Digital Commons Network^™

A Reverse Transcriptase-Pcr Assay For Detecting Filarial Infective Larvae In Mosquitoes, Sandra J. Laney, Caitlin J. Buttaro, Sabato Visconti, Nils Pilotte, Reda M.R. Ramzy, Gary J. Weil, Steven A. Williams

Biological Sciences: Faculty Publications

Background: Existing molecular assays for filarial parasite DNA in mosquitoes cannot distinguish between infected mosquitoes that contain any stage of the parasite and infective mosquitoes that harbor third stage larvae (L3) capable of establishing new infections in humans. We now report development of a molecular L3-detection assay for Brugia malayi in vectors based on RT-PCR detection of an L3-activated gene transcript.

Methodology/Principal Findings: Candidate genes identified by bioinformatics analysis of EST datasets across the B. malayilife cycle were initially screened by PCR using cDNA libraries as templates. Stage-specificity was confirmed using RNA isolated from infected mosquitoes. Mosquitoes were collected daily …

Plumage Ornamentation As An Indicator Of Female Age And An Influence In Male Mate Choice In Protonotaria Citrea, The Prothonotary Warbler In Virginia., Terry Smith

Theses and Dissertations

Flamboyant plumage and ornamentation is common and well-known in male birds; it serves as a sexual display to attract potential mates. While flamboyant plumage is less common and usually more subtle in female birds, it does occur in some species such as Dark-Eyed Juncos (Junco hyemalis) and Prothonotary Warblers (Protonotaria citrea). Prothonotary Warblers display relatively subtle sexual dimorphism. This study examines variations in tail spot patterns in Prothonotary Warblers and relates those variations to age in females. Females with fewer than six spots tend to be two years old or younger; females with six spots or more tend to be …

Zoonotic Disease Emergence : A Study Of Host-Pathogen-Ecosystem Dynamics, Laurie Jeanne Dizney

Dissertations and Theses

A growing body of work demonstrates that loss of biodiversity negatively impacts ecosystem functions. One function, or service, that biodiverse ecosystems provide is suppression of zoonotic diseases, which are defined as diseases carried by wildlife hosts that can spill over into human populations. Ebola, SARS, West Nile virus, Hantavirus, Avian Influenza and Lyme disease are just a few of the recently emerging zoonotic diseases. Disease suppression has been shown for Lyme disease by the dilution effect, whereby increasing species diversity decreases disease prevalence in the host populations. But does a dilution effect apply to other disease systems? To test this …

Effects Of Mek5/Erk5 Association On Small Ubiquitin-Related Modification Of Erk5implications For Diabetic Ventricular Dysfunction After Myocardial Infarction, Tetsuro Shishido, Chang Hoon Woo, Bo Ding, Carolyn Mcclain, Carlos Molina, Chen Yan, Jay Yang, Jun Ichi Abe

Department of Biology Faculty Scholarship and Creative Works

Diabetes mellitus (DM) contributes to the exacerbation of left ventricle (LV) dysfunction after myocardial infarction (MI). Activation of ERK5, an atypical mitogen activated protein kinase with transcriptional activity, inhibits apoptosis and LV dysfunction after doxorubicin treatment. SUMOylation has been proposed as a negative regulator of various transcription factors. In the current study, we investigated the role of ERK5-SUMOylation in ERK5 transcriptional activity as well as on DM-mediated exacerbation of LV dysfunction and apoptosis after MI. ERK5 wild-type transcriptional activity was inhibited by Ubc9 (SUMO E2 conjugase) or PIAS1 (E3 ligase), but not in the ERK5-SUMOylation-site defective mutant (K6R/K22R). H2O2 and …

Loss Of ‘Bio-Guards’ Endangering Humans Says Professor, Rachel Hatch

News and Events (Discontinued Series)

No abstract provided.

