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Slow Swimming, Fast Strikes: Effects Of Feeding Behavior On Scaling Of Anaerobic Metabolism In Epipelagic Squid, Lloyd A. Trueblood, Brad A. Seibel

Biological Sciences Faculty Publications

Many pelagic fishes engage prey at high speeds supported by high metabolic rates and anaerobic metabolic capacity. Epipelagic squids are reported to have among the highest metabolic rates in the oceans as a result of demanding foraging strategies and the use of jet propulsion, which is inherently inefficient. This study examined enzymatic proxies of anaerobic metabolism in two species of pelagic squid, Dosidicus gigas and Doryteuthis pealeii (Lesueur 1821), over a size range of six orders of magnitude. We hypothesized that activity of the anaerobically poised enzymes would be high and increase with size as in ecologically similar fishes. In …

Partial Pathogen Protection By Tick-Bite Sensitization And Epitope Recognition In Peptide-Immunized Hla Dr3 Transgenic Mice, Wendy M. C. Shattuck, Megan C. Dyer, Joe Desrosiers, Loren D. Fast, Frances E. Terry, William D. Martin, Leonard Moise, Anne S. De Groot, Thomas N. Mather

Institute for Immunology and Informatics Faculty Publications

Ticks are notorious vectors of disease for humans, and many species of ticks transmit multiple pathogens, sometimes in the same tick bite. Accordingly, a broad-spectrum vaccine that targets vector ticks and pathogen transmission at the tick/host interface, rather than multiple vaccines against every possible tickborne pathogen, could become an important tool for resolving an emerging public health crisis. The concept for such a tick protective vaccine comes from observations of an acquired tick resistance (ATR) that can develop in non-natural hosts of ticks following sensitization to tick salivary components. Mice are commonly used as models to study immune responses to …

Human Leptospirosis In The Federated States Of Micronesia: A Hospital-Based Febrile Illness Survey, Susannah Colt, Boris I. Pavlin, Jacob L. Kool, Eliaser Johnson, Judith P. Mccool, Alistair J. Woodward

Cell and Molecular Biology Faculty Publications

Background: Human leptospirosis is an emerging infectious disease of global significance, and is endemic to several countries in the Pacific. Zoonotic transmission dynamics combined with diagnostic challenges lead to difficulties in prevention and identification of cases. The Federated States of Micronesia (FSM) lacks surveillance data for human leptospirosis. This hospital-based serologic survey sought to estimate the burden of leptospirosis, collect information relating to associated factors, and assess the leptospirosis point-of-care rapid diagnostic test (RDT) commonly used in FSM. Methods: A four-month hospital-based survey was conducted in Pohnpei State, FSM in 2011. Patients with undifferentiated fevers presenting to hospital …

Post Eruption Inflation Of The East Pacific Rise At 9°50′ N, Scott L. Nooner, Spahr C. Webb, W. Roger Buck, Marie-Helene Cormier

Graduate School of Oceanography Faculty Publications

In June 2008, we installed a geodetic network at 9°50′ N on the East Pacific Rise to track the long‐term movement of magma following the 2005/6 eruption. This network consists of 10 concrete benchmarks stretching from the ridge to 9 km off‐axis. During three campaign‐style surveys, measurements of vertical seafloor motions were made at each of these benchmarks by precisely recording ambient seawater pressure as a proxy for seafloor depth with a mobile pressure recorder (MPR). The MPR was deployed using the manned submersible Alvin in 2008 and 2009 and the remotely operated vehicle Jason in 2011. The MPR observations …

Long-Term Variability Of Sea Surface Temperature In Taiwan Strait, Igor M. Belkin, Ming-An Lee

