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Variation In Genome Content And Predatory Phenotypes Between Bdellovibrio Sp. Nc01 Isolated From Soil And B. Bacteriovorus Type Strain Hd100, Laura E. Williams, Nicole Cullen, Joseph A. Degiorgis, Karla J. Martinez, Justina Mellone, Molly Oser, Jing Wang, Ying Zhang Dec 2019

Variation In Genome Content And Predatory Phenotypes Between Bdellovibrio Sp. Nc01 Isolated From Soil And B. Bacteriovorus Type Strain Hd100, Laura E. Williams, Nicole Cullen, Joseph A. Degiorgis, Karla J. Martinez, Justina Mellone, Molly Oser, Jing Wang, Ying Zhang

Cell and Molecular Biology Faculty Publications

Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a ‘core genome’ of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene …

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An Analysis Of Firestone And The Liberia Worker Struggle: Experiences On Rubber Plantations Over The Last 96 Years, Willuetee Harmon Dec 2019

An Analysis Of Firestone And The Liberia Worker Struggle: Experiences On Rubber Plantations Over The Last 96 Years, Willuetee Harmon

Senior Honors Projects

The research project examines a case study of the rubber tire giant and the largest employer in Liberia - Firestone. This project offers a comprehensive historical analysis of experiences on the rubber plantations in Haribel, Liberia. Through historical research and personal interviews, the project explores and examines the history and reform made by this company over the last 96 years and how it affected the lower-tier worker (Tappers) struggles. The researcher finds herself in a space that allows for a profound review of the company's influence on the workers' experience brought forth through multiple in-depth interviews. The intentions are to …

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Curricular Report No. 2019-20-6 From The Graduate Council To The Faculty Senate (Courses), University Of Rhode Island Faculty Senate Nov 2019

Curricular Report No. 2019-20-6 From The Graduate Council To The Faculty Senate (Courses), University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curriculum And Standards Committee Report No. #2019-20-4 (Courses), University Of Rhode Island Faculty Senate Nov 2019

Curriculum And Standards Committee Report No. #2019-20-4 (Courses), University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curricular And Standards Committee Report #2019-20-4: Curricular Proposals, University Of Rhode Island Faculty Senate Nov 2019

Curricular And Standards Committee Report #2019-20-4: Curricular Proposals, University Of Rhode Island Faculty Senate

Faculty Senate Bills

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Molecular Modeling Of Biological Systems: From A Force Field Study To Modeling Of An Anti-Microbial Peptide In Water And A Complex S. Aureus Membrane, Faramarz Joodaki Nov 2019

Molecular Modeling Of Biological Systems: From A Force Field Study To Modeling Of An Anti-Microbial Peptide In Water And A Complex S. Aureus Membrane, Faramarz Joodaki

Amgen Seminar Series in Chemical Engineering

Interest in studying anti-microbial peptides (AMPs) has increased because of their potential as a future applicable antibiotic drug. In my research under supervision of Professor Greenfield, we attempt to understand the interaction of AMPs against membrane of bacteria. We are studying the structure of two novel hybrid AMPs LM7-1 and LM7-2 that were designed previously in Professor Martin’s research group (Cell and Molecular Biology Department). These AMPs differ in sequence only at the 15th residue. Several experimental studies have been successfully investigated mechanisms of AMPs against bacteria, but there is still much uncertainty in the exact mechanisms because of experimental …

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Near-Infrared Fluorescent Carbon Nanotubes; A New Paradigm In Disease Detection And Biological Imaging, Moein Safaee Nov 2019

Near-Infrared Fluorescent Carbon Nanotubes; A New Paradigm In Disease Detection And Biological Imaging, Moein Safaee

Amgen Seminar Series in Chemical Engineering

The bandgap near-infrared photoluminescence from the semiconducting single-walled carbon nanotubes is photostable, tunable, and sensitive to the local environment. Over the last 15 years, significant progress has been made in applying carbon nanotube photoluminescence toward a range of in vitro and in vivo biomedical applications. My research at URI NanoBio Engineering Lab encompasses the design and implementation of implantable and wearable biosensors in addition to developing in vitro molecular probes, based on single-walled carbon nanotubes. We engineer the molecular corona of the SWCNTs to significantly enhance their selectivity to multiple disease biomarkers, so their spectral variations can be utilized for …

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Neurosyphilis: Old Disease, New Implications For Emergency Physicians, Laura Mercurio, E. Taylor, Angela F. Jarman Nov 2019

Neurosyphilis: Old Disease, New Implications For Emergency Physicians, Laura Mercurio, E. Taylor, Angela F. Jarman

Pharmacy Practice and Clinical Research Faculty Publications

Recent epidemiologic data demonstrate increasing rates of neurosyphilis, particularly among those in the community of men who have sex with men and those coinfected with the human immunodeficiency virus (HIV). Here we discuss a case of early neurosyphilis and new HIV diagnosis in a 27-year-old previously-healthy trans woman presenting for the second time with progressive, ascending weakness and cranial nerve VI palsy. Emergency physicians should consider this rare but highly morbid diagnosis, given the rising prevalence of neurosyphilis among at-risk patients and those with new neurologic deficits.

