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Infectious Disease And The Diversification Of The Human Genome, Jessica F. Brinkworth 2017 University of Illinois Urbana-Champaign

Infectious Disease And The Diversification Of The Human Genome, Jessica F. Brinkworth

Human Biology Open Access Pre-Prints

The human immune system is under great pathogen-mediated selective pressure. A combination of divergent infectious disease pathogenesis across human populations, and the overrepresentation of “immune genes” in genomic regions with signatures of positive selection suggests that pathogens have significantly altered the human genome. However, important features of the human immune system can confound searches for and interpretations of signatures of pathogen-mediated evolution. Immune system redundancy, immune gene pleiotropy, host ability to acquire immunity and alter the immune repertoire of their offspring through “priming”, and host microbiome complicate evolutionary interpretations of host- pathogen interactions. The overall promiscuity and sensitivity of the ...


Comparative Phylogeographic, Population Genomic, And Selection Inference With Development Of Hierarchical Co-Demographic Models, Alexander Xue 2017 The Graduate Center, City University of New York

Comparative Phylogeographic, Population Genomic, And Selection Inference With Development Of Hierarchical Co-Demographic Models, Alexander Xue

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Comparing demographic histories across assemblages of populations, species, and sister pairs has been a focus in phylogeography since its inception. Initial approaches utilized organelle genetic data and involved qualitative comparisons of genetic patterns for evaluating hypotheses of shared evolutionary responses to past environmental changes. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can analyze aggregated genomic-scale data from non-model organisms within a unified framework that considers individual taxon uncertainty and variance. To this end, the aggregate site frequency spectrum (aSFS), an expansion of the site frequency ...


Regulatory Rna: Session Introduction, Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris 2017 Iowa State University

Regulatory Rna: Session Introduction, Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris

Robert Jernigan

Advances in both experimental and computational approaches to genome-wide analysis of RNA transcripts have dramatically expanded our understanding of the ubiquitous and diverse roles of regulatory non-coding RNAs. This conference session includes presentations exploring computational approaches for detecting regulatory RNAs in RNA-Seq data, for analyzing in vivo CLIP data on RNA-protein interactions, and for predicting interfacial residues involved in RNA-protein recognition in RNA–protein complexes and interaction networks.


Amelioration Of Prenatal Alcohol Effects By Environmental Enrichment In A Mouse Model Of Fasd, Aniruddho Chokroborty-Hoque 2017 The University of Western Ontario

Amelioration Of Prenatal Alcohol Effects By Environmental Enrichment In A Mouse Model Of Fasd, Aniruddho Chokroborty-Hoque

Electronic Thesis and Dissertation Repository

Maternal alcohol consumption during pregnancy results in a spectrum of behavioural and cognitive deficits collectively known as Fetal Alcohol Spectrum Disorders (FASD). Currently, little is know about if and how the external environment may modulate these deficits. I have used C57BL/6 mice to study this interaction between prenatal alcohol exposure and the postnatal environment. Alcohol exposure during synaptogenesis produces high levels of anxiety-like traits and decreased memory performance. Alcohol-exposed mice (and matched unexposed controls) were put in 'environmentally-enriched' conditions of voluntary exercise, physical activities and cognitive stimulation to ascertain the effects of a positive postnatal environment. The results show ...


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin 2017 United States Department of Agriculture

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin

Andrew Severin

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and ...


Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela 2017 Iowa State University

Transcriptomic Responses To Environmental Temperature By Turtles With Temperature-Dependent And Genotypic Sex Determination Assessed By Rnaseq Inform The Genetic Architecture Of Embryonic Gonadal Development, Srihari Radhakrishnan, Robert A. Literman, Jennifer L. Neuwald, Andrew Severin, Nicole Valenzuela

Andrew Severin

Vertebrate sexual fate is decided primarily by the individual’s genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera—GSD), to test whether TSD’s and GSD’s transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle ...


Transcript Profiles In Longissimus Dorsi Muscle And Subcutaneous Adipose Tissue: A Comparison Of Pigs With Different Postweaning Growth Rates, C. M. Pilcher, C. K. Jones, M. Schroyen, A. J. Severin, J. F. Patience, C. K. Tuggle, J. E. Koltes 2017 Iowa State University

Transcript Profiles In Longissimus Dorsi Muscle And Subcutaneous Adipose Tissue: A Comparison Of Pigs With Different Postweaning Growth Rates, C. M. Pilcher, C. K. Jones, M. Schroyen, A. J. Severin, J. F. Patience, C. K. Tuggle, J. E. Koltes

Andrew Severin

Although most pigs recover rapidly from stresses associated with the transition of weaning, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in postweaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs was reared in commercial conditions and weighed at birth, weaning, and 3 wk postweaning. Transition ADG (tADG) was calculated as the ADG for the ...


Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti 2017 Iowa State University

Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti

Andrew Severin

The Tec family kinase, Itk (interleukin-2 tyrosine kinase), undergoes an in cis autophosphorylation on Y180 within its Src homology 3 (SH3) domain. Autophosphorylation of the Itk SH3 domain by the Itk kinase domain is strictly dependent on the presence of the intervening Src homology 2 (SH2) domain. A direct docking interaction between the Itk kinase and SH2 domains brings the Itk SH3 domain into the active site where Y180 is then phosphorylated. We now identify the residues on the surface of the Itk SH2 domain responsible for substrate docking and show that this SH2 surface mediates autophosphorylation in the full-length ...


Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima 2017 The University of Western Ontario

Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima

Electronic Thesis and Dissertation Repository

The study of organelles helped forge theories of genome evolution because of their unconventional genomes and gene expression regimes. The organelle genomics field (~35 years old) has seen the development of next generation sequencing (NGS) techniques and the consequent skyrocketing of genomic and transcriptomic data. However, these data are being underused in the studies of organelle genome transcription. My thesis investigates how NGS has affected the field of organelle genomics at both the DNA and RNA levels. First, I demonstrate that although organelle genomes are being sequenced as never before, they are un-characterized as they are published mostly as “organelle ...


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen 2017 United States Department of Agriculture

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription In The Swine Gut Microbiome, Timothy A. Johnson, Torey Looft, Andrew J. Severin, Darrell O. Bayles, Daniel J. Nasko, K. Eric Wommack, Adina Howe, Heather K. Allen

Agricultural and Biosystems Engineering Publications

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the ...


Vascular Endothelial Growth Factor A And Leptin Expression Associated With Ectopic Proliferation And Retinal Dysplasia In Zebrafish Optic Pathway Tumors, Laura E. Schultz, Staci L. Solin, Welsey A. Wierson, Janna M. Lovan, Judith Syrkin-Nikolau, Deborah E. Lincow, Andrew J. Severin, Donald S. Sakaguchi, Maura McGrail 2017 Iowa State University

Vascular Endothelial Growth Factor A And Leptin Expression Associated With Ectopic Proliferation And Retinal Dysplasia In Zebrafish Optic Pathway Tumors, Laura E. Schultz, Staci L. Solin, Welsey A. Wierson, Janna M. Lovan, Judith Syrkin-Nikolau, Deborah E. Lincow, Andrew J. Severin, Donald S. Sakaguchi, Maura Mcgrail

Genetics, Development and Cell Biology Publications

the central nervous system injury induces cellular reprogramming and progenitor proliferation, but the molecular mechanisms that limit regeneration and prevent tumorigenesis are not completely understood. We previously described a zebrafish optic pathway tumor model in which transgenic Tg(flk1:RFP)is18/+ adults develop nonmalignant retinal tumors. Key pathways driving injury-induced glial reprogramming and regeneration contributed to tumor formation. In this study, we examine a time course of proliferation and present new analyses of the Tg(flk1:RFP)is18/+ dysplastic retina and tumor transcriptomes. Retinal dysplasia was first detected in 3-month-old adults, but was not limited to a specific stem cell ...


An Approach To Identify Mycobacteriophage Diversity Prior To Dna Sequencing, Charles Gregory 2017 Western Kentucky University

An Approach To Identify Mycobacteriophage Diversity Prior To Dna Sequencing, Charles Gregory

Honors College Capstone Experience/Thesis Projects

Over 6,869 Mycobacteriophages have been isolated and purified. Of these, 1,367 genomes have been sequenced at the DNA level and more are added each year through the SEA-PHAGES program. Sequenced mycobacteriophages are grouped into clusters based on a 50% or greater nucleotide identity. The number and breadth of these clusters represents the diversity present in the environment. Each year, as new phages are discovered by students in the SEA-PHAGES program, the question arises, “Which isolates should we sequence?” In order to sequence phages that represent the greatest possible diversity, and thus broaden under-represented clusters and identify new singletons ...


Microbiome Analyses Of Pacific White Shrimp (Litopenaeus Vannamei) Collected From Disparate Geographical Locations, Arun S. Seetharam, Emily Kawaler, Zhi-Qiang Du, Max F. Rothschild, Andrew J. Severin 2017 Iowa State University

Microbiome Analyses Of Pacific White Shrimp (Litopenaeus Vannamei) Collected From Disparate Geographical Locations, Arun S. Seetharam, Emily Kawaler, Zhi-Qiang Du, Max F. Rothschild, Andrew J. Severin

Max Rothschild

In this study, the tail muscle microbiota of pacific white shrimp (Litopenaeus vannamei) sourced from five countries across Central and South America and Southeast Asia were determined and compared. The genomic DNA was sequenced at around 10 × coverage for each geographical location and was assembled de novo for comparative analysis. The assembled sequences for all the lines were classified based on their similarity to the sequences in the public database. We found that there is high correlation among the microbiota of shrimp from disparate regions, as well as the presence of some DNA from bacteria known to cause food poisoning ...