Graduate School of Oceanography Faculty Publications

Long-term variability of sea surface temperature (SST) in the Taiwan Strait was studied from the U.K. Met Office Hadley Centre climatological data set HadISST1. In 1957–2011, three epochs were identified. The first epoch of cooling SST lasted through 1976. The regime shift of 1976–1977 led to an extremely rapid warming of 2.1 °C in 22 years. Another regime shift occurred in 1998–1999, resulting in a 1.0 °C cooling by 2011. The cross-frontal gradient between the China Coastal Current and offshore Taiwan Strait waters has abruptly decreased in 1992 and remained low through 2011. The long-term warming of SST increased towards …

Determination Of In Situ Dissolved Inorganic Carbon Concentration And Alkalinity For Marine Sedimentary Porewater, Justine Sauvage, Arthur J. Spivack, Richard W. Murray, Steven D'Hondt

Graduate School of Oceanography Faculty Publications

Dissolved inorganic carbon (DIC) concentration and total alkalinity in marine sediment vary with biological activity, mineral diagenesis and past bottom ocean water composition. Reliable interpretation of this data is often compromised due to precipitation of calcium carbonate (CaCO₃) during sediment recovery, processing and sample storage.

Here we present and test a method that corrects for this precipitation and consequently allows quantification of in situ carbonate system chemistry. Our method relies on the over-determination of the dissolved carbonate system by (i) measuring DIC, alkalinity and calcium, and (ii) explicitly assuming CaCO₃ saturation in the sediment. We experimentally tested …

Targeted Search For Actinomycetes From Nearshore And Deep-Sea Marine Sediments, Alejandra Prieto-Davó, Luis J. Villarreal-Gómez, Stephanie Forschner-Dancause, Alan T. Bull, James E.M. Stach, David C. Smith, David C. Rowley, Paul R. Jensen

Graduate School of Oceanography Faculty Publications

Sediment samples collected off the coast of San Diego were analyzed for actinomycete diversity using culture-independent techniques. Eight new operational taxonomic units (OTUs) in the Streptomycetaceae were identified as well as new diversity within previously cultured marine OTUs. Sequences belonging to the marine actinomycete genus Salinispora were also detected, despite the fact that this genus has only been reported from more tropical environments. Independent analyses of marine sediments from the Canary Basin (3814 m) and the South Pacific Gyre (5126 and 5699 m) also revealed Salinispora sequences providing further support for the occurrence of this genus in deep-sea sediments. Efforts …

Does Proximity To Wetland Shrubland Increase The Habitat Value For Shrubland Birds Of Small Patches Of Upland Shrubland In The Northeastern United States?, Bill Buffum, Richard A. Mckinney

Natural Resources Science Faculty Publications

The loss of shrubland habitat is linked to population declines for many wildlife species, including several bird species of conservation concern. Conservation agencies in the northeastern United States encourage private landowners to clearcut patches of forest to create shrubland habitat. Many private landowners are only willing to create small clearcuts; therefore, it is important to understand how to maximize the impact of small clearcuts on bird habitat use. In this study we examined whether proximity to wetland shrubland increases the habitat value of small patches of upland shrubland. We conducted point counts at 22 sites containing small patches of upland …

Sensory Basis For Detection Of Benthic Prey In Two Lake Malawi Cichlids., Margot A. B. Schwalbe, Jacqueline F. Webb

Biological Sciences Faculty Publications

The adaptive radiations of African cichlids resulted in a diversity of feeding morphologies and strategies, but the role of sensory biology in prey detection and feeding ecology remains largely unexplored. Two endemic Lake Malawi cichlid genera, Tramitichromis and Aulonocara, feed on benthic invertebrates, but differ in lateral line morphology (narrow and widened lateral line canals, respectively) and foraging strategy. The hypothesis that they use their lateral line systems differently was tested by looking at the relative contribution of the lateral line system and vision in prey detection by Tramitichromis sp. and comparing results to those from a complementary study using …

