Digital Commons Network^™

Optimal Time Allocation In Parasitic Wasps Searching For Hosts And Food, Brigitte Tenhumberg, Gitta Siekmann, Michael A. Keller

School of Biological Sciences: Faculty Publications

Many species of parasitic wasp feed on sugar sources such as nectar and honeydew in order to replenish their energy reserves and so extend their life expectancy, which is often correlated with higher reproductive success. Recent research suggests that carbohydrates are also a key component in flight fuel in such insects. The importance of sugar in fuelling locomotion suggests location of sugar-rich food may be more important in parasitoid foraging behavior than has previously been assumed. If sugar sources and hosts are separated in space, parasitoids have to allocate their time between sugar-searching and host-searching. Using a stochastic dynamic programming …

Invasive Insect Abundance Varies Across The Biogeographic Distribution Of A Native Host Plant, Tatyana A. Rand, Svata M. Louda

School of Biological Sciences: Faculty Publications

Studies of biogeographic variation in species abundances are fundamental to understanding and predicting the impacts of invasive exotic species. We quantified the abundance of the introduced and now invasive biocontrol weevil, Rhinocyllus conicus, on a newly adopted native host plant, Cirsium canescens (Platte thistle), across the plant’s distributional range. We used regression and structural equation analyses to examine variation in weevil abundance at 92–108 sites over three years in relation to variation in abiotic and biotic parameters hypothesized to be important in insect or plant dynamics and distribution. We found that R. conicus now occurs throughout the majority of …

Anaerobic Nitrate-Dependent Iron(Ii) Bio-Oxidation By A Novel Lithoautotrophic Betaproteobacterium, Strain 2002, Karrie A. Weber, Jarrod Pollock, Kimberly A. Cole, Susan M. O'Connor, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Microbial nitrate-dependent Fe(II) oxidation is known to contribute to iron biogeochemical cycling; however, the microorganisms responsible are virtually unknown. In an effort to elucidate this microbial metabolic process in the context of an environmental system, a 14-cm sediment core was collected from a freshwater lake and geochemically characterized concurrently with the enumeration of the nitrate-dependent Fe(II)-oxidizing microbial community and subsequent isolation of a nitrate-dependent Fe(II)-oxidizing microorganism. Throughout the sediment core, ambient concentrations of Fe(II) and nitrate were observed to coexist. Concomitant most probable number enumeration revealed the presence of an abundant nitrate-dependent Fe(II)- oxidizing microbial community (2.4 × 10^{3 …}

Microorganisms Pumping Iron: Anaerobic Microbial Iron Oxidation And Reduction, Karrie A. Weber, Laurie A. Achenbach, John D. Coates

School of Biological Sciences: Faculty Publications

Iron (Fe) has long been a recognized physiological requirement for life, yet for many microorganisms that persist in water, soils and sediments, its role extends well beyond that of a nutritional necessity. Fe(II) can function as an electron source for iron-oxidizing microorganisms under both oxic and anoxic conditions and Fe(III) can function as a terminal electron acceptor under anoxic conditions for iron-reducing microorganisms. Given that iron is the fourth most abundant element in the Earth’s crust, iron redox reactions have the potential to support substantial microbial populations in soil and sedimentary environments. As such, biological iron apportionment has been described …

Anaerobic Redox Cycling Of Iron By Freshwater Sediment Microorganisms, Karrie A. Weber, Matilde M. Urrutia, Perry F. Churchill, Ravi K. Kukkadapu, Eric E. Roden

School of Biological Sciences: Faculty Publications

The potential for microbially mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. Most probable number enumerations revealed the presence of significant populations of Fe(III)-reducing (approximately 10⁸ cells ml^-1 ) and Fe(II)-oxidizing, nitrate-reducing organisms (approximately 10⁵ cells ml^-1 ) in the freshwater sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (approximately 1 mM) medium with a small quantity (1% v/v) of wetland sediment, and resulted in the transient accumulation of NO₂^– and production of a mixture of …

