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Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner 2015 Bowling Green State University - Main Campus

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species4. RNA-seq analysis showed that one gene, PPTG_16698 has the 5th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of the ...


A Hierarchical Graph For Nucleotide Binding Domain 2, Samuel Kakraba 2015 East Tennessee State University

A Hierarchical Graph For Nucleotide Binding Domain 2, Samuel Kakraba

Electronic Theses and Dissertations

One of the most prevalent inherited diseases is cystic fibrosis. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. Generally, most of the prevalent mutations of CFTR are located in one of two nucleotide binding domains, namely, the nucleotide binding domain 1 (NBD1). However, some mutations in nucleotide binding domain 2 (NBD2) can equally cause cystic fibrosis. In this work, a hierarchical graph is built for NBD2 ...


Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel 2015 University of Nebraska-Lincoln

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Dissertations, Theses, and Student Research Papers in Mathematics

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to ...


A Dynamic Behavioral Biometric Approach To Authenticate Users Employing Their Fingers To Interact With Touchscreen Devices, Arturo Ponce 2015 Nova Southeastern University

A Dynamic Behavioral Biometric Approach To Authenticate Users Employing Their Fingers To Interact With Touchscreen Devices, Arturo Ponce

GSCIS ETDs

The use of mobile devices has extended to all areas of human life and has changed the way people work and socialize. Mobile devices are susceptible to getting lost, stolen, or compromised. Several approaches have been adopted to protect the information stored on these devices. One of these approaches is user authentication. The two most popular methods of user authentication are knowledge based and token based methods but they present different kinds of problems.

Biometric authentication methods have emerged in recent years as a way to deal with these problems. They use an individual’s unique characteristics for identification and ...


Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University 2015 Eastern Illinois University

Darwin Core Archive File, Stover-Ebinger Herbarium, Eastern Illinois University

Darwin Core Archive Download

ZIP file contains occurrences.csv, identivications.csv, and images.csv. The meta.xml document describes the content. Fields within the occurrences.csv file are defined by the Darwin Core exchange standard.


Isolation And Genomic Analysis Of Cluster O Mycobacteriophage Vorrps, Leslie Ann Sterling, Rahul Ramaswamy, Madeleine Mullon, Peeti Sithiyopasakul 2015 Washington University in St Louis

Isolation And Genomic Analysis Of Cluster O Mycobacteriophage Vorrps, Leslie Ann Sterling, Rahul Ramaswamy, Madeleine Mullon, Peeti Sithiyopasakul

Undergraduate Research Symposium Posters & Abstracts

Mycobacteriophage Vorrps was isolated in 2014 from soil on the Washington University campus. The phage was isolated and purified by repeatedly infecting host Mycobacterium smegmatis. Vorrps produces small, circular, clear plaques approximately 1 mm in diameter, indicating that it is a lytic phage. Electron microscopy reveals that Vorrps has an unusual prolate head and a long tail characteristic of cluster O mycobacteriophage. Vorrps is very similar to the five analyzed O cluster phages Corndog, Catdawg, YungJamal, Firecracker and Dylan, as well as cluster O phage Mori, another phage isolated and analyzed by Washington University students this year. Vorrps and Mori ...


Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock 2015 Washington University in St Louis

Isolation And Comparative Genomic Analysis Of Mycobacteriophage Enkatz, Thomas Van Horn, Micah Rickles-Young, Shaarada Srivasta, Tina Zudock

Thomas Van Horn

Phage Enkatz is a temperate mycobacteriophage isolated from an un-enriched soil sample collected from the South Forty housing area of the Washington University in St. Louis campus. Enkatz displays unequally sized plaques with a clear center that become cloudier with radial distance from the center. Genome analysis indicates that Enkatz is a cluster A1 mycobacteriophage with a genome size of 49,738 bases and 82 identified genes, 33 of which have been assigned functions. This analysis reveals that the majority of the genes in the positive strand code for structural proteins, while the majority of the genes in the negative ...


The Deaf Cyborg: Analyzing Technoscience, Gender, And Ability, Callahan Roan 2015 Georgia State University

The Deaf Cyborg: Analyzing Technoscience, Gender, And Ability, Callahan Roan

Georgia State Undergraduate Research Conference

Gsurc 2015


Characterizing Orphan Gpcrs In Molluscan Neurons Through Bioinformatics, Preetham Ganupuru 2015 Georgia State University

Characterizing Orphan Gpcrs In Molluscan Neurons Through Bioinformatics, Preetham Ganupuru

Georgia State Undergraduate Research Conference

No abstract provided.


