Browsing by Subject "genetics"
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Item Admixture Effects on Coevolved Metabolic Systems(2016-05-01) Zascavage, Roxanne R.; Planz, John V.; Barber, Robert C.; Clark, Abbot F.Oxidative phosphorylation (OXPHOS) is the primary energy generating system in eukaryotic organisms. Consequently, any malfunctions or disruptions in the pathway significantly impact fitness and health. Errors in energy production have been linked to cancer, Alzheimer’s disease, Parkinson’s disease, various neuropathies, and general aging and health degeneration over time. However, there is a fundamental gap in the understanding of the genetic causes of deficiencies in energy production. The complexes within the OXPHOS pathway are of mixed origin; while most subunit-coding genes are located within the nuclear genome, thirteen are coded for in the mitochondrial genome. There is strong evidence to support coadaptation between the two genomes in these OXPHOS gene regions in order to create tight protein interactions necessary for a functional energetic system. While the effect of separating coevolved alleles is not fully understood, hybrid studies have indicated decreased energy production when combining different ancestral nuclear and mitochondrial backgrounds in various species. This suggests the common human practice of interpopulation matings between ancestrally distinct groupings influences health and relative fitness. The primary hypothesis is that admixture creates maladaptive combinations of nuclear and mitochondrial alleles in the OXPHOS-coding genes that have adverse effects on the efficiency of energy production, leading to a decrease in relative fitness. This dissertation project has: 1) identified the effects of admixture on OXPHOS activity in Mus musculus populations, showing that high admixture leads to significantly lower basal respiration rates; and 2) assessed the genetic composition of the strains of Mus musculus evaluated to identify to cause of the loss of respiration in highly admixed mice. It was determined that there were no genetic anomalies present that could explain the observations, meaning the cause is likely not due to a mutation, but instead an undetected difference, such as cyto-nuclear incompatibility. It is recommended that further energetic and genetic studies be performed to identify the source of the deficiency. Mice obtained from Jackson Laboratories and a previously published genotype dataset [82] were used for experiments. Laboratory experiments included: Liver and heart extraction, tissue preparation and bioenergetics analysis, statistical analysis, and genetic analysis.Item Allele Characterization of Ten Short Tandem Repeat Loci of North American Bears (Ursids) Using Next-Generation Sequencing(2014-05-01) Kreutzer, Mckensie; John PlanzAn identification method that provides higher genetic resolution than capillary electrophoresis (CE) is needed for isolated bear populations that possess low genetic diversity. Amplification conditions were optimized for ten bear STR loci. Amplicons were used to develop a library for next-generation sequencing (NGS) on the Ion Torrent™ PGM™ Sequencer. Through ligation of DNA barcode adaptors, seven black bear (Ursus americanus) samples were sequenced together. Sequencing reads were aligned to a virtual ladder and analyzed in NextGENe® software. Allele concordance was shown between CE and NGS. Variants within alleles (SNPs and INDELs) showed that NGS provided higher genetic resolution. These results have implications for improving individual identification and population assignment in wildlife forensics and conservation for populations with low genetic diversity.Item Bone Morphogenetic Protein 4 inhibits TGF-beta2 Stimulation of Extracellular Matrix Proteins in Optic Nerve Head Cells: Role of Gremlin in ECM Modulation(2005-05-01) Zode, Gulab S.; Wordinger, Robert J.Zode, Gulab Shalikram, Bone Morphogenetic Protein 4 Inhibits TGF-β2 Stimulation of Extracellular Matrix Proteins in Optic Nerve Head Cells: Role of Gremlin in ECM Modulation . Doctor of Philosophy (Cell Biology and Genetics), May 2008; 177pp; 34 figures; bibliography, 192 titles. The glaucomatous neuropathy is caused by irreversible loss of retinal ganglion axons in the optic nerve head (ONH). The extensive remodeling of the extracellular matrix (ECM) in the glaucomatous ONH including increased synthesis and deposition of ECM (increased collagens, basement proteins, and elastin) is associated with loss of axons. Transforming growth factor-beta2 (TGF-β2) is