Genetic polymorphisms can be seen as the occurrence of more than one form of a DNA- or protein sequence at a single locus in a group of organisms, where these different forms occur more frequently than can be attributed to mutation alone. The combination of genetic polymorphisms present in the genome of a particular individual is referred to as its genotype. A wide range of genotyping techniques have been developed to detect and visualize genetic polymorphisms. One such technique examines highly polymorphic repetitive DNA regions called microsatellites, also called “short tandem repeats” (STRs) and sometimes “simple sequence repeats” (SSRs) or “simple-sequence length polymorphisms” (SSLPs). A microsatellite region consists of a DNA sequence of identical units of usually 2-6 base pairs strung together to produce highly variable numbers of tandem repeats among individuals of a population. Microsatellite genotyping is a popular choice for many types of studies including individual identification, paternity testing, germplasm evaluation, genome mapping and diversity studies and can be used in many commercial, academic, social, and agricultural applications. There are, however, many obstacles in effectively managing and analysing microsatellite genotype data. Currently, researchers are struggling to effectively manage and analyse rapidly growing volumes of genotyping data. Management problems range from simply the lack of a secure, easily accessible central data repository to more complex issues like the merging and standardization of data from multiple sources into combined datasets. Due to these issues, genetic fingerprinting applications such as identity matching and relatedness studies can be challenging when data from different experiments or laboratories have to be combined into a central database. The main aim of this M.Sc study in Bioinformatics was to develop a bioinformatics resource for the management and analysis of genetic fingerprinting data from microsatellite marker genotyping studies, and to apply the software to the analysis of microsatellite marker data from ramets of Pinus patula clones with the purpose of analysing clonal identity in pine breeding programmes. The software resource developed here is called GenoSonic. It is a web application that provides users with a secure, easily accessible space where genotyping project data can be managed and analysed as a team. Users can upload and download large amounts of marker genotype data. Once uploaded to the system, DNA fingerprint data needs to be standardised before it can be used in further analyses. To do this, a two-step approach was implemented in GenoSonic. The first step is to assign standardized allele sizes to all of the input allele sizes of the microsatellite fingerprints automatically using a novel automated binning algorithm called CSMerge-1, which was designed specifically to bin data from multiple experiments. The second step is to manually verify the results from the automated binning function and add the verified data to a standardized dataset. Once the genetic fingerprints have been standardized, allele- and genotype frequencies can be viewed for any given marker. GenoSonic also provides functionalities for identity matching. One or more DNA fingerprints from unknown samples can be matched against a standardized dataset to establish identities or infer relatedness. Finally, GenoSonic implements a genetic distance tree construction function, which can be used to visualize relatedness among samples in a selected dataset. The bioinformatics resource developed in this study was applied to a microsatellite DNA fingerprinting project aimed at the re-establishment or confirmation of clonal identity of Pinus patula ramets from pine clonal seed orchards developed by a South African forestry company at one of their new agricultural estates in South Africa. The results from GenoSonic‟s automated binning function (CSMerge-1) and the results from the identity matching and tree construction exercise were compared to results obtained by human experts who have analysed the data manually. It was demonstrated that the results from GenoSonic equalled or surpassed the manual results in terms of accuracy and consistency, and far surpasses the manual effort in terms of the speed at which analyses could be completed. GenoSonic was developed with specific focus on reusability, and the ability to be modified or extended to solve future genotyping-related problems. This study not only provides a solution to current genotype data management and analysis needs of researchers, but is aimed at serving as a basic framework, or component library for future software development projects that may be required to address specific needs of researchers dealing with high-throughput genotyping data. / Dissertation (MSc)--University of Pretoria, 2011. / Biochemistry / unrestricted

