Characterization Of A Novel Mitochondrial Plasmid In Brassica, 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 ...
An Adaptable Pentaloop Defines A Robust Neomycin-B Rna Aptamer With Conditional Ligand-Bound Structures, 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 ...
Regulatory Rna: Session Introduction, 2017 Iowa State University
Regulatory Rna: Session Introduction, Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
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.
Reevaluating The Occurrence And Phylogeny Of The Pigtoe Unionid Mussels Fusconaia Askewi, Fusconaia Lananensis, Fusconaia Flava, And Pleurobema Riddelli In Texas, Charles J. Pratt
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
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, 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, 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 ...
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 ...
Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, 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 ...
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, 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.  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, 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 ...
Functional Analysis Of Microrna Pathway Genes In The Somatic Gonad And Germ Cells During Ovulation In C. Elegans, Carmela Rios
Dissertations (2009 -)
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in animal development and physiology, though functions for most miRNAs remain unknown. Worms with reduced miRNA biogenesis due to loss of Drosha or Pasha/DGCR8 activity are sterile and fail to ovulate, indicating that miRNAs are required for the process of oocyte maturation and ovulation. Starting with this penetrant sterile phenotype and using new strains created to perform tissue-specific RNAi, we characterize the roles of the C. elegans Pasha, pash-1, and two miRNA-specific Argonautes, alg-1 and alg-2, in somatic gonad cells and ...
Analysis Of Population Structure In A California Newt (Taricha Torosa) Metapopulation, 2017 Western Kentucky University
Analysis Of Population Structure In A California Newt (Taricha Torosa) Metapopulation, Jessica Vincent
Honors College Capstone Experience/Thesis Projects
As anthropogenic influences take an ever-increasing toll on the environment, understanding how environmental change affects species is paramount. Concern regarding decline in amphibian populations has spurred research examining the effects of habitat change on the dynamics of populations at landscape levels. One important goal is to understand how gene flow among populations is affected by changes in habitat. Biologists need to consider the relationship between gene flow and habitat alterations so that movements among individual breeding ponds can be maintained over time, reducing risk of local extinction events. This study focuses on patterns of gene flow among thirteen populations of ...
Unique Genetic Differences In Responses Of Chicken Immune Cells To An Inflammatory Stimulus And Heat Stress, 2017 Iowa State University
Unique Genetic Differences In Responses Of Chicken Immune Cells To An Inflammatory Stimulus And Heat Stress, Angelica Van Goor, Anna Slawinska, Carl Schmidt, Susan J. Lamont
Susan J. Lamont
Bone marrow antigen presenting cells (BM-APC), from Fayoumis (disease resistant and heat tolerant) and Leghorn (disease susceptible) chicken lines were evaluated for response to an inflammatory stimulus and heat stress. BM-APC from Fayoumis produced more nitric oxide (NO) and had higher Major Histocompatibility Complex (MHC) class II cell surface expression compared to those from Leghorn, indicating that BM-APC studied in vitro may be a useful tool to evaluate molecular effects of disease and/or heat tolerance in chickens.
Infection Of Commercial Laying Hens With Newcastle Disease Virus: Differing Responses Between Birds Provide Potential For Genetic Improvement Through Selection, Kaylee Rowland, Huaijun Zhou, Rodrigo Gallardo, David Bunn, Susan J. Lamont
Susan J. Lamont
Exotic Newcastle Disease Virus (ENDV) cause extremely rapid mortality in chickens after exposure to the virus. People rely heavily on poultry to provide protein and income in many places where NDV is not effectively controlled through vaccination and biosecurity. Losses from NDV contribute to worldwide hunger and poverty. It may be possible to use genetic selection to produce chickens that have a stronger immune response in the face of NDV challenge. For genetic selection to be successful, two major elements are required: differences in immune response among chickens and genetic control of these differences. This study clearly demonstrated the existence ...
Gene Expression Response To Heat Stress In Two Broiler Lines, 2017 Iowa State University
Gene Expression Response To Heat Stress In Two Broiler Lines, Jibin Zhang, Carl J. Schmidt, Susan J. Lamont
Susan J. Lamont
The fast growth rate and increased body weight of modern broilers makes them susceptible to heart failure and sensitive to heat stress. To find the genetic causes of these problems, gene expression was measured in hearts of two broiler lines that differed in their response to heat stress. Each line was separated into two groups that were kept under heat stress or at ambient temperature. The comparison of gene expression between the two lines and heat treatments suggests that expression of 325 genes were significantly changed in modern broilers under heat stress, while only 3 genes changed their expression in ...
Do Two Distinct Chicken Lines Differ In Their Response To Newcastle Disease Virus?, 2017 Iowa State University
Do Two Distinct Chicken Lines Differ In Their Response To Newcastle Disease Virus?, Melissa S. Herrmann, Rodrigo Gallardo, David A. Bunn, Huaijun Zhou, Susan J. Lamont
Susan J. Lamont
The differences between relatively resistant and susceptible chicken lines can be utilized to study the genetics behind disease resistance. To assess resistance, the viral quantity in each bird was measured after challenge with Newcastle Disease Virus (NDV) at two time points. As predicted, the resistant line was able to clear the virus more quickly than the susceptible line. Further studies are needed to determine the genetics responsible for resistance.
Effects Of Diet And Genetics On Production Traits In Response To Repeated Exposure To Heat Stress In Pigs, 2017 Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
Effects Of Diet And Genetics On Production Traits In Response To Repeated Exposure To Heat Stress In Pigs, Wendy Rauw, Johana Mayorga Lozano, Soi Lei, John Patience, Nicholas Gabler, Steven Lonergan, Jack Dekkers, Lance Baumgard
Steven M. Lonergan
Hot temperatures negatively impact global livestock production and are a serious financial burden to pig producers. Trends predict that global temperatures will continue toincrease, making this a pertinent issue now and in the future. Study objectives were to investigate the effects of genetics and dietary fiber content on growth,feed intake, and feed conversion efficiencyin response to repeated exposure to heat stress.Atotal of 103 finishing barrows from a contemporary commercial line and Yorkshire linesdivergently selected for high and low feed efficiency based on residual feed intake (RFI) were used in this experiment. All pigs were subjected three consecutivetimes to ...
Qtls Associated With Dry Matter Intake, Metabolic Mid-Test Weight, Growth And Feed Efficiency Have Little Overlap Across 4 Beef Cattle Studies, Mahdi Saatchi, Jonathan E. Beever, Jared E. Decker, Dan B. Faulkner, Harvey C. Freetly, Stephanie L. Hansen, Helen Yampara-Iquise, Kristen A. Johnson, Stephen D. Kachman, Monty S. Kerley, Jaewoo Kim, Daniel D. Loy, Elisa Marques, Holly L. Neibergs, E. John Pollak, Robert D. Schnabel, Christopher M. Seabury, Daniel W. Shike, W. M. Snelling, Matthew L. Spangler, Robert L. Weaber, D. J. Garrick, Jeremy F. Taylor
Stephanie L. Hansen
Background: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. Results: A total of 5, 6, 11 and 10 significant ...