Digital Commons Network^™

Aspartate Β-Hydroxylase Expression Promotes A Malignant Pancreatic Cellular Phenotype, Xiaoqun Dong, Qiushi Lin, Arihiro Aihara, Yu Li, Chiung-Kuei Huang, Waihong Chung, Qi Tang, Xuesong Chen, Rolf Carlson, Christina Nadolny, Gregory Gabriel, Mark Olsen, Jack Wands

Biomedical and Pharmaceutical Sciences Faculty Publications

Pancreatic cancer (PC) is one of the leading causes of cancer related deaths due to aggressive progression and metastatic spread. Aspartate β-hydroxylase (ASPH), a cell surface protein that catalyzes the hydroxylation of epidermal growth factor (EGF)-like repeats in Notch receptors and ligands, is highly overexpressed in PC. ASPH upregulation confers a malignant phenotype characterized by enhanced cell proliferation, migration, invasion and colony formation in vitro as well as PC tumor growth in vivo. The transforming properties of ASPH depend on enzymatic activity. ASPH links PC growth factor signaling cascades to Notch activation. A small molecule inhibitor of β-hydroxylase activity …

Investigating The Effects Of Mobile Bottom Fishing On Benthic Biota: A Systematic Review Protocol, Kathryn M. Hughes, Michel J. Kaiser, Simon Jennings, Robert A. Mcconnaughey, Roland Pitcher, Ray Hilborn, Ricardo O. Amoroso, Jeremy Collie, Jan Geert Hiddink, Ana M. Parma, Adriaan Rijnsdorp

Graduate School of Oceanography Faculty Publications

Background:

Mobile bottom fishing, such as trawling and dredging, is the most widespread direct human impact on marine benthic systems. Knowledge of the impacts of different gear types on different habitats, the species most sensitive to impacts and the potential for habitats to recover are often needed to inform implementation of an ecosystem approach to fisheries and strategies for biodiversity conservation. This knowledge helps to identify management options that maximise fisheries yield whilst minimising negative impacts on benthic systems.

Methods/Design:

The methods are designed to identify and collate evidence from experimental studies (e.g. before/after, control/impact) and comparative studies (spanning a …

Phlip-Fire, A Cell Insertion-Triggered Fluorescent Probe For Imaging Tumors Demonstrates Targeted Cargo Delivery In Vivo, Alexander G. Karabadzhak, Ming An, Lan Yao, Rachel Langenbacher, Anna Moshnikova, Ramona Cosmina Adochite, Oleg A. Andreev, Yana K. Reshetnyak, Donald M. Engelman

Physics Faculty Publications

We have developed an improved tool for imaging acidic tumors by reporting the insertion of a transmembrane helix: the pHLIP-Fluorescence Insertion REporter (pHLIP-FIRE). In acidic tissues, such as tumors, peptides in the pHLIP family insert as α-helices across cell membranes. The cell-inserting end of the pHLIP-FIRE peptide has a fluorophore-fluorophore or fluorophore-quencher pair. A pair member is released by disulfide cleavage after insertion into the reducing environment inside a cell, resulting in dequenching of the probe. Thus, the fluorescence of the pHLIP-FIRE probe is enhanced upon cell-insertion in the targeted tissues but is suppressed elsewhere due to quenching. Targeting studies …

Flexible And Scalable Genotyping-By-Sequencing Strategies For Population Studies, Christopher Heffelfinger, Christopher A. Fragoso, Maria A. Moreno, John D. Overton, John P. Mottinger, Hongyu Zhao, Joe Tohme, Stephen L. Dellaporta

Cell and Molecular Biology Faculty Publications

Background: Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. Genotyping-by-sequencing (GBS) is a one such method highly suited to non-human organisms. In the GBS protocol, genomic DNA is fractionated via restriction digest, then reduced representation is achieved through size selection. Since many restriction sites are conserved across a species, the sequenced portion of the genome is highly consistent within a population. This makes the GBS protocol highly suited for experiments that require surveying large numbers of markers within a population, such as those …

Insights Into Environmental Controls On Microbial Communities In A Continental Serpentinite Aquifer Using A Microcosm-Based Approach, Melitza Crespo-Medina, Katrina I. Twing, Michael D.Y. Kubo, Tori M. Hoehler, Dawn Cardace, Tom Mccollom, Matthew O. Schrenk