Separating Developmental And Environmental Effects On Fluctuating Asymmetry In Lythrum Salicaria And Penthorum Sedoides, Jennifer R. Milligan, Robert A. Krebs, Tarun K. Mal

Biological, Geological, and Environmental Faculty Publications

Environmental stress can disrupt developmental processes on biological, physiological, and chemical levels and thereby affect the symmetry of a trait. For this reason, fluctuating asymmetry is often proposed as a measure of stress encountered by an individual. One problem is that asymmetry may have multiple causes, including developmental noise and genetic background, and genetic differences may interact with any physiological stress imposed by the environment. The main objective of this research was to determine whether developmental noise and genetic stress can be separated from environmental effects on leaf asymmetry. The experiments were conducted on two wetland plants, Lythrum salicaria (purple …

Differential Exposure, Duration, And Sensitivity Of Unionoidean Bivalve Life Stages To Environmental Contaminants, W. Gregory Cope, Robert B. Bringolf, David B. Buchwalter, Teresa J. Newton, Christopher G. Ingersoll, Ning Wang, Tom Augspurger, F. James Dwyer, M. Christopher Barnhart, For Complete List Of Authors, See Publisher's Website., Edward Hammer

College of Natural and Applied Sciences

Freshwater mussels (superfamily Unionoidea) are in serious global decline and in urgent need of protection and conservation. The declines have been attributed to a wide array of human activities resulting in pollution and water-quality degradation, and habitat destruction and alteration. Linkages among poor water quality, pollutant sources, and mussel decline in rivers and streams have been associated with results of laboratory-based tests of specific pollutants. However, uncertainties remain about the relationship of laboratory data to actual contaminant exposure routes for various mussel species, life stages, and in the habitats occupied during these exposures. We evaluated the pathways of exposure to …

Soil Morphology, Depth And Grapevine Root Frequency Influence Microbial Communities In A Pinot Noir Vineyard, Rebecca E. Drenovsky, K. L. Steenwerth, J. J. Lambert, D. A. Kluepfel, K. M. Scow, D. R. Smart

Biology

The composition of microbial communities responds to soil resource availability, and has been shown to vary with increasing depth in the soil profile. Soil microorganisms partly rely on root-derived carbon (C) for growth and activity. Roots in woody perennial systems like vineyards have a deeper vertical distribution than grasslands and annual agriculture. Thus, we hypothesized that vineyard soil microbial communities along a vertical soil profile would differ from those observed in grassland and annual agricultural systems. In a Pinot noir vineyard, soil pits were excavated to ca. 1.6–2.5m, and microbial community composition in ‘bulk’ (i.e., no roots) and ‘root’ (i.e., …

Botany At Eastern Illinois University, Marissa C. Jernegan, Nancy Coutant, Janice M. Coons

Faculty Research & Creative Activity

Eastern Illinois University was established in 1899, and from its beginning recognized the importance of the botanical sciences. Two terms of botany were required for the four year program. Otis W. Caldwell, a botanist, was one of the original faculty members. He taught all of the biology courses and initiated the acquisition of a greenhouse. Caldwell was the first of a series of talented and dedicated botany professors including Edgar N. Transeau, Ernest L. Stover, Hiram F. Thut and John E. Ebinger. These and many other professors incorporated a field component into almost all classes. This dedication to the study …

Mulched Cover Crops As An Alternative To Conventional Weed Management Systems In Vineyards, Scott J. Steinmaus, C. L. Elmore, R. J. Smith, D. Donaldson, E. A. Weber, J. A. Roncoroni, P. R.M. Miller

Biological Sciences

Conventional methods of weed management in vineyards rely primarily on herbicides and tillage. The desire to adopt alternatives to these methods is driven by environmental and economic reasons. Weed suppression and grape yield under mulched cover crop systems at two rainfed northern California vineyards were similar to, and at times exceeded, those under conventional tillage or herbicide management. Cover crop productivity was positively correlated with weed suppression and mulch decomposition rates and seemed to be determined primarily by location and then by cover crop type. The mulch from mowed cover crops averaged 603(± 94) gm⁻² at the two sites. …

Climate Change And The Future Of California's Endemic Flora, Scott R. Loarie, Benjamin E. Carter, Katherine Hayhoe, Sean Mcmahon, Richard Moe, Charles A. Knight, David D. Ackerly

Biological Sciences

The flora of California, a global biodiversity hotspot, includes 2387 endemic plant taxa. With anticipated climate change, we project that up to 66% will experience >80% reductions in range size within a century. These results are comparable with other studies of fewer species or just samples of a region’s endemics. Projected reductions depend on the magnitude of future emissions and on the ability of species to disperse from their current locations. California’s varied terrain could cause species to move in very different directions, breaking up present-day floras. However, our projections also identify regions where species undergoing severe range reductions may …

A Strategy For Managing The Recreational Catch Of Demersal Scalefish In The West Coast Bioregion. Decisions By The Minister For Fisheries, Jon Ford (Minister For Fisheries; The Kimberley, Pilbara And Gascoyne)

Fisheries Management Papers

The following recreational fisheries management package is a result of an extensive public consultation process. The package has been carefully developed to deliver the required reduction in catches. It is important to understand that each management measure contributes to the reduction in catches necessary to give these stocks a chance to rebuild and that no measure on its own will deliver the required reduction in catch.

