Digital Commons Network^™

Flexible And Fast Mapping Of Peptides To A Proteome With Proteomapper., Luis Mendoza, Eric W Deutsch, Zhi Sun, David S Campbell, David Shteynberg, Robert L Moritz

Articles, Abstracts, and Reports

Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer which possible proteins are identified. Reliable mapping of peptides to proteins still poses substantial challenges when considering similar proteins, protein families, splice isoforms, sequence variation, and possible residue mass modifications, combined with an imperfect and incomplete understanding of the proteome. The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input …

Investigation Of Dengue Virus (Denv) Ns2b/3 Protease For Antiviral Development, Thimoro Cheng

Honors Capstones

Numerous studies have shown that Hepatitis C virus (HCV) and Dengue virus (DENV) are from the same family and have many characteristics in common. Despite the similarities, no adequate vaccines or antivirals have been developed for DENV yet although many are commercially available for HCV. In this research, we investigated the relationship between HCV and DENV, especially their NS3/4A and NS2B/3 proteases, to aid in the development of antiviral against DENV. To achieve this, in-depth structural analyses of the complexes were conducted; and molecular modeling stimulation software were utilized to visualize the interactions of the enzymes with different potential inhibitors …

The Daily Gamecock, Semester In Review, Fall 2018, University Of South Carolina, Office Of Student Media

December

No abstract provided.

Whalesong 2018-12-07, Erin Laughlin, Kortney Stevens, Jordan Lewis, Sierra Lissick, Caitlin Burnham, Khrystl Brouillette, Melissa Scriven, Alyssa Madrid

Whalesong

No abstract provided.

Commencement Ceremonies, University Of North Florida

Commencement Printed Materials

Program for the Fall Commencement ceremonies.

The Textbook Game, Cy Robinson

USU Student Folklore Fieldwork

The spouse game. My friend came up with this game during a biology class in 7^th grade. The game is played as such. Each participant looks through the textbook that both students have, usually one provided in class. Each would sign to the others a page number containing an “attractive” person and then make eyes as the other flipped to the respective pages. The other person would try not to smile or make eyes back to the other person as they signed the next page back to them. The game started off really juvenile until we realized that the …

A Logitudinal Feature Selection Method Identifies Relevant Genes To Distinguish Complicated Injury And Uncomplicated Injury Over Time, Suyan Tian, Chi Wang, Howard H. Chang

Biostatistics Faculty Publications

Background: Feature selection and gene set analysis are of increasing interest in the field of bioinformatics. While these two approaches have been developed for different purposes, we describe how some gene set analysis methods can be utilized to conduct feature selection.

Methods: We adopted a gene set analysis method, the significance analysis of microarray gene set reduction (SAMGSR) algorithm, to carry out feature selection for longitudinal gene expression data.

Results: Using a real-world application and simulated data, it is demonstrated that the proposed SAMGSR extension outperforms other relevant methods. In this study, we illustrate that a gene’s expression profiles over …

Adaptation Mechanism And Tolerance Of Rhodopseudomonas Palustris Psb-S Under Pyrazosulfuron-Ethyl Stress, Xiang-Wen Luo, De-Yang Zhang, Teng-Hui Zhu, Xuguo Zhou, Jing Peng, Song-Bai Zhang, Yong Liu

Entomology Faculty Publications

Background: Pyrazosulfuron-ethyl is a long lasting herbicide in the agro-ecosystem and its residue is toxic to crops and other non-target organisms. A better understanding of molecular basis in pyrazosulfuron-ethyl tolerant organisms will shed light on the adaptive mechanisms to this herbicide.

