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Practical Implications Of Erythromycin Resistance Gene Diversity On Surveillance And Monitoring Of Resistance, Elizabeth L. Rieke, Jinlyung Choi, Thomas B. Moorman, Michelle L. Soupir, Heather K. Allen, Schuyler D. Smith, Adina Howe 2018 Iowa State University

Practical Implications Of Erythromycin Resistance Gene Diversity On Surveillance And Monitoring Of Resistance, Elizabeth L. Rieke, Jinlyung Choi, Thomas B. Moorman, Michelle L. Soupir, Heather K. Allen, Schuyler D. Smith, Adina Howe

Agricultural and Biosystems Engineering Publications

Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals, and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers ...


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 ...


Conservation And Variation Of Dna Methylation In Lactuca Sativa And Lactuca Serriola, Trudi A. Baker 2017 University of Massachusetts Boston

Conservation And Variation Of Dna Methylation In Lactuca Sativa And Lactuca Serriola, Trudi A. Baker

Graduate Doctoral Dissertations

Molecular techniques for guiding plant breeding have successfully used wild progenitors of domestic crops as sources of genetic variants conveying desirable traits. However, epigenetic variation, in particular DNA methylation, is a significant source of phenotypic variation and epigenetic effects of plant domestication are poorly understood. Described herein are the first single-base pair resolution methylomes of the highly valued crop iceberg lettuce (Lactuca sativa cv. Salinas) and its close relative, and ubiquitous weed, L. serriola. This work suggests several roles for acquisition and inheritance of methylation in the evolution of Lactuca spp. in response to stress. The Lactuca spp. have conserved ...


Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli 2017 University of Massachusetts Medical School

Identification Of Factors Involved In 18s Nonfunctional Ribosomal Rna Decay And A Method For Detecting 8-Oxoguanosine By Rna-Seq, Kelly A. Limoncelli

GSBS Dissertations and Theses

The translation of mRNA into functional proteins is essential for all life. In eukaryotes, aberrant RNAs containing sequence features that stall or severely slow down ribosomes are subject to translation-dependent quality control. Targets include mRNAs encoding a strong secondary structure (No-Go Decay; NGD) or stretches of positively-charged amino acids (Peptide-dependent Translation Arrest/Ribosome Quality Control; PDTA/RQC), mRNAs lacking an in-frame stop codon (Non-Stop Decay; NSD), or defective 18S rRNAs (18S Nonfunctional rRNA Decay; 18S NRD). Previous work from our lab showed that the S. cerevisiae NGD factors DOM34 and HBS1, and PDTA/RQC factor ASC1, all participate in the ...


Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey 2017 Maseno University

Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey

Ann M. Moormann

BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells.

METHODS: Using more sensitive ...


Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens 2017 University of Dayton

Mechanical Test Methods For Assessing Porcine Carotid And Uterine Artery Burst Pressure Following Ex Vivo Ultrasonic Ligature Seal And Transection, Carissa M. Krane, Margaret Pinnell, Courtney Gardner, Mercedes Thompson, James Coleman, Robert Wilkens

Robert J. Wilkens

A test method was developed to identify those variables important for assessing the performance of ultrasonic surgical devices in ex vivo ligature sealing of porcine carotid and uterine arteries. Ruggedness testing using a small sample size in pilot experiments was conducted using a newly developed test method in an effort to assess the usefulness of this methodology and to identify test variables that might warrant further testing. The development of this test method included the use of a custom-designed prototypic tension device for load-controlled ex vivo vessel stretching during saline perfusion and subsequent seal and transection of porcine arteries with ...


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 2017 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

Michelle L. Soupir

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 ...


Development Of New Bioinformatic Approaches For Human Genetic Studies, Jose Andres Guevara Coto 2017 Clemson University

Development Of New Bioinformatic Approaches For Human Genetic Studies, Jose Andres Guevara Coto

All Dissertations

The development of bioinformatics methods for human genetic studies utilizes the vast amount of data to generate new valuable information. Machine learning and statistical coupling analysis can be used in the study of human diseases. These diseases include intellectual disabilities (ID), prevalent in 1-3% of the population and caused primarily by genetics. Although many cases of ID are caused by mutations in protein-coding genes, the possible involvement of long non-coding RNAs (lncRNAs) in ID due to their role in gene expression regulation, has been explored. In this study, we used machine learning to develop a new expression-based model trained using ...


Role Of Incompatibility Group 1 (Inci1) Plasmid-Encoded Factors On Salmonella Enterica Antimicrobial Resistance And Virulence, Pravin Raghunath Kaldhone 2017 University of Arkansas, Fayetteville

Role Of Incompatibility Group 1 (Inci1) Plasmid-Encoded Factors On Salmonella Enterica Antimicrobial Resistance And Virulence, Pravin Raghunath Kaldhone

Theses and Dissertations

Foodborne illnesses are a leading cause of infectious diseases in the world. Among enteric organisms Salmonella is a key pathogen. It’s high prevalence in poultry and other food-animal sources make it imperative to study. Salmonella has the ability to modify its genetic content with help of mobile genetic elements such as plasmids. Incompatibiltiy group 1 (IncI1) plasmids are commonly reported in Salmonella. This study evaluates role on IncI1 plasmids in antimicrobial resistance and virulence in Salmonella. Genetic determinants of resistance and virulence are noted among our IncI1-containing Salmonella isolates. These genetic elements are also transferable and reported to carry ...