Integrating External Resources Into Health Informatics And Computing Instruction: Emerging Roles For Librarians And Information Professionals, Daina R. Bouquin, Michael E. Bales 2015 Weill Cornell Medical College of Cornell University

Integrating External Resources Into Health Informatics And Computing Instruction: Emerging Roles For Librarians And Information Professionals, Daina R. Bouquin, Michael E. Bales

University of Massachusetts and New England Area Librarian e-Science Symposium

Background: In informatics courses, instructors often present materials in a didactic, module-by-module fashion; however, they may not readily integrate outside materials to facilitate learning. This may be due to a lack of time or expertise in identifying appropriate external resources. Librarians are uniquely suited to address this gap.

Setting/Participants: A librarian (D.B.) and a digital curation fellow (M.B.) taught a graduate level course on computational methods in health informatics. Students were mainly from basic science and informatics programs and had varying levels of computational experience.

Purpose: The objective of the course was to promote critical thinking about ...


A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian 2015 James Madison University

A Bioinformatics Approach To Revealing The Genetic Basis For Host Range Specificity, Hayley A. Norian

James Madison Undergraduate Research Journal

Bacteriophages, or phages, are viruses that infect bacteria. Mycobacteriophages are bacteriophages that specifically infect the genus Mycobacterium. This genus of bacteria includes human pathogens such as Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans, which cause tuberculosis, leprosy and Buruli ulcer, respectively. The full genome sequences of 654 mycobacteriophages are currently available. Collectively, these 654 phages encode 69,581 genes. Only 20.25% of these genes have at least one known homologue in NCBI, the National Center for Biotechnology Information, leaving roughly 80% of all known mycobacteriophage genes without even a predicted function. Bacteriophages are highly host-specific and typically only infect ...


Figure-Associated Text Summarization And Evaluation, Balaji Polepalli Ramesh, Ricky J. Sethi, Hong Yu 2015 University of Massachusetts Medical School

Figure-Associated Text Summarization And Evaluation, Balaji Polepalli Ramesh, Ricky J. Sethi, Hong Yu

Open Access Articles

Biomedical literature incorporates millions of figures, which are a rich and important knowledge resource for biomedical researchers. Scientists need access to the figures and the knowledge they represent in order to validate research findings and to generate new hypotheses. By themselves, these figures are nearly always incomprehensible to both humans and machines and their associated texts are therefore essential for full comprehension. The associated text of a figure, however, is scattered throughout its full-text article and contains redundant information content. In this paper, we report the continued development and evaluation of several figure summarization systems, the FigSum+ systems, that automatically ...


An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros 2015 University of Massachusetts Medical School Worcester

An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate ...


Reniform Nematode (Rotylenchulus Reniformis) Manipulation Of Host Root Gene Expression During Syncytium Formation In Upland Cotton (Gossypium Hirsutum), Wei Li 2015 Clemson University

Reniform Nematode (Rotylenchulus Reniformis) Manipulation Of Host Root Gene Expression During Syncytium Formation In Upland Cotton (Gossypium Hirsutum), Wei Li

All Theses

Background: The semi-endoparasitic reniform nematode (Rotylenchulus reniformis) is a major yield-limiting pest of multiple crops in the tropics and sub-tropics, including upland cotton (Gossypium hirsutum). Reniform-resistant cotton varieties are urgently needed, but genes that confer resistance to reniform nematode have not been identified in any species. Parasitism by reniform nematode involves significant developmental changes in plant roots, leading to the formation of multicellular feeding structures called syncytia. Here, we present de novo transcriptomes assembled from syncytial and non-syncytial cotton roots on three sampling dates across a 12-day time course. Results: Total mRNA samples extracted from reniform-infected and uninfected G. hirsutum ...


Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang 2015 University of Kentucky

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We ...


Improved Accuracy Of Genomic Prediction For Traits With Rare Qtl By Fitting Haplotypes, Xiaochen Sun, Rohan L. Fernando, Dorian J. Garrick, Jack C. M. Dekkers 2015 Iowa State University

Improved Accuracy Of Genomic Prediction For Traits With Rare Qtl By Fitting Haplotypes, Xiaochen Sun, Rohan L. Fernando, Dorian J. Garrick, Jack C. M. Dekkers

Animal Industry Report

Genomic prediction estimates breeding values by exploiting linkage disequilibrium (LD) between quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs). High LD cannot occur when QTL and SNPs have different minor allele frequencies (MAF). Marker panels tend to use SNPs with high MAF and will have limited ability to predict rare QTL alleles. In practice, increasing SNP density has not improved prediction accuracy. A possible reason is that many traits are characterized by rare QTL. In that case, linear models fitting haplotypes could have advantage because haplotypes can be in complete LD with QTL alleles. SNP genotypes were simulated to ...