Results: Pyrazosulfuron-ethyl inhibited biomass production in Rhodopseudomonas palustris PSB-S, altered cell morphology, suppressed flagella formation, and reduced pigment biosynthesis through significant suppression of carotenoids biosynthesis. A total of 1127 protein spots were detected in the two-dimensional gel electrophoresis. Among them, 72 spots representing 56 different proteins were found to be differently expressed using MALDI-TOF/TOF-MS, including 26 up- and 30 …

Synthesis And Anti-Inflammatory Activities Of Phloroglucinol-Based Derivatives, Ning Li, Shabana I. Khan, Shi Qiu, Xing-Cong Li

Faculty and Student Publications (Open Access)

The natural product phloroglucinol-based derivatives representing monoacyl-, diacyl-, dimeric acyl-, alkylated monoacyl-, and the nitrogen-containing alkylated monoacylphloro- glucinols were synthesized and evaluated for inhibitory activities against the inflammatory mediators such as inducible nitric oxide synthase (iNOS) and nuclear factor kappaB (NF-κB). The diacylphloroglucinol compound 2 and the alkylated acylphloroglucinol compound 4 inhibited iNOS with IC50 values of 19.0 and 19.5 µM, respectively, and NF-κB with IC50 values of 34.0 and 37.5 µM, respectively. These compounds may serve as leads for the synthesis of more potent anti-inflammatory compounds for future drug discovery.

Reproductive Life History And Shell Shape Variation Of Three Species Of Elimia (Pleuroceridae) In The Lower Etowah River Basin, Ellen Winant

Master of Science in Integrative Biology Theses

Pleurocerid snail diversity in the Southeastern United States is thought to be high, but estimates of overall diversity are compromised by uncertain taxonomy. This is particularly true for the genus Elimia, where reliance on conchological characters described by early naturalists for species designation failed to recognize significant variability in shell morphology. In this study we examine three putative species of Elimia to determine if quantifiable conchological characters are associated with differences in life history characteristics. Individuals of E. modesta, E. carinocostata, and E. cariniferawere collected from nine sites in three streams in the lower Etowah River …

Weekly Survivorship Curves Of Soybean Aphid Biotypes 1 And 4 On Insecticidal Seed-Treated Soybean, Carlos J. Esquivel, Christopher M. Ranger, P. Larry Phelan, Erick J. Martinez, William H. Hendrix, Andrew P. Michel

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Thiamethoxam, an insecticide used in soybean seed treatments, effectively suppresses soybean aphids (Aphis glycines) Matsumura (Hemiptera: Aphididae) for a short time after planting. However, exactly when and how quickly soybean aphid populations could increase is unknown. Likewise, we lack data on virulent soybean aphid biotypes (that can overcome soybean resistance) when fed on seed-treated soybean. Determining the survival of soybean aphids over time on insecticidal seed-treated soybean is critical for improving soybean aphid management and may provide insights to manage aphid virulence to aphid resistant-soybean. In greenhouse and field experiments, aphid-susceptible soybean plants (with and without an insecticidal seed treatment) …

Comparative Susceptibility Of Western Corn Rootworm (Coleoptera: Chrysomelidae) Neonates To Selected Insecticides And Bt Proteins In The Presence And Absence Of Feeding Stimulants, Adriano E. Pereira, Thomas A. Coudron, Kent Shelby, B. Wade French, Elisa J. Bernklau, Louis B. Bjostad, Bruce E. Hibbard

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

The susceptibility of western corn rootworm, Diabrotica virgifera virgifera LeConte, larvae to nine insecticides from five different classes and to Bt proteins eCry3.1Ab and mCry3A in the presence or absence of feeding stimulants, was estimated in filter paper and diet toxicity assays, respectively. The use of a synthetic feeding stimulant blend of the sugars glucose, sucrose, and fructose plus linoleic acid at a ratio of 30:4:4:0.3 mg/ml of distilled water was evaluated to determine whether they increase the efficacy of insecticides and Bt proteins. The efficacy of thiamethoxam diluted in solutions with feeding stimulants was significantly increased when compared to …

Chimes: December 7, 2018, Calvin College

Chimes

Evolution debate continues amongst CCCU biology profs by Joshua Polanski

New student organization 'starts up' a generation of ideas by Sam Ballast

Women In Action conference empowers women for attentiveness, self care by Ellington Smith

Calvin Center for Faith and Writing celebrates Madeleine L'Engle's 100th birthday, legacy with cake, conversation by Michal Rubingh

40% of students who visit Counselling and Wellness show signs of depression by Jose M. Hernandez

For God so loved the KOSMOS: William Matthews' latest album invites a bigger picture of God by Yolanda Chow

