Digital Commons Network^™

A Mobile Element Based Phylogeny Of Old World Monkeys, Jinchuan Xing, Hui Wang, Kyudong Han, David A. Ray, Cheney H. Huang, Leona G. Chemnick, Caro Beth Stewart, Todd R. Disotell, Oliver A. Ryder, Mark A. Batzer

Faculty Publications

SINEs (Short INterspersed Elements) are a class of non-autonomous mobile elements that are states, making them useful genetic systems for phylogenetic studies. Alu elements are the most successful SINE in primate genomes and have been utilized for resolving primate phylogenetic relationships and human population genetics. However, no Alu based phylogenetic analysis has yet been performed to resolve relationships among Old World monkeys. Using both a computational approach and polymerase chain reaction display methodology, we identified 285 new Alu insertions from sixteen Old World monkey taxa that were informative at various levels of catarrhine phylogeny. We have utilized these elements along …

Mutation Of Sac1, An Arabidopsis Sac Domain Phosphoinositide Phosphatase, Causes Alterations In Cell Morphogenesis, Cell Wall Synthesis, And Actin Organization, Ruiqin Zhong, David H. Burk, C. Joseph Nairn, Alicia Wood-Jones, W. Herbert Morrison, Zheng Hua Ye

Faculty Publications

SAC (for suppressor of actin) domain proteins in yeast and animals have been shown to modulate the levels of phosphoinositides, thereby regulating several cellular activities such as signal transduction, actin cytoskeleton organization, and vesicle trafficking. Nine genes encoding SAC domain-containing proteins are present in the Arabidopsis thaliana genome, but their roles in plant cellular functions and plant growth and development have not been characterized. In this report, we demonstrate the essential roles of one of the Arabidopsis SAC domain proteins, AtSAC1, in plant cellular functions. Mutation of the AtSAC1 gene in the fragile fiber7 (fra7) mutant caused a dramatic decrease …

Avian Hosts For West Nile Virus In St. Tammany Parish, Louisiana, 2002, Nicholas Komar, Nicholas A. Panella, Stanley A. Langevin, Aaron C. Brault, Manuel Amador, Eric Edwards, Jennifer C. Owen

Faculty Publications

West Nile virus (WNV) infections in free-ranging birds were studied in Slidell, St. Tammany Parish, Louisiana, after a human encephalitis outbreak peaked there in July 2002. Seroprevalence in resident, free-ranging wild birds in one suburban site was 25% and 24% in August and October, respectively, indicating that most transmission had ceased by early August. Mortality rates, seroprevalence rates, host competence, and crude population estimates were used in mathematical models to predict actual infection rates, population impacts, and importance as amplifying hosts for several common passerine birds. Northern cardinal (Cardinalis cardinalis) and house sparrow (Passer domesticus) were the principal amplifying hosts, …

Weather And The Salem Witch Trials, Franklin G. Mixon

Faculty Publications

No abstract provided.

Insights From The X-Ray Crystal Structure Of Coral 8r-Lipoxygenase: Calcium Activation Via A C2-Like Domain And A Structural Basis Of Product Chirality, Michael L. Oldham, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

Lipoxygenases (LOXs) catalyze the regio- and stereospecific dioxygenation of polyunsaturated membrane-embedded fatty acids. We report here the 3.2 Å resolution structure of 8R-LOX from the Caribbean sea whip coral Plexaura homomalla, a LOX isozyme with calcium dependence and the uncommon R chiral stereospecificity. Structural and spectroscopic analyses demonstrated calcium binding in a C2-like membrane-binding domain, illuminating the function of similar amino acids in calcium-activated mammalian 5-LOX, the key enzyme in the pathway to the pro-inflammatory leukotrienes. Mutation of Ca2+- ligating amino acids in 8R-LOX resulted not only in a diminished capacity to bind membranes, as monitored by fluorescence resonance energy …

Association Of The 17-Kda Extrinsic Protein With Photosystem Ii In Higher Plants, Glen D. Meades, Anne Mclachlan, Larry Sallans, Patrick A. Limbach, Laurie K. Frankel, Terry M. Bricker

Faculty Publications

The structural association of the spinach 17-kDa extrinsic protein of photosystem II with other extrinsic and membrane-bound components of the photosystem was investigated by labeling the 17-kDa extrinsic protein with the amino-group-specific reagent N-hydroxysuccinimidobiotin both on intact photosystem II membranes or as a free protein in solution. After isolation of the biotinylated molecules, the modified 17-kDa proteins were allowed to rebind to photosystem II membranes which were depleted of the 17-kDa component. Differential binding of the protein biotinylated in solution compared to unmodified 17-kDa protein or 17-kDa protein modified on PSII membranes was observed. This indicated possible steric or ionic …