Characterizing Mekk1: Candidate Behavioural Isolation Gene, Caryn Dooner 2017 The University of Western Ontario

Characterizing Mekk1: Candidate Behavioural Isolation Gene, Caryn Dooner

Electronic Thesis and Dissertation Repository

Behavioural isolation can occur due to divergence in aspects of courtship and mating, and can contribute to reproductive isolation. The purpose of this study is to determine how a gene, Mekk1, contributes to female rejection behaviour between D. melanogaster and D. simulans. Unique polymorphisms were identified within D. simulans Mekk1 that could contribute to behaviour, most of which are non-coding. Both transcripts of Mekk1 appear to be expressed at similar levels in D. simulans and D. melanogaster. These data also indicate that Mekk1 may be expressed in a specific region of the brain called the mushroom body, which has previously ...


Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly 2017 Chapman University

Genomic Data Reveal A Loss Of Diversity In Two Species Of Tuco-Tucos (Genus Ctenomys) Following A Volcanic Eruption, Jeremy L. Hsu, Jeremy Chase Crawford, Mauro N. Tammone, Uma Ramakrishnan, Eileen A. Lacey, Elizabeth A. Hadly

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Marked reductions in population size can trigger corresponding declines in genetic variation. Understanding the precise genetic consequences of such reductions, however, is often challenging due to the absence of robust pre- and post-reduction datasets. Here, we use heterochronous genomic data from samples obtained before and immediately after the 2011 eruption of the Puyehue-Cordón Caulle volcanic complex in Patagonia to explore the genetic impacts of this event on two parapatric species of rodents, the colonial tuco-tuco (Ctenomys sociabilis) and the Patagonian tuco-tuco (C. haigi). Previous analyses using microsatellites revealed no post-eruption changes in genetic variation in C. haigi, but an unexpected ...


Exploiting Fission Yeast Genetic Interaction Data To Identify Disease-Specific Drug Targets For Tuberous Sclerosis Complex, Ashyad Rayhan 2017 The University of Western Ontario

Exploiting Fission Yeast Genetic Interaction Data To Identify Disease-Specific Drug Targets For Tuberous Sclerosis Complex, Ashyad Rayhan

Electronic Thesis and Dissertation Repository

Tuberous sclerosis complex (TSC) is an inherited genetic disorder caused by loss-of-function mutations in either TSC1 or TSC2. Their respective gene products regulate the mechanistic target of rapamycin (mTOR) signaling pathway, which serves as an activator of cellular proliferation, metabolism, and cell survival. Orthologs of the TSC1 and TSC2 genes exist in a wide range of organisms, including the commonly used and genetically tractable model eukaryote, Schizosaccharomyces pombe. To better understand the functional roles of S. pombe tsc1 and tsc2, I exploited recent advances in genetic interaction biology to identify and characterize genes that modulate the phenotypic effects of tsc1 ...


Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey 2017 Maseno University

Integrative Microrna And Mrna Deep-Sequencing Expression Profiling In Endemic Burkitt Lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, Jeffrey A. Bailey

UMass Center for Clinical and Translational Science Supported Publications

BACKGROUND: Burkitt lymphoma (BL) is characterized by overexpression of the c-myc oncogene, which in the vast majority of cases is a consequence of an IGH/MYC translocation. While myc is the seminal event, BL is a complex amalgam of genetic and epigenetic changes causing dysregulation of both coding and non-coding transcripts. Emerging evidence suggest that abnormal modulation of mRNA transcription via miRNAs might be a significant factor in lymphomagenesis. However, the alterations in these miRNAs and their correlations to their putative mRNA targets have not been extensively studied relative to normal germinal center (GC) B cells.

METHODS: Using more sensitive ...


Identification Of Kit As A Suppressor Of Brafv600e-Mutant Melanoma, James V. Neiswender 2017 University of Massachusetts Medical School

Identification Of Kit As A Suppressor Of Brafv600e-Mutant Melanoma, James V. Neiswender

GSBS Dissertations and Theses

Genetic changes acquired in the pigment producing cells of the skin, called melanocytes, can lead to formation of the deadly cancer melanoma. Mutations or amplifications leading to the activation of the RAS/MAPK pathway occur in more than 90% of melanomas. Melanocyte development and survival requires the stimulation of this pathway by the receptor tyrosine kinase (RTK) KIT. In ~2% of melanomas, oncogenic KIT mutations drive tumor formation; however, the majority of melanomas lose wild-type KIT expression, suggesting that KIT could suppress melanoma formation. In human melanoma patients of The Cancer Genome Atlas (TCGA), we found an association between BRAF ...