Free food=Free students by Madalyn Buursma

The Shifting Politics Of Patient Activism: From Bio-Sociality To Bio-Digital Citizenship, Alison Anderson, Alan Petersen, Allegra Clare Schermuly

School of Law, Humanities and Social Sciences

Digital media provide novel tools for patient activists from disease- and condition-specific communities. While those with debilitating conditions or disabilities have long recognised the value of collective action for advancing their interests, digital media offers activists unparalleled opportunities to fulfil their goals. This article explores the shifting politics of ‘activism’ in the increasingly digitally mediated, commercialised context of healthcare, asking: what role have digital media played in the repertoire of activists’ strategies? And, to what extent and how has the use of such media impacted the very concept of activism? Building on sociological ideas on emergent forms of ‘biological citizenship’ …

A High-Fat Diet Alters Genome-Wide Dna Methylation And Gene Expression In Sm/J Mice, Madeline R. Keleher, Rabab Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud

Biology: Faculty Publications and Other Works

Background: While the genetics of obesity has been well defined, the epigenetics of obesity is poorly understood. Here, we used a genome-wide approach to identify genes with differences in both DNA methylation and expression associated with a high-fat diet in mice. Results: We weaned genetically identical Small (SM/J) mice onto a high-fat or low-fat diet and measured their weights weekly, tested their glucose and insulin tolerance, assessed serum biomarkers, and weighed their organs at necropsy. We measured liver gene expression with RNA-seq (using 21 total libraries, each pooled with 2 mice of the same sex and diet) and DNA methylation …

Model Vs. Experiment To Predict Crop Losses, Camille Parmesan, Michael E. Hanley, Michael C. Singer

School of Biological and Marine Sciences

No abstract provided.

Association Of Alcohol Consumption After Development Of Heart Failure With Survival Among Older Adults In The Cardiovascular Health Study, Justin S. Sadhu, Eric Novak, Kenneth J. Mukamal, Jorge R. Kizer, Bruce M. Psaty, Phyllis K. Stein, David L. Brown

Open Access Publications

Importance: More than 1 million older adults develop heart failure annually. The association of alcohol consumption with survival among these individuals after diagnosis is unknown.

Objective: To determine whether alcohol use is associated with increased survival among older adults with incident heart failure.

Design, Setting, and Participants: This prospective cohort study included 5888 community-dwelling adults aged 65 years or older who were recruited to participate in the Cardiovascular Health Study between June 12, 1989, and June 1993, from 4 US sites. Of the total participants, 393 individuals had a new diagnosis of heart failure within the first 9 years of …

Business Not As Usual: How Multisectoral Collaboration Can Promote Transformative Change For Health And Sustainable Development, Shyama Kuruvilla, Rachael Hinton, Ties Boerma, Ryan Bunney, Nuria Casamitjana, Rafael Cortez, Patrizia Fracassi, Jennifer Franz-Vasdeki, Daniel Helldén, Joanne Mcmanus, Jai K. Das

Department of Paediatrics and Child Health

No abstract provided.

Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan

Articles

Objective: This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment.

Results: It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases.

Conclusion: Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed …

The Brain In Balance: Tales From A Cellular Biochemist Studying Space And Time, Mark Decoster

Science Seminars

One definition of the brain is that it senses change. This change can be input to our traditional senses such as light, taste, and touch, to name a few. Sensing change and recording it is also important to deciding output (or not), such as responding to a question or avoiding danger. Short-term through long-term sensing of change may also be stored into memory. This process of sensing change and responding to it with storage may be defined as learning when it helps with the process. At the cellular and biochemical levels, cells in the brain may be excited or inhibited, …

Meeting Minutes, Wku Graduate Council

Graduate School

Meeting minutes.

The Impact Of Online Homework, Time On Homework, Gender, And Metacognition In Improving Student Achievement In Undergraduate Biology Courses, Donald Bishop Cook Jr

Doctoral Dissertations and Projects

This study sought to address a gap in the literature to determine whether a relationship exists between use of online homework and student achievement in undergraduate biology courses. Previous studies have examined other STEM courses, but few have considered biology. The purpose of the study was to determine whether homework grades in online homework systems can predict student achievement in introductory undergraduate biology courses. This study utilized a correlational analysis by multiple regression using archival data to determine whether final course grades in undergraduate biology courses can be predicted by grades on online homework, time spent on online homework, gender, …

Lighting Up The Season, Andrews University

Student Movement V. 103 (2018-2019)

No abstract provided.