Applications Of Phylogenetics To Issues In Freshwater Crayfish Biology, Keith A. Crandall

Faculty Publications

Freshwater crayfish have served as model organisms for over 125 years in scientific research, from areas such as neurobiology and vision research to conservation biology and evolution. Recently, evolutionary histories in the form of phylogenies have served as a critical foundation for testing hypotheses in such diverse research areas as well. In this article, I review the amazing diversity of freshwater crayfish, especially in a phylogenetic context and explore how these evolutionary histories have informed crayfish biology and can be used powerfully in the future to guide research in a diversity of areas. Throughout the article, I draw on examples …

Highly Efficient Fluorescence Detection In Picoliter Volume Liquid-Core Waveguides, Aaron R. Hawkins, John P. Barber, Dongliang Yin

Faculty Publications

We report loss improvement and fluorescence detection in integrated antiresonant reflecting optical waveguides with liquid cores. The minimum waveguide loss is reduced to 0.33/cm by compensating for thickness variations in the fabrication process. We demonstrate fluorescence detection from as few as 490 molecules in a 57 pl core using these optimized waveguides. We measure angular fluorescence collection factors as high as 15% per facet in good agreement with theory. This demonstrates the potential of integrated hollow-core waveguides as optical sensors for single-molecule spectroscopy.

Detection Of Homocysteine And Cysteine, Weihua Wang, Oleksandr Rusin, Xiangyang Xu, Kyu Kwang Kim, Jorge O. Escobedo, Sayo O. Fakayode, Kristin A. Fletcher, Mark Lowry, Corin M. Schowalter, Candace M. Lawrence, Frank R. Fronczek, Isiah M. Warner, Robert M. Strongin

Faculty Publications

At elevated levels, homocysteine (Hcy, 1) is a risk factor for cardiovascular diseases, Alzheimer's disease, neural tube defects, and osteoporosis. Both 1 and cysteine (Cys, 3) are linked to neurotoxicity. The biochemical mechanisms by which 1 and 3 are involved in disease states are relatively unclear. Herein, we describe simple methods for detecting either Hey or Cys in the visible spectral region with the highest selectivity reported to date without using biochemical techniques or preparative separations. Simple methods and readily available reagents allow for the detection of Cys and Hey in the range of their physiologically relevant levels. New HPLC …

Development And Validation Of The Theistic Spiritual Outcome Survey, P. Scott Richards, Timothy B. Smith, Marion Schowalter, Michael E. Berrett, Randy K. Hardman

Faculty Publications

We developed the Spiritual Outcome Scale (SOS) to measure the spiritual outcomes of psychotherapy from a theistic spiritual perspective. A 17-item version of the SOS was found to have adequate reliability and validity in a sample of college students. Three factors emerged from the analyses that corresponded to subscales labeled Love of God, Love of Others, and Love of Self. Correlations with measures of psychological outcomes were statistically significant. In subsequent analyses, the SOS was administered over an 8-week period to a sample of inpatient women with eating disorders and to two samples from inpatient psychological clinics in Germany. The …

Trehalose Loading Through The Mitochondrial Permeability Transition Pore Enhances Desiccation Tolerance In Rat Liver Mitochondria, Xiang Hong Liu, Alptekin Aksan, Michael A. Menze, Steven C. Hand, Mehmet Toner

Faculty Publications

Trehalose has extensively been used to improve the desiccation tolerance of mammalian cells. To test whether trehalose improves desiccation tolerance of mammalian mitochondria, we introduced trehalose into the matrix of isolated rat liver mitochondria by reversibly permeabilizing the inner membrane using the mitochondrial permeability transition pore (MPTP). Measurement of the trehalose concentration inside mitochondria using high performance liquid chromatography showed that the sugar permeated rapidly into the matrix upon opening the MPTP. The concentration of intra-matrix trehalose reached 0.29 mmol/mg protein (∼190 mM) in 5 min. Mitochondria, with and without trehalose loaded into the matrix, were desiccated in a buffer …

Host-Parasitoid Spatial Ecology: A Plea For A Landscape-Level Synthesis, James T. Cronin, John D. Reeve

Faculty Publications

A growing body of literature points to a large-scale research approach as essential for understanding population and community ecology. Many of our advances regarding the spatial ecology of predators and prey can be attributed to research with insect parasitoids and their hosts. In this review, we focus on the progress that has been made in the study of the movement and population dynamics of hosts and their parasitoids in heterogeneous landscapes, and how this research approach may be beneficial to pest management programs. To date, few studies have quantified prey and predator rates and ranges of dispersal and population dynamics …

