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Division Of Research And Economic Development Monthly Report For December 2009, Uri Division Of Research And Economic Development

Reports (Research and Economic Development)

The monthly reports include statistics for project proposals and awards received by individual academic and administrative departments at the University of Rhode Island.

Division Of Research And Economic Development Monthly Report For November 2009, Uri Division Of Research And Economic Development

Reports (Research and Economic Development)

The monthly reports include statistics for project proposals and awards received by individual academic and administrative departments at the University of Rhode Island.

Research & Innovation For 2008-2009, University Of Rhode Island

Publications (Research and Economic Development)

The 2008-2009 issue of Research & Innovation, a periodical focused on research at the University of Rhode Island.

Next Generation Transcriptomes For Next Generation Genomes Using Est2assembly, Alexie Papanicolaou, Remo Stierli, Richard H. Ffrench-Constant, David G. Heckel

Computer Science and Statistics Faculty Publications

Background: The decreasing costs of capillary-based Sanger sequencing and next generation technologies, such as 454 pyrosequencing, have prompted an explosion of transcriptome projects in non-model species, where even shallow sequencing of transcriptomes can now be used to examine a range of research questions. This rapid growth in data has outstripped the ability of researchers working on non-model species to analyze and mine transcriptome data efficiently.

Results: Here we present a semi-automated platform 'est2assembly' that processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including …

Gender And Women's Studies Newsletter For Fall 2009, Uri Gender And Women's Studies Department

Gender and Women's Studies Publications

The Fall 2009 issue of Gender and Women’s Studies Newsletter, a periodical with articles written by faculty members and some related to events within the Gender and Women’s Studies program.

Options For National Parks And Reserves For Adapting To Climate Change, Jill S. Baron, Lance Gunderson, Craig D. Allen, Erica Fleishman, Donald Mckenzie, Laura A. Meyerson, Jill Oropeza, Nate Stephenson

Natural Resources Science Faculty Publications

Past and present climate has shaped the valued ecosystems currently protected in parks and reserves, but future climate change will redefine these conditions. Continued conservation as climate changes will require thinking differently about resource management than we have in the past; we present some logical steps and tools for doing so. Three critical tenets underpin future management plans and activities: (1) climate patterns of the past will not be the climate patterns of the future; (2) climate defines the environment and influences future trajectories of the distributions of species and their habitats; (3) specific management actions may help increase the …

Forest Grazing And Natural Regeneration In A Late Successional Broadleaved Community Forest In Bhutan, Bill Buffum, Georg Gratzer, Yeshi Tenzin

Natural Resources Science Faculty Publications

This study investigated the sustainability of combining forest grazing and timber harvesting with selection felling in a cool broadleaved community forest (CF) in Bhutan. Forest grazing and timber production are critical livelihood activities for many farmers throughout the world, so it is important to understand under what conditions the 2 activities can be combined. The study was based on a household survey to quantify livestock holdings and grazing patterns, a comparison of 2 forest inventories to assess forest structure and regeneration, and a study of stumps to quantify harvesting intensities. During a 5-year period the number of cattle grazing inside …

Biological Control Of Fenusa Pusilla (Hymenoptera: Tenthredinidae) In The Northeastern United States: A Thirty-Four Year Perspective On Efficacy, Richard A. Casagrande, R. G. Van Driesche, M. Mayer, R. Fuester, D. Gilrein, L. Tewksbury, Heather H. Faubert

Past Departments Faculty Publications (CELS)

Parasitoid releases against the birch leafminer Fenusa pusilla (Lepeletier) (Hymenoptera: Tenthredinidae) in eastern North America began in 1974, with releases in eastern Canada, followed by others in the Middle Atlantic States and New England. Of 4 parasitoids released, only 1, the ichneumonid Lathrolestes nigricollis (Thompson), established and spread widely. Studies of its preliminary impacts were made in several locations in the 1980s and 1990s, but full impact of the parasitoid on host density was not yet achieved in that period. Here we report results of surveys in 7 states (MA, CT, RI, NY, PA, NJ, DE) in 2007 documenting the …

