Digital Commons Network^™

Location Of Dual Sites In E. Coli Ftsz Important For Degradation By Clpxp; One At The C-Terminus And One In The Disordered Linker, Jodi L. Camberg, Marissa G. Viola, Leslie Rea, Joel R. Hoskins, Sue Wickner

Cell and Molecular Biology Faculty Publications

ClpXP is a two-component ATP-dependent protease that unfolds and degrades proteins bearing specific recognition signals. One substrate degraded by Escherichia coli ClpXP is FtsZ, an essential cell division protein. FtsZ forms polymers that assemble into a large ring-like structure, termed the Z-ring, during cell division at the site of constriction. The FtsZ monomer is composed of an N-terminal polymerization domain, an unstructured linker region and a C-terminal conserved region. To better understand substrate selection by ClpXP, we engineered FtsZ mutant proteins containing amino acid substitutions or deletions near the FtsZ C-terminus. We identified two discrete regions of FtsZ important for …

Who's Talking About (And Citing) Me? Tracking Your Work Using Databases, Google, Web Of Knowledge, And Altmetrics Tools, Amanda Izenstark, Julia Lovett, Andrée Rathemacher

Technical Services Faculty Presentations

Slides and handouts from a presentation, "Who's Talking About (and Citing) Me? Tracking Your Work using Databases, Google, Web of Knowledge, and Altmetrics Tools," offered at the University of Rhode Island Libraries on April 9 and April 10, 2014.

"Stop using the impact factor as a measure of the value of your research. There are better ways. In this hands-on session find out about tools that can help you learn how your work is being received, used, and disseminated across scholarly platforms and social media networks."

Part of the University Libraries' Search Savvy Seminar series.

Transport Of Pathogen Surrogates In Soil Treatment Units: Numerical Modeling, Ivan Morales, Janet A. Atoyan, José A. Amador, Thomas Boving

Civil & Environmental Engineering Faculty Publications

Segmented mesocosms (n = 3) packed with sand, sandy loam or clay loam soil were used to determine the effect of soil texture and depth on transport of two septic tank effluent (STE)-borne microbial pathogen surrogates—green fluorescent protein-labeled E. coli (GFPE) and MS-2 coliphage—in soil treatment units. HYDRUS 2D/3D software was used to model the transport of these microbes from the infiltrative surface. Mesocosms were spiked with GFPE and MS-2 coliphage at 10⁵ cfu/mL STE and 10⁵–10⁶ pfu/mL STE, respectively. In all soils, removal rates were >99.99% at 25 cm. The transport simulation compared (1) …

Review: The Media Ecosystem: What Ecology Can Teach Us About Responsible Media Practice, Ju-Pong Lin

Journal of Media Literacy Education

No abstract provided.

Vibrio Vulnificus Mo6-24/O Lipopolysaccharide Stimulates Superoxide Anion, Thromboxane B2, Matrix Metalloproteinase-9, Cytokine And Chemokine Release By Rat Brain Microglia In Vitro, Alejandro M.S. Mayer, Mary L. Hall, Michael Holland, Cristina De Castro, Antonio Molinaro, Monica Aldulescu, Jeffrey Frenkel, Lauren Ottenhoff, David Rowley, Jan Powell

Biomedical and Pharmaceutical Sciences Faculty Publications

Although human exposure to Gram-negative Vibrio vulnificus (V. vulnificus) lipopolysaccharide (LPS) has been reported to result in septic shock, its impact on the central nervous system’s innate immunity remains undetermined. The purpose of this study was to determine whether V. vulnificus MO6-24/O LPS might activate rat microglia in vitro and stimulate the release of superoxide anion (O₂⁻), a reactive oxygen species known to cause oxidative stress and neuronal injury in vivo. Brain microglia were isolated from neonatal rats, and then treated with either V. vulnificus MO6-24/O LPS or Escherichia coli O26:B6 LPS for 17 …

Profiling Gene Expression To Distinguish The Likely Active Diazotrophs From A Sea Of Genetic Potential In Marine Sediments, S M. Brown, Bethany D. Jenkins

Cell and Molecular Biology Faculty Publications

Nitrogen (N) cycling microbial communities in marine sediments are extremely diverse, and it is unknown whether this diversity reflects extensive functional redundancy. Sedimentary denitrifiers remove significant amounts of N from the coastal ocean and diazotrophs are typically regarded as inconsequential. Recently, N fixation has been shown to be a potentially important source of N in estuarine and continental shelf sediments. Analysis of expressed genes for nitrite reductase (nirS) and a nitrogenase subunit (nifH) was used to identify the likely active denitrifiers and nitrogen fixers in surface sediments from different seasons in Narragansett Bay (Rhode Island, USA). …

Pan-Genome Analyses Identify Lineage- And Niche-Specific Markers Of Evolution And Adaptation In Epsilonproteobacteria, Ying Zhang, Stefan M. Sievert

Cell and Molecular Biology Faculty Publications

The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is …

Using Nocturnal Flight Calls To Assess The Fall Migration Of Warblers And Sparrows Along A Coastal Ecological Barrier, Adam D. Smith, Peter W. C. Paton, Scott R. Mcwilliams

Natural Resources Science Faculty Publications

Atmospheric conditions fundamentally influence the timing, intensity, energetics, and geography of avian migration. While radar is typically used to infer the influence of weather on the magnitude and spatiotemporal patterns of nocturnal bird migration, monitoring the flight calls produced by many bird species during nocturnal migration represents an alternative methodology and provides information regarding the species composition of nocturnal migration. We used nocturnal flight call (NFC) recordings of at least 22 migratory songbirds (14 warbler and 8 sparrow species) during fall migration from eight sites along the mainland and island coasts of Rhode Island to evaluate five hypotheses regarding NFC …

The Effect Of Normally Consumed Amounts Of Sucrose Or High Fructose Corn Syrup On Lipid Profiles, Body Composition And Related Parameters In Overweight/Obese Subjects, Joshua Lowndes, Stephanie Sinnett, Sabrina Pardo, Von T. Nguyen, Kathleen J. Melanson, Zhiping Yu, Britte E. Lowther, James M. Rippe

Nutrition Faculty Publications

The American Heart Association (AHA) has advocated that women and men not consume more than 100 and 150 kcal/day, respectively, from added sugars. These levels are currently exceeded by over 90% of the adult population in the United States. Few data exist on longer-term metabolic effects when sucrose and High Fructose Corn Syrup (HFCS), the principal sources of added dietary sugars, are consumed at levels typical of the general population. Sixty five overweight and obese individuals were placed on a eucaloric (weight stable) diet for 10-weeks, which incorporated sucrose- or HFCS-sweetened, low-fat milk at 10% or 20% of calories in …

Baseline Staging Tests Based On Molecular Subtype Is Necessary For Newly Diagnosed Breast Cancer, Xuesong Chen, Lichun Sun, Yingying Cong, Tingting Zhang, Qiushi Lin, Qingwei Meng, Hui Pang, Yanbin Zhao, Yu Li, Li Cai, Xiaoqun Dong

Biomedical and Pharmaceutical Sciences Faculty Publications

Background: Bone scanning (BS), liver ultrasonography (LUS), and chest radiography (CXR) are commonly recommended for baseline staging in patients with newly diagnosed breast cancer. The purpose of this study is to demonstrate whether these tests are indicated for specific patient subpopulation based on clinical staging and molecular subtype.

Methods: A retrospective study on 5406 patients with newly diagnosed breast cancer was conducted to identify differences in occurrence of metastasis based on clinical staging and molecular subtypes. All patients had been evaluated by BS, LUS and CXR at diagnosis.

Results: Complete information on clinical staging was available in …

Meeting Report: Ocean ‘Omics Science, Technology And Cyberinfrastructure: Current Challenges And Future Requirements (August 20-23, 2013), Jack A. Gilbert, Gregory J. Dick, Bethany D. Jenkins, John Heidelberg, Eric Allen, Katherine R.M. Mackey, Edward F. Delong

Cell and Molecular Biology Faculty Publications

The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on …

First Evidence For The Presence Of Iron Oxidizing Zetaproteobacteria At The Levantine Continental Margins, Maxim Rubin-Blum, Gilad Antler, Rami Tsadok, Eli Shemesh, James A. Austin Jr., Dwight F. Coleman, Beverly N. Goodman-Tchernov, Zvi Ben-Avraham, Dan Tchernov