Protein Binding Site Prediction Using An Empirical Scoring Function, Shide Liang, Chi Zhang, Song Liu, Yaoqi Zhou

School of Biological Sciences: Faculty Publications

Most biological processes are mediated by interactions between proteins and their interacting partners including proteins, nucleic acids and small molecules. This work establishes a method called PINUP for binding site prediction of monomeric proteins. With only two weight parameters to optimize, PINUP produces not only 42.2% coverage of actual interfaces (percentage of correctly predicted interface residues in actual interface residues) but also 44.5% accuracy in predicted interfaces (percentage of correctly predicted interface residues in the predicted interface residues) in a cross validation using a 57-protein dataset. By comparison, the expected accuracy via random prediction (percentage of actual interface residues in …

Incorporating Animal Behavior Into Seed Dispersal Models: Implications For Seed Shadows, Sabrina E. Russo, Stephen Portnoy, Carol K. Augspurger

School of Biological Sciences: Faculty Publications

Seed dispersal fundamentally influences plant population and community dynamics but is difficult to quantify directly. Consequently, models are frequently used to describe the seed shadow (the seed deposition pattern of a plant population). For vertebrate dispersed plants, animal behavior is known to influence seed shadows but is poorly integrated in seed dispersal models. Here, we illustrate a modeling approach that incorporates animal behavior and develop a stochastic, spatially explicit simulation model that predicts the seed shadow for a primate-dispersed tree species (Virola calophylla, Myristicaceae) at the forest stand scale. The model was parameterized from field-collected data on …

Spatial Associations Of Humus, Nutrients And Soils In Mixed Dipterocarp Forest At Lambir, Sarawak, Malaysian Borneo, I. C. Baillie, P.S. Ashton, S.P. Chin, S.J. Davies, P.A. Palmiotto, Sabrina E. Russo, S. Tan

School of Biological Sciences: Faculty Publications

Discrete humus layers are common on podzols under temperate coniferous and tropical heath forests, and patchy layers also occur under some temperate broadleaved forests on non-podzolic soils. We used multiple data sets to test the reported association of humus with oligotrophic but non-podzolic soils under non-heath dipterocarp forest at Lambir, Sarawak. We examined the distribution, morphology and nutrient dynamics of necromass on soils derived from sandstone and shale. Concentrations of the main mineral nutrients were lower in fresh litter on the very oligotrophic sandstone soils than on shale. The rates of litterfall were similar, so that annual litterfall fluxes of …

Can Environmental Variation Generate Positive Indirect Effects In A Model Of Shared Predation?, Chad Brassil

School of Biological Sciences: Faculty Publications

Classic models of apparent competition predict negative indirect effects between prey with a shared enemy. If predator per capita growth rates are nonlinear, then endogenously generated periodic cycles are predicted to generate less negative or even positive indirect effects between prey. Here I determine how exogenous mechanisms such as environmental variation could modify indirect effects. I find that exogenous variation can have a broader range of effects on indirect interactions than endogenously generated cycles. Indirect effects are altered by environmental variation even in simple models for which the per capita growth rate of the predator species is a linear function …

Regulation Of Mercury Resistance In The Crenarchaeote Sulfolobus Solfataricus, James Schelert, Melissa Drozda, Vidula Dixit, Amanda Dillman, Paul H. Blum

School of Biological Sciences: Faculty Publications

Mercuric ion, Hg(II), inactivates generalized transcription in the crenarchaeote Sulfolobus solfataricus. Metal

challenge simultaneously derepresses transcription of mercuric reductase (merA) by interacting with the

archaeal transcription factor aMerR. Northern blot and primer extension analyses identified two additional

