Gwaspro: A High-Performance Genome-Wide Association Analysis Server, 2018 Noble Research Institute
Gwaspro: A High-Performance Genome-Wide Association Analysis Server, Bongsong Kim, Xinbin Dai, Wenchao Zhang, Zhaohong Zhuang, Darlene L. Sanchez, Thomas Lubberstedt, Yun Kang, Michael Udvardi, William D. Beavis, Shizhong Xu, Patrick X. Zhao
We present GWASpro, a high-performance web server for the analyses of large-scale genome-wide association studies (GWAS). GWASpro was developed to provide data analyses for large-scale molecular genetic data, coupled with complex replicated experimental designs such as found in plant science investigations, and to overcome the steep learning curves of existing GWAS software tools. GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model (LMM). GWASpro is optimized to handle GWAS data that may consist of up to 10 million markers and 10 ...
Estimating The Heritability Of Thermal Tolerance In Acropora Cervicornis And The Physiological Basis Of Adaptation That Correlates To Survival At Elevated Temperatures, 2018 University of North Florida
Estimating The Heritability Of Thermal Tolerance In Acropora Cervicornis And The Physiological Basis Of Adaptation That Correlates To Survival At Elevated Temperatures, Kelsey L. Yetsko
UNF Graduate Theses and Dissertations
Human activities have substantially increased the atmospheric concentrations of greenhouse gases, resulting in warmer ocean temperatures that are having a negative impact on reef corals, which are highly susceptible to changes in temperature. Understanding the degree to which species vary in their tolerance to elevated temperatures and whether this variation is heritable is important in determining their ability to adapt to climate change. In order to address this, Acropora cervicornis fragments from 20 genetically distinct colonies were kept at either ambient or elevated temperatures, and mortality was monitored for 26 days. Heritability of thermal tolerance was estimated using a clonal ...
Emergence Of New Metabolic Pathways In Escherichia Coli, 2018 University of Colorado, Boulder
Emergence Of New Metabolic Pathways In Escherichia Coli, Michael Kristofich
Undergraduate Honors Theses
Catalytic promiscuity provides a starting point for the evolution of new enzymes. Taking this concept further, a series of promiscuous enzymes may assemble to form the basis of a new metabolic pathway (termed “serendipitous pathway”) that may emerge and become more efficient in adapting bacterial cells that require it to grow. The Copley lab at the University of Colorado at Boulder has been observing genetic changes that improve growth of Escherichia coli cells that lack the essential gene pdxB. These genetic changes are believed to improve the flux of metabolites through one or more serendipitous pathways that make up for ...
Investigating Phosphorylation Patterns And Their Effect On The Activity Of Transcription Factor Taabf1 In Imbibing Cereal Grains, Grace Uwase
The wheat transcription factor TaABF1 plays an important role in hormone-mediated regulation of seed dormancy and germination of cereal grains. Evidence shows that TaABF1 activity is regulated by phosphorylation, and previous work in our lab showed that when serine residues in its conserved regions; S36, S37, S113, S115 were altered to phosphomimetic aspartate, the 4xD TaABF1 mutant had increased activity as a transcription factor. However, when only S113 was altered, TaABF1’s activity was greatly reduced. The work presented here explored whether the S36D/S37D/S115D mutant would have stronger activity than the 4xD mutant. Using the particle bombardment technique ...
Comparing Snp Panels And Statistical Methods For Estimating Genomic Breed Composition Of Individual Animals In Ten Cattle Breeds, 2018 Hunan Agricultural University
Comparing Snp Panels And Statistical Methods For Estimating Genomic Breed Composition Of Individual Animals In Ten Cattle Breeds, Jun He, Yage Guo, Jiaqi Xu, Hao Li, Anna Fuller, Richard G. Tait Jr., Xiao-Lin Wu, Stewart Bauck
Faculty Publications, Department of Child, Youth, and Family Studies
Background: SNPs are informative to estimate genomic breed composition (GBC) of individual animals, but selected SNPs for this purpose were not made available in the commercial bovine SNP chips prior to the present study. The primary objective of the present study was to select five common SNP panels for estimating GBC of individual animals initially involving 10 cattle breeds (two dairy breeds and eight beef breeds). The performance of the five common SNP panels was evaluated based on admixture model and linear regression model, respectively. Finally, the downstream implication of GBC on genomic prediction accuracies was investigated and discussed in ...
The Effects Of Forest Degradation On Dna Methylation In Central African Songbirds, 2018 Humboldt State University
The Effects Of Forest Degradation On Dna Methylation In Central African Songbirds, Andrew K. Wiegardt
Theses and projects
Environmentally-induced stress can initiate a molecular response through DNA methylation, which can alter gene expression, thereby serving as a mechanism allowing individuals to acclimate to a changing environment within their lifetime. In addition to DNA methylation, the production and release of corticosterone is a physiological mechanism by which birds can cope with acute environmental stressors. To assess how environmental stress impacted DNA methylation and corticosterone, I collected blood and feather samples from three understory avian species (Alethe castanea, Bleda notatus and Pseudalethe poliocephala), along a disturbance gradient in the lowland Guinean rainforest adjacent to the village of Oyala, Equatorial Guinea ...