Global Dynamics Of A Competitive System Of Rational Difference Equations In The Plane, S. Kalabušic, Mustafa R. Kulenović, E. Pilav

Mathematics Faculty Publications

We investigate global dynamics of the following systems of difference equations x_n+1 = (a₁ + β₁x_n)/y_n, y_n+1 = (a₂ + y₂y_n)/(A₂ + x_n), n = 0, 1, 2, …, where the parameters a₁, β₁, a₂, y₂, and A₂ are positive numbers and initial conditions X₀ and Y₀ are arbitrary nonnegative numbers such that Y₀ > 0. We show that this system has rich dynamics which depend …

The Pic Protease Of Enteroaggregative Escherichia Coli Promotes Intestinal Colonization And Growth In The Presence Of Mucin, Susan M. Harrington, Jalaluddin Sheikh, Ian R. Henderson, Fernando Ruiz-Perez, Paul S. Cohen, James P. Nataro

Cell and Molecular Biology Faculty Publications

Enteroaggregative Escherichia coli (EAEC) is increasingly being recognized as a cause of diarrheal disease in diverse populations. No small animal model is currently available to study this pathogen. We report here that conventional mice orally inoculated with prototype EAEC strain 042 generally became colonized, though the abundance of organisms cultured from their stool varied substantially among individual animals. In contrast, mice whose water contained 5 g/liter streptomycin consistently became colonized at high levels (ca. 10⁸ CFU/g of stool). Neither conventional nor streptomycin-treated mice developed clinical signs or histopathologic abnormalities. Using specific mutants in competition with the wild-type strain, we …

Novel Features Of The Polysaccharide-Digesting Gliding Bacterium Flavobacterium Johnsoniae As Revealed By Genome Sequence Analysis, Mark J. Mcbride, Gary Xie, Eric C. Martens, Alla Lapidus, Bernard Henrissat, Ryan G. Rhodes, Eugene Goltsman, Wei Wang, Jian Xu, David W. Hunnicutt, Andrew M. Staroscik, Timothy R. Hoover, Yi-Qiang Cheng, Jennifer L. Stein

Cell and Molecular Biology Faculty Publications

The 6.10-Mb genome sequence of the aerobic chitin-digesting gliding bacterium Flavobacterium johnsoniae (phylum Bacteroidetes) is presented. F. johnsoniae is a model organism for studies of bacteroidete gliding motility, gene regulation, and biochemistry. The mechanism of F. johnsoniae gliding is novel, and genome analysis confirms that it does not involve well-studied motility organelles, such as flagella or type IV pili. The motility machinery is composed of Gld proteins in the cell envelope that are thought to comprise the “motor” and SprB, which is thought to function as a cell surface adhesin that is propelled by the motor. Analysis of the …

Direct And Specific Inactivation Of Protein Tyrosine Kinases In The Src And Fgfr Families By Reversible Cysteine Oxidation, David J. Kemble, Gongqin Sun

Cell and Molecular Biology Faculty Publications

Accumulating evidence suggests that protein tyrosine phosphorylation-based signaling pathways are under the regulation of reactive oxygen species. Although protein tyrosine phosphatases are directly regulated by reversible oxidation, it is not clear whether protein tyrosine kinases (PTKs) are also directly regulated by reduction/oxidation (redox). In this study we report a mechanism of direct oxidative inactivation specific for the PTKs in the Src and fibroblast growth factor receptor (FGFR) families, key enzymes in mammalian signal transduction. Src is fully active when reduced and retains 8–25% of the full activity toward various substrates when oxidized. This inactivation is caused by oxidation of a …

Purification And Characterization Of A Novel Salivary Antimicrobial Peptide From The Tick, Ixodes Scapularis, Sivakamasundari Pichu, José M.C. Ribeiro, Thomas N. Mather

