<p>The completion of the Human Genome Project, a remarkable feat by any measure, has provided over three billion bases of reference nucleotides for comparative studies. The next, and perhaps more challenging step is to analyse sequence variation and relate this information to important phenotypes. Most human sequence variations are characterized by structural complexity and, are hence, associated with abnormal functional dynamics. This thesis covers the assembly of a computational platform for verifying these variations, based on accurate, published, experimental data.</p>

Most clonal plants exhibit a modular structure at multiple levels. At the level of the organs, they are characterized by functional modules, such as, internodes, leaves, branches. At the level of the genetic individual (clone or genet), they possess independent evolutionary and physiological units (ramets). These evolutionary units arise through the widespread phenomenon of clonal reproduction, achieved in a variety of ways including rhizomes, stolons, bulbils, or lateral roots. The focus of this study was Populus tremuloides, trembling aspen, a dioecious tree that reproduces sexually by seed and asexually through lateral roots. Local forest patches in western populations of Populus tremuloides consisted largely of multiple genotypes. Multi-clonal patches were dominated by a single genotype, and in one population (Riske Creek) we found several patches (five out of 17) consisting of a single genotype. A second consequence of modularity is that during the repeated cycle of ramet birth, development and death, somatic mutations have the opportunity to occur. Eventually, the clone becomes a mosaic of mutant and non-mutant cell lineages. We found that neutral somatic mutations accumulated across 14 microsatellite loci at a rate of between 10^-6 and 10^-5 per locus per year. We suggest that neutral genetic divergence, under a star phylogeny model of clonal growth, is an alternative way to estimate clone age. Previous estimates of clone age couple the mean growth rate per year of shoots with the area covered by the clone. This assumes a positive linear relationship between clone age and clone size. We found, however, no repeatable pattern across our populations in terms of the relationship of either shape or size to the number of somatic changes. A final consequence of modularity is that during clonal growth, natural selection is relaxed for traits involving sexual function. This means that mutations deleterious to sexual function can accumulate, reducing the overall sexual fitness of a clone. We coupled neutral genetic divergence within clones with pollen fitness data to infer the rate and effect of mildly deleterious mutations. Mutations reduced relative sexual fitness in clonal aspen populations by about 0.12x10^-3 to 1.01x10^-3 per year. Furthermore, the decline in sexual function with clone age is evidence that clonal organisms are vulnerable to the effects of senescence.

Efficacy of tyrosine kinase inhibitor (TKI) therapy depends on epidermal growth factor receptor (EGFR) mutation status in patients with non-small cell lung cancer (NSCLC). There has been an increasing interest in studying mutation-specific rabbit monoclonal antibodies of delE746-A750 mutation in exon 19 and L858R point mutation in exon 21 for detecting EGFR mutants. These two mutations account for approximately 90% of all EGFR mutations. We evaluated the two mutation-specific monoclonal antibodies for the detection of EGFR mutations by immunohistochemistry (IHC) and the relationship with treatment outcome and survival. Twenty-five patients (58.1%) harbored EGFR mutations. These mutations include delE746-A750 mutation for seven patients, L858R point mutation for in eighteen patients. IHC showed, for the delE746-A750 and L858R mutations, sensitivity (57.1% and 66.7%), specificity (97.3% and 100%), positive predictive value (80.0% and 100%), and negative predictive value (94.7% and 80.6%). Analysis for progression-free survival was not correlated to IHC staining, but the overall survival was correlated to IHC staining. These mutation-specific antibodies for delE746-A750 and L858R mutations have high positive predictive value and specificity for predefined EGFR mutations and may be suitable for screening for these predefined mutations. However, negative IHC results required further mutation analyses before excluding EGFR TKI therapy.

Reproduction de : Thèse d'exercice : Médecine : Nancy 1 : 2006. / Titre provenant de l'écran-titre.