Coastal Water Source Of Short‐Lived Halocarbons In New England, Yong Zhou, Ruth K. Varner, Rachel S. Russo, Oliver W. Wingenter, Karl B. Haase, Robert W. Talbot, Barkley C. Sive

Faculty Publications

Short‐lived halocarbon tracers were used to investigate marine influences on air quality in a coastal region of New England. Atmospheric measurements made at the University of New Hampshire's Observing Station at Thompson Farm (TF) in Durham, New Hampshire, indicate that relatively large amounts of halocarbons are emitted from local estuarine and coastal oceanic regions. Bromine‐containing halocarbons of interest in this work include bromoform (CHBr3) and dibromomethane (CH2Br2). The mean mixing ratios of CHBr3 and CH2Br2 from 11 January to 5 March 2002 were 2.6 pptv and 1.6 pptv, and from 1 June to 31 August 2002 mean mixing ratios were …

Semiclassical Nonadiabatic Dynamics Using A Mixed Wave-Function Representation, Sophya Garashchuk, Vitaly A. Rassolov, George C. Schatz

Faculty Publications

Nonadiabatic effects in quantum dynamics are described using a mixed polar/coordinate space representation of the wave function. The polar part evolves on dynamically determined potential surfaces that have diabatic and adiabatic potentials as limiting cases of weak localized and strong extended diabatic couplings. The coordinate space part, generalized to a matrix form, describes transitions between the surfaces. Choice of the effective potentials for the polar part and partitioning of the wave function enables one to represent the total wave function in terms of smooth components that can be accurately propagated semiclassically using the approximate quantum potential and small basis sets. …

Multiple Bromodomain Genes Are Involved In Restricting The Spread Of Heterochromatic Silencing At The Saccharomyces Cerevisiae Hmr-Trna Boundary, Nithya Jambunathan, Adam W. Martinez, Elizabeth C. Robert, Nneamaka B. Agochukwu, Megan E. Ibos, Sandra L. Dugas, David Donze

Faculty Publications

The transfer RNA gene downstream from the HMR locus in S. cerevisiae functions as part of a boundary (barrier) element that restricts the spread of heterochromatic gene silencing into the downstream region of chromosome III. A genetic screen for identifying additional genes that, when mutated, allow inappropriate spreading of silencing from HMR through the tRNA gene was performed. YTA7, a gene containing bromodomain and ATPase homologies, was identified multiple times. Previously, others had shown that the bromodomain protein Bdf1p functions to restrict silencing at yeast euchromatin- heterochromatin boundaries; therefore we deleted nonessential bromodomain-containing genes to test their effects on heterochromatin …

The Case For Selection At Ccr5-Δ32, Pardis C. Sabeti, Emily Walsh, Steve F. Schaffner, Patrick Varilly, Ben Fry, Holli B. Hutcheson, Mike Cullen, Tarjei S. Mikkelsen, Jessica Roy, Nick Patterson, Richard Cooper, David Reich, David Altshuler, Stephen O'Brien, Eric S. Lander

Faculty Publications

The C-C chemokine receptor 5, 32 base-pair deletion (CCR5-Δ32) allele confers strong resistance to infection by the AIDS virus HIV. Previous studies have suggested that CCR5-Δ32 arose within the past 1,000 y and rose to its present high frequency (5%-14%) in Europe as a result of strong positive selection, perhaps by such selective agents as the bubonic plague or smallpox during the Middle Ages. This hypothesis was based on several lines of evidence, including the absence of the allele outside of Europe and long-range linkage disequilibrium at the locus. We reevaluated this evidence with the benefit of much denser genetic …

Successful Island Reintroductions Of New Zealand Robins And Saddlebacks With Small Numbers Of Founders, Sabrina S. Taylor, Ian G. Jamieson, Doug P. Armstrong

Faculty Publications

Populations established with a small number of founders are thought to have a high risk of extinction due to Allee effects, demographic stochasticity, inbreeding and reduced genetic variation. We tested whether the initial number of birds released was related to persistence in reintroductions of saddlebacks (Philesturnus carunculatus) and robins (Petroica australis) to New Zealand offshore islands. Data were analysed for 31 populations that had been observed for at least 3 years since reintroductions. The numbers released ranged from 5-188. Most of the populations (26) survived and grew, including five from less than 15 founders, and four out of the five …

