Digital Commons Network^™

Physiological, Ecological, And Phylogenetic Characterization Of Stappia, A Marine Co-Oxidizing Bacterial Genus, Carolyn F. Weber, Gary M. King

Faculty Publications

Bacteria play a major role in marine CO cycling, yet very little is known about the microbes involved. Thirteen CO-oxidizing Stappia isolates obtained from existing cultures, macroalgae, or surf samples representing geographically and ecologically diverse habitats were characterized using biochemical, physiological, and phylogenetic approaches. All isolates were aerobic chemoorganotrophs that oxidized CO at elevated (1,000 ppm) and ambient-to-subambient concentrations (<0.3 ppm). All contained the form I (OMP) coxL gene for aerobic CO dehydrogenase and also the form II (BMS) putative coxL gene. In addition, some strains possessed cbbL, the large subunit gene for ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting the possibility of lithotrophic or mixotrophic metabolism. All isolates used a wide range of sugars, organic acids, amino acids, and aromatics for growth and grew at salinities from 5 to 45 ppt. All but one isolate denitrified or respired nitrate. Phylogenetic analyses based on 16S rRNA gene sequences indicated that several isolates could not be distinguished from Stappia aggregata and contributed to a widely distributed species complex. Four isolates (of strains GA15, HI, MIO, and M4) were phylogenetically distinct from validly described Stappia species and closely related genera (e.g., Ahrensia, Pannonibacter, Pseudovibrio, and Roseibium). Substrate utilization profiles, enzymatic activity, and membrane lipid composition further distinguished these isolates and supported their designations as new Stappia species. The observed metabolic versatility of Stappia likely accounts for its cosmopolitan distribution and its ability to contribute to CO cycling as well as other important biogeochemical cycles. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Effect Of Anatomic Motion On Proton Therapy Dose Distributions In Prostate Cancer Treatment, Xiaodong Zhang, Lei Dong, Andrew K. Lee, James D. Cox, Deborah A. Kuban, Ron X. Zhu, Xiaochun Wang, Yupeng Li, Wayne D. Newhauser, Michael Gillin, Radhe Mohan

Faculty Publications

Purpose: To determine the dosimetric impact of interfraction anatomic movements in prostate cancer patients receiving proton therapy. Methods and Materials: For each of the 10 patients studied, 8 computed tomography (CT) scans were selected from sets of daily setup CT images that were acquired from a cohort of prostate cancer patients. The images were acquired in the treatment room using the CT-on-rails system. First, standard proton therapy and intensity-modulated radiation therapy (IMRT) plans were designed for each patient using standard modality-specific methods. The images, the proton plan, and the IMRT plan were then aligned to the eight CT images based …

Assessing Among-Locus Variation In The Inference Of Seed Plant Phylogeny, J. Gordon Burleigh, Sarah Mathews

Faculty Publications

Large multilocus analyses can greatly reduce sampling error in phylogenetic estimates and help resolve difficult phylogenetic questions. Yet conventional multilocus analyses may be confounded by variation in the phylogenetic signal or processes of evolution among loci. We used nonparametric bootstrapping methods to examine locus-specific variation within a 12-locus seed plant data set and to examine the effects of this variation on estimates of seed plant phylogeny. The observed maximum likelihood and maximum parsimony bootstrap support from phylogenetic analyses of sites within single loci often notably differs from the bootstrap support obtained by sampling an equal number of sites from the …

Yy1 As A Controlling Factor For The Peg3 And Gnas Imprinted Domains, Jeong Do Kim, Angela K. Hinz, Jung Ha Choo, Lisa Stubbs, Joomyeong Kim

Faculty Publications

Imprinting control regions (ICRs) often harbor tandem arrays of transcription factor binding sites, as demonstrated by the identification of multiple YY1 binding sites within the ICRs of Peg3, Nespas, and Xist/Tsix domains. In the current study, we have sought to characterize possible roles for YY1 in transcriptional control and epigenetic modification of these imprinted domains. RNA interference-based knockdown experiments in Neuro2A cells resulted in overall transcriptional up-regulation of most of the imprinted genes within the Peg3 domain and also, concomitantly, caused significant loss in the DNA methylation of the Peg3 differentially methylated region. A similar overall and coordinated expression change …

