Biology Commons^™

Weak Competition Among Tropical Tree Seedlings: Implications For Species Coexistence, C.E. Timothy Paine, Kyle E. Harms, Stefan A. Schnitzer, Walter P. Carson

Biological Sciences Faculty Research and Publications

The intensity of competition among forest tree seedlings is poorly understood, but has important ramifications for their recruitment and for the maintenance of species diversity. Intense competition among seedlings could allow competitively dominant species to exclude subordinate species. Alternatively, the low density and small stature of forest tree seedlings could preclude intense interseedling competition. In this case, other processes, such as size‐asymmetric competition with adults, interactions with consumers, or neutral dynamics would prevail as those structuring the forest understory. We tested the intensity of, and potential for, intraspecific competition among tree seedlings of three species (Brosimum alicastrum, Matisia …

Species Limits And Phylogeography Of North American Cricket Frogs (Acris: Hylidae), Tony Gamble, Peter B. Berendzen, H. Bradley Shaffer, David E. Starkey, Andrew M. Simons

Biological Sciences Faculty Research and Publications

Cricket frogs are widely distributed across the eastern United States and two species, the northern cricket frog (Acris crepitans) and the southern cricket frog (A. gryllus) are currently recognized. We generated a phylogenetic hypothesis for Acris using fragments of nuclear and mitochondrial genes in separate and combined phylogenetic analyses. We also used distance methods and fixation indices to evaluate species limits within the genus and the validity of currently recognized subspecies of A. crepitans. The distributions of existing A. crepitans subspecies, defined by morphology and call types, do not match the distributions of evolutionary lineages recovered using …

Out Of The Blue: A Novel, Trans‐Atlantic Clade Of Geckos (Gekkota, Squamata), Tony Gamble, Aaron M. Bauer, Eli Greenbaum, Todd R. Jackman

Biological Sciences Faculty Research and Publications

Phylogenetic relationships among gekkotan lizards were estimated from five nuclear protein-coding genes in separate and combined analyses using maximum parsimony, maximum likelihood and Bayesian analyses. All analyses recovered a monophyletic trans-Atlantic gecko clade (Phyllodactylidae) consisting of the genera Asaccus, Haemodracon, Homonota, Phyllodactylus, Phyllopezus, Ptyodactylus, Tarentola and Thecadactylus. No other phylogenetic or taxonomic hypotheses have proposed linking these genera, which have been consistently grouped with other taxa outside of the clade. In this paper, we determine the relationships of this new clade to other major gekkotan groups, evaluate previous phylogenetic hypotheses regarding constituent members of this novel clade, and critically …

Cloning Of The Neurodegeneration Gene Drop-Dead And Characterization Of Additional Phenotypes Of Its Mutation, Edward M. Blumenthal

Biological Sciences Faculty Research and Publications

Mutations in the Drosophila gene drop-dead (drd) result in early adult lethality and neurodegeneration, but the molecular identity of the drd gene and its mechanism of action are not known. This paper describes the characterization of a new X-linked recessive adult-lethal mutation, originally called lot's wife (lwf¹) but subsequently identified as an allele of drd (drd^lwf); drd^lwf mutants die within two weeks of eclosion. Through mapping and complementation, the drd gene has been identified as CG33968, which encodes a putative integral membrane protein of unknown function. The drd^lwf allele is associated …

Dune And Vegetation Stability At South Padre Island, Texas, United States Of America, Frank W. Judd, Kenneth R. Summy, Robert I. Lonard, Ruben A. Mazariegos

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

Padre Island is the longest of five barrier islands occurring along the Texas Gulf Coast. South Padre Island is separated from the northern two-thirds of the island by the Mansfield Channel. The composition and pattern of vegetation on South Padre Island are relatively well known, but data on the interrelationship of dune and vegetation stability are lacking. We hypothesized that (1) there should be an inverse relationship between elevation change and percent cover on transects across the nearshore dunes of South Padre Island; and (2) percent cover, species composition, and species importance should be most stable where elevation change was …

Reproductive And Social Dynamics Of A Lek Breeding Bird, Thomas Brandt Ryder

Dissertations

Sociality and the unequal apportionment of reproductive success among social individuals is a common characteristic of many vertebrate taxa. To date, our understanding of what factors drive high variance in reproductive success (i.e., intra vs. inter-sexual selection) and which male attributes contribute to that variance, are still fragmentary for most species. Moreover, how social structure interacts with individual behavior and fitness remains understudied despite its potential importance to the evolution of cooperation. This dissertation research focused on understanding this complex synergistic interplay between social and reproductive dynamics in a lek-breeding bird, the wire-tailed manakin. The first chapter examines the complex …

The Effect Of Ginseng On Biofilm Formation By Wild Type And Mutant Strains Of Pseudomonas Aeruginosa, Premi Shekar

Morehead State Theses and Dissertations

A thesis presented to the faculty of the College of Science and Technology at Morehead State University in partial fulfillment of the requirements for the Degree of Master of Science by Premi Shekar on June 25, 2008.

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 …

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 …

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 …

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 …

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.

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.