Hg(II)-inducible S. solfataricus genes, merH and merI (SSO2690), located on either side of merA. Transcription

initiating upstream of merH at promoter merHp was metal inducible and extended through merA and merI,

producing a merHAI transcript. Northern analysis of a merRA double mutant produced by linear DNA

recombination demonstrated merHp promoter activity was dependent on aMerR to overcome Hg(II) …

Anatomy And Physiology Of Giant Neurons In The Antenniform Leg Of The Amblypygid Phrynus Marginemaculatus, A. J. Spence, Eileen Hebets

Eileen Hebets Publications

Amblypygids have modified front legs that are not used for locomotion, but rather to probe the environment in the manner of antennae. These elongate, motile sense organs are referred to as antenniform legs. We have found remarkable replication in structure and function of giant neurons in the antenniform leg of the amblypygid Phrynus marginemaculatus C.L. Koch 1841 when compared with other amblypygids. These neurons have such large diameter axons (several μm) that their action potentials can be recorded outside the cuticle. Their cell bodies are found in the periphery, in the distal-most segments of the antenniform leg, centimeters away from …

Regional Seismic Song Differences In Sky Island Populations Of The Jumping Spider Harbonattus Pugillis Griswold (Araneae, Salticidae), Damian O. Elias, Eileen Hebets, Ronald R. Hoy, Wayne P. Maddison, Andrew C. Mason

Eileen Hebets Publications

Jumping spiders have long been used as model organisms to study visual communication. However, recent studies documenting the presence of intricate multicomponent seismic songs during courtship displays suggest an important role of seismic communication as well. Given the relatively recent focus on seismic communication, the extent to which seismic songs vary among jumping spider species or even among populations remains poorly understood. Here, we use the extensively studied Habronattus pugillis Griswold 1987 complex to explore putative seismic song diversity among males from isolated populations. H. pugillis populations have been studied extensively because of the tremendous diversification of male visual secondary …

Superoxide Dismutase Activities In Long-Lived Drosophila Melanogaster Females: Chico1 Genotypes And Dietary Dilution, Hadise Kabil, Linda Partridge, Lawrence G. Harshman

Lawrence G. Harshman Publications

Superoxide dismutase (SOD) activities were determined for dietary dilution conditions that extend the life span of Drosophila melanogaster. The hypothesis motivating this research was that elevated SOD activity is associated with increased life span resulting from flies being held on a restricted diet. SOD activities were also measured for chico¹ which is a mutation in the insulin receptor substrate protein gene associated with life span extension. This allowed us to confirm the results of (Clancy et al. 2001) and extend the results by measuring CuZn SOD and Mn SOD activities in addition to the previously determined overall SOD activity. …

A Quantitative Trait Locus Analysis Of Natural Genetic Variation For Drosophila Melanogaster Oxidative Stress Survival, Yue Wang, David Pot, Stephen D. Kachman, Sergey V. Nuzhdin, Lawrence G. Harshman

Lawrence G. Harshman Publications

Little is known about natural genetic variation for survival under oxidative stress conditions or whether genetic variation for oxidative stress survival is associated with that for life-history traits. We have investigated survival in a high-oxygen environment at 2 adult densities using a set of re-combinant inbred lines (RILs) isolated from a natural population of Drosophila melanogaster. Female and male oxidative stress survival was highly correlated. Quantitative trait loci (QTLs) for oxidative stress survival were identified on both autosomes. These QTLs were sometimes sex or density spe-cific but were most often not. QTLs were identified that colocalize to the same …

Hyla Squirella (Squirrel Treefrog): Refugia., Louis A. Somma, David Serrano

Papers in Herpetology

HYLA SQUiREUA (Squirrel Treefrog). REFUGIA. Entomologists commonly use trap-nests to monitor cavity-nesting Hymenoptera. These trap-nests consist of 5 x 10 cm pine timber cut into 12-cm lengths. Five lengths are then stacked and strapped together. Each pIece of timber is predrilled in each side to have either a 3.2, 4.8, 6.4, 7.9, or 12.7 Iiundiameterhole, 8 cmindepth. Thus, each trap-nest consisted of five pieces of wood containing 2 holes of each diameter. They are suspended with wire from tree trunks and branches. We set these wooden traps (N = 10) at Devil's Millhopper Geological State Park, Gainesville, Alachua Co., Florida, …