Graduate Council Report No. 2013-2014-3, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Do Tregitopes Have The Potential To Impact The Current Treatment Landscape Of Autoimmune Diseases?, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Current treatment of autoimmune disease usually involves the use of cytotoxic drugs or biologic agents that interfere with the activity of B cells, T cells or key cytokines, such as TNF, IL-1 and IL-6. On occasion, polyclonal immunoglobulin G (IgG), intravenous (IVIg) is used. The discovery of IgG- (and hence IVIg-) derived T regulatory (Treg) epitopes that trigger the expansion of Tregs in vitro and in vivo provides a novel explanation for the effect of IVIg. These IgG-derived Treg epitopes (also known as Tregitopes) appear to be effective on their own (in vivo, in autoimmune disease models) and when co-administered …

Chromatin-Induced Spindle Assembly Plays An Important Role In Metaphase Congression Of Silkworm Holocentric Chromosomes, Hiroaki Mon, Jae Man Lee, Kazuei Mita, Marian R. Goldsmith, Takahiro Kusakabe

Biological Sciences Faculty Publications

The kinetochore plays important roles in cell cycle progression. Interactions between 4 chromosomes and spindle microtubules allow chromosomes to congress to the middle of the 5 cell and to segregate the sister chromatids into daughter cells in mitosis. The chromosome 6 passenger complex (CPC), composed of the Aurora B kinase and its regulatory subunits 7 INCENP, Survivin, and Borealin, plays multiple roles in these chromosomal events. In the 8 genome of the silkworm, Bombyx mori, which has holocentric chromosomes, the CPC 9 components and their molecular interactions were highly conserved. In contrast to 10 monocentric species, however, the silkworm CPC …

Failure Under Stress: The Effect Of The Exotic Herbivore Adelges Tsugae On Biomechanics Of Tsuga Canadensis, Nicole E. Soltis, Sara Gomez, Gary G. Leisk, Patrick Sherwood, Evan L. Preisser, Pierluigi Bonello, Colin M. Orians

Biological Sciences Faculty Publications

Background and Aims Exotic herbivores that lack a coevolutionary history with their host plants can benefit from poorly adapted host defences, potentially leading to rapid population growth of the herbivore and severe damage to its plant hosts. The hemlock woolly adelgid (Adelges tsugae) is an exotic hemipteran that feeds on the long-lived conifer eastern hemlock (Tsuga canadensis), causing rapid mortality of infested trees. While the mechanism of this mortality is unknown, evidence indicates that A. tsugae feeding causes a hypersensitive response and alters wood anatomy. This study investigated the effect of A. tsugae feeding on biomechanical …

Ph Dependent Transfer Of Nano-Pores Into Membrane Of Cancer Cells To Induce Apoptosis, Dayanjali Wijesinghe, Mohan C. M. Arachchige, Andrew Lu, Yana K. Reshetnyak, Oleg A. Andreev

Physics Faculty Publications

Proper balance of ions in intracellular and extracellular space is the key for normal cell functioning. Changes in the conductance of membranes for ions will lead to cell death. One of the main differences between normal and cancerous cells is the low extracellular pH_e and the reverse pH gradient: intracellular pH_i is higher than extracellular pH_e. We report here pH-selective transfer of nano-pores to cancer cells for the dis-regulation of balance of monovalent cations to induce cell death at mildly acidic pH_e as it is in most solid tumors. Our approach is based on the …

Analysis Of Energy Flow In Us Globec Ecosystems Using End-To-End Models, James J. Ruzicka, John H. Steele, Sarah K. Gaichas, Tosca Ballerini, Dian J. Gifford, Richard D. Brodeur, Eileen E. Hofmann

Graduate School of Oceanography Faculty Publications

End-to-end models were constructed to examine and compare the trophic structure and energy flow in coastal shelf ecosystems of four US Global Ocean Ecosystem Dynamics (GLOBEC) study regions: the Northern California Current, the Central Gulf of Alaska, Georges Bank, and the Southwestern Antarctic Peninsula. High-quality data collected on system components and processes over the life of the program were used as input to the models. Although the US GLOBEC program was species-centric, focused on the study of a selected set of target species of ecological or economic importance, we took a broader community-level approach to describe end-to-end energy flow, from …