Bioassay-Guided Fractionation Of Rubus Suavissimus Leaf Extracts Possessing Nf-Κb Inhibitory Activities And A Separable Cytotoxicity, Dong Liu, Zhanguo Gao, Jian Zhang, Jianping Ye, Zhijun Liu

Faculty Publications

Leaf extract of Rubus suavissimus S. Lee (Rosaceae), a perennial woody shrub indigenous to southern China, was tested for its biological activity in the regulation of transcription factor NF-κB (nuclear factor kappa B) A NF-κB luciferase reporter cell line was used in this study. The crude extract inhibited NF-κB at 100-1000 μg/ml concentrations with minor cytotoxicity. This finding prompted two more rounds of fractionation toward separating the active fraction from the cytotoxic fraction. Five fractions were obtained in the first round of fractionation, of which RUS-C20 was found to be the most potent in inhibiting NF-κB without signs of cytotoxicity …

Genomic Rearrangements By Line-1 Insertion-Mediated Deletion In The Human And Chimpanzee Lineages, Kyudong Han, Shurjo K. Sen, Jianxin Wang, Pauline A. Callinan, Jungnam Lee, Richard Cordaux, Ping Liang, Mark A. Batzer

Faculty Publications

Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of ∼18 kb of sequence from the human genome and ∼15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of …

Influences Of Dietary Soy Isoflavones On Metabolism But Not Nociception And Stress Hormone Responses In Ovariectomized Female Rats, Edwin D. Lephart, Lihong H. Bu, Kenneth Setchell

Faculty Publications

Isoflavones, the most abundant phytoestrogens in soy foods, are structurally similar to 17beta-estradiol. Few studies have examined the nociception and stress hormone responses after consumption of soy isoflavones. Methods: In this study, ovariectomized (OVX) female Long-Evans rats were fed either an isoflavone-rich diet (Phyto-600) or an isoflavone-free diet (Phyto-free). We examined the effects of soy isoflavones on metabolism by measuring body weights, food/water intake, adipose tissue weights as well as serum leptin levels. Also, circulating isoflavone levels were quantified. During chemically induced estrous, nociceptive thresholds were recorded. Then, the animals were subjected to a stressor and stress hormone levels were …

Using Genetic Algorithms To Map First-Principles Results To Model Hamiltonians: Application To The Generalized Ising Model For Alloys, Gus L. W. Hart, Volker Blum, Michael J. Walorski, Alex Zunger

Faculty Publications

The cluster expansion method provides a standard framework to map first-principles generated energies for a few selected configurations of a binary alloy onto a finite set of pair and many-body interactions between the alloyed elements. These interactions describe the energetics of all possible configurations of the same alloy, which can hence be readily used to identify ground state structures and, through statistical mechanics solutions, find finite-temperature properties. In practice, the biggest challenge is to identify the types of interactions which are most important for a given alloy out of the many possibilities. We describe a genetic algorithm which automates this …

Controls On The Seasonal Exchange Of Ch3br In Temperate Peatlands, Marguerite L. White, Ruth K. Varner, Patrick M. Crill, Cindy H. Mosedale

Faculty Publications

Measurements of CH3Br exchange at two New Hampshire peatlands (Sallie's Fen and Angie's Bog) indicate that net flux from these ecosystems is the sum of competing production and consumption processes. Net CH3Br fluxes were highly variable and ranged from net emission to net uptake between locations within a single peatland. At Sallie's Fen, net CH3Br flux exhibited positive correlations with peat temperature and air temperature during all seasons sampled, but these relationships were not observed at Angie's Bog where flux varied according to microtopography. The major CH3Br production process at Sallie's Fen appeared dependent on aerobic conditions within the peat, …

A Role For Airway Remodeling During Respiratory Syncytial Virus Infection, David Becnel, Dahui You, Joshua Erskin, Dawn M. Dimina, Stephania A. Cormier

Faculty Publications

Background: Severe respiratory syncytial virus infection (RSV) during infancy has been shown to be a major risk factor for the development of subsequent wheeze. However, the reasons for this link remain unclear. The objective of this research was to determine the consequences of early exposure to RSV and allergen in the development of subsequent airway hyperreactivity (AHR) using a developmental time point in the mouse that parallels that of the human neonate. Methods: Weanling mice were sensitized and challeged with ovalbumin (Ova) and/or infected with RSV. Eight days after the last allergen challenge, various pathophysiological endpoints were examined. Results: AHR …

Limitations And Potentials Of Current Motif Discovery Algorithms, Jianjun Hu, Bin Li, Daisuke Kihara

