Environmental Stress Proteomics Of Two Blue Mussel (Genus Mytilus) Congeners, Lars Tomanek

Biological Sciences

Abstract of paper presented at the 28th Congress of the New European Society of Comparative Physiology and Biochemistry Proceedings: Bilbao, Spain.

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Long-Term Effects Of Estradiol Replacement In The Olfactory System, Britto P. Nathan, Michael Tonsor, Robert G. Struble

Faculty Research & Creative Activity

Olfactory dysfunction often precedes other clinical symptoms in chronic neurodegenerative diseases like Alzheimer’s and Parkinson’s disease. Estrogen deficiency and apoE genotype are known risk factors in these diseases and these factors also affect olfaction. Therefore we examined the effects of estradiol replacement following ovariectomy on expression of apoE and markers of cell proliferation, neuronal maturation, synaptogenesis and reactive gliosis in the primary olfactory pathway of wild-type (WT) and apoE knockout (KO) mice. Estradiol replacement increased apoE staining in the olfactory nerve and glomerular layers. Estradiol increased astrocyte density and olfactory epithelium (OE) thickness regardless of the genotype. In addition estradiol …

Long-Term Effects Of Estradiol Replacement In The Olfactory System, Britto Nathan, Michael Tonsor, Robert Struble

Faculty Research & Creative Activity

Olfactory dysfunction often precedes other clinical symptoms in chronic neurodegenerative diseases like Alzheimer’s and Parkinson’s disease. Estrogen deficiency and apoE genotype are known risk factors in these diseases and these factors also affect olfaction. Therefore we examined the effects of estradiol replacement following ovariectomy on expression of apoE and markers of cell proliferation, neuronal maturation, synaptogenesis and reactive gliosis in the primary olfactory pathway of wild-type (WT) and apoE knockout (KO) mice. Estradiol replacement increased apoE staining in the olfactory nerve and glomerular layers. Estradiol increased astrocyte density and olfactory epithelium (OE) thickness regardless of the genotype. In addition estradiol …

Gene Transcripts Encoding Hypoxia-Inducible Factor (Hif) Exhibit Tissue- And Muscle Fiber Type-Dependent Responses To Hypoxia And Hypercapnic Hypoxia In The Atlantic Blue Crab, Callinectes Sapidus, Kristin M. Hardy, Chandler R. Follett, Louis E. Burnett, Sean Lema

Biological Sciences

Hypoxia inducible factor (HIF) is a transcription factor that under low environmental oxygen regulates the expression of suites of genes involved in metabolism, angiogenesis, erythropoiesis, immune function, and growth. Here, we isolated and sequenced partial cDNAs encoding hif-α and arnt/hif-β from the Atlantic blue crab, Callinectes sapidus, an estuarine species that frequently encounters concurrent hypoxia (low O₂) and hypercapnia (elevated CO₂). We then examined the effects of acute exposure (1 h) to hypoxia (H) and hypercapnic hypoxia (HH) on relative transcript abundance for hif-α and arnt/hif-β in …

Investigation Of The Importance Of Rock Chemistry For Saxicolous Lichen Communities Of The New Idria Serpentinite Mass, San Benito County, California, Usa, Nishanta Rajakaruna, Kerry Knudsen, Alan M. Fryday, Ryan E. O'Dell, Nathaniel S. Pope, Fred C. Olday, Suzie Woolhouse

Biological Sciences

Although several lichen inventories exist for European ultramafic sites, only four surveys of serpentine lichens for North America have been published to date. Of those, only one has been conducted in California. We conducted a survey of saxicolous lichens from ultramafic rocks (including nephrite, partially serpentinized peridotite, and serpentinite) and non-ultramafic rocks (including silica-carbonate, shale, and sandstone) at the New Idria serpentinite mass, San Benito County, California. X-ray Fluorescence Analysis of the rocks from which the lichens were collected revealed significant elemental differences between the ultramafic and non-ultramafic rocks for 26 of the 32 major and trace elements analyzed. We …

Reinterpreting Bateman Gradients: Multiple Mating And Selection In Both Sexes Of A Songbird Species, N.M. Gerlach, J.W Mcglothlin, P.G Parker, E.D Ketterson