Characterization Of Plp, A Phosphatidylcholine-Specific Phospholipase And Hemolysin Of Vibrio Anguillarum, Ling Li, Xiangyu Mou, David R. Nelson

Cell and Molecular Biology Faculty Publications

Background: Vibrio anguillarum is the causative agent of vibriosis in fish. Several extracellular proteins secreted by V. anguillarum have been shown to contribute to virulence. While two hemolysin gene clusters, vah1-plp and rtxACHBDE, have been previously identified and described, the activities of the protein encoded by the plp gene were not known. Here we describe the biochemical activities of the plp-encoded protein and its role in pathogenesis.

Results: The plp gene, one of the components in vah1 cluster, encodes a 416-amino-acid protein (Plp), which has homology to lipolytic enzymes containing the catalytic site amino acid signature SGNH. Hemolytic …

Conservation In The Context Of Climate Change: Practical Guidelines For Land Protection At Local Scales, Kevin Ruddock, Peter V. August, Christopher Damon, Charles Labash, Pamela Rubinoff, Donald Robadue Jr.

Natural Resources Science Faculty Publications

Climate change will affect the composition of plant and animal communities in many habitats and geographic settings. This presents a dilemma for conservation programs – will the portfolio of protected lands we now have achieve a goal of conserving biodiversity in the future when the ecological communities occurring within them change? Climate change will significantly alter many plant communities, but the geophysical underpinnings of these landscapes, such as landform, elevation, soil, and geological properties, will largely remain the same. Studies show that extant landscapes with a diversity of geophysical characteristics support diverse plant and animal communities. Therefore, geophysically diverse landscapes …

Coordinate Nuclear Targeting Of The Fancd2 And Fanci Proteins Via A Fancd2 Nuclear Localization Signal, Rebecca A. Boisvert, Meghan A. Rego, Paul A. Azzinaro, Maurizio Mauro, Niall G. Howlett

Cell and Molecular Biology Faculty Publications

Fanconi anemia (FA) is a rare recessive disease, characterized by congenital defects, bone marrow failure, and increased cancer susceptibility. FA is caused by biallelic mutation of any one of sixteen genes. The protein products of these genes function cooperatively in the FA-BRCA pathway to repair DNA interstrand crosslinks (ICLs). A central step in the activation of this pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Monoubiquitinated FANCD2 and FANCI localize to discrete chromatin regions where they function in ICL repair. Despite their critical role in ICL repair, very little is known about the structure, function, and regulation of …

Concentrations, Fluxes And Residence Time Of Pbdes Across The Tropical Atlantic Ocean, Rainer Lohmann, Jana Klanova, Petr Kukucka, Shifra Yonis, Kevyn Bollinger

Graduate School of Oceanography Faculty Publications

Little is known about the fate of polybrominated diphenylethers (PBDEs) across the Oceans. Air and water were sampled using both active and passive polyethylene samplers on an east-west transect across the tropical Atlantic Ocean in 2009 and analyzed for PBDEs. Typical particle-bound concentrations of PBDEs in the surface water were low, atL(-1). Truly dissolved concentrations from passive samplers were ∼0.5 pg L(-1) for BDE 47 and around 0.1 pg L(-1) for BDEs 28, 99, and 100 (results from active samples were compromised). In the atmosphere, particle-bound BDE 209 dominated overall concentrations (median 1.2 pg m(-3)), followed by BDE 99 (0.13 …

Field Calibration Of Low Density Polyethylene Passive Samplers For Gaseous Pops, Mohammed A. Khairy, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

A field calibration study of low density polyethylene (LDPE) for measuring atmospheric concentrations of persistent organic pollutants (POPs) was performed in East Providence (RI), USA. LDPE samplers were collected after 3, 7, 10, 14, 17 and 21 days of exposure along with samples from a co-deployed high volume sampler. Uptake kinetics of POPs by LDPEs were confirmed both by using an uptake study over time and the inclusion of performance reference compounds (PRCs). Results indicated that only POPs with log sampler-air partitioning coefficient (K_PE-A) ≤ 7.6 were approaching equilibrium by the end of the deployment period, whereas all the …