Chemical Topping Burley Tobacco, 2018 University of Kentucky
Chemical Topping Burley Tobacco, Mitchell D. Richmond
Theses and Dissertations--Plant and Soil Sciences
The act of topping tobacco (Nicotiana tabacum L.) involves the removal of the terminal bud or inflorescence of the tobacco plant. This practice ordinarily is accomplished by manually removing the top of each tobacco plant in an entire field which is labor intensive and costly. Chemical topping utilizes sucker control products to inhibit the terminal bud and axillary bud growth without manually removing the top of the tobacco plant. There were several research objectives in order to determine the utility of a chemical topping system: 1) determine if burley tobacco could be chemically topped with currently registered suckercide products while ...
Aptamer-Enabled Uptake Of Small Molecule Ligands, 2018 Iowa State University
Aptamer-Enabled Uptake Of Small Molecule Ligands, Supipi Liyamali Auwardt, Yeon-Jung Seo, Muslum Ilgu, Judhajeet Ray, Robert R. Feldges, Shambhavi Shubham, Lee Bendickson, Howard A. Levine, Marit Nilsen-Hamilton
Biochemistry, Biophysics and Molecular Biology Publications
The relative ease of isolating aptamers with high specificity for target molecules suggests that molecular recognition may be common in the folds of natural RNAs. We show here that, when expressed in cells, aptamers can increase the intracellular concentrations of their small molecule ligands. We have named these aptamers as DRAGINs (Drug Binding Aptamers for Growing Intracellular Numbers). The DRAGIN property, assessed here by the ability to enhance the toxicity of their ligands, was found for some, but not all, aminoglycoside aptamers. One aptamer protected cells against killing by its ligand. Another aptamer promoted killing as a singlemer and protected ...
Cattle Infection Response Network And Its Functional Modules, 2018 Iowa State University
Cattle Infection Response Network And Its Functional Modules, Hamid Beiki, Abbas Pakdel, Ardeshir Nejati Javaremi, Ali Masoudi-Nejad, James M. Reecy
Animal Science Publications
Background: Weighted Gene Co-expression Network analysis, a powerful technique used to extract co-expressed gene pattern from mRNA expression data, was constructed to infer common immune strategies used by cattle in response to five different bacterial species (Escherichia coli, Mycobacterium avium, Mycobacterium bovis, Salmonella and Staphylococcus aureus) and a protozoa (Trypanosoma Congolense) using 604 publicly available gene expression microarrays from 12 cattle infection experiments.
Results: A total of 14,999 transcripts that were differentially expressed (DE) in at least three different infection experiments were consolidated into 15 modules that contained between 43 and 4441 transcripts. The high number of shared DE ...
An Integrative Transcriptome Analysis Indicates Regulatory Mrna-Mirna Networks For Residual Feed Intake In Nelore Cattle, 2018 Embrapa Pecuária Sudeste
An Integrative Transcriptome Analysis Indicates Regulatory Mrna-Mirna Networks For Residual Feed Intake In Nelore Cattle, Priscila S.N. De Oliveira, Luiz L. Coutinho, Polyana C. Tizioto, Aline S. M. Cesar, Gabriella B. De Oliveira, Wellison J. Da S. Diniz, Andressa O. De Lima, James M. Reecy, Gerson B. Mourão, Adhemar Zerlotini, Luciana C. A. Regitano
Animal Science Publications
Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such ...
In Silico Modeling Of Epigenetic-Induced Changes In Photoreceptor Cis-Regulatory Elements, Reafa A. Hossain, Nicholas R. Dunham, Raymond A. Enke, Christopher E. Berndsen
Ray Enke Ph.D.
No abstract provided.
Comparison Between Listeria Sensu Stricto And Listeria Sensu Lato Strains Identifies Novel Determinants Involved In Infection, 2017 Technische Universität München, Germany
Comparison Between Listeria Sensu Stricto And Listeria Sensu Lato Strains Identifies Novel Determinants Involved In Infection, Jakob Schardt, Grant Jones, Stefanie Müller-Herbst, Kristina Schauer, Sarah E. F. D'Orazio, Thilo M. Fuchs
Microbiology, Immunology, and Molecular Genetics Faculty Publications
The human pathogen L. monocytogenes and the animal pathogen L. ivanovii, together with four other species isolated from symptom-free animals, form the "Listeria sensu stricto" clade. The members of the second clade, "Listeria sensu lato", are believed to be solely environmental bacteria without the ability to colonize mammalian hosts. To identify novel determinants that contribute to infection by L. monocytogenes, the causative agent of the foodborne disease listeriosis, we performed a genome comparison of the two clades and found 151 candidate genes that are conserved in the Listeria sensu stricto species. Two factors were investigated further in vitro and in ...