Biology Department Faculty Works

Bateman’s principle, which states that male reproductive success should increase with multiple mating, whereas female reproductive success should not, has long been used to explain sex differences in behavior. The statistical relationship between mating success and reproductive success, or Bateman gradient, has been proposed as a way to quantify sex differences in sexual selection. We used a long-term data set on the distribution of paternity in the socially monogamous dark-eyed junco to examine the effect of multiple mating on lifetime reproductive success and to determine the relative contributions of within-pair and extra-pair mating. Both sexes exhibited a strong positive Bateman …

Poliovirus Infection Transiently Increases Copii Vesicle Budding, Meg Trahey, Hyung Suk Oh, Craig E. Cameron, Jesse C. Hay

Biological Sciences Faculty Publications

Poliovirus (PV) requires membranes of the host cell's secretory pathway to generate replication complexes (RCs) for viral RNA synthesis. Recent work identified the intermediate compartment and the Golgi apparatus as the precursors of the replication "organelles" of PV (N. Y. Hsu et al., Cell 141:799-811, 2010). In this study, we examined the effect of PV on COPII vesicles, the secretory cargo carriers that bud from the endoplasmic reticulum and homotypically fuse to form the intermediate compartment that matures into the Golgi apparatus. We found that infection by PV results in a biphasic change in functional COPII vesicle biogenesis in cells, …

The Genus Plectrocnemia Stephens In China (Trichoptera, Polycentropodidae), Hua Zhong, Lian-Fang Yang, John C. Morse

Publications

Currently, 21 species of the genus Plectrocnemia are known from China. Examination of material collected from 13 provinces of China from 1990–2005 has revealed 9 new species and 3 new records of this genus, bringing the number of Chinese Plectrocnemia species to 33. Newly described species include: P. monacanthus sp. nov., P. huangi sp. nov., P. maoerensis sp. nov., P. pectinata sp. nov., P. fanjingensis sp. nov., P. platilobus sp. nov., P. paragryphalis sp. nov., P. bifoliolata sp. nov., and P. wuyiensis sp. nov. Two species, Plectrocnemia sinualis Wang & Yang and P. uncata Wang & Yang are synonymized with …

Arabidopsis Scaffold Protein Rack1a Modulates Rare Sugar D-Allose Regulated Gibberellin Signaling, Hemayet Ullah

Department of Biology Faculty Publications

As energy sources and structural components, sugars are the central regulators of plant growth and development. In addition to the abundant natural sugars in plants, more than 50 different kinds of rare sugars exist in nature, several of which show distinct roles in plant growth and development. Recently, one of the rare sugars, D-allose, an epimer of D-glucose at C3, is found to suppress plant hormone gibberellin (GA) signaling in rice. Scaffold protein RACK1A in the model plant Arabidopsis is implicated in the GA pathway as rack1a knockout mutants show insensitivity to GA in GA-induced seed germination. Using genetic knockout …

Rapid Range Expansion In The Great Plains Narrow-Mouthed Toad (Gastrophryne Olivacea) And A Revised Taxonomy For North American Microhylids, Jeffrey W. Streicher, Christian L. Cox, Jonathan A. Campbell, Eric N. Smith, Rafael O. De Sá

Biology Faculty Publications

We investigated genetic variation within the Great Plains narrow-mouthed toad, Gastrophryne olivacea, across its geographic range in the United States and Mexico. An analysis of mitochondrial DNA (mtDNA) from 105 frogs revealed remarkably low levels of genetic diversity in individuals inhabiting the central United States and northern Mexico. We found that this widespread matrilineal lineage is divergent (ca. 2% in mtDNA) from haplotypes that originate from the western United States and western coast of Mexico. Using a dataset that included all five species of Gastrophryne and both species of the closely related genus Hypopachus, we investigated the phylogenetic …

High Prevalence Of The Amphibian Chytrid Fungus (Batrachochytrium Dendrobatidis) Across Multiple Taxa And Localities In The Highlands Of Ethiopia, David J. Gower, Thomas M. Doherty-Bone, Roman K. Aberra, Abebe Mengistu, Silvia Schwaller, Michele Menegon, Rafael O. De Sá, Samy A. Saber, Andrew A. Cunningham, Simon P. Loader

