Biology Commons^™

Assessing The Use Of Non-Lethal Tail Clips For Measuring Stable Isotopes Of Plethodontid Salamanders, Joseph Milanovich, John C. Maerz

Biology: Faculty Publications and Other Works

Stable isotopes are increasingly used in ecology to study the diets, trophic position, and migratory patterns of wildlife including herpetofauna. When using stable isotopes, it is important to consider which tissues can or should be sampled, and how selecting tissues may affect the inferences drawn from stable isotope data. Amphibians offer fewer tissues than other larger organisms that can be harvested in sufficient quantity without killing the animal; however, many salamanders have tails that readily autotomize and regenerate. We used three species of plethodontid salamander (Plethodon cinereus, P. metcalfi, and Desmognathus quadramaculatus) to determine whether distal tail tissue had carbon …

Creation Of A Natural History Information Database With Mobile Device Access For The Pace Campus In Pleasantville, Joshua J. Schwartz, Martina Blackwood

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Testing Phylogenetic Hypotheses Of The Subgenera Of The Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, Keith A Crandall

Computational Biology Institute

BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.

METHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene …

Introduction: Why People Do Not Accept Evolution: Using Protistan Diversity To Promote Evolution Literacy, Guillermo Paz-Y-Miño-C, Avelina Espinosa

Arts & Sciences Faculty Publications

The controversy evolution vs. creationism is inherent to the incompatibility between scientific rationalism/empiricism and the belief in supernatural causation. To test this hypothesis, we conceptualized a Cartesian landscape where the dependent variable acceptance of evolution was plotted as function of three factors, each represented by an index (value range 0 to 3): Religiosity Index (RI), Science Index (SI), and Evolution Index (EI). The indexes summarized an individual's personal religious convictions, familiarity with the processes and forces of change in organisms (= concept of evolution), and understanding the essence of science (= method to explore …

Internet Reviews: Livescience, John Creech

Library Scholarship

This column provides a review of LiveScience, a website created by TechMediaNetwork. The site is recommended for undergraduates seeking background information or professionals seeking quick facts.

Survey Of Erwinia Amylovora, Causal Agent Of Fire Blight, From Apple And Pear Orchards In Utah For Streptomycin Resistance, Christine Dhiman

NCUR

Fire blight caused by the bacterium Erwinia amylovora results in millions of dollar in losses worldwide. It is the most important disease problem for apple and pear growers in Utah. Currently the only effective management strategy is application of the antibiotic streptomycin. In 2006, resistant isolates were detected in an apple orchard in Utah County. To determine the distribution of resistant isolates, samples collected in 2006, 2007, 2010 and 2011 from orchards across Utah were tested for resistance to streptomycin. Isolates were screened at 0, 100 and 1000ppm of streptomycin. Bacteria were spread on LB agar. A hole was punched …

Saté-Ii: Very Fast And Accurate Simultaneous Estimation Of Multiple Sequence Alignments And Phylogenetic Trees, Kevin Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen

University Faculty Publications and Creative Works

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of …

Phylogenetic Community Structure Of Aquatic Beetle Assemblages In A Multi-Wetland Experiment, Sandor Lawrence Kelly

Electronic Theses and Dissertations

Phylogenetic Community Structure (PCS) metrics are becoming more common in community ecology. PCS metrics estimate the phylogenetic relatedness among members of an ecological community or assemblage. If ecological traits are conserved, then phylogenetic clustering (i.e., taxa are more closely related than expected by chance) indicates habitat filtering as the key process in community assembly. On the other hand, a pattern of phylogenetic overdispersion (i.e., taxa are more distantly related than expected by chance) suggests competition is dominant. Most studies to date have used PCS of unmanipulated ecosystems, but the value of PCS metrics will be best revealed in experiments. This …

Soil C And N Changes With Afforestation Of Grasslands Across Gradients Of Precipitation And Plantation Age, Sean T. Berthrong, Gervasio Pinero, Esteban G. Jobbagy, Robert B. Jackson

Scholarship and Professional Work - LAS

Afforestation, the conversion of unforested lands to forests, is a tool for sequestering anthropogenic carbon dioxide into plant biomass. However, in addition to altering biomass, afforestation can have substantial effects on soil organic carbon (SOC) pools, some of which have much longer turnover times than plant biomass. An increasing body of evidence suggests that the effect of afforestation on SOC may depend on mean annual precipitation (MAP). The goal of this study was to test how labile and bulk pools of SOC and total soil nitrogen (TN) change with afforestation across a rainfall gradient of 600–1500 mm in the Rio …

Congenic Strain Analysis Reveals Genes That Are Rapidly Evolving Components Of A Prezygotic Isolation Mechanism Mediating Incipient Reinforcement, Christina M. Laukaitis, Corina Mauss, Robert C. Karn