For over a century, documented scientific research and debate has revolved around the therapeutic properties of the medicinal plant Echinacea angustifolia. With overwhelming evidence demonstrating the biological activity of its root phytochemical constituents, the genetic improvement of E. angustifolia by selecting phytochemically rich genotypes has garnered both scientific and commercial interest. This dissertation presents results of multi-disciplinary experiments intended to help establish scientifically based guidelines for breeding efforts aimed at developing therapeutically superior varieties of E. angustifolia in British Columbia. Cultivated E. angustifolia populations from British Columbia and Washington were grown in a common greenhouse environment to identify possible genetically superior populations with respect to root concentrations of therapeutically relevant caffeic acid derivatives (CAD) and alkamides. However, none of the studied cultivated E. angustifolia populations showed significant genetic differences in terms of root phytochemical traits. In the second part, an investigation into correlations between root and shoot phytochemical concentrations in field- and greenhouse-grown plants revealed that concentrations of therapeutically relevant marker compounds in shoots were generally poor predictors of concentrations in roots. Some weak yet significant positive correlations were observed between root and shoot concentrations of CADs but were inconsistent between the two environments. Significant genotype by environment interactions were documented for the first time in phytochemical traits of E. angustifolia in a study of five genetically homogeneous populations grown in three different environments, including 1 greenhouse and 2 field sites in British Columbia. For the final objective, in vitro bioassays showed that environmentally and genotypically related differences in concentrations of CADs and alkamides in E. angustifolia ethanolic root extracts did not translate into significant differences in their anti-inflammatory potential as measured by pro-inflammatory interleukin (IL-6 and IL-8) secretion in human bronchial epithelial (BEAS-2B) cells challenged with rhinovirus. When used in isolation however, pure tetraene alkamide showed a significant inhibitory effect on secretion, thereby further supporting the use of high alkamide production as a selection criterion for therapeutic E. angustifolia cultivar development. A series of recommendations derived from these findings are presented along with ideas for important future studies in the field of Echinacea research. / Land and Food Systems, Faculty of / Graduate

No description available.

Campylobacter species are the primary cause of bacterial food-borne diarrhoea worldwide. Comparative genomic analyses of Campylobacter strains reveal genome plasticity providing insight into the evolution of virulence traits. The goal of this study was to identify genes important for infectivity and for naturally occurring variability in phenotypic traits in C. jejuni and C. coli strains. Transcriptome and phenotype analyses were conducted to determine if genetic and phenotypic characteristics could be attributed to the source of the strains. Isolates from water sources had higher biofilm formation than animal strains. Clinical strains had decreased sensitivity to hydrogen peroxide as well as increased adherence and invasion when compared to animal strains. A number of genetic differences were observed; however, without further analysis it is difficult to determine which of these impact virulence in Campylobacter. Ultimately, this project will lead to the identification of markers associated with strains of Campylobacter causing illness.

Apolipoproteins have important roles in the transport of lipids and the regulation of lipoprotein metabolism as cofactors for enzymes and ligands for receptor-binding. Their function and metabolism are closely related to the development of many diseases. This dissertation describes the investigation of the distribution and metabolism of apoE and glycated apoE in diabetes, obesity and hyperlipidaemia in comparison with healthy people. In order to carry out the research, I developed several robust laboratory methods and techniques for the isolation and measurement of apoE and glycated apoE. These included (1) a modified in-house ultracentrifugation for isolation of lipoprotein fractions (2) high sensitivity sandwich enzyme-linked immunosorbent assay (ELISA) for apoE and (3) m-aminophenylboronate affinity chromatography for the separation of glycated and non- glycated apoE.In healthy people the apoE concentration in different lipoprotein fractions is influenced by age, gender and apoE genotype. The effect of atorvastatin on serum apoE concentration in patients with type 2 diabetes with nephropathy was dependent on the dose of atorvastatin and apoE genotype and was strongly correlated with the reduction in triglycerides (TG) in very low density lipoprotein (VLDL).The effect of bariatric surgery on obese patients with and without diabetes demonstrated that after bariatric surgery, VLDL-apoE increased and apoE in low density lipoprotein (LDL), high density lipoprotein (HDL) and d>1.21g/ml fractions decreased; both glycated LDL-apoE and glycated HDL-apoE decreased. Total apoE and glycated apoE concentrations in plasma decreased to levels comparable to those of healthy controls. However, the distribution within the lipoprotein fractions was very different. The effect of niacin/laropiprant (LRPT) on lipoproteins in hyperlipidaemia patients was assessed in a blind crossover trial. Niacin/LRPT slightly decreased VLDL-apoE and LDL-apoE. It had no effect on apoE in HDL. Glycated apoE did not change in hyperlipidaemia. These results show that, compared with healthy people, the apoE distribution in obese and hyperlipidaemia patients is abnormal despite no change in total apoE concentration in some cases. The results also demonstrate that glycated apoE originates preferentially from VLDL. Various mechanisms for these results and relationships with other lipids are discussed. Furthermore, I suggest several potential directions, especially in vitro, for further research on apoE function and metabolism.