increased in glaucomatous ONH and is thought to be responsible for increased synthesis and deposition of ECM proteins of the ONH. Bone morphogenetic proteins (BMPs) normally maintain the balance of ECM proteins via opposing TGF-β2 stimulated ECM proteins in various cell types. BMP antagonist gremlin inhibits BMPs function, thus may plan an important role in ECM modulation. We previously demonstrated that human ONH expresses BMP-4, BMP receptor and BMP antagonist gremlin. Therefore, we hypothesize that elevated TGF-β2 in the glaucomatous ONH induces gremlin expression that blocks BMP-4 inhibition of TGF-β2 signaling, leading to increased ECM synthesis and deposition. First, we examined whether human ONH tissues and ONH cells express the canonical BMP signaling pathway. This study demonstrated that ONH tissues and ONH cells express BMP-4 and Smad signaling pathway. Treatment of ONH cells with BMP-4 increased phosphorylation of R-Smad/1/58/ phosphorylation and interaction with Co-Smad4 indicating activation of the Smad signaling pathway. Therefore, cells within the human ONH can respond to locally released BMP via activation of Smad signaling. Second, we examined the signaling pathways utilized by TGF-β2 to stimulate ECM in ONH cells. This study demonstrated that TGF-β2 is increased in glaucomatous ONH. Recombinant TGF-β2 increased ECM deposition in ONH cells. TGF-β2 activated phosphorylation of R-smad2/3 but did not alter phosphorylation of ERK1/2, p38, and JNK1/2 in ONH cells. Inhibition of either TGF-β I receptor activity or phosphorylation of R-Smad3 or knockdown of R-Smad2/3 via siRNA reduced TGF-β2 stimulated ECM in ONH cells. Thus, TGF-β2 requires R-Smad2/3 to stimulate ECM proteins in ONH cells. Lastly, we investigated the potential effects of BMP-4 and gremlin on TGF-β2 stimulated ECM in ONH cells. BMP-4 significantly reduced TGF-β2 stimulation of ECM proteins. Addition of gremlin blocked the BMP-4 effect, increasing ECM proteins in ONH cells. Gremlin levels were significantly increased in the human glaucomatous ONH tissues. Interestingly, recombinant gremlin also increased ECM proteins in ONH cells. Gremlin stimulation of ECM proteins required activation of the TGF-β receptor and R-Smad3. TGF-β2 increased gremlin mRNA and protein in ONH cells. Thus, TGF-β2 induced gremlin expression intensifies TGF-β2 effects on ECM metabolism by inhibiting BMP-4 antagonism of TGF-β2 signaling. In conclusion, elevated TGF-β2 and gremlin in the glaucomatous ONH are involved in the pathogenesis of glaucomatous ONH. Elevated TGF-β2 directly increases ECM and also induces gremlin expression, which further aids TGF-β2 to stimulate ECM via inhibiting BMPs antagonism of TGF-β2 signaling, leading to unopposed TGF-β2 stimulated ECM proteins. Interestingly, R-smad3 is required for TGF-β2 or gremlin induced ECM remodeling in ONH cells. Therefore, modulation of R-smad3 provides a novel therapeutic target for preventing ECM remodeling in glaucoma.Item Dr. Joseph Warren(2013-08-02)Item Effects of a Synthetic Amino Acid Diet: Insights from the Guy Microbiome, Inflammation, and Behavior(2021-05) Mancilla, Viviana J.; Allen, Michael S.; Jones, Harlan P.; Phillips, Nicole R.; Planz, John V.; Ellis, DorettePhenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treated through a phenylalanine-restrictive diet and frequently supplemented with an amino acid formula to maintain proper nutrition. PKU patients often report high levels of anxiety along with symptoms of gastrointestinal distress (i.e., chronic diarrhea, constipation, cramps); symptoms previously associated with gut microbiome dysbiosis. Little is known of the effects of these dietary interventions on the gut microbiome of PKU patients, particularly in adults. The gut microbiome is a collection of microbes residing primarily in the large intestine. The colon is a major production site for short chain fatty acids (SCFAs) through anaerobic fermentation by commensal bacteria. SCFAs provide a source of energy for the colonocytes, as well as provide anti-inflammatory benefits. The production of SCFA appears to be dependent on the availability of soluble fibers and members of the gut microbiota capable of fermentation. We characterized the gut microbiome of adults with PKU for the first time and identified signs of dysbiosis. We then focused on the synthetic, low fiber, nature of the amino acid diet in a murine model. In this interdisciplinary study, we monitored the effect of a consuming synthetic diet on the composition of the murine gut microbiome over the course of 13 weeks, beginning