Fire Does Not Alter Vegetation In Infertile Prairie, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

The paradigm in prairie ecology is that fire is one of the key factors deter-mining vegetation composition. fire can impact grassland ecosystems in various ways, including changing plant species composition and inducing nitro-gen loss. I found that 17 years of different burning frequencies in infertile grassland had only a minor impact on the vegetation composition and diversity. The only major impact from increasing the frequency of fires was a decrease of Poa pratensis abundance. However, other plant species did not r-spond to the change in Poa abundance. This result contrasts with previous studies in savannas and more productive grasslands, where …

Invasive Insect Abundance Varies Across The Biogeographic Distribution Of A Native Host Plant, Tatyana A. Rand, Svata M. Louda

Svata M. Louda Publications

Studies of biogeographic variation in species abundances are fundamental to understanding and predicting the impacts of invasive exotic species. We quantified the abundance of the introduced and now invasive biocontrol weevil, Rhinocyllus conicus, on a newly adopted native host plant, Cirsium canescens (Platte thistle), across the plant’s distributional range. We used regression and structural equation analyses to examine variation in weevil abundance at 92–108 sites over three years in relation to variation in abiotic and biotic parameters hypothesized to be important in insect or plant dynamics and distribution. We found that R. conicus now occurs throughout the majority of …

Determination Of Mrna Half-Lives In Candida Albicans Using Thiolutin As A Transcription Inhibitor, Bessie W. Kebaara, Lindsey E. Nielsen, Kenneth Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

A method for determining mRNA half-lives in the polymorphic fungus Candida albicans is described. It employs growth in a defined medium, the inhibition of transcription with thiolutin (10–20 μg/mL), and quantitative Northern blotting. The method is effective for the A72, SC5314, and CAI-4 strains of C. albicans, and for mRNAs that have a wide variety of decay rates and steady-state abundances. The range of half-lives detected (from 4–168 min) shows that this method is effective for mRNAs with widely varying half-lives. The mRNA decay rates obtained are compared with those for orthologous mRNAs from Saccharomyces cerevisiae. This procedure …

Hen1 Recognizes 21–24 Nt Small Rna Duplexes And Deposits A Methyl Group Onto The 2' Oh Of The 3' Terminal Nucleotide, Zhiyong Yang, Yon W. Ebright, Bin Yu, Xuemei Chen

Bin Yu Publications

microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants bear a methyl group on the ribose of the 3' terminal nucleotide. We showed previously that the methylation of miRNAs and siRNAs requires the protein HEN1 in vivo and that purified HEN1 protein methylates miRNA/miRNA* duplexes in vitro. In this study, we show that HEN1 methylates both miRNA/miRNA* and siRNA/siRNA* duplexes in vitro with a preference for 21–24 nt RNA duplexes with 2 nt overhangs. We also demonstrate that HEN1 deposits the methyl group on to the 2' OH of the 3' terminal nucleotide. Among various modifications thatcanoccuronthe ribose of …

First Report Of Mites And Fleas Associated With Sigmodontine Rodents From Corrientes Province, Argentina, Marcela Lareschi, Donald Gettinger, Santiago Nava, Agustín Abba, Mariano L. Merino

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Fleas (Insecta: Siphonaptera) and mesostigmate mites (Acari: Laelapidae) are common ectoparasitic associates of sigmodontine rodents in the Neotropics of South America. In Argentina, most of the research on ectoparasitic arthropods has been carried out on rodents from Buenos Aires Province (Autino and Lareschi, 1998; Lareschi and Mauri, 1998), while only a few small studies have been done in other areas of the country, such as the northwest (Lareschi et al., 2003a), and the Monte Desert Biome in Mendoza Province (Lareschi et al., 2004). Unfortunately, very little information is available from the region between the Paraná and Uruguay rivers in northeastern …