To ensure the ongoing recovery of stocks, an adaptive approach to management has been adopted. This approach will involve an ongoing review of the effectiveness of these management arrangements, and take into account the …

Variation In Resource Acquisition And Utilization Traits Between Native And Invasive Perennial Forbs, Rebecca E. Drenovsky, Christina E. Martin, Molly R. Falasco, Jeremy J. James

Biology

Understanding the functional traits that allow invasives to outperform natives is a necessary first step in improving our ability to predict and manage the spread of invaders. In nutrient-limited systems, plant competitive ability is expected to be closely tied to the ability of a plant to exploit nutrient-rich microsites and use these captured nutrients efficiently. The broad objective of this work was to compare the ability of native and invasive perennial forbs to acquire and use nutrients from nutrient-rich microsites. We evaluated morphological and physiological responses among four native and four invasive species exposed to heterogeneous (patch) or homogeneous (control) …

Rules Of Engagement: Interspecies Interactions That Regulate Microbial Communities, Ainslie Little, Courtney Robinson, S Peterson, Kenneth Raffa, Jo Handelsman

Department of Biology Faculty Publications

Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important …

Movement And Habitat Use Of Two Aquatic Turtles (Graptemys Geographic And Trachemys Scripta) In An Urban Landscape, Travis J. Ryan, C A. Conner, B A. Douthitt, S C. Sterrett, Carmen M. Salsbury

Scholarship and Professional Work - LAS

Our study focuses on the spatial ecology and seasonal habitat use of two aquatic turtles in order to understand the manner in which upland habitat use by humans shapes the aquatic activity, movement, and habitat selection of these species in an urban setting. We used radiotelemetry to follow 15 female Graptemys geographica (common map turtle) and each of ten male and female Trachemys scripta (red-eared slider) living in a man-made canal within a highly urbanized region of Indianapolis, IN, USA. During the active season (between May and September) of 2002, we located 33 of the 35 individuals a total of …

Estimating Gene Signals From Noisy Microarray Images, Pinaki Sarder, Arye Nehorai, Paul H. Davis, Samuel L. Stanley Jr.

Biology Faculty Publications

In oligonucleotide microarray experiments, noise is a challenging problem, as biologists now are studying their organisms not in isolation but in the context of a natural environment. In low photomultiplier tube (PMT) voltage images, weak gene signals and their interactions with the background fluorescence noise are most problematic. In addition, nonspecific sequences bind to array spots intermittently causing inaccurate measurements. Conventional techniques cannot precisely separate the foreground and the background signals. In this paper, we propose analytically based estimation technique. We assume a priori spot-shape information using a circular outer periphery with an elliptical center hole. We assume Gaussian statistics …

Undetected Species Losses, Food Webs, And Ecological Baselines: A Cautionary Tale From The Greater Yellowstone Ecosystem, Usa, Joel Berger

Biological Sciences Faculty Publications

Large protected areas are often considered natural yet outside pressures may compromise ecological integrity. This paper points to a problem in assessing ecological baselines: what if species' extirpations go undetected? I present a data set spanning 130 years that demonstrates the loss of white-tailed jack rabbits Lepus townsendii from two National Parks in the well studied 60,000 km(2) Greater Yellowstone Ecosystem, USA. While these extirpations have been unnoticed until now, an ecological consequence may be elevated predation on juvenile ungulates. A critical challenge we face is how to apply better the concept of shifting baselines to the restoration of functional …

Reproduction Within Marmotine Ground Squirrels (Sciuridae, Xerinae, Marmotini): Patterns Among Genera, Virginia Hayssen

Biological Sciences: Faculty Publications

The sciurid tribe Marmotini has a distinctive, highly specialized reproductive profile characterized by annually produced litters of many offspring, each of small mass and fast growth rate. However, not all genera of marmotines follow the reproductive profile of the tribe. In fact, included in the tribe are squirrels with the highest and lowest energetic investment into reproduction of the entire family. Because of its large litter size, Ammospermophilus has the largest energetic investment into reproduction of nearly all squirrels. Also, Ammospermophilus is not limited to 1 litter per year. At the opposite extreme, Marmota has the smallest energetic investment into …