Plant Sciences and Entomology Faculty Publications

A novel antimicrobial peptide was isolated from the saliva of the Lyme disease tick vector, Ixodes scapularis, henceforth designated as ISAMP (I. scapularis Antimicrobial Peptide). ISAMP was purified using a sequential method including ultra filtration, gel filtration and reverse-phase high performance liquid chromatography. The purified peak had a molecular weight of 5.3 kDa by MALDI/TOF-MS and its amino acid sequence, determined by Edman degradation was PDxGxPxxVKAGRxPxxSI. A BLASTP search revealed that the protein is a putative 5.3 kDa secreted protein (AAM93656) from I. scapularis. The predicted protein is composed of 69 amino acids with no conserved …

Freshman Record : The University Of Rhode Island, The Interfraternity/Panhellenic Councils

Freshman Record

No abstract provided.

Recalculated Diet And Daily Ration Of The Shortfin Mako (Isurus Oxyrinchus), With A Focus On Quantifying Predation On Bluefish (Pomatomus Saltatrix) In The Northwest Atlantic Ocean, Anthony D. Wood, Bradley M. Wetherbee, Francis Juanes, Nancy E. Kohler, Cheryl Wilga

Biological Sciences Faculty Publications

The diet and daily ration of the shortfin mako (Isurus oxyrinchus) in the northwest Atlantic were re-examined to determine whether fluctuations in prey abundance and availability are ref lected in these two biological variables. During the summers of 2001 and 2002, stomach content data were collected from fishing tournaments along the northeast coast of the United States. These data were quantified by using four diet indices and were compared to index calculations from historical diet data collected from 1972 through 1983. Bluefish (Pomatomus saltatrix) were the predominant prey in the 1972–83 and 2001–02 diets, accounting for …

Population Size And Survivorship For Juvenile Lemon Sharks (Negaprion Brevirostris) On Their Nursery Grounds At A Marine Protected Area In Brazil, Renato Hajenius Aché De Freitas, Ricardo S. Rosa, Bradley M. Wetherbee, Samuel H. Gruber

Biological Sciences Faculty Publications

Sharks face a number of obstacles for surviving their first several years of life and many species occupy nursery areas. Although estimates of survival, particularly for young age classes, are essential for assessing, monitoring and effectively managing animal populations, there have been relatively few calculations of survival within shark populations and even fewer estimates based on direct methods for sharks on their nursery grounds. We used tag-recapture methods to estimate the population size and survival of juvenile lemon sharks (Negaprion brevirostris) on their nursery grounds at Atol das Rocas, a marine protected area in Brazil. Sharks were sampled …

Human Carboxylesterases Hce1 And Hce2: Ontogenic Expression, Inter-Individual Variability And Differential Hydrolysis Of Oseltamivir, Aspirin, Deltamethrin And Permethrin, Dongfang Yang, Robin E. Pearce, Xiliang Wang, Roger Gaedigk, Yu-Jui Yvonne Wan, Bingfang Yan

Biomedical and Pharmaceutical Sciences Faculty Publications

Carboxylesterases hydrolyze chemicals containing such functional groups as a carboxylic acid ester, amide and thioester. The liver contains the highest carboxylesterase activity and expresses two major carboxylesterases: HCE1 and HCE2. In this study, we analyzed 104 individual liver samples for the expression patterns of both carboxylesterases. These samples were divided into three age groups: adults (≥ 18 years of age), children (0 days–10 years) and fetuses (82–224 gestation days). In general, the adult group expressed significantly higher HCE1 and HCE2 than the child group, which expressed significantly higher than the fetal group. The age-related expression was confirmed by RT-qPCR and …

Pyrethroid Insecticides: Isoform-Dependent Hydrolysis, Induction Of Cytochrome P450 3a4 And Evidence On The Involvement Of The Pregnane X Receptor, Dongfeng Yang, Xiliang Wang, Yi-Tzai Chen, Ruitang Deng, Bingfang Yan