Parelaphostrongylus Odocoilei In Columbia Black-Tailed Deer From Oregon, Jack A. Mortenson, Arthur Abrams, Benjamin M. Rosenthal, Detiger Dunams, Eric P. Hoberg, Robert J. Bildfell, Richard L. Green

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Documenting the occurrence of Parelaphostrongylus odocoilei has historically relied on the morphological examination of adult worms collected from the skeletal muscle of definitive hosts, including deer. Recent advances in the knowledge of protostrongylid genetic sequences now permit larvae to be identified. Dorsal-spined larvae (DSLs) collected in 2003–2004 from the lung and feces of six Columbian black-tailed deer (Odocoileus hemionus columbianus) from Oregon were characterized genetically. The sequences from unknown DSLs were compared to those from morphologically validated adults and larvae of P. odocoilei at both the second internal transcribed spacer (ITS-2) of ribosomal DNA and the mitochondrial cytochrome …

Dissolution Kinetics Of High Explosives Particles In A Saturated Sandy Soil, Matthew C. Morley, Hiroshi Yamamoto, Gerald E. Speitel, Jr., Jay Clausen

Department of Civil and Environmental Engineering: Faculty Publications

Solid phase high explosive (HE) residues from munitions detonation may be a persistent source of soil and groundwater contamination at military training ranges. Saturated soil column tests were conducted to observe the dissolution behavior of individual components (RDX, HMX, and TNT) from two HE formulations (Comp B and C4). HE particles dissolved readily, with higher velocities yielding higher dissolution rates, higher mass transfer coefficients, and lower effluent concentrations. Effluent concentrations were below solubility limits for all components at superficial velocities of 10–50 cm day^-1. Under continuous flow at 50 cm day^-1, RDX dissolution rates from Comp …

Fast-Nmr - Functional Annotation Screening Technology Using Nmr Spectroscopy, Kelly A. Mercier, Michael Baranski, Viswanathan Ramanathan, Peter Z. Revesz, Rong Xiao, Gaetano T. Montelione, Robert Powers

Robert Powers Publications

An abundance of protein structures emerging from structural genomics and the Protein Structure Initiative (PSI) are not amenable to ready functional assignment because of a lack of sequence and structural homology to proteins of known function. We describe a high-throughput NMR methodology (FAST-NMR) to annotate the biological function of novel proteins through the structural and sequence analysis of protein-ligand interactions. This is based on basic tenets of biochemistry where proteins with similar functions will have similar active sites and exhibit similar ligand binding interactions, despite global differences in sequence and structure. Protein-ligand interactions are determined through a tiered NMR screen …

Prairie Suite: A Celebration, Twyla Hansen, Paul A. Johnsgard

Paul Johnsgard Collection

25 poems by Twyla Hansen, with illustrations by Paul A. Johnsgard, including:

Walk on the Prairie

There is mystery here, in the shapes of grass,
in the dim movements of an inland sea,
connections to an earlier time. Wander barefoot,
hypothesize the dance of millennia, the unbearable
carvings of the built environment, this ragtag escape.

Let its divine simplicity ooze into your pores.
Comb the steel from your hair, blanket your
tongue with orange. Your breathing will slow.
Breathing slow, unbutton the child within.
Give her permission to go fly a kite.