Number Born Alive Accuracy Changes Based On The Number Of Crossbred Records Included For Large White And Landrace Breeding Value Estimation From A Large Seedstock Supplier, Denise Beam, John W. Mabry, Kenneth J. Stalder 2017 Iowa State University

Number Born Alive Accuracy Changes Based On The Number Of Crossbred Records Included For Large White And Landrace Breeding Value Estimation From A Large Seedstock Supplier, Denise Beam, John W. Mabry, Kenneth J. Stalder

Kenneth J Stalder

Data from a large pig breeding company which included number born alive records from company nucleus farms, company multiplier farms, customer-owned daughter nucleus farms, and customer-owned closed herd commercial farms were used to estimate breeding values and prediction accuracies of selection for purebred Landrace and Large White females. Prediction accuracies when breeding values were estimated using purebred information only and purebred and crossbred information were compared for three customer-owned commercial herds with pedigree information on more than 70% of their Landrace/Large White crossbred females. Change in accuracy and Pearson correlations with and without crossbred daughter records were calculated for ...


Genetic Parameters For Growth, Body Composition, And Structural Soundness Traits In Commercial Gilts, Marja Tellervo Nikkila, Kenneth J. Stalder, B. E. Mote, Max F. Rothschild, F. C. Gunsett, Anna K. Butters-Johnson, Locke A. Karriker, Mark Boggess, T. V. Serenius 2017 Iowa State University

Genetic Parameters For Growth, Body Composition, And Structural Soundness Traits In Commercial Gilts, Marja Tellervo Nikkila, Kenneth J. Stalder, B. E. Mote, Max F. Rothschild, F. C. Gunsett, Anna K. Butters-Johnson, Locke A. Karriker, Mark Boggess, T. V. Serenius

Kenneth J Stalder

The objective of this study was to estimate genetic parameters for growth, body composition, and structural soundness traits in commercial gilt lines. The data included 1,449 gilts: 462 females from a grandparent maternal line and 987 from a parent maternal line. Growth was expressed as number of days to a constant 113.5 kg BW (DAYS) and compositional traits included loin muscle area (LMA), 10th rib backfat (BF10), and last rib backfat (LRF). Subjective structural soundness evaluation was completed using a 9-point scale and included: body length (BL), body depth (BD), body width (BWD), rib shape (BRS), top line ...


Genetics Of Sow Longevity, T. Serenius, Kenneth J. Stalder 2017 Iowa State University

Genetics Of Sow Longevity, T. Serenius, Kenneth J. Stalder

Kenneth J Stalder

The objective of this study was to estimate direct and indirect selection potential for length of productive life and lifetime prolificacy. In order to study the direct selection potential, the heritabilities of these traits were estimated. The genetic correlations of length of productive life and lifetime prolificacy with prolificacy traits and overall leg conformation were estimated to evaluate if selection for these traits could indirectly improve measures of sow longevity. In addition, correlations between length of productive life, lifetime prolificacy, daily gain, and backfat thickness were estimated. Records were utilized from Finnish purebred Landrace (n=26,744) and Large White ...


Identification Of The Range Of Hock Angles In Lame And Non-Lame Replacement Gilt, Jared Mumm, Kenneth J. Stalder, Joe Stock, Julia A. Calderón Díaz 2017 Iowa State University

Identification Of The Range Of Hock Angles In Lame And Non-Lame Replacement Gilt, Jared Mumm, Kenneth J. Stalder, Joe Stock, Julia A. Calderón Díaz

Kenneth J Stalder

Hock angle ranges were measured in Yorkshire gilts from the 10th generation of gilts divergently selected for residual feed intake (RFI) at Iowa State University. Fifty-five gilts (low RFI n= 26 and high RFI n= 29) were included in the study. Digital profile images were taken from each gilt and hock angles were measured while the gilt’s leg was positioned forward, standing squarely, and backwards. Angles were calculated by tracing the front and back of the joint between the fibula/tibia and tarsals, with the anterior and posterior positions acting as the anchor. Additionally, gilts were classified as lame ...


Selfish Little Circles: Transmission Bias And Evolution Of Large Deletion-Bearing Mitochondrial Dna In Caenorhabditis Briggsae Nematodes, Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika Kusuma, Sita Ping, Suzanne Estes 2017 Oregon State University

Selfish Little Circles: Transmission Bias And Evolution Of Large Deletion-Bearing Mitochondrial Dna In Caenorhabditis Briggsae Nematodes, Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika Kusuma, Sita Ping, Suzanne Estes

Suzanne Estes

Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ ...


Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta IV, Dee R. Denver, Suzanne Estes 2017 South Dakota State University

Endogenous Ros Levels In C. Elegans Under Exogenous Stress Support Revision Of Oxidative Stress Theory Of Life-History Tradeoffs, Samson W. Smith, Leigh C. Latta Iv, Dee R. Denver, Suzanne Estes

Suzanne Estes

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with ...


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