Evolution Into And Out Of The Andes: A Bayesian Analysis Of Historical Diversification In Thamnophilus Antshrikes, Robb T. Brumfield, Scott V. Edwards

Faculty Publications

The Andean uplift played important roles in the historical diversification of Neotropical organisms, both by producing new high-elevation habitats that could be colonized and by isolating organisms on either side of the mountains. Here, we present a molecular phylogeny of Thamnophlius antshrikes, a clade of 30 species whose collective distribution spans nearly the entirety of lowland habitats in tropical South America, the eastern slope foothills of the Andes, and the tepuis of northern South America. Our goal was to examine the role of the Andes in the diversification of lowland and foothill species. Using parsimony and Bayesian ancestral state reconstructions …

Generation And Characterization Of Rabbit Embryonic Stem Cells, Shufen Wang, Xianghui Tang, Yuyu Niu, Hongwei Chen, Bin Li, Tianqing Li, Xiuzhen Zhang, Zhixin Hu, Qi Zhou, Weizhi Ji

Faculty Publications

We described the derivation of four stable pluripotent rabbit embryonic stem cell (ESC) lines, one (RF) from blastocysts fertilized in vivo and cultured in vitro and three (RP01, RP02, and RP03) from parthenogenetic blastocysts. These ESC lines have been cultivated for extended periods (RF >1 year, RP01 >8 months, RP02 >8 months, and RP03 >6 months) in vitro while maintaining expression of pluripotent ESC markers and a normal XY or XX karyotype. The ESCs from all lines expressed alkaline phosphatase, transcription factor Oct-4, stage-specific embryonic antigens (SSEA-1, SSEA-3, and SSEA-4), and the tumor-related antigens (TRA-1-60 and TRA-1-81). Similar to human …

Threshold Power Of Canonical Antennas For Inducing Sar At Compliance Limits In The 300-3000 Mhz Frequency Range, Mohammod Ali, Mark G. Douglas, Abu T.M. Sayem, Antonio Faraone, Chung-Kwang Chou

Faculty Publications

A study of the specific absorption rate (SAR) in an exposed body induced by canonical antennas is presented, with the aim of determining an upper bound for the antenna transmit power that demonstrates that a product is inherently compliant with internationally accepted radio frequency (RF) exposure limits. Starting from the fundamental limits in antenna quality factor (Q) and the corresponding bandwidth, several antenna sizes are selected, and their SAR distributions are computed using the method of moments (MoM) and finite-difference time domain (FDTD) method in the frequency range 300-3000 MHz. The threshold powers are then determined, below which the peak …

Food Insecurity And Subsequent Weight Gain In Women, Sonya J. Jones, Edward A. Frongillo Jr.

Faculty Publications

Objective: Cross-sectional data indicate that a relationship between household food insecurity and overweight exists among women in the USA. Cross-sectional data cannot determine if food insecurity leads to overweight as some have hypothesised. The purpose of the present study was to examine the relationship of food insecurity with subsequent weight gain in women using data from the Panel Study of Income Dynamics (PSID).

Design, setting and subjects:Panel data from the 1999 and 2001 PSID, a nationally representative sample of households, were analysed using multivariate regression procedures.