Most clonal plants exhibit a modular structure at multiple levels. At the level of the organs, they are characterized by functional modules, such as, internodes, leaves, branches. At the level of the genetic individual (clone or genet), they possess independent evolutionary and physiological units (ramets). These evolutionary units arise through the widespread phenomenon of clonal reproduction, achieved in a variety of ways including rhizomes, stolons, bulbils, or lateral roots. The focus of this study was Populus tremuloides, trembling aspen, a dioecious tree that reproduces sexually by seed and asexually through lateral roots. Local forest patches in western populations of Populus tremuloides consisted largely of multiple genotypes. Multi-clonal patches were dominated by a single genotype, and in one population (Riske Creek) we found several patches (five out of 17) consisting of a single genotype. A second consequence of modularity is that during the repeated cycle of ramet birth, development and death, somatic mutations have the opportunity to occur. Eventually, the clone becomes a mosaic of mutant and non-mutant cell lineages. We found that neutral somatic mutations accumulated across 14 microsatellite loci at a rate of between 10^-6 and 10^-5 per locus per year. We suggest that neutral genetic divergence, under a star phylogeny model of clonal growth, is an alternative way to estimate clone age. Previous estimates of clone age couple the mean growth rate per year of shoots with the area covered by the clone. This assumes a positive linear relationship between clone age and clone size. We found, however, no repeatable pattern across our populations in terms of the relationship of either shape or size to the number of somatic changes. A final consequence of modularity is that during clonal growth, natural selection is relaxed for traits involving sexual function. This means that mutations deleterious to sexual function can accumulate, reducing the overall sexual fitness of a clone. We coupled neutral genetic divergence within clones with pollen fitness data to infer the rate and effect of mildly deleterious mutations. Mutations reduced relative sexual fitness in clonal aspen populations by about 0.12x10^-3 to 1.01x10^-3 per year. Furthermore, the decline in sexual function with clone age is evidence that clonal organisms are vulnerable to the effects of senescence.

Fenugreek (Trigonella foenum-graecum L.) is an annual legume mainly used as a spice crop in many parts of the world. "Tristar" is a new forage cultivar that requires - 120 days to produce mature seed in western Canada where only - 100 frost-free days are available. The goal for this study was to reduce maturity duration for the crop through a series of studies on the genetics and agronomic aspects of fenugreek. This two year study suggests that: 1)mutation breeding using Tristar seed as a base population could be successfull; 2)multi-location trials using world accessions exhibited genotype X environment interaction; 3)swathing of plants before freezing temperatures set in; 4)application of phosphate fertilizer increased seed yield and; 5)foliar sprays of chemicals can be used for production of high quality seed. In this study some short duration, high yielding and determine lines of fenugreek were produced improving the potential for use of fenugreek and the economics of beef production in western Canada. / xix, 184 leaves : ill. (some col.) ; 29 cm.

The effects of a mutation in one gene can occasionally be suppressed by mutation in another gene. Genetic suppression indicates functional relationships and provides clues about the mechanism and order of action in genetic pathways. Here I explored the existing yeast deletion collection to identify suppressor relationships. The collection was released in 2000 and it is known that some strains in the collection have acquired mutations. Whole genome sequencing of 48 yeast deletion strains corresponding to 26 genome integrity genes was performed. High-throughput sequencing revealed a broad mutational spectrum including point mutations, indels, and copy number variations. I identified and experimentally validated two new suppressor mutations (sgs1 mutations in both top3Δ and rmi1Δ strains) corresponding to gene pairs with previously known suppressor relationships. Thus, high-throughput sequencing and analysis of yeast deletion strains can identify suppressor mutations. The resulting genome sequences also provide a baseline for future laboratory evolution experiments.

<p>The completion of the Human Genome Project, a remarkable feat by any measure, has provided over three billion bases of reference nucleotides for comparative studies. The next, and perhaps more challenging step is to analyse sequence variation and relate this information to important phenotypes. Most human sequence variations are characterized by structural complexity and, are hence, associated with abnormal functional dynamics. This thesis covers the assembly of a computational platform for verifying these variations, based on accurate, published, experimental data.</p>

Base rivalry arises at replication of monotonous DNA – sequences. Irreparable mutations can arise by tunnel processes if the developed energy is high enough. The tunnel probability depends not only on the base rivalry energy but also depends on the temperature of surroundings. The tunnel probability diminishes with decreasing temperature. The cytoplasm viscosity increases in the long term with decreasing temperature. The length of the monotonous sequence in which happens an irreparable mutation (caused by base rivalry) then will be larger than at higher temperatures. This means that the possible distribution variety of all base components on the given matrix will diminish; therefore the probability increases that one base component which possesses the necessary energy, comes into the certain monotonous sequence to provoke a tunnel process. These different temperature dependences are the subject of the following examinations; they lead to the equation (32) which is valid for coming off of an irreparable mutation which is caused by base rivalry. Because of the dependence between temperature change and mutating sequence length from s1 to s1+1 (expressed in this equation), there result informations about evolution, and informations about mutation of DNA – viruses. The calculations are performed with very small DNA fragments so called residual fragments.

Diss. Linköping : Univ., 2003.