Coupling Between Primary Terrestrial Succession And The Trophic Development Of Lakes At Glacier Bay, Alaska, D. R. Engstrom, Sherilyn C. Fritz

Department of Earth and Atmospheric Sciences: Faculty Publications

The natural eutrophication of lakes is still an accepted concept in limnology, arising as it does from the earliest efforts to classify lakes and place them in an evolutionary sequence. Recent studies of newly formed lakes at Glacier Bay, Alaska, only partially support this idea, and suggest more variable trends in lake trophic development which are under local (catchment-level) control. Here we use sediment cores from several lakes in Glacier Bay National Park to examine the relationship between successional changes in catchment vegetation and trends in water-column nitrogen (a limiting nutrient) and lake primary production. Terrestrial succession at Glacier Bay …

Reconstructing Sea-Level Change From The Internal Architecture Of Stromatolite Reefs: An Example From The Mesoproterozoic Sulky Formation, Dismal Lakes Group, Arctic Canada, L C. Kah, Julie K. Bartley, Tracy D. Frank, Timothy W. Lyons

Department of Earth and Atmospheric Sciences: Faculty Publications

The Mesoproterozoic Dismal Lakes Group, arctic Canada, contains a relatively thin, yet regionally extensive stromatolitic reef complex that developed subtidally during a major transgression, shoaled to sea level, and was overlain by intertidal to supratidal carbonate and evaporite strata. The September Lake reef complex exhibits a complex internal architecture that records the interaction between stromatolite growth and changes in accommodation space derived from both higher order (4th- or 5th-order, parasequence-scale) changes in sea level and the variable bathymetry of the sea floor. Reef growth, which was initiated during three sea-level cycles, records progressive marine transgression over depositional lows that were …

Advances In Data Modeling Research, G. Allen, A. Bajaj, V. Khatri, S. Ram, Keng Siau

Research Collection School Of Computing and Information Systems

In this paper, we summarize the discussions of the panel on "Advances in Data Modeling Research," held at the Americas Conference on Information Systems (AMCIS) in 2005. We focus on four primary areas where data modeling research offers rich opportunities: spatio-temporal semantics, genome research, ontological analysis and empirical evaluation of existing models. We highlight past work in each area and also discuss open questions, with a view to promoting future research in the overall data modeling area.

Molecular Basis Of Breast Cancer, Layla J. Al-Mansouri, Majed S. Alokail

Saudi Medical Journal

Breast cancer is the most frequent cancer in women and represents the second leading cause of cancer death among women after lung cancer. A common phenotypic abnormality of breast cancer cells is dysregulation of cell cycle control. The transformation of normal cell to a cancer cell appears to depend on mutation in genes that normally control cell cycle progression, thus leading to loss of the regulatory cell growth. We summarize here the molecular regulation of mammary carcinoma with regards to the most prominent oncogenes and tumor suppressor genes and their outcome in terms of cellular prognosis, and tumor development.

Treatment Of Acne Vulgaris With 2% Topical Tea Lotion, Khalifa E. Sharquie, Ihsan A. Al-Turfi, Wathik M. Al-Shimary

Saudi Medical Journal

OBJECTIVE: To use 2% tea lotion as natural plant remedy in the treatment of acne vulgaris. METHODS: We conducted this study in the Department of Dermatology and Venereology in Baghdad Teaching Hospital, Iraq during the period between October 2002 and October 2004. In this single blind randomly controlled therapeutic study, we enrolled 60 patients, their ages ranged from 14-22 years. There were 35 females and 25 males. We divided the patients equally into 2 groups; we instructed group A to use freshly prepared 2% tea lotion twice daily for 2 months, while group B used a control solution. We graded …

Simulation Model And Analysis Of A Data Warehouse, Vikas Agrawal, Udayan Nandkeolyar, P.S. Sundararaghavan, Mesbah U. Ahmed

Journal of International Technology and Information Management

Data warehouses are large complex systems with many interacting nonlinear components. It is an amalgamation of many different systems and integration of such diverse elements is its primary concern. It is often difficult for a data warehouse manager to predict the performance of the system especially when demand pattern for the required data keeps changing. We have developed a simulation model using ARENA simulation package that will simulate the behavior and performance of a data warehouse system environment based on its overall design. Given such a model, a data warehouse manager can walk through various what-if scenarios and can pinpoint …