Reproductive Effort In Squirrels: Ecological, Phylogenetic, Allometric, And Latitudinal Patterns, Virginia Hayssen

Biological Sciences: Faculty Publications

The distinctive features of reproduction in squirrels are the lack of allometric influences on the duration of reproductive investment; the strong allometric influences on offspring mass; and a trade-off between number and size of young, suggesting an important developmental component to reproduction. Lengths of gestation and lactation do not vary with body size but neonatal and weaning mass do. Apparently, the major constraint on reproduction in squirrels is not resources per se (food, calories, minerals, or water) but rather the length of time such resources are available. Squirrels adjust growth rate to fit the timing of resource abundance. Within the …

Contribution Of Cystine-Glutamate Antiporters To The Psychotomimetic Effects Of Phencyclidine, David A. Baker, Aric Madayag, Lars V. Kristiansen, James H. Meador-Woodruff, Vahram Haroutunian, Ilangovan Raju

Biological Sciences Faculty Research and Publications

Altered glutamate signaling contributes to a myriad of neural disorders, including schizophrenia. While synaptic levels are intensely studied, nonvesicular release mechanisms, including cystine–glutamate exchange, maintain high steady-state glutamate levels in the extrasynaptic space. The existence of extrasynaptic receptors, including metabotropic group II glutamate receptors (mGluR), pose nonvesicular release mechanisms as unrecognized targets capable of contributing to pathological glutamate signaling. We tested the hypothesis that activation of cystine–glutamate antiporters using the cysteine prodrug N-acetylcysteine would blunt psychotomimetic effects in the rodent phencyclidine (PCP) model of schizophrenia. First, we demonstrate that PCP elevates extracellular glutamate in the prefrontal cortex, an effect …

Neural Network Models For Solving The Maximum Flow Problem, S. Effati, M. Ranjbar

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, two new neural network models for solving the maximum flow problem are presented. The maximum flow problem in networks is formulated as a special type of linear programming problem and it is solved by appropriately defined neural networks. The nonlinear neural networks are able to generate optimal solution for maximum flow problem. We solve neural network models by one of the numerical method. Finally, some numerical examples are provided for the sake of illustration.

Behavioral And Physiological Ecology Of Scorpion Venom Expenditure: Stinging, Spraying, And Venom Regeneration, Zia Nisani

Loma Linda University Electronic Theses, Dissertations & Projects

In this dissertation, I reviewed the functional aspects of venom from a behavioral perspective to develop a comprehensive understanding of the behavioral ecology of venom. To explore the behavioral and physiological ecology of venom expenditure by scorpions, I conducted four studies of the medically significant Buthid scorpion Parabuthus transvaalicus. The first two experiments revealed that scorpions regulate their venom expenditure during defensive stinging and squirting in the most complex manner yet described for any venomous organism. When stinging, these scorpions can choose between delivering a dry or wet sting. Should they deliver a wet sting, they meter the volume …

Improving The Computer Science In Bioinformatics Through Open Source Pedagogy, John David N. Dionisio, Kam D. Dahlquist

Biology Faculty Works

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total "incubation time" of six months.

The Reproductive And Conservation Biology Of The Spotted Towhee In Urban Forest Fragments, Sarah Bartos Smith

Dissertations and Theses

I studied the demography, reproductive biology, and mating behavior of Spotted Towhees (Pipilo maculatus) in four urban parks in relation to park area, the presence of recreational trails, and the effects of habitat edges. Despite high towhee abundance in the parks, two of the four are population sinks with levels of yearly reproductive productivity that do not offset adult survival. The other two parks have sufficient reproduction to adequately result in stable or growing population sizes. Park area and the proportion of habitat edge had no influence on population growth rate, reproductive productivity, or survival. However, trail density …

Complementary Dna Sequencing And Identification Of Mrnas From Venomous Gland Of Agkistrodon Piscivorus Leucostoma, Ying Jia, Bruno A. Cantu, Elda E. Sánchez, John C. Pérez

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

To advance our knowledge on the snake venom composition and transcripts expressed in venom gland at the molecular level, we constructed a cDNA library from venom gland of Agkistrodon piscivorus leucostoma for the generation of expressed sequence tags (ESTs) database. From the randomly sequenced 2,112 independent clones, we have obtained ESTs for 1,309 (62%) cDNAs which showed significant deduced amino acid sequence similarity (scores > 80) to previously characterized proteins in NCBI database. Ribosomal proteins make up 47 clones (2%) and the remaining 756 (36%) cDNAs represent either unknown identity or show BLASTX sequence identity scores of < 80 with known GenBank accessions. The most highly expressed gene encoding phospholipase A2 (PLA2) accounting for 35% of A. p. leucostoma venom …

Mutational Studies In The Dntp Binding Pocket Of Human Immunodeficiency Virus Type 1 Reverse Transcriptase, Smita Shukla

Theses

It was earlier postulated that Gln 91 of HIV-1 RT stabilizes the side chain of Tyr 183 via hydrogen bonding interaction between 0(H) of Y1 83 and CO of Q91 (Harris et al., BIOCHEMISTRY 37: 9630, 1998). In an attempt to understand the function of Gln 91 in the catalytic mechanism, mutants of this residue (Gln91 - -> Ala and Gln91 - ->Asn) were generated and subjected to an in-depth analysis. The efficiency of reverse transcription of natural U5-PBS HIV-1 RNA template was severely impaired by both conservative and non-conservative substitutions from Gln—>Asn and Gln—> Ala, a result …

An Improved String Composition Method For Sequence Comparison, Guoquing Lu, Shunpu Zhang, Xiang Fang

Biology Faculty Publications

Background: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector (CV) methods, which use the frequencies of nucleotide or amino acid strings to represent sequence information, show promising results in genome sequence comparison of prokaryotes. The existing CV-based methods, however, suffer certain statistical problems, thereby underestimating the amount of evolutionary …

The Cul7 E3 Ubiquitin Ligase Targets Insulin Receptor Substrate 1 For Ubiquitin-Dependent Degradation, Pascal J. Lafontant

Biology Faculty publications

Recent genetic studies have documented a pivotal growth regulatory role played by the Cullin 7 (CUL7) E3 ubiquitin ligase complex containing the Fbw8-substrate-targeting subunit, Skp1, and the ROC1 RING finger protein. In this report, we identified insulin receptor substrate 1 (IRS-1), a critical mediator of the insulin/insulin-like growth factor 1 signaling, as a proteolytic target of the CUL7 E3 ligase in a manner that depends on mammalian target of rapamycin and the p70 S6 kinase activities. Interestingly, while embryonic fibroblasts of Cul7-/- mice were found to accumulate IRS-1 and exhibit increased activation of IRS-1’s downstream Akt and MEK/ERK pathways, these …

The Parallel Worm Tracker: A Platform For Measuring Average Speed And Drug-Induced Paralysis In Nematodes, Daniel Ramot, Brandon E. Johnson, Tommie L. Berry Jr., Lucinda Carnell, Miriam B. Goodman

All Faculty Scholarship for the College of the Sciences

Background

Caenorhabditis elegans locomotion is a simple behavior that has been widely used to dissect genetic components of behavior, synaptic transmission, and muscle function. Many of the paradigms that have been created to study C. elegans locomotion rely on qualitative experimenter observation. Here we report the implementation of an automated tracking system developed to quantify the locomotion of multiple individual worms in parallel.

Methodology/Principal Findings

Our tracking system generates a consistent measurement of locomotion that allows direct comparison of results across experiments and experimenters and provides a standard method to share data between laboratories. The tracker utilizes a video camera …

Grazing And Virus-Induced Mortality Of Microbial Populations Before And During The Onset Of Annual Hypoxia In Lake Erie, Christopher J. Gobler, Timothy W. Davis, Sarah N. Deonarine, Matthew A. Saxton, Peter J. Lavrentyev, Frank J. Jochem

Biology Faculty Research

Lake Erie is the most productive of the North American Great Lakes and experiences annual periods of hypolimnetic hypoxia with unknown consequences for the microbial food web. We established the abundances and mortality rates of microbes in Lake Erie during thermal stratification and determined how they varied with changes in bottom-water dissolved oxygen concentrations. The microbial plankton community (heterotrophic bacteria, Cyanobacteria, eukaryotic phytoplankton, nanozooplankton, microzooplankton) was quantified in surface and bottom waters along with measurements of herbivory and bacterivory rates on eukaryotic and prokaryotic picoplankton and rates of viral lysis of bacteria. High rates of grazing mortality of prokaryotic picoplankton …