Genome-Wide Association Analyses Of Biological Responses To Heat Stress In Pigs, Kwan-Suk Kim, Eui-Soo Kim, Jacob T. Seibert, Aileen F. Keating, Lance H. Baumgard, Jason W. Ross, Max F. Rothschild 2015 Iowa State University

Genome-Wide Association Analyses Of Biological Responses To Heat Stress In Pigs, Kwan-Suk Kim, Eui-Soo Kim, Jacob T. Seibert, Aileen F. Keating, Lance H. Baumgard, Jason W. Ross, Max F. Rothschild

Animal Industry Report

With genetic selection for rapid, lean tissue accretion, pigs are becoming increasingly sensitive to heat stress (HS) due to their physiological limitations such as the lack of functional sweat glands to effectively dissipate heat. Increased respiration rate and reduced feed intake are immediate and conserved biological responses to HS in pigs and other livestock species. Genetic differences in how animals respond to high ambient temperatures have been previously reported, but genetic factors contributing to the response variability remain ill-defined. In this study, porcine high density single nucleotide polymorphism (SNP) beadchips were used to genotype 236 female pigs who had been ...


A Comparison Of The Genetic Factors Influencing Host Response To Infection With One Of Two Isolates Of Porcine Reproductive And Respiratory Syndrome Virus, Andrew S. Hess, Nicholas Boddicker, Bob Rowland, Joan Lunney, Graham Plastow, Jack C. M. Dekkers 2015 Iowa State University

A Comparison Of The Genetic Factors Influencing Host Response To Infection With One Of Two Isolates Of Porcine Reproductive And Respiratory Syndrome Virus, Andrew S. Hess, Nicholas Boddicker, Bob Rowland, Joan Lunney, Graham Plastow, Jack C. M. Dekkers

Animal Industry Report

Host genetic differences in viral load (VL) and weight gain (WG) during porcine reproductive and respiratory syndrome virus (PRRSV) challenge were assessed for thirteen trials of ~200 commercial crossbred piglets each, from several different commercial suppliers. Piglets were experimentally infected with PRRSV isolates NVSL-97-7895 (NVSL) or KS-2006-72109 (KS06). VL and WG were moderately heritable and were antagonistically related for both virus isolates. The genetic correlation of host response to NVSL with host response to KS06 was high for both VL and WG. Consistent with previous findings, animals that were heterozygous (AB) for the WUR10000125 (WUR) marker on Chromosome 4 (SSC4 ...


Accuracies Of Genomic Prediction Of Traits Associated With Lactation And Reproduction In Yorkshire And Landrace Sows, Dinesh M. Thekkoot, Bob Kemp, Max F. Rothschild, Graham Plastow, Jack C. M. Dekkers 2015 Iowa State University

Accuracies Of Genomic Prediction Of Traits Associated With Lactation And Reproduction In Yorkshire And Landrace Sows, Dinesh M. Thekkoot, Bob Kemp, Max F. Rothschild, Graham Plastow, Jack C. M. Dekkers

Animal Industry Report

Genomic prediction involves statistical methods to estimate the genetic merit of selection candidates based on genetic markers spaced across the genome. The benefit of genomic prediction depends on the accuracies with which we can predict the genomic estimated breeding values (GEBV) of selection candidates based on their marker genotypes. The objective of this study was to estimate the accuracies of GEBV for traits associated with lactation and reproduction in Yorkshire and Landrace sows. Across both breeds, genomic predictions had greater accuracy than pedigree-based predictions. This result suggests that accuracy of selection can be improved by genomic prediction and, thereby, increase ...


Understanding Social Effects In Online Networks, Huda Alhazmi, Swapna S. Gokhale, Derek Doran 2015 Wright State University - Main Campus

Understanding Social Effects In Online Networks, Huda Alhazmi, Swapna S. Gokhale, Derek Doran

Kno.e.sis Publications

Understanding the motives behind people’s interactions online can offer sound bases to predict how a social network may evolve and also support a host of applications. We hypothesize that three offline social factors, namely, stature, relationship strength, and egocentricity may also play an important role in driving users’ interactions online. Therefore, we study the influence of these three social factors in online interactions by analyzing the transitivity in triads or three-way relationships among users. Analyzing transitivity through the lens of triad census for four popular social networks, namely, Facebook, Twitter, YouTube and Slashdot, we find that: (i) users’ interactions ...


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