Faculty Publications

Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithms, their strengths and weaknesses are not sufficiently understood. Here, we designed a comprehensive set of performance measures and benchmarked five modern sequence-based motif discovery algorithms using large datasets generated from Escherichia coli RegulonDB. Factors that affect the prediction accuracy, scalability and reliability are characterized. It is revealed that the nucleotide and the binding site level accuracy are very low, while the motif level accuracy …

A Numerical Study Of The Western Cosmonaut Polynya In A Coupled Ocean-Sea Ice Model, T.G. Prasad, Julie L. Mcclean, Elizabeth C. Hunke, Albert J. Semtner, Detelina Ivanova

Faculty Publications

[1] Employing results from a 0.4 degrees, 40-level fully global, coupled ocean - sea ice model, we investigated the role of physical processes emanating from atmosphere, ocean, and ice in the initiation, maintenance, and termination of a sensible heat polynya with a focus on the western Cosmonaut polynya that occurred during May - July 1999. The Cosmonaut polynya first appeared in early May 1999 in the form of an ice-free embayment, transformed into an enclosed polynya on 5 - 9 July, and disappeared by late July, when the ice from the surrounding regions began to encircle the embayment. Except for …

Remotely Sensed Data To Map Forest Age Class By Cover Type In East Texas, Daniel Unger, I-Kuai Hung, Jeffrey M. Williams, James Kroll, Dean W. Coble, Jason Grogan

Faculty Publications

• Remote sensing in conjunction with ground truthing, can accurately quantify forest composition and age distributions in East Texas.
• Method uses standardized and readily available data available to the general public.
• Method was shown to be effective in terms of time and cost.

Cross-Talk Among Gp130 Cytokines In Adipocytes, Sanjin Zvonic, James E. Baugh, Patricia Arbour-Reily, Randall L. Mynatt, Jacqueline M. Stephens

Faculty Publications

The interleukin-6 (IL-6) family of cytokines is a family of structurally and functionally related proteins, including IL-6, IL-11, leukemia inhibitory factor (LIF), oncostatin M (OSM), ciliary neurotrophic factor (CNTF), and cardiotrophin-1 (CT-1). These proteins are also known as gp130 cytokines because they all share gp130 as a common transducer protein within their functional receptor complexes. Several of these cytokines (LIF, OSM, CNTF, and CT-1) also utilize the LIF receptor (LIFR) as a component of their receptor complex. We have shown that all of these cytokines are capable of activating both the JAK/STAT and p42/44 mitogen-activated protein kinase signaling pathways in …

Tracking Alu Evolution In New World Primates, David A. Ray, Mark A. Batzer

Faculty Publications

Background: Alu elements are Short INterspersed Elements (SINEs) in primate genomes that have proven useful as markers for studying genome evolution, population biology and phylogenetics. Most of these applications, however, have been limited to humans and their nearest relatives, chimpanzees. In an effort to expand our understanding of Alu sequence evolution and to increase the applicability of these markers to non-human primate biology, we have analyzed available Alu sequences for loci specific to platyrrhine (New World) primates. Results: Branching patterns along an Alu sequence phylogeny indicate three major classes of platyrrhine-specific Alu sequences. Sequence comparisons further reveal at least three …

The Role Of Cavitation In Acoustically Activated Drug Delivery, Mario A. Diaz, Ghaleb A. Husseini, William G. Pitt, Eric S. Richardson, Douglas A. Christensen

Faculty Publications

The triblock copolymer, Pluronic P105, has been found to be an ideal ultrasonically activated drug delivery vehicle because it forms micelles with hydrophobic polypropylene oxide cores that sequester hydrophobic drugs (Fig. 1). These micelles release their contents upon the application of low frequency ultrasound [1]such that drugs can be released specifically at the ultrasonicated region (Fig. 2). Such ultrasonically controlled release has been effective against cancer cells in vitro [2] and in vivo [3]. This poster presents our results showing that collapse cavitation is associated with drug release. Cavitation is generally divided into two types of behavior. Stable cavitation is …

Analysis Of Gaits For A Rotating Tripedal Robot, Damian M. Lyons, Kiran Pamnany

Faculty Publications

A goal of robotics has been to develop mechanisms that have the efficiency and speed of wheeled robots with the terrain flexibility of legged robots. In previous work, we have proposed a unique three-legged mechanism, the rotopod, designed to integrate these two useful approaches to locomotion. In this paper, we present an analysis of the variety of gaits that can be exhibited by the rotopod. We present examples of many of these gaits and discuss their potential use. A trajectory generation algorithm is presented that can be used to generate point to point trajectories using one of three different styles …