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Seasonal Variation Of Macrolide Resistance Gene Abundances In The South Fork Iowa River Watershed, Elizabeth Luby Rieki, Thomas B. Moorman, Elizabeth L. Douglass, Michelle L. Soupir 2018 Iowa State University

Seasonal Variation Of Macrolide Resistance Gene Abundances In The South Fork Iowa River Watershed, Elizabeth Luby Rieki, Thomas B. Moorman, Elizabeth L. Douglass, Michelle L. Soupir

Agricultural and Biosystems Engineering Publications

The Midwestern United States is dominated by agricultural production with high concentrations of swine, leading to application of swine manure onto lands with artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations which administer antimicrobials. While previous studies have examined the occurrence of ARGs around confined swine feeding operations, little information is known how their transport from tile-drained fields receiving swine manure application impacts downstream environments. To further our knowledge in this area, water samples were collected from five locations in the agriculturally dominated South ...


Genetic Diversity In Hypericum And Aflp Markers For Species-Specific Identification Of H. Perforatum L., Ryan J. Percifield, Jennifer S. Hawkins, Joe-Ann McCoy, Mark P. Widrlechner, Jonathan F. Wendel 2017 Iowa State University

Genetic Diversity In Hypericum And Aflp Markers For Species-Specific Identification Of H. Perforatum L., Ryan J. Percifield, Jennifer S. Hawkins, Joe-Ann Mccoy, Mark P. Widrlechner, Jonathan F. Wendel

Jonathan F. Wendel

One of the top-selling medicinal products worldwide is Hypericum perforatum (St. John's Wort). Despite its cosmopolitan distribution and utilization, little is known regarding the relationship of the bioactive compounds in H. perforatum to the plants from which they are purportedly derived. In this study, amplified fragment length polymorphism (AFLP) analysis of 56 Hypericum accessions, representing 11 species, was conducted to gain a better understanding of diversity within Hypericum species, especially within cultivated accessions of H. perforatum, and to establish a molecular methodology that will provide breeders and regulators with a simple, affordable, and accurate tool with which to identify ...


Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin 2017 The University of Western Ontario

Characterization Of Acaricide Resistance, Plant-Mediated Rnai Against Two-Spotted Spider Mites (Tetranychus Urticae Koch), And Assessing Off- And Non-Target Effects, Hooman Hosseinzadeh Namin

Electronic Thesis and Dissertation Repository

The two-spotted spider mite (TSSM), Tetranychus urticae (Koch), is one of the most damaging agricultural pests in the world. It feeds on over 150 crops, causing considerable yield losses in greenhouses and agricultural fields. Currently, using synthetic acaricides is the main method to control TSSM. However, it can develop resistance to acaricides with repeated exposure, and typically resistance can occur within two to four years. To understand the underlying mechanisms of spider mite adaptation to acaricides is an essential part of resistance management strategy. The resistance ratio of the pyridaben-selected strain compared with the pre-selection strain was estimated at greater ...


Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle 2017 University of Nebraska - Lincoln

Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle

UCARE Research Products

Possessing some of the largest and most complex genomes of any eukaryotic organelles, plant mitochondria are notorious for their rapidly rearranging genetic framework. In addition to containing a large and complex mitochondrial genome, the mitochondria of several plants in the genus Brassica have also been shown to contain an independent, self-replicating linear plasmid. Interestingly, the plasmid appears to be able to move independently between the cytoplasm and the mitochondria, and it can be paternally inherited, unlike the rest of the mitochondrial genome. The plasmid also has features similar to those of adenoviruses, including terminal inverted repeats and covalently bound proteins ...


Affine Cipher Cryptanalysis Using Genetic Algorithms, Yaqeen S. Mezaal, Seevan Fahmy 2017 Al-Esraa University College

Affine Cipher Cryptanalysis Using Genetic Algorithms, Yaqeen S. Mezaal, Seevan Fahmy

Seevan F. Abdulkareem

Genetic algorithms (GAs) have been used as a powerful tool for cryptanalyzing affine ciphers in this paper for the first time. They are one of heuristic search techniques which use natural selection. They select the optimal solution by using selection, crossover and mutation operations. The useful parameters in GAs are kept in the memory and the best values of fitness have been selected to represent the next generation. The frequencies of single letter have been used as an essential factor in the fitness function of the adopted GAs operations for affine cryptanalysis. By this tool, a high number of letters ...


Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering 2017 Loyola University Chicago

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Catherine Putonti

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the ...


An Adaptable Pentaloop Defines A Robust Neomycin-B Rna Aptamer With Conditional Ligand-Bound Structures, Muslum Ilgu, D. Bruce Fulton, Ragothaman M. Yennamalli, Monica H. Lamm, Taner Z. Sen, Marit Nilsen-Hamilton 2017 Iowa State University

An Adaptable Pentaloop Defines A Robust Neomycin-B Rna Aptamer With Conditional Ligand-Bound Structures, Muslum Ilgu, D. Bruce Fulton, Ragothaman M. Yennamalli, Monica H. Lamm, Taner Z. Sen, Marit Nilsen-Hamilton

Monica H. Lamm

Aptamers can be highly specific for their targets, which implies precise molecular recognition between aptamer and target. However, as small polymers, their structures are more subject to environmental conditions than the more constrained longer RNAs such as those that constitute the ribosome. To understand the balance between structural and environmental factors in establishing ligand specificity of aptamers, we examined the RNA aptamer (NEO1A) previously reported as specific for neomycin-B. We show that NEO1A can recognize other aminoglycosides with similar affinities as for neomycin-B and its aminoglycoside specificity is strongly influenced by ionic strength and buffer composition. NMR and 2-aminopurine (2AP ...


Life’S Late Digital Revolution And Why It Matters For The Study Of The Origins Of Life, David A. Baum, Niles Lehman 2017 University of Wisconsin-Madison

Life’S Late Digital Revolution And Why It Matters For The Study Of The Origins Of Life, David A. Baum, Niles Lehman

Chemistry Faculty Publications and Presentations

The information contained in life exists in two forms, analog and digital. Analog information is manifest mainly in the differing concentrations of chemicals that get passed from generation to generation and can vary from cell to cell. Digital information is encoded in linear polymers such as DNA and RNA, whose side chains come in discrete chemical forms. Here, we argue that the analog form of information preceded the digital. Acceptance of this dichotomy, and this progression, can help direct future studies on how life originated and initially complexified on the primordial Earth, as well as expected trajectories for other, independent ...


Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt 2017 University of Texas at Tyler

Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt

Biology Theses

The recent development of DNA-based species classification methods has led to the revision of many morphology-based species designations as genetic data has provided new information for species delineation. Analysis of standardized DNA ‘barcoding’ gene regions has proven particularly effective in resolving the taxonomic status of taxa that display phenotypic and habitat overlap.

Freshwater Unionid and Margaritiferid mussels comprise one of the most diverse aquatic taxa in North America, but are also among the most threatened, with over 70% of the approximately 300 native species considered at-risk or in decline. Although mussels face extensive threats from anthropogenic activity, conservation efforts have ...


Accurate Cytogenetic Biodosimetry Through Automated Dicentric Chromosome Curation And Metaphase Cell Selection, Jin Liu, Yanxin Li, Ruth Wilkins, Canadian Nuclear Laboratories, Joan H. Knoll, Peter Rogan 2017 Western University

Accurate Cytogenetic Biodosimetry Through Automated Dicentric Chromosome Curation And Metaphase Cell Selection, Jin Liu, Yanxin Li, Ruth Wilkins, Canadian Nuclear Laboratories, Joan H. Knoll, Peter Rogan

Biochemistry Publications

Accurate digital image analysis of abnormal microscopic structures relies on high quality images and on minimizing the rates of false positive (FP) and negative objects in images. Cytogenetic biodosimetry detects dicentric chromosomes (DCs) that arise from exposure to ionizing radiation, and determines radiation dose received based on DC frequency. Improvements in automated DC recognition increase the accuracy of dose estimates by reclassifying FP DCs as monocentric chromosomes or chromosome fragments. We also present image segmentation methods to rank high quality digital metaphase images and eliminate suboptimal metaphase cells. A set of chromosome morphology segmentation methods selectively filtered out FP DCs ...


Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster 2017 University of Massachusetts Medical School

Intergenerational Effects Of Nicotine In An Animal Model Of Paternal Nicotine Exposure, Markus Parzival Vallaster

GSBS Dissertations and Theses

Environmental conditions imposed onto organisms during certain phases of their life cycles such as embryogenesis or puberty can not only impact the organisms’ own health, but also affect subsequent generations. The underlying mechanisms causing intergenerational phenotypes are not encoded in the genome, but the result of reversible epigenetic modifications. This work investigates in a mouse model the impact of paternal nicotine exposure on the next generation regarding addictive behavior modulation, metabolic changes, and molecular mechanisms. It provides evidence that male offspring from nicotine-exposed fathers (NIC offspring) is more resistant to lethal doses of nicotine. This phenotype is gender-specific and depends ...


Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran 2017 Purdue University

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being ...


Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey 2017 University of Arkansas, Fayetteville

Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey

Theses and Dissertations

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens ...


The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers 2017 University of Louisville

The Dlk1-Meg3 Locus In Malignant Cells Of Proposed Primordial Germ Cell Origins., Zachariah Payne Sellers

Electronic Theses and Dissertations

Primordial germ cells (PGCs) are hypothesized to deposit hematopoietic stem cells (HSCs) along their migration route through the embryo during the early stages of embryogenesis. PGCs also undergo global chromatin remodeling, including the erasure and reestablishment of genomic imprints, during this migration. While PGCs do not spontaneously form teratomas, their malignant development into germ cell tumors (GCTs) in vivo is often accompanied by the retention of hypomethylation at the IGF2-H19 imprinting control differentially methylated region (DMR). Previous studies in bimaternal embryos determined that proper genomic imprinting at two paternally imprinted loci was necessary for their growth and development: Igf2-H19 and ...


Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta 2017 Old Dominion University

Anaplasma Phagocytophilum Infection Modulates Expression Of Megakaryocyte Cell Cycle Genes Through Phosphatidylinositol-3-Kinase Signaling, Supreet Khanal, Hameeda Sultana, John D. Catravas, Jason A. Carlyon, Girish Neelakanta

Biological Sciences Faculty Publications

Anaplasma phagocytophilum, the agent of human granulocytic anaplasmosis infects neutrophils and other cells from hematopoietic origin. Using human megakaryocytic cell line, MEG-01, we show that expression of cell cycle genes in these cells are altered upon A. phagocytophilum infection. Expression of several cell cycle genes in MEG-01 cells was significantly up regulated at early and then down regulated at later stages of A. phagocytophilum infection. Lactate dehydrogenase (LDH) assays revealed reduced cellular cytotoxicity in MEG-01 cells upon A. phagocytophilum infection. The levels of both PI3KCA (p110 alpha, catalytic subunit) and PI3KR1 (p85, regulatory subunit) of Class I PI3 kinases and ...


Identifying Three-Way Gene Interactions From Microarray Data Using Kolmogorov-Smirnov And Cross-Match Tests, Shubhashree Khadka 2017 University of Arkansas, Fayetteville

Identifying Three-Way Gene Interactions From Microarray Data Using Kolmogorov-Smirnov And Cross-Match Tests, Shubhashree Khadka

Theses and Dissertations

Human gene network is much more complex than just pairwise interaction among the genes. Zhang et al. [6] extracted microarray data from International Genomics Consortium (IGC), and presented the detection of three-way gene interactions in their paper using Fisher’s z-transformation test. Three-way gene interactions are closer than pairwise correlations in representing the complex gene structures. Additionally, it was more tractable than assessing four or more gene interactions. In this paper, we are simulating different models where Fisher’s test might not be as effective. Zhang et al.’s approach utilized Pearson’s correlation coefficients and involved detection of linear ...