Biomedical and Pharmaceutical Sciences Faculty Publications

Pyrethroids account for more than one-third of the insecticides currently marketed in the world. In mammals, these insecticides undergo extensive metabolism by carboxylesterases and cytochrome P450s (CYPs). In addition, some pyrethroids are found to induce the expression of CYPs. The aim of this study was to determine whether pyrethroids induce carboxylesterases and CYP3A4, and whether the induction is correlated inversely with their hydrolysis. Human liver microsomes were pooled and tested for the hydrolysis of 11 pyrethroids. All pyrethroids were hydrolyzed by the pooled microsomes, but the hydrolytic rates varied by as many as 14 fold. Some pyrethroids such as bioresmethrin …

Precolonized Human Commensal Escherichia Coli Strains Serve As A Barrier To E. Coli O157:H7 Growth In The Streptomycin-Treated Mouse Intestine, Mary P. Leatham, Swati Banerjee, Steven M. Autieri, Regino Mercado-Lubo, Tyrrell Conway, Paul S. Cohen

Cell and Molecular Biology Faculty Publications

Different Escherichia coli strains generally have the same metabolic capacity for growth on sugars in vitro, but they appear to use different sugars in the streptomycin-treated mouse intestine (Fabich et al., Infect. Immun. 76:1143-1152, 2008). Here, mice were precolonized with any of three human commensal strains (E. coli MG1655, E. coli HS, or E. coli Nissle 1917) and 10 days later were fed 10⁵ CFU of the same strains. While each precolonized strain nearly eliminated its isogenic strain, confirming that colonization resistance can be modeled in mice, each allowed growth of the other commensal strains to higher numbers, …

Functional Interaction Between The Fanconi Anemia D2 Protein And Proliferating Cell Nuclear Antigen (Pcna) Via A Conserved Putative Pcna Interaction Motif, Niall G. Howlett, Julie A. Harney, Meghan A. Rego, Frederick W. Kolling Iv, Thomas W. Glover

Cell and Molecular Biology Faculty Publications

Fanconi Anemia (FA) is a rare recessive disease characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The FA proteins and the familial breast cancer susceptibility gene products, BRCA1 and FANCD1/BRCA2, function cooperatively in the FA-BRCA pathway to repair damaged DNA and to prevent cellular transformation. Activation of this pathway occurs via the mono-ubiquitination of the FANCD2 protein, targeting it to nuclear foci where it co-localizes with FANCD1/BRCA2, RAD51, and PCNA. The regulation of the mono-ubiquitination of FANCD2, as well as its function in DNA repair remain poorly understood. In this study, we have further characterized the interaction between …

Salmonella Enterica Serovar Typhimurium Mutants Unable To Convert Malate To Pyruvate And Oxaloacetate Are Avirulent And Immunogenic In Balb/C Mice, Regino Mercado-Lubo, Mary P. Leatham, Tyrrell Conway, Paul S. Cohen

Cell and Molecular Biology Faculty Publications

Previously, we showed that the Salmonella enterica serovar Typhimurium SR-11 tricarboxylic acid (TCA) cycle must operate as a complete cycle for full virulence after oral infection of BALB/c mice (M. Tchawa Yimga, M. P. Leatham, J. H. Allen, D. C. Laux, T. Conway, and P. S. Cohen, Infect. Immun. 74:1130-1140, 2006). In the same study, we showed that for full virulence, malate must be converted to both oxaloacetate and pyruvate. Moreover, it was recently demonstrated that blocking conversion of succinyl-coenzyme A to succinate attenuates serovar Typhimurium SR-11 but does not make it avirulent; however, blocking conversion of succinate to …

Identification Of N-Terminal Lobe Motifs That Determine The Kinase Activity Of The Catalytic Domains And Regulatory Strategies Of Src And Csk Protein Tyrosine Kinases, Kezhen Huang, Yue-Hao Wang, Alex Brown, Gongqin Sun