Biology Faculty Publications

Surveys of the potentially lethal amphibian chytrid fungus (Batrachochytrium dendrobatidis - Bd) in Africa are patchy, especially in some regions of high species endemicity. We present results of the first Bd surveys of wild amphibians in Ethiopia, for two upland regions on either side of the Rift Valley: the Bale Mountains and the Kaffa region. Surveys were opportunistic so that robust interpretation of the data is limited. Utilizing diagnostic qPCR assays, 51 out of 120 frogs (14 species in 10 genera) tested positive for Bd at altitudes of 1,620–3,225 m, across all genera and species, and all but …

Euscorpius Sicanus (Scorpiones: Euscorpiidae) From Tunisia: Dna Barcoding Confirms Ancient Disjunctions Across The Mediterranean Sea, Matthew R. Graham, Pavel Stoev, Nesrine Akkari, Gergin Blagoev, Victor Fet

Biological Sciences Faculty Research

We used a DNA barcoding marker (mitochondrial cox1) to investigate the controversial natural occurrence of Euscorpius sicanus (C.L. Koch) in North Africa. We tested this hypothesis by comparing a sample collected from a mountain in Tunisia to disjunct populations in Sardinia, Malta, and Greece. Using these samples, and a few additional Euscorpius spp. from southern Europe as outgroups, we reconstructed the maternal phylogeny. We then used a molecular clock to place the phylogeny in a temporal context. The Tunisian sample grouped closest to a specimen from Sardinia, with both being more distantly related to E. sicanus from Malta, which is …

Ectoparasites Of American Kestrels In Northwestern New Jersey And Their Relationship To Nestling Growth And Survival, Mark J. Lesko, John Smallwood

Department of Biology Faculty Scholarship and Creative Works

American Kestrel (Falco sparverius) populations have been declining throughout much of North America during recent decades. To determine if the ectoparasite burdens of nestlings may be a contributing factor, we examined broods of kestrels in nest boxes in northwestern New Jersey. Our objectives were to identify and quantify the arthropod ectoparasites of nestlings, and to determine if removing these parasites from nestlings would increase kestrel nesting success. Of 26 broods we examined, we randomly chose 13 and manually removed from the nestlings all visible arthropods during three visits, when nestlings were age 57, 1012, and 1517 d old; we handled …

Enrichment Of Hp1a On Drosophila Chromosome 4 Genes Creates An Alternate Chromatin Structure Critical For Regulation In This Heterochromatic Domain, Nicole Riddle, Youngsook Jung, Tingting Gu, Artyom Alekseyenko, Dalal Asker, Hongxing Gui, Peter Kharchenko, Aki Minoda, Annette Plachetka, Yuri Schwartz, Michael Tolstorukov, Mitzi Kuroda, Vincenzo Pirrotta, Gary Karpen, Peter Park, Sarah C.R. Elgin

Biology Faculty Research

Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in …

Resource‐Based Habitat Associations In A Neotropical Liana Community, James W. Dalling, Stefan A. Schnitzer, Claire Baldeck, Kyle E. Harms, Robert John, Scott A. Mangan, Elena Lobo, Joseph B. Yavitt, Stephen P. Hubbell

Biological Sciences Faculty Research and Publications

Summary

1. Lianas are a conspicuous element of many tropical forests, accounting for up to 40% of woody stem density and 20% of species richness in seasonal forests. However, lianas have seldom been surveyed at sufficiently large spatial scales to allow an assessment of the importance of habitat variables in structuring liana communities.

2. We compare the association patterns of 82 liana species and an equivalent sample of tree species on the 50 ha Forest Dynamics Project plot on Barro Colorado Island, Panama, with topographic habitat variables (high and low plateau, slope, swamp and streamside), and thirteen mapped soil chemical …

Long Noncoding Rnas Are Rarely Translated In Two Human Cell Lines, Jainab Khatun, Brian Risk, Morgan Giddings

Biology Faculty Publications and Presentations

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA– fractions in the cell lines K562 and GM12878. We used the machinelearning algorithm RuleFit3 to regress the peptide data against RNA …

The Conflict Within And The Escalating War Between The Sex Chromosomes, Jeffrey M. Good

Biological Sciences Faculty Publications

No abstract provided.