Graduate School of Oceanography Faculty Publications

During the 2010–2011 E/V Nautilus exploration of the Levantine basin’s sediments at the depth of 300–1300 m, densely patched orange-yellow flocculent mats were observed at various locations along the continental margin of Israel. Cores from the mat and the control locations were collected by remotely operated vehicle system (ROV) operated by the E/V Nautilus team. Microscopic observation and phylogenetic analysis of microbial 16S and 23S rRNA gene sequences indicated the presence of zetaproteobacterial stalk forming Mariprofundus spp. – like prokaryotes in the mats. Bacterial tag-encoded FLX amplicon pyrosequencing determined that zetaproteobacterial populations were a dominant fraction of microbial community in …

Barcode Microchips For Single-Cell Proteomic And Transcriptomic Analyses, Jun Wang

Amgen Seminar Series in Chemical Engineering

With recent progress in high-throughput single-cell analysis, we gradually realize that most multicellular systems are intrinsically heterogeneous. However, how the cellular heterogeneity emerges is not well understood, which is largely limited by the availability of single-cell tools. To answer this question and address the need for clinical diagnosis, I have developed two high-throughput barcode microchips for the analysis of single-cell proteome and transcriptome. Compelling evidences show that cell-cell interactions can significantly induce heterogeneity and redirect cell development. In the first part of my talk, I will describe the principle of the barcode microchip for single-cell or two-cell proteomic analysis and …

Targeting Diseased Tissues By Phlip Insertion At Low Cell Surface Ph, Oleg A. Andreev, Donald M. Engelman, Yana K. Reshetnyak

Physics Faculty Publications

The discovery of the pH Low Insertion Peptides (pHLIPs^®) provides an opportunity to develop imaging and drug delivery agents targeting extracellular acidity. Extracellular acidity is associated with many pathological states, such as those in cancer, ischemic stroke, neurotrauma, infection, lacerations, and others. The metabolism of cells in injured or diseased tissues often results in the acidification of the extracellular environment, so acidosis might be useful as a general marker for the imaging and treatment of diseased states if an effective targeting method can be developed. The molecular mechanism of a pHLIP peptide is based on pH-dependent membrane-associated folding. …

Changing Ph In The Surface Ocean, Michael E.Q. Pilson

Graduate School of Oceanography Faculty Publications

In 1896, Arrhenius provided the first roughly quantitative sense of the plausible magnitude of human-induced changes in the concentration of CO2 in the atmosphere. Since then, all chemists could be aware that increasing CO2 in the atmosphere must lead to increasing amounts in the ocean and a corresponding increase in acidity. For a long time, however, no one appears to have thought much about this latter consequence, probably because the likely effects were small and were, in any case, rather troublesome to calculate. It was only in 1909 that Sørensen proposed the concept of the pH scale. The negligible level …

Electromagnetically Inspired Biomaterials For Directing Biology, Stephen Kennedy

Amgen Seminar Series in Chemical Engineering

The ability to spatially and temporally regulate the delivery of biomolecules in vivo is pervasively desired in contemporary and emerging biotechnological and therapeutic contexts. 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 development of biomaterial systems—using simple electromagnetic principles as inspiration—that are capable of releasing molecular payloads in response to externally administered stimuli. I will describe how these systems may provide a high …

Copyright, Fair Use, And Education: Your Rights As A Student, Faculty Member, And Researcher, Julia Lovett, Andrée Rathemacher, Angel Ferria

Technical Services Faculty Presentations

Slides, handouts, and classroom examples from a presentation, "Copyright, Fair Use, and Education: Your Rights as a Student, Faculty Member, and Researcher," offered at the University of Rhode Island Libraries on February 24 and February 25, 2014.

"Learn how Fair Use can help you incorporate copyrighted works (written material, images, video, etc.) into your research, teaching, and academic projects. Have questions about Fair Use and Copyright? Please bring them to these interactive sessions!"

Part of the University Libraries' Search Savvy Seminar series.