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Head Size Of Male And Female Lizards Increases With Population Density Across Island Populations In The Bahamas, Johanna E. Wegener, Kevin P. Mulder, Robert M. Pringle, Jonathan B. Losos, Jason J. Kolbe Nov 2019

Head Size Of Male And Female Lizards Increases With Population Density Across Island Populations In The Bahamas, Johanna E. Wegener, Kevin P. Mulder, Robert M. Pringle, Jonathan B. Losos, Jason J. Kolbe

Biological Sciences Faculty Publications

In polygynous lizards, male–male competition is an important driver of morphologic and behavioral traits associated with intraspecific dominance. The extent to which females engage in aggressive behavior and thus contribute to competition-driven morphologic variation is not well studied. We used injury frequencies of brown anoles (Anolis sagrei) in 16 island populations to test the hypothesis that injury-inducing aggressive encounters increase with population density in both male and female lizards. We further asked whether intraspecific competition is a potential driver of phenotypic traits related to dominance by using population density as proxy for intraspecific competition. We found that the proportion of …

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Suppressing Mir-21 Activity In Tumor-Associated Macrophages Promotes An Antitumor Immune Response, Mahnaz Sahraei, Balkrishna Chaube, Yuting Liu, Jonathan Sun, Alanna Kaplan, Nathan L. Price, Wen Ding, Stanley Oyaghire, Rolando Garcia-Milian, Sameet Mehta, Yana Reshetnyak, Raman Bahal, Paolo Fiorina, Peter M. Glazer, David L. Rimm, Carlos Fernandez-Hernando, Yajaira Suarez Nov 2019

Suppressing Mir-21 Activity In Tumor-Associated Macrophages Promotes An Antitumor Immune Response, Mahnaz Sahraei, Balkrishna Chaube, Yuting Liu, Jonathan Sun, Alanna Kaplan, Nathan L. Price, Wen Ding, Stanley Oyaghire, Rolando Garcia-Milian, Sameet Mehta, Yana Reshetnyak, Raman Bahal, Paolo Fiorina, Peter M. Glazer, David L. Rimm, Carlos Fernandez-Hernando, Yajaira Suarez

Physics Faculty Publications

microRNA-21 (miR-21) is the most commonly upregulated miRNA in solid tumors. This cancer-associated microRNA (oncomiR) regulates various downstream effectors associated with tumor pathogenesis during all stages of carcinogenesis. In this study, we analyzed the function of miR-21 in noncancer cells of the tumor microenvironment to further evaluate its contribution to tumor progression. We report that the expression of miR-21 in cells of the tumor immune infiltrate, and in particular in macrophages, was responsible for promoting tumor growth. Absence of miR-21 expression in tumor- associated macrophages (TAMs), caused a global rewiring of their transcriptional regulatory network that was skewed toward a …

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The Why, When, And How Of Computing In Biology Classrooms [Version 1; Peer Review: 2 Approved], April M. Wright, Rachel Schwartz, Jamie R. Oaks, Catherine E. Newman, Sarah P. Flanagan Nov 2019

The Why, When, And How Of Computing In Biology Classrooms [Version 1; Peer Review: 2 Approved], April M. Wright, Rachel Schwartz, Jamie R. Oaks, Catherine E. Newman, Sarah P. Flanagan

Biological Sciences Faculty Publications

Many biologists are interested in teaching computing skills or using computing in the classroom, despite not being formally trained in these skills themselves. Thus biologists may find themselves researching how to teach these skills, and therefore many individuals are individually attempting to discover resources and methods to do so. Recent years have seen an expansion of new technologies to assist in delivering course content interactively. Educational research provides insights into how learners absorb and process information during interactive learning. In this review, we discuss the value of teaching foundational computing skills to biologists, and strategies and tools to do so. …

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Career Choice Among First-Generation, Minority Stem College Students, Bryan Dewsbury, Cynthia Taylor, Amy Reid, Connie Viamonte Oct 2019

Career Choice Among First-Generation, Minority Stem College Students, Bryan Dewsbury, Cynthia Taylor, Amy Reid, Connie Viamonte

Biological Sciences Faculty Publications

We qualitatively investigated ways in which undergraduates unpacked their perceptions of STEM careers after attending a seminar series that introduced them to diverse scientists. Using Social Cognitive Career Theory (SCCT) as a guiding framework, we explored how culturally-specific realities impacted students’ career choices. Our findings suggest that familial ties and cultural expectations played key roles in determining how students navigated career choice. Our results have implications for how institutions navigate career pursuit discussions with students.