Effect Of Egf-Receptor Tyrosine Kinase Inhibitor On Rab5 Function During Endocytosis, Ivan Jozic, Samar C. Saliba, M. Alejandro Barbieri

Biology Faculty Articles

Tyrosine autophosphorylation within the cytoplasmic tail of EGF-receptor is a key event, which in turn recruits several factors including Shc, Grb2 and Rin1 that are essential activities for receptor-mediated endocytosis and signaling. In this study, we demonstrated that treatment with AG1478, an EGF-receptor kinase inhibitor, blocked the formation of Rab5-positive endosomes as well as the activation of Rab5 upon addition of EGF. We also found that EGF-receptor catalytically inactive mutant failed to activate Rab5 upon EGF stimulation. Additionally, endosomal co-localization of Rab5 and EGF-receptor was inhibited by AG1478. Interestingly, AG1478 inhibitor did not block the formation of enlarged Rab5-positive endosomes …

Non-Photoperiodic Regulation Of Reproductive Physiology In The Flexibly Breeding Pine Siskin (Spinus Pinus), Heather E. Watts, Thomas P. Hahn

Biology Faculty Works

In order to time reproduction to coincide with favorable conditions, animals use environmental cues to up- and down-regulate the reproductive axis appropriately. Although photoperiodic cues are one of the best studied of such environmental cues, animals also attend to others such as temperature, food availability, rainfall and social cues. Such non-photic cues are expected to be particularly important for tropical species and temperate-zone species that exhibit flexible or opportunistic breeding schedules. In this study, we investigate the use of non-photic cues, specifically food availability and social cues, to time the initiation of reproductive development in the pine siskin (Spinus …

The Development Of Dermatonotus Muelleri (Anura: Microhylidae: Gastrophryninae), Marissa Fabrezi, Silvia Quinzio, Javier Goldberg, Rafael O. De Sá

Biology Faculty Publications

The monophyly of Microhylidae is supported by an overwhelming accumulation of synapomorphic larval features. Despite the distinctiveness of the microhylid tadpole, few studies have focused on larval development. Microhylid larval morphology is usually described and based on standard tables that imply that developmental events at equivalent stages of overall tadpole development are independent from species-specific patterns of developmental timing. Herein, we present additional developmental data based on external morphology and field data on larval growth for the gastrophrynine microhylid Dermatonotus muelleri. We describe internal morphological variation (e.g., skeletal and soft systems) during larval development. The results indicate that the onset …

Expression Of Recombinant Earli1, A Hybrid Proline-Rich Protein Of Arabidopsis, In Escherichia Coli And Its Inhibition Effect To The Growth Of Fungal Pathogens And Saccharomyces Cerevisiae, Lan Li, Chen Zhang, Dan Xu, Michael Schläppi, Zi-Qin Xu

Biological Sciences Faculty Research and Publications

EARLI1 is an Arabidopsis gene with pleiotropic effects previously shown to have auxiliary functions in protecting plants against freezing-induced cellular damage and promoting germinability under low-temperature and salinity stresses. Here we determined whether recombinant EARLI1 protein has anti-fungal activity. Recombinant EARLI1 protein lacking its signal peptide was produced in Escherichia coli BL21(DE3) using isopropyl β-d-1-thiogalactopyranoside (IPTG) induction and the prokaryotic expression vector pET28a. Expression of EARLI1 was analyzed by Western blotting and the protein was purified using affinity chromatography. Recombinant EARLI1 protein was applied to fungal cultures of Saccharomyces cerevisiae, Botrytis cinerea and Fusarium oxysporum, and membrane permeability …

Sub-Antarctic And High Antarctic Notothenioid Fishes: Ecology And Adaptational Biology Revealed By The Icefish 2004 Cruise Of Rvib Nathaniel B. Palmer, H. William Detrich Iii, Bradley A. Buckley, Daniel F. Doolittle, Christopher D. Jones, Susanne J. Lockhart