Marketing Archaeology, William H. Krieger

Philosophy Faculty Publications

In the 19th century, ‘scientific archaeologists’ split from their antiquarian colleagues over the role that provenience (context) plays in the value of an artifact. These archaeologists focus on documenting an artifact’s context when they remove it from its original location. Archaeologists then use this contextual information to place these artifacts within a particular larger assemblage, in a particular time and space. Once analyzed, the artifacts found in a site or region can be used to document, to understand, and explain the past. Given the central place of context for archaeological excavation, archaeologists have done everything in their power to combat …

Curricular Affairs Committee Report #512, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Faculty Senate Meeting Minutes February 20, 2014, University Of Rhode Island Faculty Senate

Faculty Senate Meeting Minutes

No abstract provided.

2014-02-17 Library Impact Statement For Bio 444 Insect Ecology, Michael Cerbo

Library Impact Statements

This is the Library Impact statement for BIO 444 Insect Ecology. No new library resources are required for this proposal.

Cross-Conservation Of T-Cell Epitopes: Now Even More Relevant To (H7n9) Influenza Vaccine Design, Anne S. De Groot, Lenny Moise, Rui Liu, Andres H. Gutierrez, Frances Terry, Ousmane A. Koita, Ted M. Ross, William Martin

Institute for Immunology and Informatics Faculty Publications

A novel avian-origin H7N9 influenza strain emerged in China in April 2013. Since its re-emergence in October–November 2013, the number of reported cases has accelerated; more than 220 laboratory-confirmed cases and 112 deaths (case fatality rate of 20–30%) have been reported. The resurgence of H7N9 has re-emphasized the importance of making faster and more effective influenza vaccines than those that are currently available. Recombinant H7 hemagglutinin (H7-HA) vaccines have been produced, addressing the first problem. Unfortunately, these recombinant subunit vaccine products appear to have failed to address the second problem, influenza vaccine efficacy. Reported unadjuvanted H7N9 vaccine seroconversion rates were …

Graduate Council Report No. 2013-2014-5a, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Identification Of The Maize Gravitropism Gene Lazy Plant1 By A Transposon-Tagging Genome Resequencing Strategy, Thomas P. Howard Iii, Andrew P. Hayward, Anthony Tordillos, Christopher Fragoso, Maria A. Moreno, Joe Tohme, Albert P. Kausch, John P. Mottinger, Stephen L. Dellaporta

Cell and Molecular Biology Faculty Publications

Since their initial discovery, transposons have been widely used as mutagens for forward and reverse genetic screens in a range of organisms. The problems of high copy number and sequence divergence among related transposons have often limited the efficiency at which tagged genes can be identified. A method was developed to identity the locations of Mutator (Mu) transposons in the Zea mays genome using a simple enrichment method combined with genome resequencing to identify transposon junction fragments. The sequencing library was prepared from genomic DNA by digesting with a restriction enzyme that cuts within a perfectly conserved motif of the …

Curricular Affairs Committee Report #511 Appendix C, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Fsec Meeting Minutes January 21, 2014, University Of Rhode Island Faculty Senate

Faculty Senate Executive Committee Minutes

No abstract provided.

Birkhoff Normal Forms And Kam Theory For Gumowski-Mira Equation, Mustafa Kulenovic, Zehra Nurkanović, Esmir Pilav

Mathematics Faculty Publications

By using the KAMtheory we investigate the stability of equilibrium solutions of the Gumowski-Mira equation: x_n+1 = (2ax_n)/(1 + x²_n) – x_n-1, n = 0, 1, …, where x_-1, x₀, ∈ (−∞,∞), and we obtain the Birkhoff normal forms for this equation for different equilibrium solutions.

2014-01-06 Bio 498 Teaching Practicum In Biological Sciences, Michael Cerbo

Library Impact Statements

This is the Library Impact Statement for BIO 498 Teaching Practicum in Biological Sciences. No new library resources are need to support this course.

Division Of Research And Economic Development Annual Report For Fy2014, Uri Division Of Research And Economic Development

Reports (Research and Economic Development)

Annual report for the Division of Research and Economic Development of the University of Rhode Island for the year 2013-2014.

Includes statistics of project proposals, expenditures, URI Foundation Awards, previous annual report summaries and awards received by individual academic and administrative departments.

Division Of Research And Economic Development Monthly Report For July 2013 - March 2014, 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.