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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 ...


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.


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 ...


Faces: Diversity-Aware Entity Summarization Using Incremental Hierarchical Conceptual Clustering, Kalpa Gunaratna, Krishnaprasad Thirunarayan, Amit P. Sheth 2015 Wright State University

Faces: Diversity-Aware Entity Summarization Using Incremental Hierarchical Conceptual Clustering, Kalpa Gunaratna, Krishnaprasad Thirunarayan, Amit P. Sheth

Kno.e.sis Publications

Semantic Web documents that encode facts about entities on the Web have been growing rapidly in size and evolving over time. Creating summaries on lengthy Semantic Web documents for quick identification of the corresponding entity has been of great contemporary interest. In this paper, we explore automatic summarization techniques that characterize and enable identification of an entity and create summaries that are human friendly. Specifically, we highlight the importance of diversified (faceted) summaries by combining three dimensions: diversity, uniqueness, and popularity. Our novel diversity-aware entity summarization approach mimics human conceptual clustering techniques to group facts, and picks representative facts from ...


Discovering Perceptions In Online Social Media: A Probabilistic Approach, Derek Doran, Swapna S. Gokhale, Aldo Dagnino 2015 Wright State University - Main Campus

Discovering Perceptions In Online Social Media: A Probabilistic Approach, Derek Doran, Swapna S. Gokhale, Aldo Dagnino

Kno.e.sis Publications

People across the world habitually turn to online social media to share their experiences, thoughts, ideas, and opinions as they go about their daily lives. These posts collectively contain a wealth of insights into how masses perceive their surroundings. Therefore, extracting people’s perceptions from social media posts can provide valuable information about pertinent issues such as public transportation, emergency conditions, and even reactions to political actions or other activities. This paper proposes a novel approach to extract such perceptions from a corpus of social media posts originating from a given broad geographical region. The approach divides the broad region ...


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 ...


Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle 2015 Iowa State University

Differentially Expressed Genes In Blood From Young Pigs Between Two Swine Lines Divergently Selected For Feed Efficiency: Potential Biomarkers For Improving Feed Efficiency, Haibo Liu, Yet T. Nguyen, Daniel S. Nettleton, Jack C. M. Dekkers, Christopher K. Tuggle

Animal Industry Report

The goal of this study was to find potential gene expression biomarkers in blood of piglets that can be used to predict pigs’ future feed efficiency. Using RNA-seq technology, we found 453 genes were differentially expressed (false discovery rate (FDR) ≤ 0.05) in the blood of two Yorkshire lines of pigs divergently selected for feed efficiency (FE) based on residual feed intake (RFI). Genes involved in several biosynthetic processes were overrepresented among genes more highly expressed in the low RFI line compared to the high RFI line. Weighted gene co-expression network analysis (WGCNA) also revealed genes involved in some of ...


Identifying Molecular Differences In Pigs With Extreme Phenotypes For Weight Gain And Viral Load In Response To Prrs, Martine Schroyen, Juan Pedro Steibel, Igseo Choi, James E. Koltes, Christopher J. Eisley, Eric R. Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, Bob R. R. Rowland, Joan K. Lunney, Catherine W. Ernst, Christopher K. Tuggle 2015 Iowa State University

Identifying Molecular Differences In Pigs With Extreme Phenotypes For Weight Gain And Viral Load In Response To Prrs, Martine Schroyen, Juan Pedro Steibel, Igseo Choi, James E. Koltes, Christopher J. Eisley, Eric R. Fritz-Waters, James M. Reecy, Jack C. M. Dekkers, Bob R. R. Rowland, Joan K. Lunney, Catherine W. Ernst, Christopher K. Tuggle

Animal Industry Report

Blood transcriptome analyses in the early phase after infection with the Porcine Reproductive and Respiratory Syndrome virus (PRRSv) revealed differential gene expression patterns and regulatory networks between pigs with extreme phenotypes for weight gain and viral load. Understanding these differences could lead to identifying biomarkers that would predict which pigs would be more resistant to PRRS.


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 ...


Effect Of Wur Genotype And Prrs Vaccination On Pigs Co-Infected With Prrs And Pcv2b, Jenelle R. Dunkelberger, Nick Vergara Lopes Serão, Maureen Kerrigan, Joan Lunney, Bob Rowland, Jack C. M. Dekkers 2015 Iowa State University

Effect Of Wur Genotype And Prrs Vaccination On Pigs Co-Infected With Prrs And Pcv2b, Jenelle R. Dunkelberger, Nick Vergara Lopes Serão, Maureen Kerrigan, Joan Lunney, Bob Rowland, Jack C. M. Dekkers

Animal Industry Report

Average daily gain (ADG) and viral load (VL) were evaluated for pigs co-infected with porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) and porcine circovirus type 2b (PCV2b). Pigs were pre-selected for WUR genotype (a marker on chromosome 4 associated with weight gain and VL under PRRSV-challenge), half were vaccinated for PRRS, and half were not. Results indicate that vaccination for PRRS resulted in slower growth prior to co-infection and that the AB WUR genotype was associated with faster growth prior to co-infection, lower PRRS VL, and lower PCV2b VL in vaccinated pigs.


Accuracy Of Genomic Prediction For Prrs Antibody Response, Nicholas Vergara Lopes Serão, Bob Kemp, Benny Mote, Philip Willson, John Harding, Steve Bishop, Graham Plastow, Jack C. M. Dekkers 2015 Iowa State University

Accuracy Of Genomic Prediction For Prrs Antibody Response, Nicholas Vergara Lopes Serão, Bob Kemp, Benny Mote, Philip Willson, John Harding, Steve Bishop, Graham Plastow, Jack C. M. Dekkers

Animal Industry Report

The accuracy of genomic prediction for antibody response to Porcine Reproductive and Respiratory Syndrome (PRRS), measured as S/P ratio, was evaluated using two independent datasets of Landrace x Large White females. Results demonstrate that antibody response during a PRRS outbreak can be predicted with high accuracy using genetic markers in two regions on chromosome 7. One of these regions includes the Major Histocompatibility Complex. The high accuracy for this region indicates that marker effects are consistent across Landrace x Large White populations.


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 ...


Identifying Glioblastoma Gene Networks Based On Hypergeometric Test Analysis, Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad 2014 University of Miami Miller School of Medicine

Identifying Glioblastoma Gene Networks Based On Hypergeometric Test Analysis, Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo Komotar, Jennifer Clarke, Ming Zhang, Nagi G. Ayad

Faculty Publications, Department of Statistics

Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA). To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in ...


Regulation Of Phialide Morphogenesis In Aspergillus Nidulans, Hu Yin 2014 University of Nebraska-Lincoln

Regulation Of Phialide Morphogenesis In Aspergillus Nidulans, Hu Yin

Dissertations and Theses in Biological Sciences

Filamentous fungi have two distinctive life cycles, vegetative growth and development for sexual or asexual spore formation. The asexual reproduction in development as conidiation in A. nidulans is the dominant form of producing spores effectively. A complex conidiophore structure is developed during asexual reproduction process. The conidiophore is formed from hyphal cell and consists of stalk, vesicle, metulae, phialide and conidial spores. Phialides are essential sporogenous cells in the conidiophore structure. The growth pattern is switched from acropetal to basipetal between phialide and spores, which makes phialide a unique cell type in A. nidulans and other phialide producing fungi. Study ...


Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood 2014 University of Tennessee - Knoxville

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous ...


Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel L. Speiser, Molly S. Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley 2014 University of California - Santa Barbara

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel L. Speiser, Molly S. Pankey, Alexander K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Biology Faculty Publications and Presentations

Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis ...


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