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, 2017 Cuny Graduate School of Journalism
Unseen Science: Modern Discoveries Too Far Away Or Tiny For Human Eyes, Lucy Huang
As science has progressed, scientists have realized that evidence goes beyond the realms of physical sight. Whether it is too small or difficult to find, scientists have developed different ways to get around this problem. We see this in cancer genomics and in extrasolar planetary research. Scientists use what they know and what they measure to validate their work.
Effects Of Crude Oil On Tumor Suppressor P53 Polymorphisms In Laboratory-Exposed Atlantic Killifish, Fundulus Heteroclitus, Allison Margaret Nadler
Seton Hall University Dissertations and Theses (ETDs)
Polycyclic aromatic hydrocarbons (PAHs), constituents of crude oil, are implicated as a potent source of adverse toxicological effects on living organisms. To model the effects of PAHs in response to environmental oil spill disasters a species of killifish (Fundulus heteroclitus) was captured and exposed to crude oil in a laboratory-controlled setting. Over a period of 7 days, fish were dosed with crude oil by gavage, culled, and organs were harvested for analysis. Excitation-emission matrix spectroscopy (EEMS) of gall bladder tissue homogenates was used to verify exposure. Effects of PAHs on the p53 gene were evaluated as an indicator of genotoxicity ...
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 ...
Stressing Out: Dynamics Of Chromatin Insulator Body Formation In Eukaryotes Under Osmotic Stress, 2017 University of Tennessee, Knoxville
Stressing Out: Dynamics Of Chromatin Insulator Body Formation In Eukaryotes Under Osmotic Stress, Shannon Marie Garland
Higher order genome organization and the role it plays in governing cell dynamics and protein expression has become a widely studied field. Chromatin insulators are important to this organization in their ability to form long range contacts between distant regions on the genome. During times of osmotic stress, insulator proteins leave their binding sites on the DNA to form insulator bodies in the nucleus. This phenomenon relieves the DNA of its structure and is rapidly reversible. Using a variety of immunofluorescent staining methods, this work looked to further characterize this process while attempting to identify molecular mechanisms that mediate chromatin ...
Activation Of A Cryptic 5′ Splice Site Reverses The Impact Of Pathogenic Splice Site Mutations In The Spinal Muscular Atrophy Gene, Natalia N. Singh, Jose Bruno Del Rio-Malewski, Diou Luo, Eric W. Ottesen, Matthew D. Howell, Ravindra N. Singh
Biomedical Sciences Publications
Spinal muscular atrophy (SMA) is caused by deletions or mutations of the Survival Motor Neuron 1 (SMN1) gene coupled with predominant skipping of SMN2 exon 7. The only approved SMA treatment is an antisense oligonucleotide that targets the intronic splicing silencer N1 (ISS-N1), located downstream of the 5′ splice site (5′ss) of exon 7. Here, we describe a novel approach to exon 7 splicing modulation through activation of a cryptic 5′ss (Cr1). We discovered the activation of Cr1 in transcripts derived from SMN1 that carries a pathogenic G-to-C mutation at the first position (G1C) of intron 7. We ...
The Role Of Rnf4 In Stripping Transcriptionally-Active Huntingtin, 2017 College of William and Mary
The Role Of Rnf4 In Stripping Transcriptionally-Active Huntingtin, Jen Peek
Undergraduate Honors Theses
Altered gene expression is a hallmark of neurodegenerative disorders such as Huntington’s disease. The causative agent of Huntington’s is a mutant, aggregation-prone fragment of huntingtin (htt) that aggregates in the cytosol and nuclei of neuronal cells. The severity and onset of Huntington’s is correlated with the length of a polyglutamine (Q) tract encoded in the N-terminus of htt. Little is known about the nuclear accumulation of polyQ expanded htt, how it interacts with chromatin, and dysregulates transcriptional activity. In this thesis, we investigate the effect of nuclear localized htt on reporter gene activation and demonstrate that the ...
Exploiting Fission Yeast Genetic Interaction Data To Identify Disease-Specific Drug Targets For Tuberous Sclerosis Complex, 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 ...
Ablation Of An Ovarian Tumor Family Deubiquitinase Exposes The Underlying Regulation Governing The Plasticity Of Cell Cycle Progression In Toxoplasma Gondii, Animesh Dhara, Rodrigo De Paula Baptista, Jessica C. Kissinger, Ernest Charles Snow, Anthony P. Sinai
Microbiology, Immunology, and Molecular Genetics Faculty Publications
The Toxoplasma genome encodes the capacity for distinct architectures underlying cell cycle progression in a life cycle stage-dependent manner. Replication in intermediate hosts occurs by endodyogeny, whereas a hybrid of schizogony and endopolygeny occurs in the gut of the definitive feline host. Here, we characterize the consequence of the loss of a cell cycle-regulated ovarian tumor (OTU family) deubiquitinase, OTUD3A of Toxoplasma gondii (TgOTUD3A; TGGT1_258780), in T. gondii tachyzoites. Rather than the mutation being detrimental, mutant parasites exhibited a fitness advantage, outcompeting the wild type. This phenotype was due to roughly one-third of TgOTUD3A-knockout (TgOTUD3A-KO) tachyzoites exhibiting deviations from endodyogeny ...