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Comparing Ocean Surface Boundary Vertical Mixing Schemes Including Langmuir Turbulence, Tetsu Hara, Et Al Oct 2019

Comparing Ocean Surface Boundary Vertical Mixing Schemes Including Langmuir Turbulence, Tetsu Hara, Et Al

Graduate School of Oceanography Faculty Publications

Six recent Langmuir turbulence parameterization schemes and five traditional schemes are implemented in a common single‐column modeling framework and consistently compared. These schemes are tested in scenarios versus matched large eddy simulations, across the globe with realistic forcing (JRA55‐do, WAVEWATCH‐III simulated waves) and initial conditions (Argo), and under realistic conditions as observed at ocean moorings. Traditional non‐Langmuir schemes systematically underpredict large eddy simulation vertical mixing under weak convective forcing, while Langmuir schemes vary in accuracy. Under global, realistic forcing Langmuir schemes produce 6% (−1% to 14% for 90% confidence) or 5.2 m (−0.2 m to 17.4 m for 90% confidence) …

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Zoo Animal Management Avs 327, Michael Cerbo Oct 2019

Zoo Animal Management Avs 327, Michael Cerbo

Library Impact Statements

No abstract provided.

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Curricular Report No. 2019-20-1, University Of Rhode Island Faculty Senate Oct 2019

Curricular Report No. 2019-20-1, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curricular Report #2019-20-2, University Of Rhode Island Faculty Senate Oct 2019

Curricular Report #2019-20-2, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curricular Report No. 2019-20-1 From The Graduate Council To The Faculty Senate (Courses), University Of Rhode Island Faculty Senate Oct 2019

Curricular Report No. 2019-20-1 From The Graduate Council To The Faculty Senate (Courses), University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curricular Report No. #2019-20-2 From The Graduate Council To The Faculty Senate: Ph.D. Program In Health Sciences, University Of Rhode Island Faculty Senate Oct 2019

Curricular Report No. #2019-20-2 From The Graduate Council To The Faculty Senate: Ph.D. Program In Health Sciences, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Curricular And Standards Committee Report No. #2019-20-2: Bs In Chemistry, With Tracks Of General Chemistry And Forensic Chemistry, University Of Rhode Island Faculty Senate Oct 2019

Curricular And Standards Committee Report No. #2019-20-2: Bs In Chemistry, With Tracks Of General Chemistry And Forensic Chemistry, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

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Associations Between Pre-Pregnancy Bmi, Gestational Weight Gain, And Prenatal Diet Quality In A National Sample, Haley W. Parker, Alison Tovar, Karen Mccurdy, Maya Vadiveloo Oct 2019

Associations Between Pre-Pregnancy Bmi, Gestational Weight Gain, And Prenatal Diet Quality In A National Sample, Haley W. Parker, Alison Tovar, Karen Mccurdy, Maya Vadiveloo

Nutrition Faculty Publications

This secondary analysis explored the association between gestational weight gain, pre-pregnancy body mass index (BMI), and prenatal diet quality in a United States national sample. The sample comprised 1322 pregnant women in the longitudinal Infant Feeding Practices Study II with Diet History Questionnaire data. Diet quality in the third trimester was assessed using the Alternative Healthy Eating Index for Pregnancy. Self-reported pre-pregnancy BMI (categorized as underweight

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Chemical Process Safety In The Chemical Engineering Curriculum, Stephen J. Kmiotek Oct 2019

Chemical Process Safety In The Chemical Engineering Curriculum, Stephen J. Kmiotek

Amgen Seminar Series in Chemical Engineering

In 2011, ABET modified its accreditation criteria for Chemical Engineering programs to include “….. the hazards associated with (chemical, physical and/or biological) processes.” The new criterion was added in large part because of continued serious process safety incidents within the chemical industry and, based on the incident investigations, an apparent lack of understanding of these hazards by chemical engineering graduates. ABET left it to universities to address how best to meet the criterion at their institutions. Despite resources provided by, for instance, the Center for Chemical Process Safety, it has proven a challenge to add significant new content to a …

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A Newcomer's Guide To Functional Near Infrared Spectroscopy Experiments, Rand K. Almajidy, Kunal Mankodiya, Mohammadreza Abtahi, Ulrich G. Hofmann Oct 2019