Biology Faculty Publications and Presentations

The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat …

Competitive Abilities In Experimental Microcosms Are Accurately Predicted By A Demographic Index For R*, Ebony G. Murrell, Steven A. Juliano

Faculty Publications – Biological Sciences

Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (R-index) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether R-index yielded accurate predictions of competitive abilities using mosquitoes as …

Origin Of Great Lakes Brown Trout, Salmo Trutta: A Phylogeographic Analysis Using Mtdna Sequence Variation, David Baisch

Masters Theses

The brown trout, Salmo trutta, was first introduced to the Laurentian Great Lakes in 1887 from European broodstocks to found a recreational salmonid fishery; however, the origins of these progenitor lineages remain largely unknown. Trout from these regions are very specialized to their native habitats and matching North American stocks to similar watersheds may help increase survivability by introducing the stock to a more appropriate environment. The objective of this study was to determine the European origins of brown trout found in the Great Lakes. We analyzed 144 brown trout from ten watersheds across Michigan and Wisconsin and identified …

The Ranging Costs Of A Fallback Food: Liana Consumption Supplements Diet But Increases Foraging Effort In Howler Monkeys, Jacob C. Dunn, Norberto Asensio, Victor Arroyo-Rodriguez, Stefan A. Schnitzer, Jurgi Cristóbal‐Azkarate

Biological Sciences Faculty Research and Publications

Lianas are important components in the dynamics of tropical forests and represent fallback foods for some primates, yet little is known about their impact on primate ecology, behavior or fitness. Using 2 yr of field data, we investigated liana consumption and foraging effort in four groups of howler monkeys (two in bigger, more conserved forest fragments and two in smaller, less conserved fragments) to assess whether howler monkeys use lianas when and where food availability is scarce, and how liana consumption is related to foraging effort. Howler monkeys in smaller fragments spent more time consuming lianas and liana consumption was …

Land Snails In Ephemeral Pools At Ottine Swamp, Gonzales County, Texas, Frank J. Dirrigl, Robert H. Mohlenbrock

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

We found five species of terrestrial land snails in dried ephemeral pools at Ottine Swamp, Palmetto State Park, Gonzales County, Texas. We recorded four species previously known (Anguispira stronglyodes, Mesomphix friabilis, Olygyra orbiculata, and Rabdotus dealbatus) and added a new occurrence (Mesodon thyroidus) to the list of species in the park.

Se encontraron cinco especies de caracoles terrestres en los fondos secos de unos charcos efímeros en Ottine Swamp, Palmetto State Park, en el condado de Gonzales, Texas. Registramos cuatro especies conocidas anteriormente (Anguispira stronglyodes, Mesomphix friabilis, Olygyra orbiculata y …

Stable Bifurcations In Semelparous Leslie Models, J. M. Cushing, Shandelle M. Henson

Faculty Publications

In this paper, we consider nonlinear Leslie models for the dynamics of semelparous age-structured populations. We establish stability and instability criteria for positive equilibria that bifurcate from the extinction equilibrium at R0=1. When the bifurcation is to the right (forward or super-critical), the criteria consist of inequalities involving the (low-density) between-class and within-class competition intensities. Roughly speaking, stability (respectively, instability) occurs if between-class competition is weaker (respectively, stronger) than within-class competition. When the bifurcation is to the left (backward or sub-critical), the bifurcating equilibria are unstable. We also give criteria that determine whether the boundary of the positive cone is …

Urban Development In Costa Rica: The Direct And Indirect Impacts On Local And Regional Avian Assemblages, Jeff L. Norris

Dissertations

Urban development, the pinnacle of human land use, has drastic effects on native ecosystems and the species they contain. For the first time in recorded history there are more people living in cities than in the rural areas surrounding them. Furthermore, the global rate of urbanization continues increasing; raising serious concerns for earth's tropical regions as they harbor a disproportionate amount of the earth's species, and where the impacts of urban development on natural communities are poorly known. Therefore, for my dissertation research I investigated the impacts of urban development on avian community structure and organization at both local and …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …