Les variations de nombre de copies (CNVs) sont des séquences supérieures à 1kb ayant subi une délétion, une duplication ou une inversion de fragments d'ADNs et sont présents avec une fréquence de 12% dans le génoe humain. Leur caractérisation ainsi que leur association dans les maladies complexes sont, à ce jour, en plein essor. Nous avons donc entrepris l'étude des CNVs de gènes candidats dans les familles de patients atteints de polyarthrite rhumatoïde (PR) en utilisant plusieurs outils de biologie moléculaire. Les CNVs de quatre gènes candidats (GSTMI, GSTT1, FCGR3B et CCL3L1) ont été investigués par PCR classique, qPCR ou Droplet Digital PCR (ddPCR). Mais très vite, la PCR classique a montré qu'elle n'est pas applicable à tous les gènes et que la qPCR était peu sensible et reproductible. Par contre, grâce à la ddPCR, nous avons tout d'abord pu quantifier avec précision les CNVs des gènes GSTM1, FCGR3B et CCL3L1. Par la suite, nous avons pu identifier les génotypes en nombre de copies pour le gène GSTM1 et mettre en évidence une duplication en tandem qui a été confirmée par une Lone Range PCR. La transmission des CNVs au sein des familles étudiées nous a ensuite permis d'identifier tous les génotypes en nombre de copies du gène FCGR3B et certains génotypes du gène CCL3LI. Des événements de recombinaison de novo ont été mis en évidence pour le gène FCGR3B ainsi que des duplications en tandem transmises des parents aux patients pour les trois gènes investigués par ddPCR. Aucune association n'a été mise en évidence entre la PR et les CNVs des quatre gènes candidats. Néanmoins, une transmission préférentielle de la délétion du gène GSTT1 a été mise en évidence, après stratification dans le sous-groupe de patients séropositifs pour le facteur rhumatoïde. Des tendances non significatives ont été observées dans les sous-groupes de cas index avec un âge de début de la maladie inférieur à 40 ans, avec présence de modules (pour le gêne GSTM1), et avec la présence d'auto-anticorps (pur les gènes FCGR3B et CCL3L1). En conclusion, le développement de l'utilisation d'une technologie de pointe et l'accès à des échantillons familiaux sont des atouts indispensables pour caractériser les variants génomiques de nombre de copies, facteurs de risque potentiels des maladies complexes. / Copy number variations (CNVs) are sequences up to 1kb resulting from deletion, duplication and inversion of DNA regions ans are present with a frequency of 12% in the human genome. CNVs characterization and association to complex diseases are still subjects of controversies. We then enhanced the study of CNV's for candidate genes in rhemuatoid arthritis (RA) families, with different methodologies. CNVs of our candidate genes (GSTM1, GSTT1, FCGR3B et CCL3L1) were investigated with standard PCR, quantitative PCR (qPCR) or with Droplet Digital PCR (ddPCR). First we found that standard PCR was not applicable for all genes and that the qPCR was not sensitive and reproductible for CNVs quantification. Second, the ddPCR methodology allowed us to quantify CNVs of GSTM1, FCGR3B, and CCL3L1 with high resolution and to characterize copy number genotypes og GSTM1 gene, leading to the identification of tandem duplicated copies. A long range PCR confirmed this result. CNVs transmission in families allowed the identification of all copy number genotypes for FCGR3B gene and some of CCL3L1 with high resolution and to characterize copy numbers genotypes of GSTM1 gene, leading to the identification of tandem duplicated copies. A long Range PCR confirmed this result. CNVs transmission in families allowed the identification of all copy number genotypes for FCGR3B gene and some of CCL3L1 genotypes. De novo recombination events were highllighted for FCGR3B gene and transmission of the duplication from one parent to the offspring was observed for all genes characterized by ddPCR. No association between RA and candidate genes CNVs was found, but after stratification, we observed a significant preferential transmission of GSTT1 deletion in the subgroup of patients seropositive for rheumatoid factor. We also showed a non-significant tendency in the subgroups of patient with an age at onset inferior to 40 years, with presence of nodules (for GSTM1 gene), and with presence of auto-antibodies (for FCGR3B and CCL3L1 gene). In conclusion, digital PCR is currently the most adequate methodology to accurately genotype CNVs. Analysis of familial sample leads to the identification of duplication events and to the characterization of genotypes, essential for CNVs association in complex diseases.