Geosciences Faculty Publications

Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO) in northern California during …

Organic Pollutants And Ocean Fronts Across The Atlantic Ocean: A Review, Rainer Lohmann, Igor M. Belkin

Graduate School of Oceanography Faculty Publications

Little is known about the effect of ocean fronts on pollutants dynamics, particularly organic pollutants. Since fronts are associated with convergent currents and productive fishing grounds, any possible convergence of pollutants at fronts would raise concerns. The focus here is on relatively persistent organic pollutants, POPs, as non-persistent organic pollutants are rarely found in the open ocean. Results from recent cruises in the Atlantic Ocean are examined for POP distributions across ocean fronts in (i) the Canary Current; (ii) the Gulf Stream; and (iii) the Amazon and Rio de la Plata Plumes. Few studies achieved a spatial resolution of 10–20 …

Basins Of Attraction For Two Species Competitive Model With Quadratic Terms And The Singular Allee Effect, Ann Brett, Mustafa Rs Kulenović

Mathematics Faculty Publications

We consider the following system of difference equations:

χ_n+1 = χ²_n/(B₁χ²_n + C₁y²_n), y_n+1 = y²_n/(A₂ + B₂χ²_n + C₂y²_n), n = 0, 1, ..., where B₁, C₁, A₂, B₂, C₂ are positive constrants and χ0, y0 ≥ 0 are initial conditions. This system has interesting dynamics and it can have up to seven equilibrium points as well as a singular …

Reproduction Of Endangered Big-Headed Turtle, Platysternon Megacephalum (Reptilia: Testudines: Platysternidae), Yik-Hei Sung, Billy C.H. Hau, Nancy E. Karraker

Natural Resources Science Faculty Publications

The big-headed turtle (Platysternon megacephalum) is heavily harvested to support tremendous demands from food and pet markets, and thus its ecology remains poorly understood. The presence of self-sustaining populations in Hong Kong (22°09’-22°37’N, 113°50’-114°30’E) provides important opportunities to advance our understanding of this species. We employed mark-recapture surveying, radio-tracking of two gravid females, and directed streamside searches to document the reproductive ecology of the species between September 2009 and June 2011 in Hong Kong. We found seven gravid females between 20-27 June 2010 and 2011, and which subsequently oviposited on average three eggs (range 2-8), with mean length …

Dengue Virus Neutralizing Antibody Levels Associated With Protection From Infection In Thai Cluster Studies, Darunee Buddhari, Jared Aldstadt, Timothy P. Endy, Anon Srikiatkhachorn, Butsaya Thaisomboonsuk, Chonticha Klungthong, Ananda Nisalak, Benjawan Khuntirat, Richard G. Jarman, Stefan Fernandez, Stephen J. Thomas, Thomas W. Scott, Alan Rothman, In-Kyu Yoon

Institute for Immunology and Informatics Faculty Publications

Background

Long-term homologous and temporary heterologous protection from dengue virus (DENV) infection may be mediated by neutralizing antibodies. However, neutralizing antibody titers (NTs) have not been clearly associated with protection from infection.

Methodology/Principal Findings

Data from two geographic cluster studies conducted in Kamphaeng Phet, Thailand were used for this analysis. In the first study (2004–2007), cluster investigations of 100-meter radius were triggered by DENV-infected index cases from a concurrent prospective cohort. Subjects between 6 months and 15 years old were evaluated for DENV infection at days 0 and 15 by DENV PCR and IgM ELISA. In the second study (2009–2012), …

Large-Scale Computational Modeling Of The Metabolism And Evolution Of Microorganisms, Ying Zhang

Amgen Seminar Series in Chemical Engineering

Microorganisms are ubiquitous on Earth and dominate the diversity, productivity, and persistence of various ecosystems. The development of next-generation sequencing and many high-throughput technologies has enabled the large-scale molecular identification of microbial communities. However, today a comprehensive understanding is still lacking about the connections between microbial genome evolution and niche adaptation. This talk will highlight some latest developments in the integrated, large-scale modeling of the metabolism and evolution of microbial species. Examples will also be given to highlight the importance of high-performance computing systems in the analyses of big and heterogeneous biological data.