Comprehensive Assessments Of The Genetic Determinants In Salmonella Typhimurium For Fitness Under Host Stressors: Oxidative Stress And Iron Restriction, Sardar Abdullah 2017 University of Arkansas, Fayetteville

Comprehensive Assessments Of The Genetic Determinants In Salmonella Typhimurium For Fitness Under Host Stressors: Oxidative Stress And Iron Restriction, Sardar Abdullah

Theses and Dissertations

Salmonella is an intracellular pathogen that infects a wide range of hosts. The infected host utilizes reactive oxygen species (ROS) and iron-restriction to eliminate the pathogen. We used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a highly saturated Tn5 library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes that are required for resistance of S. Typhimurium to H2O2L and H2O2H, and the results were validated via phenotypic evaluation of 50 selected mutants ...


Molecular And Pathological Analyses Of Three New Mouse Mutations That Affect Ear Development And Function, Cong Tian 2017 University of Maine

Molecular And Pathological Analyses Of Three New Mouse Mutations That Affect Ear Development And Function, Cong Tian

Electronic Theses and Dissertations

This dissertation presents three new mouse models that help to study the functions of Enpp1, Atp6v1b1, and Tbx1 for ear development and function. asj (aging with stiffened joints) carries a missense mutation in the mouse Enpp1 gene. Enpp1 encodes the enzyme ENPP1 that regulate soft-tissue calcification and bone mineralization, and is associated with generalized arterial calcification of infancy and hypophosphatemic rickets in human patients. asj mutant mice show severe middle ear infection and tissue calcification, which provide a new mouse model to study otitis media and tympanoscleorosis. Atp6v1b1 encode a protein that is a subunit of the V-ATPase pump, which ...


Characterization Of The Biological Role Of The Ciliopathy Gene Serologically Defined Colon Cancer Antigen 8 (Sdccag8), Katie A. Weihbrecht 2017 University of Iowa

Characterization Of The Biological Role Of The Ciliopathy Gene Serologically Defined Colon Cancer Antigen 8 (Sdccag8), Katie A. Weihbrecht

Theses and Dissertations

The primary cilium is vital for the health and well being of the organism. Diseases of the cilia, referred to as ciliopathies, present with overlapping phenotypes due to a protein defect in the same organelle. Three such disorders are Nephronophthisis (NPHP), Bardet-Biedl Syndrome (BBS), and Senior-Loken Syndrome (SLS). Mutations in serologically defined colon cancer antigen 8(SDCCAG8 [MIM 613524]) have been associated with all of these disorders (BBS16, NPHP10, SLSN7). Little is known about the role of SDCCAG8 in ciliary function, and the mechanisms through which SDCCAG8 leads to ciliopathy phenotypes are potentially novel and may identify therapeutic targets for ...


A State-Wide Initiative To Promote Genetic Testing In An Underserved Population, Meghan L. Underhill, Traci M. Blonquist, Karleen Habin, Debra Lundquist, Kristen Shannon, Kathryn Robinson, Mary-Lou Woodford, Jean Boucher 2017 Dana-Farber Cancer Institute

A State-Wide Initiative To Promote Genetic Testing In An Underserved Population, Meghan L. Underhill, Traci M. Blonquist, Karleen Habin, Debra Lundquist, Kristen Shannon, Kathryn Robinson, Mary-Lou Woodford, Jean Boucher

Open Access Articles

Genetic testing for cancer susceptibility has been widely studied and utilized clinically. Access to genetic services in research and practice is largely limited to well-insured, Caucasian individuals. In 2009, the Cancer Resource Foundation (CRF) implemented the Genetic Information for Treatment Surveillance and Support (GIFTSS) program to cover the out-of-pocket expenses associated with cancer genetic testing, targeting high-risk individuals with limited financial means and limited health insurance coverage. Here, we (i) describe the characteristics of participants in the Massachusetts (MA) GIFTSS program and (ii) evaluate mutations found in this diverse sample. A secondary retrospective data analysis was performed using de-identified demographic ...


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