Reconstructing Genome-Wide Regulatory Network Of E. Coli Using Transcriptome Data And Predicted Transcription Factor Activities, Yao Fu, Laura R. Jarboe, Julie A. Dickerson 2017 Iowa State University

Reconstructing Genome-Wide Regulatory Network Of E. Coli Using Transcriptome Data And Predicted Transcription Factor Activities, Yao Fu, Laura R. Jarboe, Julie A. Dickerson

Laura R. Jarboe

Background: Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes. Understanding the connections and the activity levels of regulators is important for the research of gene regulatory networks. While relevance score based algorithms that reconstruct gene regulatory networks from transcriptome data can infer genome-wide gene regulatory networks, they are unfortunately prone to false positive results. Transcription factor activities (TFAs) quantitatively reflect the ability of the transcription factor to regulate target genes. However, classic relevance score based gene regulatory network reconstruction algorithms use models do not include the ...


Genome Sequence Of The Psychrophilic Deep-Sea Bacterium Moritella Marina Mp-1 (Atcc 15381), Kumar Babu Kautharapu, Laura R. Jarboe 2017 Iowa State University

Genome Sequence Of The Psychrophilic Deep-Sea Bacterium Moritella Marina Mp-1 (Atcc 15381), Kumar Babu Kautharapu, Laura R. Jarboe

Laura R. Jarboe

Moritella marina MP-1 is a bacterial species known for its production of docosahexaenoic acid. We present the draft genome sequence of the type strainMoritella marina MP-1 (ATCC 15381), having 4,636,778 bp with a G+C content of 40.5% and consisting of 83 contigs.


Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan 2017 The Graduate Center, City University of New York

Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 ...


Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti 2017 Iowa State University

Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti

Amy Andreotti

The Tec family kinase, Itk (interleukin-2 tyrosine kinase), undergoes an in cis autophosphorylation on Y180 within its Src homology 3 (SH3) domain. Autophosphorylation of the Itk SH3 domain by the Itk kinase domain is strictly dependent on the presence of the intervening Src homology 2 (SH2) domain. A direct docking interaction between the Itk kinase and SH2 domains brings the Itk SH3 domain into the active site where Y180 is then phosphorylated. We now identify the residues on the surface of the Itk SH2 domain responsible for substrate docking and show that this SH2 surface mediates autophosphorylation in the full-length ...


Shelterin Components Mediate Genome Reorganization In Response To Replication Stress, Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter FitzGerald, Job Dekker, Shiv I. Grewal S 2017 National Institutes of Health

Shelterin Components Mediate Genome Reorganization In Response To Replication Stress, Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter Fitzgerald, Job Dekker, Shiv I. Grewal S

Program in Systems Biology Publications and Presentations

The dynamic nature of genome organization impacts critical nuclear functions including the regulation of gene expression, replication, and DNA damage repair. Despite significant progress, the mechanisms responsible for reorganization of the genome in response to cellular stress, such as aberrant DNA replication, are poorly understood. Here, we show that fission yeast cells carrying a mutation in the DNA-binding protein Sap1 show defects in DNA replication progression and genome stability and display extensive changes in genome organization. Chromosomal regions such as subtelomeres that show defects in replication progression associate with the nuclear envelope in sap1 mutant cells. Moreover, high-resolution, genome-wide chromosome ...


Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew McDermut 2017 Washington University in St. Louis

Isolation And Comparative Genomic Analysis Of Final Third Of Satis Genome, Kelly Hartigan, Nicole Curnutt, Matthew Mcdermut

Undergraduate Research Symposium Posters

A highly novel Streptomyces phage, Satis, was isolated from a direct environmental sample collected from outside Danforth House on the Washington University campus. Satis infects bacterial species Streptomyces lividans producing pinpoint, cloudy plaques less than 1mm in diameter. Electron microscope data shows rare atypical physical features. Rather than the common octahedral capsid shape, Satis has a prolate head with visible cross-linked hexagonal protein structure and average measurements of 285 nm by 47 nm with a long, flexible tail measuring 268 nm. Upon sequencing, it was found that Satis contains the longest phage genome discovered to date through the SEA-PHAGE program ...


Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, Keira C. Davis 2017 Clark Atlanta University

Characterization Of Zic2 As An Oncoprotein In Prostate Cancer, Keira C. Davis

Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University

The field of prostate cancer research is in need of biological markers that predict which cancers do not need treatment, those that can be treated successfully with a localized treatment and more specific cases in which patients are likely to have an aggressive form of cancer that will require more aggressive surgical and chemotherapeutic treatments. ZIC2 is one of five members of a family of proteins that play critical roles in neural crest and mesoderm growth in normal embryonic brain development and in the adult cerebellum of vertebrates. Found throughout the animal kingdom, ZIC1-5 genes encode five distinct ZIC proteins ...


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