Living On The Edge: Voltage-Driven Extreme Deformation Of Bilayer Membranes, Petia Vlahovska

Amgen Seminar Series in Chemical Engineering

Living cells maintain electric potential difference across their plasma membrane. Changes in the transmembrane electric field are biologically important signals in physiological processes such as electric-field-directed cell migration in development and regeneration. Pulsed electric fields are used to open pores in the membrane, which enable the delivery of material inside the cell, e.g. for gene transfection.

I will present our theoretical and experimental work on the deformation and stability of biomimetic membranes (bilayers assembled from lipids or polymers) in electric fields. Gant vesicles exposed to DC pulses adopt peculiar drum-like shapes and may collapse. Our experiments suggest that the edge …

Reference Databases Usage Statistics 2013-2014, Michael A. Cerbo Ii, Sarah Bannister

Technical Services Reports and Statistics

Statistics on the use of online reference databases at the University of Rhode Island during the period from July 2013 through June 2014. Includes COUNTER-compliant data on sessions, searches, turnaways, full text articles downloaded, and other metrics.

A Polymorphic Microdeletion In The Rgs9 Gene Suppresses Ptb Binding And Associates With Obesity, Chong Shen, Meenakshi Sharma, Daniel C. Reid, Pengtao Li, Jeremy Celver, Norhashimah Abu Seman, Jinfeng Chen, Senthil K. Vasan, Hairu Wang, Tianwei Gu, Ying Liu, Wan Nazaimoon Wan Mohamud, Hongbing Shen, Kerstin Brismar, William G. Fairbrother, Abraham Kovoor, Harvest F. Gu

Biomedical and Pharmaceutical Sciences Faculty Publications

Objective: RGS9 is a member of the family of Regulators of G-Protein Signaling (RGS) proteins defined by the presence of an RGS domain which can accelerate the GTPase-activity of G protein Gα subunits. An insertion/deletion (I/D) polymorphism of the nucleotide sequence TTTCT (rs3215227) has been identified in the human RGS9 gene, which matches the consensus high affinity binding motif for the ubiquitously expressed RNA binding Polypyrimidine Tract Binding Protein (PTB). In this study, we evaluate the genetic association and functional relevance of this polymorphism in type 2 diabetes and obesity.

Subjects and methods: We genotyped a larger population …

Circulating Micrornas In Pancreatic Juice As Candidate Biomarkers Of Pancreatic Cancer, Jin Wang, Massimo Raimondo, Sushovan Guha, Jinyun Chen, Lixia Diao, Xiaoqun Dong, Michael B. Wallace, Ann M. Killary, Marsha L. Frazier, Timothy A. Woodward, Jing Wang, Subrata Sen

Biomedical and Pharmaceutical Sciences Faculty Publications

Development of sensitive and specific biomarkers, preferably those circulating in body fluids is critical for early diagnosis of cancer. This study performed profiling of microRNAs (miRNAs) in exocrine pancreatic secretions (pancreatic juice) by microarray analysis utilizing pancreatic juice from 6 pancreatic ductal adenocarcinoma (PDAC) patients and two pooled samples from 6 non-pancreatic, non-healthy (NPNH) as controls. Differentially circulating miRNAs were subsequently validated in 88 pancreatic juice samples from 50 PDAC, 19 chronic pancreatitis (CP) patients and 19 NPNH controls. A marked difference in the profiles of four circulating miRNAs (miR-205, miR-210, miR-492, and miR-1427) was observed in pancreatic juice collected …

Refworks Usage Statistics Through June 2014, Andrée J. Rathemacher

Technical Services Reports and Statistics

RefWorks is a subscription-based, online software product that helps researchers save, organize, and format bibliographic citations. This report provides monthly statistics on the usage of RefWorks by the University of Rhode Island community from 2002 through June 2014. Data provided includes: user type summary, focus area summary, references created per month, accounts created per month, all user accounts by user type, all user accounts by focus area, last quarter number of accounts by user type, reference type detail, all references by focus area, last quarter references by focus area, last quarter references by user type, all references by user type, …

Public Services Annual Report 2013-2014, Deborah Mongeau

Public Services Reports

Annual report of the Public Services Department of the University of Rhode Island Libraries.

Acquisitions Unit Annual Report 2013-2014, Andrée J. Rathemacher

Technical Services Reports and Statistics

Annual Report of the Acquisitions Unit, University Libraries, University of Rhode Island for FY14. Covers personnel, work flow, special projects, and serial, monograph, and e-resource acquisitions. Supplemental files include data on library materials expenditures by a number of variables as well as important working documents from the year.