Orientadores: Fernando Lopes Gonçales Junior, Neiva Sellan Lopes Gonçales / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-07T22:44:35Z (GMT). No. of bitstreams: 1 Tonetto_PriscilaAparecida_M.pdf: 2027435 bytes, checksum: ec4453a66ae541917395dc0f14142ed8 (MD5) Previous issue date: 2006 / Resumo: O vírus da hepatite B (VHB) pode ser classificado em oito principais genótipos (A-H), e essa classificação tem uma distribuição geográfica determinada. Os genótipos do VHB podem influenciar na progressão de doença. O objetivo foi determinar os genótipos e os subtipos do VHB e correlacioná-los com as variáveis clínicas epidemiológicas, laboratoriais e histológicas. Foram determinados os genótipos de 139 amostras de soro de pacientes infectados pelo VHB, coletadas em Campinas, no estado de São Paulo, Brasil. O método para genotipagem utilizado foi o seqüenciamento parcial do gene S do VHB. Os primers utilizados foram desenhados a partir de seqüências do gene S, com genótipo determinado, depositadas no GenBank. Todas as seqüências obtidas foram comparadas com as seqüências depositadas no GenBank para determinação dos genótipos. O genótipo A (55%) do VHB foi o mais predominante na população, seguido pelos genótipos C (3%), D (38%) e F (4%). Entre os pacientes infectados pelos genótipos A e D, observou-se uma provável descendência africana de 18% (14/76) e 11% (6/53), respectivamente. Entre os quatro pacientes infectados pelo genótipo C, dois possuíam descendência asiática e dois eram caucasianos. Todos os pacientes infectados pelo genótipo F eram caucasianos sem ascendência indígena relatada. Aproximadamente 30% dos pacientes eram HBeAg positivo e 70% eram HBeAg negativo. A carga viral do DNA-VHB foi aproximadamente cinco vezes mais alta entre os HBeAg positivo quando comparada aos HBeAg negativo. Os genótipos A e D são os mais prevalentes entre os pacientes, aparentemente em virtude da imigração européia em nossa região / Abstract: Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression. Our objective was to determine the genotypes and the subtypes of HBV and to correlate them with the with variables clinical epidemiologies, laboratories and histological. Hepatitis B virus genotypes were determined in 139 plasma samples collected in Campinas, in the state of São Paulo, Brazil from HBV-infected patients. A method for genotyping hepatitis B virus by partial HBsAg gene sequencing with primers common to all known genotypes was developed. The results of sequencing corresponded to those found in HBV isolates obtained from GenBank, including all of the known HBV genotypes. HBV genotype A was predominant in our sample, appearing in 76 patients (55%), while genotypes C, D and F was found in 4 (3%), 53 (38%) and 6 (4%) of the patients, respectively. Among the patients infected by genotypes A and D, were observed a probably African descendents of the 18.3% (14/76) and 11.3% (6/53), respectively. Among the genotype C infected patients, 2 (50%) were of Asian descendents and 2 were Caucasians. The genotype F infected patients were all Caucasians without told indigenous origin. About 30% of the patients were HBeAg positive and 70% were HBeAg negative. The viral load of HBV-DNA was about 5 times higher among HBeAg positive than in HBeAg-negative patients. Genotypes A and D were the most prevalent among our HBV-infected patients, apparently a consequence of the types of immigration to our region / Mestrado / Ciencias Basicas / Mestre em Ciências Médicas