Scholarship and Professional Work - LAS

Two decades ago, we developed a congenic strain of Mus musculus, called b-congenic, by replacing the androgen-binding protein Abpa27^a allele in the C3H/HeJ genome with the Abpa27^b allele from DBA/2J. We and other researchers used this b-congenic strain and its C3H counterpart, the a-congenic strain, to test the hypothesis that, given the choice between signals from two strains with different a27 alleles on the same genetic background, test subjects would prefer the homosubspecific one. It was our purpose in undertaking this study to characterize the segment transferred from DBA to the C3H background in producing the b-congenic …

The Roles Of Gene Duplication, Gene Conversion And Positive Selection In Rodent Esp And Mup Pheromone Gene Families With Comparison To The Abp Family, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although …

Salinity Preference Of Alaskan Threespine Stickleback: Test For Divergence In Halotaxis Between Ancestral And Landlocked Populations, David Fryxell, Eric T. Schultz

EEB Articles

Glacial retreat during the Pleistocene caused landlocking of anadromous Alaskan threespine stickleback, Gasterosteus aculeatus, furnishing a natural ‘experiment’ in osmoregulatory divergence. The objective of this study was to assess the effects of individual acclimation and population divergence on salinity preference. Full-sibling families of marine, anadromous, and freshwater-landlocked populations of stickleback were reared in common environments until 3 weeks post-hatch, then were split and acclimated to low or high salinity. At 6 to 8 weeks of age the six experimental groups were tested for salinity preference in a tank that offers fish a choice of compartments with different salinities arranged …

Flow Structure And Transport Characteristics Of Feeding And Exchange Currents Generated By Upside-Down Cassiopea Jellyfish, Arvind Santhanakrishnan, Makani Dollinger, Christina L. Hamlet, Sean Colin, Laura A. Miller

Arts & Sciences Faculty Publications

Quantifying the flows generated by the pulsations of jellyfish bells is crucial for understanding the mechanics and efficiency of their swimming and feeding. Recent experimental and theoretical work has focused on the dynamics of vortices in the wakes of swimming jellyfish with relatively simple oral arms and tentacles. The significance of bell pulsations for generating feeding currents through elaborate oral arms and the consequences for particle capture are not as well understood. To isolate the generation of feeding currents from swimming, the pulsing kinematics and fluid flow around the benthic jellyfish Cassiopea spp. were investigated using a combination of videography, …

Cbdb: The Codon Bias Database, Adam Hilterbrand, Joseph Saelens, Catherine Putonti

Bioinformatics Faculty Publications

Background

In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift. Furthermore, correlations between codon usage within host genomes and their viral pathogens have been observed for a myriad of host-virus systems. As such, numerous studies have investigated codon usage and codon bias in an effort to better understand how species evolve. Numerous metrics have been developed to identify biases in codon usage. In addition, a few data repositories of codon bias data are available, …

Cam Kinase Control Of Akt And Lncap Cell Survival, John M. Schmitt, Samantha Smith, Brendon Hart, Luke Fletcher

Faculty Publications - Department of Biological & Molecular Science

AKT and its substrate BAD have been shown to promote prostate cancer cell survival. Agonists, such as carbachol, and hormones that increase intracellular calcium concentration can activate AKT leading to cancer cell survival. The LNCaP prostate cancer cells express the carbacholsensitive M3-subtype of G protein-coupled receptors that cause increases in intracellular calcium and activate the family of Ca2þ/calmodulindependent protein kinases (CaM Ks). One type of CaM Kinase, CaM Kinase Kinase (CaM KK), phosphorylates several substrates including AKT on threonine 308. AKT phosphorylation and activation enhances cell survival through phosphorylation of BAD protein and the subsequent blockade of caspase activation. Our …

Estrogen And Vitamin D Control Of Transcription In Mcf-7 Cells, John M. Schmitt, N. Magill

Faculty Publications - Department of Biological & Molecular Science

Abstract The Extracellular Signal-Regulated Kinase (ERK) is part of a key, signaling pathway that regulates both transcription and translation in many cell types. Increases in intracellular calcium levels results in the CaM Kinase-dependent activation of ERK and cell growth in MCF-7 breast cancer cells. ERK has also been shown to play a role in the regulation of MCF-7 cell proliferation through control of downstream transcription factors including Elk-1. The hormone, Vitamin D has been suggested to play an inhibitory role on cancer cells by blocking ERK activation. Our goal was to evaluate the ability of E2 to activate Elk-1, through …

Estrogen Receptor Activation Of Cam Kinase I And Erk, John M. Schmitt, Mikayla S. Todd