Journal Usage Report For Fiscal Year 2014, Michael A. Cerbo Ii

Technical Services Reports and Statistics

Journal usage for the University Libraries are listed alphabetically by authority title. The report includes the usage statistics taken from each vendor and incorporated in Serials Solutions 360 Counter.

The report is broken down monthly for fiscal year 2014 and shows each journal's usage per month and the total usage for the year..

Electronic Journals Overlap Analysis 2014, Michael A. Cerbo Ii

Technical Services Reports and Statistics

Overlap analysis for the University of Rhode Island's electronic journals are complied alphabetically by database name. The report shows the number or titles that are exclusive to that database as compiled by Serials Solutions.

The table located under the report gives a brief explanation of the headings used in the analysis.

The Glanville Fritillary Genome Retains An Ancient Karyotype And Reveals Selective Chromosomal Fusions In Lepidoptera, Virpi Ahola, Marian R. Goldsmith, Et Al

Biological Sciences Faculty Publications

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n¼31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n¼31 for at least 140My. We show that fusion chromosomes have retained the ancestral chromosome segments and …

Quantitative Factors Proposed To Influence The Prevalence Of Canine Tick-Borne Disease Agents In The United States, Roger W. Stich, Byron L. Blagburn, Dwight D. Bowman, Christopher Carpenter, M. Roberto Cortinas, Sidney A. Ewing, Desmond Foley, Janet E. Foley, Holly Gaff, Graham J. Hickling, R. Ryan Lash, Susan E. Little, Catherine Lund, Robert Lund, Thomas N. Mather, Glen R. Needham, William L. Nicholson, Julia Sharp, Andrea Varela-Stokes, Dongmei Wang

Plant Sciences and Entomology Faculty Publications

The Companion Animal Parasite Council hosted a meeting to identify quantifiable factors that can influence the prevalence of tick-borne disease agents among dogs in North America. This report summarizes the approach used and the factors identified for further analysis with mathematical models of canine exposure to tick-borne pathogens.

Cyclic Peptide-Capped Gold Nanoparticles For Enhanced Sirna Delivery, Amir Nasrolahi Shirazi, Karissa L. Paquin, Niall G. Howlett, Dindyal Mandal, Keykavous Parang

Cell and Molecular Biology Faculty Publications

Previously, we have reported the synthesis of a homochiral l-cyclic peptide [WR]₅ and its use for delivery of anti-HIV drugs and biomolecules. A physical mixture of HAuCl₄ and the peptide generated peptide-capped gold nanoparticles. Here, [WR]₅ and [WR]₅-AuNPs were tested for their efficiency to deliver a small interfering RNA molecule (siRNA) in human cervix adenocarcinoma (HeLa) cells. Flow cytometry investigation revealed that the intracellular uptake of a fluorescence-labeled non-targeting siRNA (200 nM) was enhanced in the presence of [WR]₅ and [WR]₅-AuNPs by 2- and 3.8-fold when compared with that of siRNA alone …

Estimates Of Micro-, Nano-, And Picoplankton Contributions To Particle Export In The Northeast Pacific, B. L. Mackinson, S. Bradley Moran, M. W. Lomas, G. M. Stewart, R. P. Kelly

Graduate School of Oceanography Faculty Publications

The contributions of micro-, nano-, and picoplankton to particle export were estimated from measurements of size-fractionated particulate ²³⁴Th, organic carbon, and phytoplankton indicator pigments obtained during five cruises between 2010 and 2012 along Line P in the subarctic northeast Pacific Ocean. Sinking fluxes of particulate organic carbon (POC) and indicator pigments were calculated from ²³⁴Th–²³⁸U disequilibria and, during two cruises, measured by sediment trap at Ocean Station Papa. POC fluxes at 100 m ranged from 0.65–7.95 mmol m⁻² d⁻¹, similar in magnitude to previous results at Line P. Microplankton pigments dominate indicator pigment …

Comparison Of Survival Patterns Of Northern And Southern Genotypes Of The North American Tick Ixodes Scapularis (Acari: Ixodidae) Under Northern And Southern Conditions, Howard S. Ginsberg, Eric L. Rulison, Alexandra Azevedo, Genevieve C. Pang, Isis M. Kuczaj, Jean I. Tsao, Roger A. Lebrun

Plant Sciences and Entomology Faculty Publications

Background: Several investigators have reported genetic differences between northern and southern populations of Ixodes scapularis in North America, as well as differences in patterns of disease transmission. Ecological and behavioral correlates of these genetic differences, which might have implications for disease transmission, have not been reported. We compared survival of northern with that of southern genotypes under both northern and southern environmental conditions in laboratory trials.