at weaning. At the conclusion of the feeding period, mice we observed for anxiolytic behavior, locomotion, and cognition. We also searched for markers of inflammation through colon shrinkage, changes in cytokine levels within several tissues, and determined the concentration of SCFAs in the colon at the conclusion of the feeding period. The gut microbiome of mice fed the synthetic diet experienced significant deviation from the control group which affected relative abundance of beneficial bacteria. Mice on the synthetic diet were found to have shorter colons, lower concentration of SCFAs in the colon, and demonstrated elevated exploratory behavior.Item Health Games: Questions and Answers from Free Online NLM Resources(2016-11-01) Gibson D. Lewis Health Science Library; Sheldon, Lorraine; Smith, Jacqui E.This document is a printable card game for children and youth that provides samples of questions from health games online. Print double sided and cut on dotted lines. The purpose of this document is to promote the National Library of Medicine as part of Gibson D. Lewis Library’s function as a Resource Library.Item Heredity In Relation to Evolution and Animal Breeding(D. Appleton and Company, 1911-01-01) Castle, WilliamItem Mitochondrial Genetics and Function among Men Screened for Prostate Cancer(2015-12-01) Sprouse, Marc L.; Arthur J. Eisenberg; Rhonda Roby; Robert C. BarberGenetic alterations are associated with sporadic cancer development, progression and metastasis. Until now, more was known about nuclear DNA (nDNA) mutations and their role in cancer than the types of genetic changes that occur in the mitochondrial genome (mtGenome). Changes to mitochondrial DNA (mtDNA) are frequent in prostate cancer (PCa). Further, these changes have been associated with enhanced tumorigenesis and progression to an aggressive phenotype. However, it is unclear whether changes to the mtGenome can delineate PCa progression from indolent cancer to an advanced metastatic disease. An exhaustive characterization of the mtGenome of men screened for PCa was performed to determine if genetic differences between varying PCa disease states can be measured. Two genetic techniques (copy number and genome sequencing) were used to perform a comprehensive characterization of the changes to mtDNA in whole blood extracts from three groups of men screened for prostate cancer: normal control (NC), no evidence of disease (NED), and, biochemical recurrence/metastasis (BCR/MET). Mitochondrial DNA copies per cell and mtGenome deletion ratio (whole mtGenomes:truncated mtGenomes) were measured using a multiplex real-time quantitative PCR (qPCR) assay. Whole mtGenome sequence data were generated using a massively parallel sequencing platform, the Ion Torrent Personal Genome Machine (PGM). Real-time qPCR revealed a higher dispersion of mtDNA copies per cell and mtGenomes harboring a large scale deletion in samples from men with advanced stages of PCa when compared to normal controls and indolent PCa. Whole mtGenome sequencing showed a higher number of genetic variants in men with PCa, some of which are predicted to be pathological. A significant positive correlation was observed between mutational load and PCa disease status. Further, three-dimensional comparative modeling evidenced the negative effect of a single mtDNA missense mutation on a protein’s structural integrity. Overall, the presented data suggest there are differences in the mtGenome between men with and without PCa that are measurable in peripheral blood and may be used as a potential risk assessment tool. Future analyses with a larger sample size may lead to more compelling evidence that supports the role of changes to the mtGenome with PCa progression.Item Optimization and Validation of the Bode TM Buccal DNA CollectorTM in Conjunction with the AmpFLSTR® Identifiler® Direct PCR Amplification Kit for Single Source Reference Samples.