Cell and Molecular Biology Faculty Publications

Csk and Src protein tyrosine kinases are structurally homologous but use opposite regulatory strategies. The isolated catalytic domain of Csk is intrinsically inactive and is activated by interactions with the regulatory Src homology 3 (SH3) and SH2 domains, while the isolated catalytic domain of Src is intrinsically active and is suppressed by interactions with the regulatory SH3 and SH2 domains. The structural basis for why one isolated catalytic domain is intrinsically active while the other is inactive is not clear. In this study, we identified structural elements in the N-terminal lobe of the catalytic domain that render the Src catalytic …

Communication Competence And Moral Competence: A Confucian Perspective, Xiaosui Xiao, Guo-Ming Chen

Communication Studies Faculty Publications

How can meaningful and productive communication take place among people of different cultural backgrounds? This question has become increasingly important in the age of the global village. Confucians, who long ago learned to live harmoniously with those from other parts of the world, have much to offer in response to the question. Western scholars and practitioners tend to see communication competence as a goal-achieving capability and self-assertive skill. Confucians believe that every human being is endowed with a moral nature and the capacity to feel, appreciate, and respect others. From this perspective, communication is seen primarily as an ethical and …

Epigenetics, Oxidative Stress, And Alzheimer Disease, Nasser H. Zawia, Debomoy K. Lahiri, Fernando Cardozo-Pelaez

Biomedical and Pharmaceutical Sciences Faculty Publications

Alzheimer disease (AD) is a progressive neurodegenerative disorder whose clinical manifestations appear in old age. The sporadic nature of 90% of AD cases, the differential susceptibility to and course of the illness, as well as the late age onset of the disease suggest that epigenetic and environmental components play a role in the etiology of late-onset AD. Animal exposure studies demonstrated that AD may begin early in life and may involve an interplay between the environment, epigenetics, and oxidative stress. Early life exposure of rodents and primates to the xenobiotic metal lead (Pb) enhanced the expression of genes associated with …

Eugenia Jambolana Lam. Berry Extract Inhibits Growth And Induces Apoptosis Of Human Breast Cancer But Not Non-Tumorigenic Breast Cells, Liya Li, Lynn S. Adams, Shiuan Chen, Caroline Killian, Aftab Ahmed, Navindra P. Seeram

Biomedical and Pharmaceutical Sciences Faculty Publications

The ripe purple berries of the native Indian plant Eugenia jambolana Lam., known as Jamun, are popularly consumed and available in the United States in Florida and Hawaii. Despite the growing body of data on the chemopreventive potential of edible berry extracts, there is paucity of such data for Jamun fruit. Therefore our laboratory initiated the current study with the following objectives: (1) to prepare a standardized Jamun fruit extract (JFE) for biological studies and (2) to investigate the antiproliferative and pro-apoptotic effects of JFE in estrogen dependent/aromatase positive (MCF-7aro), and estrogen independent (MDA-MB-231) breast cancer cells, and in a …

Synthesis And Evaluation Of Phosphopeptides Containing Iminodiacetate Groups As Binding Ligands Of The Src Sh2 Domain, Guofeng Ye, Aaron D. Schuler, Yousef Ahmadibeni, Joel R. Morgan, Absar Faruqui, Kezhen Huang, Gongqin Sun, John A. Zebala, Keykavous Parang

Biomedical and Pharmaceutical Sciences Faculty Publications

Phosphopeptide pTyr-Glu-Glu-Ile (pYEEI) has been introduced as an optimal Src SH2 domain ligand. Peptides, Ac-K(IDA)pYEEIEK(IDA) (1), Ac-KpYEEIEK (2), Ac-K(IDA)pYEEIEK (3), and Ac-KpYEEIEK(IDA) (4), containing 0–2 iminodiacetate (IDA) groups at the N- and C-terminal lysine residues were synthesized and evaluated as the Src SH2 domain binding ligands. Fluorescence polarization assays showed that peptide 1 had a higher binding affinity (K_d = 0.6 μM) to the Src SH2 domain when compared with Ac-pYEEI (K_d = 1.7 μM), an optimal Src SH2 domain ligand, and peptides 2–4 …