acase@tulane.edu / Background It is estimated 3 to 5 million individuals in the U.S. are chronically infected with the Hepatitis C virus (HCV). (Durham DP, 2016) More than 12,000 deaths occur annually in the U.S. as a result of HCV-related liver disease. (Wieland A, 2015) The cost of treatment medication for an individual with HCV genotype-1 is approximately $100,000 for 12 weeks of therapy. (Reau N, 2014) The exorbitant cost of HCV treatment has led to fears that many who could benefit from treatment will not receive it considering many with HCV are uninsured or have Medicaid. Purpose The purpose of this study is to quantify the cost, cost-effectiveness, and adverse outcomes associated with denying or delaying HCV treatment among the Louisiana Medicaid (LA-Medicaid) HCV GT-1 population. Methodology This project evaluates the cost and cost-effectiveness of treating HCV compared to not treating; initiating early treatment compared to late treatment and HCV-related health outcomes. A decision tree and Markov model simulates progression through the various states of health involved in progressive HCV disease, including death (hepatic and other causes). Results Don’t Treat/Treat Comparison Treatment was generally cost-effective, exhibiting an incremental cost-effectiveness ratio (ICER) of $21,670/life-year and $37,067/QALY (Quality-Adjusted Life-Years) gained. Optimal Treatment Stage Comparison Treatment of a person at F0 was cost effective, exhibiting an ICER of $6,482/QALY and $6,194/year of life compared to not treating at all and treating at F1, F2, F3, F4 or after LT. Conclusion Treatment of HCV-infected patients without liver fibrosis or in early stages of liver fibrosis appear to be more cost-effective than treating in advance stages of liver fibrosis or denying treatment. / 1 / Dwana Green

Two sets of durum samples were used to determine kernel characteristics and milling properties of durum genotypes grown in North Dakota, USA. Kernels were characterized for kernel size (length, width, and thickness), germ size (length and width), and shape (kernel width/kernel length, volume, sphericity, germ width/germ length, germ length/kernel length, and germ width/kernel width). Kernels were also characterized for their test weight, kernel weight, vitreousness and hardness. Milling properties evaluated were break release, milling rate, total extraction, semolina extraction, and semolina quality. All kernel characteristics and milling properties varied with genotype and growing location. First break release and milling rate were influenced by kernel shape and size. Larger, wider, and rounder kernels tended to result in better milling performance in the first break. Kernel hardness and vitreousness were strongly correlated and both were positively correlated to semolina extraction but not total extraction.

White mold (Sclerotinia sclerotiorum Lib. de Bary) is one of the most important diseases of common bean in the U.S. with seed yield losses up to 100%. White mold resistance is hard to incorporate into breeding materials because of low heritability, cumbersome screening methods, and few sources of resistance. A Multi-parent Advanced Generation Inter-Crosses population was created to develop resistant germplasm and map the genetics factors controlling the resistance. A seedling straw test method was used to identify resistant lines. Twenty genotypes were found to be resistant based on its response when inoculated with isolate 1980 of white mold. GWAS using quantitative, polynomial and binomial phenotypic distribution data, identified 30 genomic regions associated with resistance on Pv01, Pv02, Pv04, Pv05, Pv07, Pv08, Pv10 and Pv11. Cumulative R2 values were 57% for binomial distribution using 13 genomic intervals, 41% for polynomial using 8 intervals, and 40% for quantitative using 11 intervals.

No description available.