Results: Average weight gain among all women (n=5595) was 1.1 kg …

Human–Robot Interaction: A Survey, Michael A. Goodrich, Alan C. Schultz

Faculty Publications

Human–Robot Interaction (HRI) has recently received considerable attention in the academic community, in labs, in technology companies, and through the media. Because of this attention, it is desirable to present a survey of HRI to serve as a tutorial to people outside the field and to promote discussion of a unified vision of HRI within the field. The goal of this review is to present a unified treatment of HRI-related problems, to identify key themes, and discuss challenge problems that are likely to shape the field in the near future. Although the review follows a survey structure, the goal of …

Avpv Neurons Containing Estrogen Receptor-Beta In Adult Male Rats Are Influenced By Soy Isoflavones, Edwin D. Lephart, Lihong H. Bu

Faculty Publications

Background Isoflavones, the most abundant phytoestrogens in soy foods, are structurally similar to 17beta-estradiol. It is known that 17beta-estradiol induces apoptosis in anteroventral periventricular nucleus (AVPV) in rat brain. Also, there is evidence that consumption of soy isoflavones reduces the volume of AVPV in male rats. Therefore, in this study, we examined the influence of dietary soy isoflavones on apoptosis in AVPV of 150 day-old male rats fed either a soy isoflavone-free diet (Phyto-free) or a soy isoflavone-rich diet (Phyto-600). Results: The occurrence of apoptosis in AVPV was examined by TUNEL staining. The incidence of apoptosis was about 10 times …

Understanding The Experiences Of Instructors As They Adopt A Course Management System, Charles R. Graham, Gregory L. Waddoups, Richard E. West

Faculty Publications

In this study, we used qualitative methods to help us better understand the experiences of instructors as they are persuaded to adopt a course management system and integrate it into their teaching. We discuss several patterns explaining how instructors implemented Blackboard, a CMS, by experimenting with individual features, facing both technical and integration challenges, and attempting to adapt Blackboard features to match their goals and practices. We also give explanations for why instructors either a) embraced the tool and grew more dependent on it, b) reduced their use of the tool to only some features, or c) discontinued the tool …

Modeling And Sensitivity Analysis Of Acoustic Release Of Doxorubicin From Unstabilized Pluronic P105 Using An Artificial Neural Network Model, Ghaleb A. Husseini, Nabil M. Abdel-Jabbar, Farouq S. Mjalli, William G. Pitt

Faculty Publications

This paper models steady state acoustic release of Doxorubicin (Dox) from Pluronic P105micelles using Artificial Neural Networks (ANN). Previously collected release data werecompiled and used to train, validate, and test an ANN model. Sensitivity analysis was thenperformed on the following operating conditions: ultrasonic frequency, power density, Plu-ronic P105 concentration, and temperature. The model showed that drug release was mostefficient at lower frequencies. The analysis also demonstrated that release increases as thepower density increases. Sensitivity plots of ultrasound intensity revealed a drug releasethreshold of 0.015 W/cm2 and 0.38 W/cm2 at 20 and 70 kHz, respectively. The presence ofa power density threshold …

Model-Based Compartmental Analysis Indicates A Reduced Mobilization Of Hepatic Vitamin A During Inflammation In Rats, Sin Gieng, Michael Green, Joanne Green, Francisco Rosales

Faculty Publications

Vitamin A (VA) kinetics was studied in rats with marginal VA stores before, during, and after inflammation. Rats received orally [11,12-3H(N)]retinol ([3H]VA; day 0), and inflammation was induced on day 21 with lipopolysacchride (LPS) for 3 days (n = 5) or recombinant human interleukin-6 (rhIL-6) for 7 days (n = 5). Both the fraction of [3H]VA and retinol concentrations in plasma were reduced significantly by LPS or rhIL-6. Compartmental analysis using the Windows version of Simulation, Analysis, and Modeling software was applied to group mean data, and non-steady-state models were developed. After absorption, VA kinetics was described by a three-compartment …

Gene Sampling Strategies For Multi-Locus Population Estimates Of Genetic Diversity (Θ), Matthew D. Carling, Robb T. Brumfield

Faculty Publications

Background. Theoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored. Methodology/Principle Findings. To investigate how much data is required to estimate the population genetic parameter θ(4 Neμ) accurately under ideal circumstances, we simulated datasets of DNA sequences under three values of θ per site (0.1, 0.01, 0.001), varying in both the total number of base pairs sequenced per individual and the number of equal-length loci. From these datasets we estimated …