Establishment Of The Coast Range Ophiolite Microbial Observatory (Cromo): Drilling Objectives And Preliminary Outcomes, Dawn Cardace, T. Hoehler, T. Mccollom, M. Schrenk, D. Carnevale, M. Kubo, K. Twing

Geosciences Faculty Publications

This project aimed to establish a subsurface microbial observatory in ultramafic rocks, by drilling into an actively serpentinizing peridotite body, characterizing cored rocks, and outfitting the boreholes for a program of long-term observation and experimentation to resolve the serpentinite-hosted subsurface biosphere. We completed drilling in August 2011, drilling two boreholes with core recovery and possibility for down-hole experimentation, and six smaller-diameter monitoring wells arrayed around the two primary holes, in the Coast Range ophiolite (CRO) locality in the UC-Davis McLaughlin Natural Reserve, Lower Lake, CA. Every effort was made during drilling to keep the cores and wells as free of …

Keap1-Knockdown Decreases Fasting-Induced Fatty Liver Via Altered Lipid Metabolism And Decreased Fatty Acid Mobilization From Adipose Tissue, Jialin Xu, Ajay C. Donepudi, Jamie E. Moscovitz, Angela Slitt

Biomedical and Pharmaceutical Sciences Faculty Publications

Aims: The purpose of this study was to determine whether Nrf2 activation, via Keap1-knockdown (Keap1-KD), regulates lipid metabolism and mobilization induced by food deprivation (e.g. fasting).

Methods and Results: Male C57BL/6 (WT) and Keap1-KD mice were either fed ad libitum or food deprived for 24 hours. After fasting, WT mice exhibited a marked increase in hepatic lipid accumulation, but Keap1-KD mice had an attenuated increase of lipid accumulation, along with reduced expression of lipogenic genes (acetyl-coA carboxylase, stearoyl-CoA desaturase-1, and fatty acid synthase) and reduced expression of genes related to fatty acid transport, such as fatty acid translocase/CD36 …

No-Boundary Thinking In Bioinformatics Research, Xiuzhen Huang, Barry Bruce, Alison Buchan, Clare Bates Congdon, Carole L. Cramer, Steven F. Jennings, Hongmei Jiang, Zenglu Li, Gail Mcclure, Rick Mcmullen, Jason H. Moore, Bindu Nanduri, Joan Peckham, Andy Perkins, Shawn W. Polson, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Donald Wunsch, Donghai Xiong, Shuzhong Zhang, Zhongming Zhao

Computer Science and Statistics Faculty Publications

Currently there are definitions from many agencies and research societies defining “bioinformatics” as deriving knowledge from computational analysis of large volumes of biological and biomedical data. Should this be the bioinformatics research focus? We will discuss this issue in this review article. We would like to promote the idea of supporting human-infrastructure (HI) with no-boundary thinking (NT) in bioinformatics (HINT).

Spatially Explicit Model Of Wintering Common Loons: Conservation Implications, Kristopher J. Winiarski, David L. Miller, Peter W. C. Patton, Scott R. Mcwilliams

Natural Resources Science Faculty Publications

Common loons Gavia immer are a conservation concern in New England due to a variety of anthropogenic factors, yet little is known about biotic and abiotic environmental factors determining their wintering distribution and abundance in nearshore and offshore waters. The primary objective of this study was to develop a spatially explicit abundance model of wintering common loons in the maritime waters of southern New England (USA) that could inform decisions about offshore development. Aerial line-transect surveys were conducted throughout a 3800 km² study area off the coast of Rhode Island during the winters of 2010–2011 and 2011–2012. A density …

Peptide-Amphiphile Containing Arginine And Fatty Acyl Chains As Molecular Transporters, Amir Nasrolahi Shirazi, Donghoon Oh, Rakesh Kumar Tiwari, Brian Sullivan, Anju Gupta, Geoffrey D. Bothun, Keykavous Parang