Methods: Subadult I. scapularis from laboratory colonies that originated from adults collected from deer from several sites in the northeastern, north central, and southern U.S. were exposed to controlled conditions in environmental …

Diurnal Variability Of Persistent Organic Pollutants In The Atmosphere Over The Remote Southern Atlantic Ocean, Rosalinda Gioia, Matthew Macleod, Javier Castro-Jiménez, Luca Nizzetto, Jordi Dachs, Rainer Lohmann, Kevin C. Jones

Graduate School of Oceanography Faculty Publications

A diel (24-h) cycle with daytime atmospheric concentrations higher than nighttime concentrations by a factor of 1.5–3 was observed for several low molecular weight polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) in remote areas of the tropical South Atlantic during a cruise in October–November 2005. In contrast, high molecular weight PCBs and PAHs did not display diurnal variability. A model which has successfully explained diel variability of persistent organic pollutants (POPs) over land could not reproduce the observed diel cycle by considering variability in temperature, atmospheric OH radical concentrations, atmospheric boundary layer height and wind speed as causal factors. …

Serials Solutions Click-Through Statistics By Provider And Database 2013-2014, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics on the total number of database and journal-level clicks, by provider and database, of Serials Solutions tools at the University of Rhode Island Libraries by month for 2013-2014. Clicks may have originated from the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/), from OpenURL links ("360 Link"), or the 856 fields of Serials Solutions-generated MARC records ("360 MARC Updates").

Serials Solutions 360 Link Referring Sources Report 2013-2014, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics for 2013-2014 on the number of OpenURL requests made to the "Serials Solutions 360 Link" OpenURL link resolver (at http://zu4tq4pb5v.search.serialssolutions.com/) for items held by the University of Rhode Island Libraries.

Information provided includes Referring Source ID, total Number of Requests for the year, and %Total (Number of Requests).

Note: "36520" = EBSCOhost

Serials Solutions Subject Search Report 2013-2014, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics on the total number of Serials Solutions subject searches at the University of Rhode Island Libraries by month for 2013-2014. Shows how many times the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/) was browsed by specific subjects.

Transcriptome Of American Oysters, Crassostrea Virginica, In Response To Bacterial Challenge: Insights Into Potential Mechanisms Of Disease Resistance, Ian C. Mcdowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gomez-Chiarri

Biological Sciences Faculty Publications

The American oyster Crassostrea virginica, an ecologically and economically important estuarine organism, can suffer high mortalities in areas in the Northeast United States due to Roseovarius Oyster Disease (ROD), caused by the gram-negative bacterial pathogen Roseovarius crassostreae. The goals of this research were to provide insights into: 1) the responses of American oysters to R. crassostreae, and 2) potential mechanisms of resistance or susceptibility to ROD. The responses of oysters to bacterial challenge were characterized by exposing oysters from ROD-resistant and susceptible families to R. crassostreae, followed by high-throughput sequencing of cDNA samples from various timepoints after …

Targeting Breast Tumors With Ph (Low) Insertion Peptides, Ramona Cosmina Adochite, Anna Moshnikova, Sean D. Carlin, Renato A. Guerrieri, Oleg A. Andreev, Jason S. Lewis, Yana K. Reshetnyak

Physics Faculty Publications

Extracellular acidity is associated with tumor progression. Elevated glycolysis and acidosis promote the appearance of aggressive malignant cells with enhanced multidrug resistance. Thus, targeting of tumor acidity can open new avenues in diagnosis and treatment of aggressive tumors and targeting metastatic cancers cells within a tumor. pH (low) insertion peptides (pHLIPs) belong to the class of pH-sensitive agents capable of delivering imaging and/or therapeutic agents to cancer cells within tumors. Here, we investigated targeting of highly metastatic 4T1 mammary tumors and spontaneous breast tumors in FVB/N-Tg (MMTV-PyMT)634Mul transgenic mice with three fluorescently labeled pHLIP variants including well-characterized WT-pHLIP and, recently …