(2010-05-01) DeLillo, Sandy D.; Warren, JosephDNA analysis for human identification is a multi-step process culminating in the generation of a DNA profile unique to the contributor of the biological sample. In order for human identification by way of DNA analysis to be successful, comparisons of a known sample to an unknown sample must be made. Processing of the known or reference samples should be efficient, reliable and reproducible. The Buccal DNA Collector™ (Bode Technology Group, Lorton, VA) used in conjunction with the AmpFLSTR® Identifiler® Direct PCR Amplification Kit (Applied Biosystems, Foster City, CA) has been shown to be an effective method for processing single source reference samples. This technique can be reliably applied to the processing of samples for DNA databasing, paternity or reference samples for forensic casework.Item Optimization of Spermatozoa Capture During the Differential Extraction Process for STR Typing with the Potential for Automation(2002-05-01) Marshall, Pamela L.; Eisenberg, Arthur; Martin, Michael W.; Wordinger, Robert J.Marshall, Pamela. Optimization of Spermatozoa Capture During the Differential Extraction Process for STR Typing With the Potential for Automation. Master of Science (Forensic Genetics). May, 2002. In 1998, within the United States, it is estimated that a rape occurred every 2.3 minutes. In 1995, according to the Bureau of Justice Statistics, an estimated 350,000 rapes or sexual assaults (R/SA0 were experienced by persons age 12 or older. Of the estimated 100,000 R/SA reported, there were only approximately, 25,000 cases analyzed by crime labs nationwide. The majority of crime laboratories throughout the U.S., especially those in major metropolitan cities, have a significant backlog of unresolved R/SA cases. With the implementation of the Convicted Offender Database (CODIS), it is essential that all R/SA cases by analyzed, especially those lacking a known suspect. The comparison of the short tandem repeat (STR) profiles derived from sperm DNA recovered from evidentiary material with CODIS samples would provide the police with critical investigative leads resulting in the identification of the assailant. The goal of this research is to develop a cellular sorting method for the isolation of sperm cells from sexual assault samples which will: 1) take advantage of differentiating features (extracellular antigenic sites) for complete separation of cell types, 2) provide a more efficient means of sperm recovery, increasing DNA yield from the male fraction, and 3) ensure the DNA isolation process is compatible with the amplification of the CODIS core STR loci. Overall, the proposed technique will increase the probability of success in the analysis of sexual assault case samples. (NIJGrant #: 2000-IJ-CX-K009).Item Production of Extracellular Matrix-Degrading Proteases by a Rat B Cell Line.CRL-1631(2002-05-01) Badeaux, Kathleen S.; R. GoldfarbBadeaux, K. Production of Extracellular Matrix-Degrading Proteases by a Rat B Cell Line.CRL-1631. Master of Science (Microbiology and Immunology), May 2002. 30 pp., 9 illustrations, 1 table, 16 bibliography titles. Previously B lymphocytes have been reported to accumulate at the site of tumor development and to play a role in immune surveillance against metastatic tumors. Investigating this mechanism, we studied B lymphocyte production of extracellular matrix-degrading proteinases: matrix metalloproteinases (MMPs) and components of the urokinase plasminogen activator (uP A) system. Our studies include RT-PCR of CRL-1631 eDNA revealing mRNA for MMP-2, MMP-9, TIMP-1, TIMP-2 and uPAR. MMP-2 and MMP-9 activity was verified by gelatin zymography. TIMP-1, TIMP-2 and uPAR protein expression was confirmed by Western blot analyses. I also report, for the first time, MT -1 MMP gene and protein expression in B cells by RT-PCR and Western blot, respectively. CRL-1631 invasion through Matrigel model basement membrane was significantly inhibited by BB-94, confirming MMP involvement in this cell line's invasiveness. Therefore, B cells use multiple proteases in the degradation of the extracellular matrix, ECM, and this may be one factor responsible for their accumulation at the site of established tumors.Item Scientific Proceedings of the Royal Dublin Society, Simplified Solutions of Certain Mendelian Problems in which factors have inseparable effects(The Royal Dublin Society; Williams and Norgate, 1915-04-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; Unsound Mendelian Developments Especially as Regards the Presence and Absence Theory(The Royal Dublin Society; Williams and Norgate, 1912-12-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; AN EXAMPLE OF THE MULTIPLE COUPLINGOF MENDELIAN FACTORS .(The Royal Dublin Society; Williams and Norgate, 1913-03-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; Inter-Alternative as Opposed to Coupled Mendelian Factors: A Solution of the Agouti-Black Colour in Rabbits(The Royal Dublin Society; Williams and Norgate, 1915-01-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; THE INHERITANCE OF COAT COLOUR IN HORSES.