradation of the Q1070X transcript precludes the expression of truncated but functional mutant channels. In the present study, we tested the hypothesis that inhibition of NMD can restore functional expression of LQT2 mutations that are targeted by NMD. We showed that inhibition of NMD by RNA interference-mediated knockdown of UPF1 increased Q1070X mutant channel protein expression and hERG current …

Mutational Studies Uncover Non-Native Structure In The Dimeric Kinetic Intermediate Of The H2a–H2b Heterodimer, Matthew R. Stump, Lisa M. Gloss

Faculty Publications - Department of Biological & Molecular Science

The folding pathway of the histone H2A–H2B heterodimer minimally includes an on-pathway, dimeric, burst-phase intermediate, I2. The partially folded H2A and H2B monomers populated at equilibrium were characterized as potential monomeric kinetic intermediates. Folding kinetics were compared for initiation from isolated, folded monomers and the heterodimer unfolded in 4 M urea. The observed rates were virtually identical above 0.4Murea, exhibiting a log-linear relationship on the final denaturant concentration. Below ∼0.4 M urea (concentrations inaccessible from the 4-M urea unfolded state), a rollover in the rates was observed; this suggests that a component of the I2 ensemble contains non-native structure that …

Mitochondrial Physiology Of Diapausing And Developing Embryos Of The Annual Killifsh Austrofundulus Limnaeus: Implications For Extreme Anoxia Tolerance, Jeff Duerr, Jason E. Podrabsky

Faculty Publications - Department of Biological & Molecular Science

Diapausing embryos of the annual killiWsh Austrofundulus limnaeus have the highest reported anoxia tolerance of any vertebrate and previous studies indicate modified mitochondrial physiology likely supports anoxic metabolism. Functional mitochondria isolated from diapausing and developing embryos of the annual killifish exhibited VO2, respiratory control ratios (RCR), and P:O ratios consistent with those obtained from other ectothermic vertebrate species. Reduced oxygen consumption associated with dormancy in whole animal respiration rates are correlated with maximal respiration rates of mitochondria isolated from diapausing versus developing embryos. P:O ratios for developing embryos were similar to those obtained from adult liver, but were diminished in …

Explorations Of Aspects Of Mixotrophy Using Mathematical Models, Kenneth W. Crane

Biology Dissertations - Archive

This work examined three theoretical aspects of mixotrophy, the simultaneous use of phototrophic and heterotrophic nutritional modes, and one practical application. The first study addressed the coexistence of microorganisms pursuing diverse nutritional strategies. It was found that in the range of model environments explored that all four types of organisms were predicted to persist for certain parameter combinations. The most successful mixotrophs were predicted to be primarily autotrophic, supplementing photosynthesis with bacterivory. The second study extended the first one by focusing on the effects of environmental parameters governing resource supplies and the responses of populations and ecosystem properties in relation …

Genetic Conflict And Sex Chromosome Evolution, Colin D. Meiklejohn, Yun Tao

School of Biological Sciences: Faculty Publications

Chromosomal sex determination systems create the opportunity for the evolution of selfish genetic elements that increase the transmission of one sex chromosome at the expense of its homolog. Because such selfish elements on sex chromosomes can reduce fertility and distort the sex ratio of progeny, unlinked suppressors are expected to evolve, bringing different regions of the genome into conflict over the meiotic transmission of the sex chromosomes. Here we argue that recurrent genetic conflict over sex chromosome transmission is an important evolutionary force that has shaped a wide range of seemingly disparate phenomena including the epigenetic regulation of genes expressed …

Effect Of Ingestion By Alligator Snapping Turtles (Macrochelys Temminckii) On Seeds Of Riparian Vegetation, Jean Pierre Elbers

Graduate Theses/Dissertations

The alligator snapping turtle (Macrochelys temminckii) is a large freshwater turtle that inhabits many lotic water bodies in the Southeastern United States. The species consumes primarily fish but also consumes large amounts of vegetation including seeds of common persimmon (Diospyros virginiana), tupelos (Nyssa sp.), willow oak (Quercus phellos), and pecan (Carya illinoensis). Captive specimens of M. temminckii were fed samples of the above-mentioned seeds to assess how the species affects ingested seeds in order to evaluate the potential role this species may play as a seed disperser. The proportion of seeds defecated intact varied with species (57−99 %), was lowest …

Nutritional Analysis Of High Fructose Corn Syrup, Emily Pitts

A with Honors Projects

An analysis of high fructose corn syrup and its positive and/or negative aspects.