Soil Nutrients Influence Spatial Distributions Of Tropical Trees Species, Robert John, James W. Dalling, Kyle E. Harms, Joseph B. Yavitt, Robert F. Stallard, Matthew Mirabello, Stephen P. Hubbell, Renato Valencia, Hugo Navarrete, Martha Vallejo, Robin B. Foster

Faculty Publications

The importance of niche vs. neutral assembly mechanisms in structuring tropical tree communities remains an important unsettled question in community ecology [Bell G (2005) Ecology 86:1757-1770]. There is ample evidence that species distributions are determined by soils and habitat factors at landscape (<104 >km2) and regional scales. At local scales (<1 >km2), however, habitat factors and species distributions show comparable spatial aggregation, making it difficult to disentangle the importance of niche and dispersal processes. In this article, we test soil resource-based niche assembly at a local scale, using species and soil nutrient distributions obtained at high spatial resolution in three …

A Large-Scale Deforestation Experiment: Effects Of Patch Area And Isolation On Amazon Birds, Gonçalo Ferraz, James D. Nichols, James E. Hines, Philip C. Stouffer, Richard O. Bierregaard, Thomas E. Lovejoy

Faculty Publications

As compared with extensive contiguous areas, small isolated habitat patches lack many species. Some species disappear after isolation; others are rarely found in any small patch, regardless of isolation. We used a 13-year data set of bird captures from a large landscape-manipulation experiment in a Brazilian Amazon forest to model the extinction-colonization dynamics of 55 species and tested basic predictions of island biogeography and metapopulation theory. From our models, we derived two metrics of species vulnerability to changes in isolation and patch area. We found a strong effect of area and a variable effect of isolation on the predicted patch …

5-Methyltetrahydrofolate Is Bound In Intersubunit Areas Of Rat Liver Folate-Binding Protein Glycine N-Methyltransferase, Zigmund Luka, Svetlana Pakhomova, Lioudmila V. Loukachevitch, Martin Egli, Marcia E. Newcomer, Conrad Wagner

Faculty Publications

Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. It is abundant in the liver, where it uses excess S-adenosylmethionine (AdoMet) to methylate glycine to N-methylglycine (sarcosine) and produces S-adenosylhomocysteine (AdoHcy), thereby controlling the methylating potential of the cell. GNMT also links utilization of preformed methyl groups, in the form of methionine, to their de novo synthesis, because it is inhibited by a specific form of folate, 5-methyltetrahydrofolate. Although the structure of the enzyme has been elucidated by x-ray crystallography of the apoenzyme and in the presence of the substrate, the location of the folate inhibitor in …

A New Species Of Ophiomegistus Banks (Acari: Paramegistidae) From Papua New Guinea, Hans Klompen, Christopher C. Austin

Faculty Publications

A new species of Ophiomegistus, O. spectabilis, is described from New Guinea. This represents the 13th species of this genus from New Guinea skinks. A re-evaluation of host and locality data for the genus shows a host range restricted to squamates, especially skinks, but no obvious specificity for individual skink species. Specificity for small geographical areas seems more likely. Copyright © 2007 · Magnolia Press.

Assignment Of The Ferriheme Resonances Of The High-Spin Forms Of Nitrophorins 1 And 4 By 1H Nmr Spectroscopy: Comparison To Structural Data Obtained From X-Ray Crystallography, Tatiana Kh Shokhireva, Kevin M. Smith, Robert E. Berry, Nikolai V. Shokhirev, Celia A. Balfour, Hongjun Zhang, F. Ann Walker

Faculty Publications

In this work, we report the assignment of the majority of the ferriheme resonances of high-spin nitrophorins (NPs) 1 and 4 and compare them to those of NP2, published previously. It is found that the structures of the ferriheme complexes of NP1 and NP4, in terms of the orientation of the histidine imidazole ligand, can be described with good accuracy by NMR techniques and that the angle plot proposed previously for the high-spin form of the NPs (Shokhireva, T. Kh.; Shokhirev, N. V.; Walker, F. A. Biochemistry 2003, 42, 679-693) describes the angle of the effective nodal plane of the …