Synthesis Of Nucleoside Mono-, Di-, And Triphosphoramidates From Solid-Phase Cyclosaligenyl Phosphitylating Reagents, Yousef Ahmadibeni, Rakesh K. Tiwari, Gongqin Sun, Keykavous Parang

Biomedical and Pharmaceutical Sciences Faculty Publications

Chloromethyl polystyrene resin was reacted with 5-hydroxysalicylaldehyde in the presence of potassium carbonate to afford polymer-bound 2-hydroxybenzaldehyde. Subsequent reduction with borane solution produced polymer-bound 2-hydroxybenzyl alcohol. The reaction of immobilized 2-hydroxybenzyl alcohol with appropriate phosphitylating reagents yielded solid-phase cycloSaligenyl mono-, di-, and triphosphitylating reagents, which were reacted with unprotected nucleosides, followed by iodine oxidation, deprotection of cyanoethoxy groups, and the basic cleavage, respectively, to afford 5′-O-nucleoside mono-, di-, and triphosphoramidates in 52−73% overall yield.

In Silico-Accelerated Identification Of Conserved And Immunogenic Variola/Vaccinia T-Cell Epitopes, Leonard Moise, Julie A. Mcmurry, Soren Buus, Sharon Frey, William D. Martin, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Epitopes shared by the vaccinia and variola viruses underlie the protective effect of vaccinia immunization against variola infection. We set out to identify a subset of cross-reactive epitopes using bioinformatics and immunological methods. Putative T-cell epitopes were computationally predicted from highly conserved open reading frames from seven complete vaccinia and variola genomes using EpiMatrix. Over 100 epitopes bearing low human sequence homology were selected and assessed in HLA binding assays and in T-cell antigenicity assays using PBMCs isolated from Dryvax-immunized subjects. This experimental validation of computational predictions illustrates the potential for immunoinformatics methods to identify candidate immunogens for a new, …

T Cell Epitope: Friend Or Foe? Immunogenicity Of Biologics In Context, Constanze A. Weber, Preema J. Mehta, Matthew Ardito, Leonard Moise, William Martin, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Like vaccines, biologic proteins can be very immunogenic for reasons including route of administration, dose frequency and the underlying antigenicity of the therapeutic protein. Because the impact of immunogenicity can be quite severe, regulatory agencies are developing risk-based guidelines for immunogenicity screening. T cell epitopes are at the root of the immunogenicity issue. Through their presentation to T cells, they activate the process of anti-drug antibody development. Preclinical screening for T cell epitopes can be performed in silico, followed by in vitro and in vivo validation. Importantly, screening for immunogenicity is complicated by the discovery of regulatory T cell …

Coastal Lagoons And Climate Change: Ecological And Social Ramifications In The U.S. Atlantic And Gulf Coast Ecosystems, Abigail Anthony, Joshua Atwood, Peter V. August, Carrie Byron, J. Stanley Cobb, Cheryl Foster, Crystal Fry, Arthur Gold, Kifle Hagos, Leanna Heffner, D. Q. Kellogg, Kimberly Lellis-Dibble, James J. Opaluch, Candace A. Oviatt, Anna Pfeiffer-Herbert, Nicole Rohr, Leslie Smith, Tiffany Smythe, Judith Swift, Nathan Vinhateiro

Biological Sciences Faculty Publications

Lagoons are highly productive coastal features that provide a range of natural services that society values. Their setting within the coastal landscape leaves them especially vulnerable to profound physical, ecological, and associated societal disturbance from global climate change. Expected shifts in physical and ecological characteristics range from changes in flushing regime, freshwater inputs, and water chemistry to complete inundation and loss and the concomitant loss of natural and human communities. Therefore, managing coastal lagoons in the context of global climate change is critical. Although management approaches will vary depending on local conditions and cultural norms, all management scenarios will need …