Identification Of A Nuclear Export Signal In The Catalytic Subunit Of Amp-Activated Protein Kinase, N. Kazgan, Tyisha Williams, L. J. Forsberg, J. E. Brenman

Biology Faculty Research

The metabolic regulator AMP-activated protein kinase (AMPK) maintains cellular homeostasis through regulation of proteins involved in energy-producing and -consuming pathways. Although AMPK phosphorylation targets include cytoplasmic and nuclear proteins, the precise mechanisms that regulate AMPK localization, and thus its access to these substrates, are unclear. We identify highly conserved carboxy-terminal hydrophobic amino acids that function as a leptomycin B–sensitive, CRM1-dependent nuclear export sequence (NES) in the AMPK catalytic subunit (AMPKα). When this sequence is modified AMPKα shows increased nuclear localization via a Ran-dependent import pathway. Cytoplasmic localization can be restored by substituting well-defined snurportin-1 or protein kinase A inhibitor (PKIA) …

Figs, Wasps, Gophers, And Lice: A Computational Exploration Of Coevolution, Ran Libeskind-Hadas

All HMC Faculty Publications and Research

This chapter explores the topic of coevolution: the genetic change in one species in response to the change in another. For example, in some cases, a parasite species might evolve to specialize with its host species. In other cases, the relationship between two species may be mutually beneficial and coevolution may serve to strengthen the benefits of that relationship.

Using Shewanella Baltica Ecotypes As A Model For Transcriptional Variation At The Population Level, William Sealy Hambright

Biology Theses - Archive

Eukaryotic studies have shown considerable transcriptional variation among individuals of the same population. Owing to the cost of sequencing entire eukaryotic genomes, tested organisms were assumed to be genomically similar or even identical. We overcame this necessary assumption by using four sequenced strains of the bacterium Shewanella baltica, (OS155, OS185, OS195, OS223), as models to assess transcriptional variation and ecotype formation within a prokaryotic population. The strains were isolated from various depths throughout a water column of the Baltic Sea occupying different ecological niches characterized by various abiotic parameters. Although their genome sequences are strikingly similar, when grown in the …

A Tale Of Three Phytopathogens: Impact Of Transposable Elements On Genome Evolution, Komal Vadnagara

Biology Theses - Archive

The genus Phytophthora harbors some notorious plant pathogens like Phytophthora infestans (causal of Irish potato famine), Phytophthora sojae (soybean rot agent), and Phytophthora ramorum (responsible for sudden oak death) that have significant economic, ecological and environmental impact. These phytopathogens exhibit remarkable phenotypic instability and vary tremendously in genome size from 65 Mb (P. ramorum) to 240 Mb (P. infestans). Complete draft genome sequences revealed that a substantial portion of their genome is occupied by highly repetitive DNA. This extreme genome plasticity is due to an infestation of repetitive virus-like genomic parasites called transposable elements (TEs). TEs are sometimes called jumping …

Environmental Regulation Of Stomate-Based Defense Against Bacterial Infection In Arabidopsis, Reejana Chitrakar

Biology Theses - Archive

Stomata are natural openings in the plant epidermis responsible for gas (O2 and CO2) exchange between plant interior and environment. They are formed by a pair of guard cells, which are able to close the stomatal pore in response to a number of external factors including light intensity, carbon dioxide concentration, and relative humidity. The stomatal pore is also the main route for pathogen entry into leaves, a crucial step for disease development. Recent studies have unveiled that closure of the pore is effective in preventing bacterial disease in Arabidopsis plants and the successful plant pathogen Pseudomonas syringae pv. tomato …

Comparing The Genome Expression Profiles Of Verrucomicrobium Sp. Strain Tav2 Cells Grown Under Two Different Oxygen Concentrations, Austin Willis

Biology Theses - Archive

Termites are significantly different in their lifestyles and organization but most are linked by the common trait in degrading plant material, whether it is leaf litter, wood, soil or animal waste. They consume the cellulose, hemicelluloses and lignin that make up the plant material but rely on a food web consisting of about 270 different phylotypes of microorganisms to break down the biomass into usable nutrients. Isolated from the hindgut of the termite Reticulitermis flavipes, one such organism is Verrucomicrobium sp. strain TAV2. Members of this relatively new bacterium phylum have rigid peptidoglycan with some possessing prosthecae. They have been …

Characterization Of Anti-Rotavirus Activities Of Saponin Extracts From Quillaja Saponaria, Ka Ian Tam

Biology Dissertations - Archive

Rotavirus is the leading cause of severe diarrhea disease in newborns and young children worldwide, estimated to be responsible for over 500,000 adolescent deaths mostly in developing countries each year. Rotavirus-related deaths represent approximately 5% of all deaths in children younger than five years of age worldwide. Previous research has shown that Quillaja saponins demonstrate strong antiviral activity against 7 different viruses, including rotavirus, in vitro. Quillaja saponins, a natural, aqueous extract of triterpenoid saponins obtained from Quillaja saponaria, the Chilean Soap Bark tree that display strong adjuvant activity when used in vaccines. In this study, Quillaja saponins are stable …