Digital Commons Network^™

A Marine Autonomous Surface Craft For Long-Duration, Spatially Explicit, Multidisciplinary Water Column Sampling In Coastal And Estuarine Systems, Daniel L. Codiga

Graduate School of Oceanography Faculty Publications

The Surveying Coastal Ocean Autonomous Profiler (SCOAP) is a large catamaran marine autonomous surface craft (MASC) for unattended weeks-long, spatially explicit, multidisciplinary oceanographic water column profile sampling in coastal/estuarine waterbodies. Material transport rates/pathways, crucial to understanding these ecosystems, are typically poorly known. SCOAP addresses demanding spatiotemporal sampling needs and operational challenges (strong currents, open coastal sea states, complex bathymetry, heavy vessel traffic). Its large size (11-m length, 5-m beam) provides seaworthiness/stability. The average speed of 2.5 m s⁻¹ meets the representative goal to traverse an 18-km transect, sampling 10 min at each of 10 stations 2 km apart, nominally …

The Effect Of Light Intensity On Prey Detection Behavior In Two Lake Malawi Cichlids, Aulonocara Stuartgranti And Tramitichromis Sp., Margot A.B. Schwalbe, Jacqueline F. Webb

Biological Sciences Faculty Publications

Two sand-dwelling cichlids from Lake Malawi (Aulonocara stuartgranti, Tramitichromis sp.) that feed on benthic invertebrates, but have different lateral line phenotypes, use lateral line and/or visual cues to detect prey under light versus dark conditions. The current study examined how ecologically relevant variation in light intensity [0–800 lux (lx)] influences detection of prey (mobile, immobile) in each species by analyzing six behavioral parameters. Both species fed at light intensities ≥1 lx and trends in behavior among light intensities were informative. However, prey type and/or time of day (but not light intensity) predicted all four parameters analyzed with generalized …

2015-02 Library Impact Statement For Bch/Mic 421 Physical Chemistry For The Life Sciences, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for BCH/MIC 421 Physical Chemistry for the Life Sciences. This class was supported with no need for additional resources. Responding library faculty: Michael Cerbo. Requesting faculty: Lenore M. Martin.

Electromagnetically Inspired Approaches In Biomaterials And Drug Delivery, Stephen Kennedy

Amgen Seminar Series in Chemical Engineering

The ability to spatially and temporally regulate the delivery of therapeutic biomolecules in vivo is pervasively desired in contemporary and emerging biotechnological and therapeutic contexts. That is, because biology varies greatly in space and time, the medical community requires biomaterials and biosystems that can communicate/direct biology with a high degree of spatial and temporal precision. The ability to regulate the timing, dose, and directionality of multiple biomolecules is particularly desirable in the realm of tissue engineering, where the engineering/repair of functional tissues requires a highly choreographed sequence of localized biomolecular presentations. Here, I will describe works in progress towards the …

Out Of The Dark: Transitional Subsurface-To-Surface Microbial Diversity In A Terrestrial Serpentinizing Seep (Manleluag, Pangasinan, The Philippines), Kristin M. Woycheese, D'Arcy R. Meyer-Dombard, Dawn Cardace, Anacleto M. Argayosa, Carlo A. Arcilla

Geosciences Faculty Publications

In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca²⁺-OH⁻-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO₂) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the …

2015-02 Library Impact Statement For Cmb 320 Introduction To Computational Biology, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for CMB 320 Introduction to Computational Biology. This class was supported with no need for additional resources. Responding library faculty member: Michael Cerbo. Requesting faculty member: Ying Zhang.

2015-02 Library Impact Statement For Nrs 543 Public Engagement With Science, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for NRS 543 Public Engagement with Science. This class was supported with no need for additional resources. Responding library faculty member: Michael Cerbo. Requesting faculty member: Caroline Gottschalk Druschke.

Radiative Energy And Momentum Transfer For Various Spherical Shapes: A Single Sphere, A Bubble, A Spherical Shell And A Coated Sphere, Yi Zheng, Alok Ghanekar

Mechanical, Industrial & Systems Engineering Faculty Publications

We use fluctuational electrodynamics to determine spectral emissivity and van der Waals contribution to surface energy for various spherical shapes, such as a sphere, a bubble, a spherical shell, and a coated sphere, in a homogeneous and isotropic medium. The dyadic Green's function formalism of radiative energy and fluctuation-induced van der Waals stress for different spherical configurations has been developed. We show (1) emission spectra of micro- and nano-sized single and coated spheres display several emissivity sharp peaks as the size of object reduces and (2) surface energy becomes size dependent due to van der Waals phenomena when size of …

Feasible Metabolisms In High Ph Springs Of The Philippines, Dawn Cardace, D'Arcy R. Meyer-Dombard, Kristin M. Woycheese, Carlo A. Arcilla

Geosciences Faculty Publications

A field campaign targeting high pH, H₂-, and CH₄-emitting serpentinite-associated springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to rank feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these …

Herbivore Impacts On Two Morphologically Similar Bloom-Forming Ulva Species In A Eutrophic Bay, Michele Guidone, Carol S. Thornber, Kathryn L. Van Alstyne

Biological Sciences Faculty Publications

Herbivore impacts on macrophyte growth vary with the identity of the herbivores and macrophytes, as well as under different abiotic conditions. This interaction is further complicated by anthropogenic alterations to the environment, such as eutrophication. In this study, we utilized in situ herbivore exclusion experiments and mesocosm feeding preference assays to examine the impacts of different herbivores on the growth of two morphologically similar, co-occurring macroalgal bloom Ulva species in a nutrient-rich environment. We found that herbivory had a measurable impact on Ulva biomass, though the rate of consumption rarely surpassed growth for either Ulva species. We determined that the …

Big Data - A 21st Century Science Maginot Line? No-Boundary Thinking: Shifting From The Big Data Paradigm, Xiuzhen Huang, Steven F. Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L. Cramer, Weihua Guan, Uwe K.K. Hilgert, Hongmei Jiang, Zenglu Li, Gail Mcclure, Donald F. Mcmullen, Bindu Nanduri, Andy Perkins, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Karl Walker, Donald Wunsch, Donghai Xiong, Shuzhong Zhang, Yu Zhang, Zhongming Zhao, Jason H. Moore

Graduate School of Oceanography Faculty Publications

Whether your interests lie in scientific arenas, the corporate world, or in government, you have certainly heard the praises of big data: Big data will give you new insights, allow you to become more efficient, and/or will solve your problems. While big data has had some outstanding successes, many are now beginning to see that it is not the Silver Bullet that it has been touted to be. Here our main concern is the overall impact of big data; the current manifestation of big data is constructing a Maginot Line in science in the 21st century. Big data is not …

The Secreted Proteins Of Achlya Hypogyna And Thraustotheca Clavata Identify The Ancestral Oomycete Secretome And Reveal Gene Acquisitions By Horizontal Gene Transfer, Ian Misner, Nic Blouin, Guy Leonard, Thomas A. Richards, Christopher E. Lane

Biological Sciences Faculty Publications

Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the “secretome” and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here,we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the …

Study Protocol For Young & Strong: A Cluster Randomized Design To Increase Attention To Unique Issues Faced By Young Women With Newly Diagnosed Breast Cancer, Mary L. Greaney, Kim Sprunck-Harrild, Kathryn J. Ruddy, Jennifer Ligibel, William T. Barry, Emily Baker, Meghan Meyer, Karen M. Emmons, Ann H. Partridge

Kinesiology Faculty Publications

Background: Each year, approximately 11% of women diagnosed with breast cancer in the United States are 45 years of age or younger. These women have concerns specific to or accentuated by their age, including fertility-related concerns, and have higher rates of psychosocial distress than women diagnosed at older ages. Current guidelines recommend that fertility risks be considered early in all treatment plans; however, the extant research indicates that attention to fertility by the healthcare team is limited. Importantly, attention to fertility may be a proxy for whether or not other important issues warranting attention in younger women with breast cancer …

2015-01 Library Impact Statement For Avs/Pls 275 Pasture And Grazing Management In Sustainable Agriculture, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for AVS/PLS 275 Pasture and Grazing Management in Sustainable Agriculture. This course was supported with no need for additional resources.

2015-01 Library Impact Statement For Pls 395 Agroecology And Food Systems: Global Experiences, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for PLS 395 Agroecology and Food Systems: Global Experiences. This course was supported with no need for additional resources.

Testing Sample Stability Using Four Storage Methods And The Macroalgae Ulva And Gracilaria, Autumn Oczkowski, Carol S. Thornber, Erin E. Markham, Ryann Rossi, Amanda Ziegler, Shelby Rinehart

Biological Sciences Faculty Publications

Concern over the relative importance of different sample preparation and storage techniques frequently used in stable isotope analysis of particulate nitrogen (δ¹⁵N) and carbon (δ¹³C) prompted an experiment to determine how important such factors were to measured values in marine organisms. We stored the marine macroalgae Ulva and Gracilaria in four different ways and analyzed replicates every three months over the course of a year to assess treatment effects on stability. Treatments consisted of algae dried at 65°C, ground to a powder, and stored in a desiccator until analysis; algae left in a drying oven or …

Coil-Helix Transition Of Polypeptide At Water-Lipid Interface, Ganga P. Sharma, Yana Reshetnyak, Oleg A. Andreev, Michael Karbach, Gerhard Müller

Physics Faculty Publications

We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an α-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order …

Manipulation Of Host Quality And Defense By A Plant Virus Improves Performance Of Whitefly Vectors, Qi Su, Evan L. Preisser, Wen Xie, Shao Li Wang, Qin Jun Wu, You Jun Zhang

Biological Sciences Faculty Publications

Pathogen-mediated interactions between insect vectors and their host plants can affect herbivore fitness and the epidemiology of plant diseases. While the role of plant quality and defense in mediating these tripartite interactions has been recognized, there are many ecologically- and economically-important cases where the nature of the interaction has yet to be characterized. The Bemisia tabaci cryptic species MED is an important vector of tomato yellow leaf curl virus (TYLCV), and performs better on virus-infected tomato than on uninfected controls. We assessed the impact of TYLCV infection on plant quality and defense, and the direct impact of TYLCV infection on …

Rapid And Gradual Modes Of Aerosol Trace Metal Dissolution In Seawater, Katherine R.M. Mackey, Chia-Te Chien, Anton F. Post, Mak A. Saito, Adina Paytan

Graduate School of Oceanography Faculty Publications

Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence …

High Ph Microbial Ecosystems In A Newly Discovered, Ephemeral, Serpentinizing Fluid Seep At Yanartaş (Chimera), Turkey, D'Arcy R. Meyer-Dombard, Kristin M. Woycheese, Erin N. Yargıçoğlu, Dawn Cardace, Yasemin Güleçal-Pektas, Mustafa Temel

Geosciences Faculty Publications

Gas seeps emanating from Yanartaş (Chimera), Turkey, have been documented for thousands of years. Active serpentinization produces hydrogen and a range of carbon gases that may provide fuel for life. Here we report a newly discovered, ephemeral fluid seep emanating from a small gas vent at Yanartaş. Fluids and biofilms were sampled at the source and points downstream. We describe site conditions, and provide microbiological data in the form of enrichment cultures, Scanning electron microscopy (SEM), carbon and nitrogen isotopic composition of solids, and PCR screens of nitrogen cycle genes. Source fluids are pH 11.95, with a Ca:Mg of ~200, …

2015-01 Library Impact Statement For Mic 420 Introduction To Biological Data Integration, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for MIC 240 Introduction to BIological Data Integration. Additional resources were purchased to support this course. Responding library faculty member: Michael Cerbo. Requesting faculty member: Ying Zhang.

Collagen Gel Formation In The Presence Of A Carbon Nanobrush, George W. Dombi, Kaushalkumar Purohit, Lenore M. Martin, Sze C. Yang

Chemistry Faculty Publications

Type I, bovine skin collagen was allowed to gel in the presence of various concentrations of a carbon nanotube material covered with a polystyrene/polyaniline copolymer, called a carbon nanobrush (CNB). The rate of collagen gelation was enhanced by the presence of the CNB in a dose dependent manner. The extent of collagen gelation was due to the concentration of collagen and not the amount of CNB. Collagen D-periodicity, and average fibril diameter were unchanged by the CNB material as seen in transmission electron micrographs. Gel tensile strength was reduced by the presence of the CNB in a dose related manner. …

Basins Of Attraction For Two-Species Competitive Model With Quadratic Terms And The Singular Allee Effect, A. Brett, M. R.S. Kulenović

Mathematics Faculty Publications

We consider the following system of difference equations: xn+1=xn2/B1xn2+C1yn2, yn+1=yn2/A2+B2xn2+C2yn2, n=0, 1,., where B1, C1, A2, B2, C2 are positive constants and x0, y0≥0 are initial conditions. This system has interesting dynamics and it can have up to seven equilibrium points as well as a singular point at (0,0), which always possesses a basin of attraction. We characterize the basins of attractions of all equilibrium points as well as the singular point at (0,0) and thus describe the global dynamics of this system. Since the singular point at (0,0) always possesses a basin of attraction this system exhibits Allee's effect.

City Slickers: Poor Performance Does Not Deter Anolis Lizards From Using Artificial Substrates In Human‐Modified Habitats, Jason J. Kolbe, Andrew C. Battles, Kevin J. Avilés-Rodríguez

Biological Sciences Faculty Publications

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1. As animals move through their environments, they encounter a variety of substrates, which have important effects on their locomotor performance. Habitat modification can alter the types of substrates available for locomotion. In particular, many types of artificial substrates have been added to urban areas, but effects of these novel surfaces on animal locomotion are little known.
2. In this study, we assessed locomotor performance of two Anolis lizard species (A. cristatellus and A. stratulus) on substrates that varied in inclination and surface roughness. Rough substrates represented the tree trunks and branches typically used in natural forest habitats, whereas …

Division Of Research And Economic Development Monthly Report For February 2015, 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 January 2015, 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 March 2015, 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 December 2015, 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 July 2015, 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 April - June 2015, 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.