Biomedical and Pharmaceutical Sciences Faculty Publications

Peptide amphiphiles (PAs) are promising tools for the intracellular delivery of numerous drugs. PAs are known to be biodegradable systems. Here, four PA derivatives containing arginine and lysine conjugated with fatty acyl groups with different chain length, namely PA1: R-K(C₁₄)-R, PA2: R-K(C₁₆)-R, PA3: K(C₁₄)-R-K(C₁₄), and PA4: K(C₁₆)-R-K(C₁₆), where C₁₆ = palmitic acid and C₁₄ = myristic acid, were synthesized through Fmoc chemistry. Flow cytometry studies showed that among all synthesized PAs, only K(C₁₆)-R-K(C₁₆), PA4 was able to enhance the cellular uptake of …

Feasibility Of Using Low Density Polyethylene Sheets To Detect Atmospheric Organochlorine Pesticides In Alexandria, Egypt, Mohammed A. Khairy, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

Egypt is a major agricultural country in Africa with a known past of organochlorine pesticides (OCPs) application, yet data on atmospheric levels of OCPs in Egypt is sparse. Low density polyethylene (LDPE) passive samplers were therefore deployed for 3 weeks each at 11 locations in July, 2010 and January, 2011 in Alexandria to screen for gas-phase OCPs. Performance reference compounds were used to investigate the uptake kinetics. Field-derived sampler-air partitioning coefficients (K_PE-As) for OCPs were significantly correlated against the compounds' subcooled liquid vapor pressure (log P_L): [log K_PE-A = −0.77 ± 0.07*log P_{L …}

Thalassiosira Spp. Community Composition Shifts In Response To Chemical And Physical Forcing In The Northeast Pacific Ocean, P. Dreux Chappell, Leann P. Whitney, Traci L. Haddock, Susanne Menden-Deuer, Eric G. Roy, Mark L. Wells, Bethany D. Jenkins

Cell and Molecular Biology Faculty Publications

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., …

Curricular Affairs Committee Report #507, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Immunization With Cross-Conserved H1n1 Influenza Cd4+ T-Cell Epitopes Lowers Viral Burden In Hla Dr3 Transgenic Mice, Leonard Moise, Ryan Tassone, Howard Latimer, Frances Terry, Lauren Levitz, John P. Haran, Ted M. Ross, Christine Boyle, William D. Martin, Anne S. De Groot

Cell and Molecular Biology Faculty Publications

The emergence of the pandemic H1N1 strain of influenza in 2009 was associated with a unique w-shaped age-related susceptibility curve, with higher incidence of morbidity and mortality among young persons and lower incidence among older persons, also observed during the 1918 influenza pandemic. Pre-existing H1N1 antibodies were not cross-reactive with the prior seasonal vaccine, forcing influenza experts to scramble to develop a new vaccine specific for the pandemic virus. We hypothesized that response to T-cell epitopes that are cross-conserved between pandemic H1N1 and the 2008 seasonal influenza vaccine strains might have contributed to partial protection from clinical illness among older …

Nanopore Surface Coating Delivers Nanopore Size And Shape Through Conductance-Based Sizing, Cameron M. Frament, Y. M. Nuwan D.Y. Bandara, Jason R. Dwyer

Chemistry Faculty Publications

The performance of nanopore single-molecule sensing elements depends intimately on their physical dimensions and surface chemical properties. These factors underpin the dependence of the nanopore ionic conductance on electrolyte concentration, yet the measured, or modeled, dependence only partially illuminates the details of geometry and surface chemistry. Using the electrolyte-dependent conductance data before and after selective surface functionalization of solid-state nanopores, however, introduces more degrees of freedom and improves the performance of conductance-based nanopore characterizations. Sets of representative nanopore profiles were used to generate conductance data, and the nanopore shape and exact dimensions were identified, through conductance alone, by orders-of-magnitude 3 …