Faculty Publications - Department of Biological & Molecular Science

Cell growth and development is regulated by the cell signaling second messenger, calcium, that regulates key enzymes and genes in cells including the Calcium/Calmodulin-dependent protein kinases (CaM Ks) and their downstream target ERK. In particular, CaM KK and its substrate CaM KI promote ERK and Elk-1 activation in MCF-7 breast cancer cells. Estrogen (E2) may utilize CaM KK and ERK to promote breast cancer cell proliferation, however it is unclear which E2 receptor promotes cell proliferation through CaM Ks. Estrogen is a ligand for estrogen receptors (ER) of the alpha(α) and beta(β) forms, as well as G protein-coupled receptor 30 …

Early Lqt2 Nonsense Mutation Generates N-Terminally Truncated Herg Channels With Altered Gating Properties By The Reinitiation Of Translation, Matthew R. Stump, Qiuming Gong, Jonathan D. Packer, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

Mutations in the human ether-a-go-go-related gene (hERG) result in long QT syndrome type 2 (LQT2). The hERG gene encodes a K+ channel that contributes to the repolarization of the cardiac action potential. We have previously shown that hERG mRNA transcripts that contain premature termination codon mutations are rapidly degraded by nonsense-mediated mRNA decay (NMD). In this study, we identified a LQT2 nonsense mutation, Q81X, which escapes degradation by the reinitiation of translation and generates N-terminally truncated channels. RNA analysis of hERG minigenes revealed equivalent levels of wild-type and Q81X mRNA while the mRNA expressed from minigenes containing the LQT2 frameshift …

Isoform-Specific Dominant-Negative Effects Associated With Herg1 G628s Mutation In Long Qt Syndrome, Matthew R. Stump, Qiuming Gong, Zhengfeng Zhou

Faculty Publications - Department of Biological & Molecular Science

Background: Mutations in the human ether-a-go-go-related gene 1 (hERG1) cause type 2 long QT syndrome (LQT2). The hERG1 gene encodes a K+ channel with properties similar to the rapidly activating delayed rectifying K+ current in the heart. Several hERG1 isoforms with unique structural and functional properties have been identified. To date, the pathogenic mechanisms of LQT2 mutations have been predominantly described in the context of the hERG1a isoform. In the present study, we investigated the functional consequences of the LQT2 mutation G628S in the hERG1b and hERG1aUSO isoforms.

Methods: A double-stable, mammalian expression system was developed to characterize …

Anoxia Tolerance During Vertebrate Development - Insights From Studies On The Annual Killifish Austrofundulus Limnaeus, Jason E. Podrabsky, Claire L. Riggs, Jeffrey M. Duerr

Faculty Publications - Department of Biological & Molecular Science

No abstract provided.

A Comparative Approach To Elucidating The Physiological Response In Symbiodinium To Changes In Temperature, Elizabeth S. Mcginty

Biology Dissertations - Archive

Coral reefs are one of the most biodiverse ecosystems, and play a large role in the functioning of oceanic and coastal ecosystems. They are currently declining around the world, largely due to the effects of climate change and local anthropogenic issues. Temperature stress in particular has been associated with significant coral mortality over the last 30 years due to adverse effects on the relationship between reef-building corals and their algal endosymbionts from the genus Symbiodinium. Periods of elevated temperature have led to the phenomenon of coral bleaching, a disruption of the symbiosis that is characterized by the loss of the …

The Effects Of Mine Land Reclamation Of Herpetofaunal Communities, Jayme L. Walton

Biology Theses - Archive

Succession describes the process of community change over time after a disturbance. Understanding these processes allows ecological restoration projects to take advantage of natural community trajectories. Reclamation efforts often "jump-start" succession to restore anthropogenically disturbed land and water features to their former state. This is often accomplished by seeding for desired species or planting tree seedlings. One way of gauging whether reclamation was successful is to compare floral and faunal communities of reclaimed land with that of nearby land that was not disturbed. Most such studies have focused on plant and bird species while few have looked at the effects …

Survival Of The Fittest: Overcoming Oxidative Stress At The Extremes Of Acid, Heat And Metal, Yukari Maezato, Paul H. Blum

School of Biological Sciences: Faculty Publications

The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid ����� ��������� ������������ ������������ ������������� ��� ���� ���������� ��� ������ �������� carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly …

Metal Resistance And Lithoautotrophy In The Extreme Thermoacidophile Metallosphaera Sedula, Yukari Maezato, Tyler Johnson, Samuel Mccarthy, Karl Dana, Paul H. Blum