Selective Cholesterol Dynamics Between Lipoproteins And Caveolae/Lipid Rafts, Stephen M. Storey, Adalberto M. Gallegos, Barbara P. Atshaves, Avery L. Mcintosh, Gregory G. Martin, Rebecca D. Parr, Kerstin K. Landrock, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although low-density lipoprotein (LDL) receptor-mediated cholesterol uptake through clathrin-coated pits is now well understood, the molecular details and organizing principles for selective cholesterol uptake/efflux (reverse cholesterol transport, RCT) from peripheral cells remain to be resolved. It is not yet completely clear whether RCT between serum lipoproteins and the plasma membrane occurs primarily through lipid rafts/caveolae or from non-raft domains. To begin to address these issues, lipid raft/caveolae-, caveolae-, and non-raft-enriched fractions were resolved from purified plasma membranes isolated from L-cell fibroblasts and MDCK cells by detergent-free affinity chromatography and compared with detergent-resistant membranes isolated from the same cells. Fluorescent sterol …

India’S Emergence As A “Responsible” Nuclear Power, Karthika Sasikumar

Faculty Publications

In 2005, India and the United States announced a nuclear “deal” that would seek to clarify India’s ambiguous status in the nuclear order. The sole superpower appeared to be recognizing India’s status as a nuclear-armed state by opening up the possibility of nuclear cooperation. This announcement represented the fruit of many years of careful Indian diplomacy aimed at establishing its identity as a responsible possessor of nuclear weapons and forging a closer alliance with the US. This article provides a concise description of the provisions of the 2005 India-US nuclear agreement, and analyzes its global, regional, and domestic implications. While …

How Heel Oxygenation Changes Under Pressure, Vivian K. Wong, N. A. Stotts, H. W. Hopf, E. S. Froelicher, G. A. Dowling

Faculty Publications

The mechanism of heel pressure ulcers after hip surgery is not entirely understood. The purpose of this one-group, prospective, repeated-measures design study was to examine how the external pressure of the bed surface affects heel skin oxygen tension in adults on the first 3 days after hip surgery. Transcutaneous oxygen sensors were placed on the plantar surface of each foot, close to the heels. Measures were taken on room air and with an oxygen challenge with the heels (1) suspended above the bed surface (preload), (2) on the bed surface for 15 minutes (loading), and (3) again suspended above the …

Outsourcing In Biopharmaceutical Industry: India's Value Propositions, S. Dhar, Mahesh N. Rajan

Faculty Publications

In this paper we discuss the rationale behind biopharmaceutical outsourcing. We then discuss the benefits, challenges, current trends and market opportunities. From January 2005, India has agreed to comply with the product patent protection in accordance with the obligation under the TRIPS Agreement of the WTO. This has created new opportunities as well as challenges for the Indian biopharmaceutical companies. We analyze the value proposition of India as a suitable destination for outsourcing in biopharmaceutical industry in this new business environment. This research will help managers to understand the benefits of biopharmaceutical outsourcing along with its challenges under the current …

Analysis And Kinetics Of The Sequencing Batch Reactors, Udeme J. Ndon

Faculty Publications

Fundamental analysis and kinetics of treatment reactors are major topics in environmental engineering literature. These fundamental topics in reactor processes are well known for the ideal batch reactor, the continuous stirred tank reactor, and the plug flow reactor. The sequencing batch reactors (SBRs) are relatively new in the field, but are widely used. Despite the wide application of sequencing batch reactors in the field, information is lacking on the fundamental analysis and kinetics, especially with comparison to the ideal batch reactor. This report presents analysis and kinetics of the sequencing batch reactors and compares the kinetics equations developed with those …

Ultrastructure Of Teliospores And Promycelium And Basidiospore Formation In The Four-Spored Form Of Gymnoconia Nitens, One Of The Causes Of Orange Rust Of Rubus, C. W. Mims, E. A. Richardson, Josephine Taylor