A Newcomer's Guide To Functional Near Infrared Spectroscopy Experiments, Rand K. Almajidy, Kunal Mankodiya, Mohammadreza Abtahi, Ulrich G. Hofmann

Electrical, Computer, and Biomedical Engineering Faculty Publications

This review presents a practical primer for functional near-infrared spectroscopy (fNIRS) with respect to technology, experimentation, and analysis software. Its purpose is to jump-start interested practitioners considering utilizing a non-invasive, versatile, nevertheless challenging window into the brain using optical methods. We briefly recapitulate relevant anatomical and optical foundations and give a short historical overview. We describe competing types of illumination (trans-illumination, reflectance, and differential reflectance) and data collection methods (continuous wave, time domain and frequency domain). Basic components (light sources, detection, and recording components) of fNIRS systems are presented. Advantages and limitations of fNIRS techniques are offered, followed by a …

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Introduction To Ecological Data Analysis Bio 263, Michael Cerbo Oct 2019

Introduction To Ecological Data Analysis Bio 263, Michael Cerbo

Library Impact Statements

No abstract provided.

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Genetic Deficiency Or Pharmacological Inhibition Of Mir-33 Protects From Kidney Fibrosis, Nathan L. Price, Veronica Miguel, Wen Ding, Abhishek K. Singh, Shipra Malik, Noemi Rotllan, Anna Moshnikova, Jakub Toczek, Caroline Zeiss, Mehran M. Sadeghi, Noemi Arias, Angel Baldan, Oleg A. Andreev, Diego Rodriguez-Puyol, Raman Bahal, Yana K. Reshetnyak, Yajaira Suarez, Carlos Fernandez-Hernando, Santiago Lamas Oct 2019

Genetic Deficiency Or Pharmacological Inhibition Of Mir-33 Protects From Kidney Fibrosis, Nathan L. Price, Veronica Miguel, Wen Ding, Abhishek K. Singh, Shipra Malik, Noemi Rotllan, Anna Moshnikova, Jakub Toczek, Caroline Zeiss, Mehran M. Sadeghi, Noemi Arias, Angel Baldan, Oleg A. Andreev, Diego Rodriguez-Puyol, Raman Bahal, Yana K. Reshetnyak, Yajaira Suarez, Carlos Fernandez-Hernando, Santiago Lamas

Physics Faculty Publications

Previous work has reported the important links between cellular bioenergetics and the development of chronic kidney disease, highlighting the potential for targeting metabolic functions to regulate disease progression. More recently, it has been shown that alterations in fatty acid oxidation (FAO) can have an important impact on the progression of kidney disease. In this work, we demonstrate that loss of miR-33, an important regulator of lipid metabolism, can partially prevent the repression of FAO in fibrotic kidneys and reduce lipid accumulation. These changes were associated with a dramatic reduction in the extent of fibrosis induced in 2 mouse models of …

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“Got Water?” The Effects Of Globalized Agribusiness On Consumers’ Access To Water Sources, Lorena Garcia-Ramon Oct 2019

“Got Water?” The Effects Of Globalized Agribusiness On Consumers’ Access To Water Sources, Lorena Garcia-Ramon

Markets, Globalization & Development Review

This paper conceptually examines the consequences of globalized industrial agriculture on consumers’ access to clean water sources. It identifies the historical conditioners that allowed contemporary agribusiness corporations to gain the influence they currently hold over global water consumption, and it discusses the struggles that consumers face without access to clean water. The paper makes an original contribution by shifting the focus from the fact that vulnerable consumers do not have access to clean water to the reasons why they do not have access. It is suggested that water conservation strategies should not only be implemented at the consumer level, but …

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Spatial Patterns Of Arctic Sponge Ground Fauna And Demersal Fish Are Detectable In Autonomous Underwater Vehicle (Auv) Imagery, H.K. Meyer, E.M. Roberts, H.T. Rapp, Andrew J. Davies Oct 2019

Spatial Patterns Of Arctic Sponge Ground Fauna And Demersal Fish Are Detectable In Autonomous Underwater Vehicle (Auv) Imagery, H.K. Meyer, E.M. Roberts, H.T. Rapp, Andrew J. Davies

Biological Sciences Faculty Publications

Deep-sea sponge grounds are important habitats that provide several ecosystem services, yet relatively little is known about their distribution and ecology. While most surveys have focused on the broad-scale distribution patterns of sponge grounds (100s–1000s m), only rarely have the finer-scale (<10 m) spatial distribution patterns of the primary organisms been studied. In this study, the autonomous underwater vehicle (AUV) Hugin 1000 was used to map an area of an arctic sponge ground located on the summit of the Schulz Bank (Arctic Mid-Ocean Ridge), with the aim of detecting small-scale spatial patterns produced by the dominant megafauna. Using low-light cameras to construct a photomosaic comprising of 9,953 images and a virtual quadrat spatial sampling approach, density hotspots of …

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Undergraduate Research Science: Principles And Practice Bio 200, Michael Cerbo Oct 2019

Undergraduate Research Science: Principles And Practice Bio 200, Michael Cerbo

Library Impact Statements

No abstract provided.