(The Royal Dublin Society; Williams and Norgate, 1910-04-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; The Inheritance of Milk Yield in Cattle(The Royal Dublin Society; Williams and Norgate, 1911-06-01) Wilson, JamesItem Scientific Proceedings of the Royal Dublin Society; The Inheritance of the Dun Coat-Colour in Horses(The Royal Dublin Society; Williams and Norgate, 1912-01-01) Wilson, JamesItem Single Nucleotide Polymorphisms and Haplotype Analyses of Complex Medical Disorders(2008-05-01) Gonzalez, Suzanne D.; Arthur Eisenberg; Robert Luedtke; Rustin ReevesGonzalez, Suzanne D., Doctor of Philosophy. Cell Biology and Genetics. Single Nucleotide Polymorphisms and Haplotype Analyses of Complex Medical Disorders. Number of Pages: 129. Number of Tables: 25. Number of Illustrations: 5. Number of Titles Included in References: 197. There has been great difficulty in identifying genes involved in complex disorders. The complex genetic basis of these diseases indicates that either several genes act together to cause disease, or genetic heterogeneity is present in the population. This dissertation was aimed at developing new assays to identify polymorphisms in novel candidate genes that potentially contribute to two classes of common complex disorders: psychiatric diseases and metabolic disorders. Genotyping assays were developed to investigate single nucleotide polymorphisms (SNPs) and haplotypes in complex genetic disorders using multiplexed SNP panels, restriction fragment length polymorphism technology, and cycle sequencing platforms. An introduction to the study is provided in Chapter 1. Manuscripts focus on association studies of candidate genes in Bipolar Disorder and Schizophrenia (Chapter 2), Type 2 Diabetes, Hypertension and Metabolic Syndrome (Chapter 3), and baseline blood pressure in African Americans (Chapter 4). The summary of these manuscripts (Chapter 5) describes the significant associations made between SNPs/haplotypes in psychiatric and metabolic complex genetic disorders. Significant genetic associations of SNPs within the PHLPP gene were detected among schizophrenics (Chapter 2). The G allele of SNP rs8087170 was associated with the control population with the T allele of SNP rs12966002 was found only in schizophrenics. A significant variance was detected at SNP rs12457020 between bipolar and schizophrenic datasets, as there was a 10 fold increase in the A allele in the bipolar group. Significant associations of ATP1A2 5’ SNPs C-1489T and G-1253A were detected in metabolic syndrome and hypertensive groups (Chapter 3). Haplotypes based on these 3 SNPs were significantly associated with metabolic syndrome and hypertensive populations. Four linked ATP1A2 SNPs, G3756C, G3853A, C3913T and C3915T, were associated with baseline blood pressure (Chapter 4). Haplotypes associated with blood pressure in an ethnic specific manner. GGCC associated with lower blood pressures, while haplotype GGTT associated with higher blood pressures in African Americans. These studies provide new mechanisms to identify mutations and provide evidence supporting the pathophysiology of these disorders.Item The Underlying Relationship between Keratoconus and Down Syndrome(MDPI, 2022-09-24) Akoto, Theresa; Li, Jiemin J.; Estes, Amy J.; Karamichos, Dimitrios; Liu, YutaoKeratoconus (KC) is one of the most significant corneal disorders worldwide, characterized by the progressive thinning and cone-shaped protrusion of the cornea, which can lead to severe visual impairment. The prevalence of KC varies greatly by ethnic groups and geographic regions and has been observed to be higher in recent years. Although studies reveal a possible link between KC and genetics, hormonal disturbances, environmental factors, and specific comorbidities such as Down Syndrome (DS), the exact cause of KC remains unknown. The incidence of KC ranges from 0% to 71% in DS patients, implying that as the worldwide population of DS patients grows, the number of KC patients may continue to rise significantly. As a result, this review aims to shed more light on the underlying relationship between KC and DS by examining the genetics relating to the cornea, central corneal thickness (CCT), and mechanical forces on the cornea, such as vigorous eye rubbing. Furthermore, this review discusses KC diagnostic and treatment strategies that may help detect KC in DS patients, as well as the available DS mouse models that could be used in modeling KC in DS patients. In summary, this review will provide improved clinical knowledge of KC in DS patients and promote additional KC-related research in these patients to enhance their eyesight and provide suitable treatment targets.