Faculty Publications

Orange rust of Rubus is an interesting disease because of the fact that it can be caused by three different rust fungi that produce virtually identical symptoms. One is Gymnoconia peckiana (Howe in Peck) Trotter, which is a demicyclic species, while the other two are endocyclic forms historically referred to as Gymnoconia nitens (Schwein.) Kern & H.W. Thurston. Although the spores produced on infected Rubus leaves by these latter two forms are morphologically identical to the aeciospores of G. peckiana, they actually function as teliospores. However, the teliospores of one of the forms gives rise to two-celled promycelia that …

Updated And New Amphibian And Reptile Records From Clark County, Illinois [Abstract], C. Drew Foster, Stephen J. Mullin

Faculty Publications

No abstract provided.

Population Responses Of Wood Frog (Rana Sylvatica) Tadpoles To Overwintered Bullfrog (Rana Catesbeiana) Tadpoles, Leroy J. Walston, Stephen J. Mullin

Faculty Publications

A fundamental goal in ecology is to understand how environmental variation influences the distribution of individuals within a population. In this study, we used laboratory experiments to examine the population responses of sympatric Wood Frog (Rana sylvatica) tadpoles to native overwintered Bullfrog (Rana catesbeiana) tadpoles. For periods of up to two weeks, we measured growth, activity, and refuge use of Wood Frog tadpoles in small mesocosms with and without an overwintered Bullfrog tadpole present. Bullfrog tadpoles had a negative effect on the growth of Wood Frog tadpoles allotopic (naive) to Bullfrogs, whereas the presence of Bullfrogs had no effect on …

A New N-Terminal Recognition Domain In Caveolin-1 Interacts With Sterol Carrier Protein-2 (Scp-2), Rebecca D. Parr, Gregory G. Martin, Heather A. Hostetler, Megan E. Schroeder, Kiran D. Mir, Ann B. Kier, Judith M. Ball, Friedhelm Schroeder

Faculty Publications

Although plasma membrane domains, such as caveolae, provide an organizing principle for signaling pathways and cholesterol homeostasis in the cell, relatively little is known regarding specific mechanisms, whereby intracellular lipid-binding proteins are targeted to caveolae. Therefore, the interaction between caveolin-1 and sterol carrier protein-2 (SCP-2), a protein that binds and transfers both cholesterol and signaling lipids (e.g., phosphatidylinositides and sphingolipids), was examined by yeast two-hybrid, in vitro binding and fluorescence resonance energy transfer (FRET) analyses. Results of the in vivo and in vitro assays identified for the first time the N-terminal amino acids (aa) 1−32 amphipathic α helix of SCP-2 …

Full-Length, Glycosylated Nsp4 Is Localized To Plasma Membrane Caveolae By A Novel Raft Isolation Technique, Stephen M. Storey, Thomas F. Gibbons, Cecelia V. Williams, Rebecca D. Parr, Friedhelm Schroeder, Judith M. Ball

Faculty Publications

Rotavirus NSP4, initially characterized as an endoplasmic reticulum intracellular receptor, is a multifunctional viral enterotoxin that induces diarrhea in murine pups. There have been recent reports of the secretion of a cleaved NSP4 fragment (residues 112 to 175) and of the association of NSP4 with LC3-positive autophagosomes, raft membranes, and microtubules. To determine if NSP4 traffics to a specific subset of rafts at the plasma membrane, we isolated caveolae from plasma membrane-enriched material that yielded caveola membranes free of endoplasmic reticulum and nonraft plasma membrane markers. Analyses of the newly isolated caveolae from rotavirus-infected MDCK cells revealed full-length, high-mannose glycosylated …

Assessment Of Genetic Diversity In The Usda And Cip-Fao International Nursery Collections Of Quinoa (Chenopodium Quinoa Willd.) Using Microsatellite Markers [Abstract], S. A. Christensen, Donald B. Pratt, C. Pratt, P. T. Nelson, M. R. Stevens, Eric N. Jellen, C. E. Coleman, D. J. Fairbanks, A. Bonifacio, Peter J. Maughan

Faculty Publications

No abstract provided.