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Polymer-Grafted Nanoparticle Membranes With Unusual Gas Separation Properties, Sanat K. Kumar Oct 2019

Polymer-Grafted Nanoparticle Membranes With Unusual Gas Separation Properties, Sanat K. Kumar

Amgen Seminar Series in Chemical Engineering

Polymer membranes are employed in several critical sustainability applications involving the separation of gas mixtures based on size differences. In spite of their widespread use, important performance challenges remain outstanding - the need to dramatically affect the transport of a desired mixture component and improving mechanical resilience relative to the current state-of-the-art. Here, we develop novel membranes based on polymer-grafted nanoparticles (GNPs) which possess controllable, spatially inhomogeneous gas transport behavior. We show that smaller gases are transported more uniformly than larger solutes in the polymer layer of pure GNPs; these larger gases preferentially move through the interstices between the NPs. …

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Golgi Membrane Protein Gp73 Modified-Liposome Mediates The Antitumor Effect Of Survivin Promoter-Driven Hsvtk In Hepatocellular Carcinoma, Chang Liu, Chaochao Wen, Xi Wang, Yan Wei, Chunyang Xu, Xiuli Mu, Lina Zhang, Xuan Wang, Jiubo Tian, Peiyuan Ma, Fanxiu Meng, Qi Zhang, Na Zhao, Baofeng Yu, Tao Gong, Rui Guo, Hailong Wang, Jun Xie, Gongqin Sun, Gaopeng Li, Hongwei Zhang, Qin Qin, Jun Xu, Xiushan Dong, Lumei Wang Oct 2019

Golgi Membrane Protein Gp73 Modified-Liposome Mediates The Antitumor Effect Of Survivin Promoter-Driven Hsvtk In Hepatocellular Carcinoma, Chang Liu, Chaochao Wen, Xi Wang, Yan Wei, Chunyang Xu, Xiuli Mu, Lina Zhang, Xuan Wang, Jiubo Tian, Peiyuan Ma, Fanxiu Meng, Qi Zhang, Na Zhao, Baofeng Yu, Tao Gong, Rui Guo, Hailong Wang, Jun Xie, Gongqin Sun, Gaopeng Li, Hongwei Zhang, Qin Qin, Jun Xu, Xiushan Dong, Lumei Wang

Cell and Molecular Biology Faculty Publications

Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide, and there is currently no effective therapeutic strategy in clinical practice. Gene therapy has great potential for decreasing tumor-induced mortality but has been clinically limited because of the lack of tumor-specific targets and insufficient gene transfer. The study of targeted transport of therapeutic genes in HCC treatment seems to be very important. In this study, we evaluated a gene therapy approach targeting HCC using the herpes simplex virus thymidine kinase/ganciclovir (HSVtk/GCV) suicide gene system in HCC cell lines and in an in vivo human HCC xenograft mouse …

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Oyster Reefs In Northern Gulf Of Mexico Estuaries Harbor Diverse Fish And Decapod Crustacean Assemblages: A Meta-Synthesis, Megan K. La Peyre, Danielle Aguilar Marshall, Lindsay S. Miller, Austin T. Humphries Oct 2019

Oyster Reefs In Northern Gulf Of Mexico Estuaries Harbor Diverse Fish And Decapod Crustacean Assemblages: A Meta-Synthesis, Megan K. La Peyre, Danielle Aguilar Marshall, Lindsay S. Miller, Austin T. Humphries

Fisheries, Animal and Veterinary Sciences Faculty Publications

Oyster reefs provide habitat for numerous fish and decapod crustacean species that mediate ecosystem functioning and support vibrant fisheries. Recent focus on the restoration of eastern oyster (Crassostrea virginica) reefs stems from this role as a critical ecosystem engineer. Within the shallow estuaries of the northern Gulf of Mexico (nGoM), the eastern oyster is the dominant reef building organism. This study synthesizes data on fish and decapod crustacean occupancy of oyster reefs across nGoM with the goal of providing management and restoration benchmarks, something that is currently lacking for the region. Relevant data from 23 studies were identified, representing …

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