Kaposi’S Sarcoma-Associated Herpesvirus-Encoded Viral Il-6 (Vil-6) Enhances Immunoglobulin Class-Switch Recombination, Santas Ana Rosario

Open Access Dissertations

Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gamma-herpesvirus that causes several AIDS-defining malignancies, including Kaposi's sarcoma (KS) and other lymphoproliferative disorders. These malignancies continue to burden AIDS patients, particularly one-seventh of the world’s population in sub-Saharan Africa, where highly active antiretroviral therapy (HAART) is poorly accessible. To successfully establish lifelong persistence within a host, KSHV employs several strategies, including mimicry of host cytokines, to modulate the immune response and usurp cellular signaling pathways. One crucial cytokine is vIL-6, a viral homolog to human IL-6 (hIL-6) and mouse IL-6 (mIL-6). Although the immune system plays a pivotal role in the pathogenesis …

The Formation Of Climate Change Beliefs Among Young Adults In Appalachian Kentucky: A Consideration Of The Role Played By Economic Risk Perception, Rebecca Johnson

Morehead State Theses and Dissertations

A thesis presented to the faculty of the Caudill College of Arts, Humanities, and Social Sciences at Morehead State University in partial fulfillment of the requirements for the Degree Master of Arts by Rebecca Johnson on December 6, 2018.

Residents' Opinions On Fracking In Utah, Kelsey Gale

Fall Student Research Symposium 2018

Fracking is the process of drilling down into the earth before a high-pressure water mixture is directed at the rock to release gas inside.

Water, sand and chemicals are injected into the rock at high pressure which allows the gas to flow out to the head of the well.

This can be a very controversial topic, especially in the Western United States where fracking is a major part of the economic growth of the states.

The public forms opinions both negative and positive regarding fracking in the state of Utah.

Studies have been done to discover the impacts, good or …

Modeling The Effect Of Post-Dispersal Seed Predation On Tropical Tree Species In Panama, Justin Tirrell

Fall Student Research Symposium 2018

Palm trees provide a unique opportunity to study what conditions optimize the probability that a seed will grow successfully. The seeds of palm trees, endocarps, are large and easy to locate. When they don't grow, predators leave marks on them that tell the story of their fate. The focus of my experiment is to determine how the current distribution pattern of parent palm trees in Panama Palm trees affects the the future distribution of seedlings. I have programmed a versatile model that takes the assumption that bruchid beetles are the sole predators acting on the seeds, and that these fall …

Hawks' Herald -- Dec. 6, 2018, Roger Williams University

Hawk's Herald

No abstract provided.

Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf

Fall Student Research Symposium 2018

Aerosol particles are thought to impact climate properties. The ability to probe aerosols to understand their chemical properties has been difficult due to a lack of appropriate analytical techniques. Here we present interface-specific SHS techniques to allow for in situ analysis of aerosol particles. Transportation of aerosols from their collection site to the laboratory disturbs their chemical and physical properties thus making it difficult to take accurate measurements of aerosol particles. We show that using a CCD detector is a more effective option for producing more sensitive results and can greatly reduce sampling time and could possibly detect measurements from …

Potential Impacts Of The Purple Salt Marsh Crab, Sesarma Reticulatum, On Long Island Sound Salt Marshes, Jaymie Frederick

Master's Theses

Salt marshes are important, highly productive ecosystems that provide many ecological benefits, including shoreline protection. Salt marshes were long believed to be driven by bottom up forces, however, recent research has suggested that top down influences may impact the foundation species Spartina alterniflora, and consequently marsh structure. This study looked at patterns of Spartina alterniflora dieback along creek bank areas and assessed Sesarma reticulatum abundance spatially throughout the marsh to improve understanding as to whether Sesarma may be influencing the dieback phenomenon. Dieback was occurring in all three salt marshes studied, at two of those marsh sites the rate of …