School of Biological Sciences: Faculty Publications

Archaea such as Metallosphaera sedula are thermophilic lithoautotrophs that occupy unusually acidic and metal-rich environments. These traits are thought to underlie their industrial importance for bioleaching of base and precious metals. In this study, a genetic approach was taken to investigate the specific relationship between metal resistance and lithoautotrophy during biotransformation of the primary copper ore, chalcopyrite (CuFeS₂). In this study, a genetic system was developed for M. sedula to investigate parameters that limit bioleaching of chalcopyrite. The functional role of the M. sedula copRTA operon was demonstrated by cross-species complementation of a copper-sensitive Sulfolobus solfataricus copR mutant. …

Carbohydrate Hydrolysis And Transport In The Extreme Thermoacidophile Sulfolobus Solfataricus, Sreedevi Lalithambika, Landon Peterson, Karl Dana, Paul H. Blum

School of Biological Sciences: Faculty Publications

Extremely thermoacidophilic microbes, such as Sulfolobus solfataricus, are strict chemoheterotrophs despite their geologic niche. To clarify their ecophysiology, the overlapping roles of endoglucanases and carbohydrate transporters were examined during growth on soluble cellodextrins as the sole carbon and energy source. Strain-specific differences in genome structure implied a unique role for one of three endogenous endoglucanases. Plasmid-based endoglucanase expression promoted the consumption of oligosaccharides, including cellohexaose (G6) through cellonanaose (G9). Protein transporters required for cellodextrin uptake were identified through

mutagenesis and complementation of an ABC transporter cassette, including a putative oligosaccharide binding protein. In addition, ablation of the binding protein …

Multiple Exposures To Drought ‘Train’ Transcriptional Responses In Arabidopsis, Yong Ding, Michael Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Pre-exposure to stress may alter plants’ subsequent responses by producing faster and/or stronger reactions implying that plants exercise a form of ‘stress memory’. The mechanisms of plants’ stress memory responses are poorly understood leaving this fundamental biological question unanswered. Here we show that during recurring dehydration stresses Arabidopsis plants display transcriptional stress memory demonstrated by an increase in the rate of transcription and elevated transcript levels of a subset of the stress–response genes (trainable genes). During recovery (watered) states, trainable genes produce transcripts at basal (preinduced) levels, but remain associated with atypically high H3K4me3 and Ser5P polymerase II levels, indicating …

Divergent Functions Of The Myotubularin (Mtm) Homologs Atmtm1 And Atmtm2 In Arabidopsis Thaliana: Evolution Of The Plant Mtm Family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, Zoya Avramova

School of Biological Sciences: Faculty Publications

Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases, and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes …

Dfvf: Database Of Fungal Virulence Factors, Tao Lu, Bo Yao, Chi Zhang

School of Biological Sciences: Faculty Publications

Fungal pathogens cause various diseases for plant and animal hosts. Despite the extensive impact of fungi on human health and life, the threats posed by emerging fungal pathogens are poorly understood. Specifically, there exist few fungal virulence gene databases, which prevent effective bioinformatics studies on fungal pathogens. Therefore, we constructed a comprehensive online database of known fungal virulence factors, which collected 2058 pathogenic genes produced by 228 fungal strains from 85 genera. This database creates a pivotal platform capable of stimulating and facilitating further bench studies on fungal pathogens.

Sex Allocation In California Oaks: Trade-Offs Or Resource Tracking?, Johannes Knops, Walter D. Koenig

School of Biological Sciences: Faculty Publications

Trade-offs in sex resource allocation are commonly inferred from a negative correlation between male and female reproduction. We found that for three California oak species, aboveground annual net productivity (ANP) differences among individuals were primarily correlated with water availability and soil fertility. Reproductive biomass increased with ANP, but the relative allocation to reproduction was constant, indicating that reproduction tracked productivity, which in turn tracked site quality. Although there was a negative correlation between male and female reproduction, this was not the result of a resource investment trade-off, but rather a byproduct of the positive correlation between female reproductive biomass and …

Urea Amidolyase (Dur1,2) Contributes To Virulence And Kidney Pathogenesis Of Candida Albicans, Dhammika H. M. L. P Navarathna, Michail S. Lionakis, Martin J. Lizak, Jeeva Munasinghe, Kenneth W. Nickerson, David D. Roberts

School of Biological Sciences: Faculty Publications

The intracellular enzyme urea amidolyase (Dur1,2p) enables C. albicans to utilize urea as a sole nitrogen source. Because deletion of the DUR1,2 gene reduces survival of C. albicans co-cultured with a murine macrophage cell line, we investigated the role of Dur1,2p in pathogenesis using a mouse model of disseminated candidiasis. A dur1,2Δ/dur1,2Δ strain was significantly less virulent than the wild-type strain, showing significantly higher survival rate, better renal function, and decreased and less sustained fungal colonization in kidney and brain. Complementation of the mutant restored virulence. DUR1,2 deletion resulted in a milder host inflammatory reaction. Immunohistochemistry, flow …