Tuber crops such as potato (Solanum tuberosum L.) can take up high levels of soil cadmium (Cd) which can be accumulated in their tubers. Thus, they can act as vehicles for transporting Cd to human body which can seriously threaten our health due to its high toxicity. In some circumstances, consumption of potato can contribute to more than 50 percent of human dietary Cd intake. In the present research two approaches were used to probe the potential for genetic improvement to contribute towards the goal of “minimisation of Cd level in potato” which is a novel food safety strategy: (1) assess the natural occurrence of variation in Cd accumulating potential among different potato cultivars already in cultivation in New Zealand, and (2) as a proof-of-concept study to generate potato plants with improved Cd resistance from a model experimental potato cultivar Iwa based on plant cell culture-selection (in vitro breeding approach). In the first approach, 10 New Zealand cultivars, namely Red Rascal (RR), Russet Burbank (RB), Fianna (F), Agria (A), Laura (L), Purple Heart (PH), Purple Passion (PP), Yukon Gold (YG), Moonlight (M) and Summer Delight (SD) were chosen randomly among over 30 cultivars grown for seed production in a block situated approximately one kilometre east of Lincoln, Canterbury within the 2011-2012 growing season. The tubers as well as the soil samples immediately surrounding the tubers were harvested and prepared for analytical analyses using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The results showed that the soil samples were low in Cd level (0.06 mg kg-1), compared with the national soil average (0.35 mg kg-1), while the tubers varied widely in Cd content from 0.04 to 0.34 mg kg-1 among different cultivars. Therefore, SD with the lowest mean Cd content (0.05 mg kg-1) and an Enrichment Factor (EF) of just below one showed promise as a potential cadmium safe cultivar (CSC). There might be of concern if L, YG, PP with the highest mean Cd contents (0.18-0.21 mg kg-1) are grown in soils with higher Cd levels. Potato tissue culture required for the second approach based on somaclonal variation was established from the model experimental genotype Iwa in the lab. Leaf and internode explants were used as the starting plant materials to initiate two morphologically distinct calli (type-A and -B). Upon morphological assessment and analysis of antioxidative enzymes such as peroxidase, it was revealed that they exhibited differential Cd sensitivity. The more Cd-resistant callus type (type-B) was chosen for in vitro selection using 18 different Cd treatments varying in Cd exposure timing and duration. Following shoot and root regeneration from these calli, 18 different new Iwa plant lines were obtained. After at least three months of sub-culturing of all 18 plant lines on Cd-free media, in vitro screening of the lines was carried out to identify the most promising plant lines as far as Cd resistance was concerned. After two rounds of in vitro growth screening under a low and high Cd levels, two lines including line 9 (L9) and line 11 (L11) were found to exhibit enhanced Cd resistance compared to control Iwa plants. Further studies of L9 and L11 compared to control Iwa plants including biochemical analysis of reactive oxygen species such as hydrogen peroxide, and transmission electron microscopic studies uncovered that L11 was more resistant to Cd than L9 and control plants. L11 plantlets had about 20 and 10 percent less H2O2 level than control and L9 plantlets, while antioxidative activities were four and two times higher in L11 compared with control and L9, respectively. Moreover, L11 seemed to exhibit a high rate of Cd compartmentalisation in the vacuoles and Cd binding to the cell walls in the roots, suggesting a potential to exclude or limit Cd translocation to other parts of the plant.

Transposons are mobile genetic elements that have the potential to cause mutations as a result of different aspects of their life cycle. Because most of these mutations are detrimental and due to a selfish life cycle seemingly aiming at increasing their numbers, transposons have been regarded as "junk" DNA that contributes no evolutionary function to the host organism. In this thesis, I argue that although most of the transposon-induced mutations are detrimental, some may lead to benefits for the host and become adaptive. I discuss recent evidence from the literature that points to several mechanisms by which transposons and transposon activity may lead to the diversification of host genes and gene functions. I also provide evidence that transposons have inserted in the 5' flanking region of the gene coding for maize and teosinte auxin-binding protein 1 (Abp1). These transposons do not change the structure of the Abp1 transcripts but may modulate Abp1 gene expression quantitatively. In addition, I document the first case outside of oncogenic retroviruses, of a retrotransposon (called Bs1) that transduced portions from three different maize genes. I show that the Bs1-associated transduction events resulted in the formation of one uninterrupted open reading frame that is both transcribed and translated in reproductive tissues. I suggest that, such as in the case of Bs1, gene transduction by retroelements may be a general mechanism for the evolution of new hybrid genes by the shuffling of host sequences. I conclude that transposons are better regarded as means for the generation of gene and genomic diversity. Natural selection will favor and fix adaptive variants whereas detrimental mutations are likely to be purged out of the population.

Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references (leaves [178]-193).

abstract: Genomic structural variation (SV) is defined as gross alterations in the genome broadly classified as insertions/duplications, deletions inversions and translocations. DNA sequencing ushered structural variant discovery beyond laboratory detection techniques to high resolution informatics approaches. Bioinformatics tools for computational discovery of SVs however are still missing variants in the complex cancer genome. This study aimed to define genomic context leading to tool failure and design novel algorithm addressing this context. Methods: The study tested the widely held but unproven hypothesis that tools fail to detect variants which lie in repeat regions. Publicly available 1000-Genomes dataset with experimentally validated variants was tested with SVDetect-tool for presence of true positives (TP) SVs versus false negative (FN) SVs, expecting that FNs would be overrepresented in repeat regions. Further, the novel algorithm designed to informatically capture the biological etiology of translocations (non-allelic homologous recombination and 3&ndashD; placement of chromosomes in cells –context) was tested using simulated dataset. Translocations were created in known translocation hotspots and the novel&ndashalgorithm; tool compared with SVDetect and BreakDancer. Results: 53% of false negative (FN) deletions were within repeat structure compared to 81% true positive (TP) deletions. Similarly, 33% FN insertions versus 42% TP, 26% FN duplication versus 57% TP and 54% FN novel sequences versus 62% TP were within repeats. Repeat structure was not driving the tool's inability to detect variants and could not be used as context. The novel algorithm with a redefined context, when tested against SVDetect and BreakDancer was able to detect 10/10 simulated translocations with 30X coverage dataset and 100% allele frequency, while SVDetect captured 4/10 and BreakDancer detected 6/10. For 15X coverage dataset with 100% allele frequency, novel algorithm was able to detect all ten translocations albeit with fewer reads supporting the same. BreakDancer detected 4/10 and SVDetect detected 2/10 Conclusion: This study showed that presence of repetitive elements in general within a structural variant did not influence the tool's ability to capture it. This context-based algorithm proved better than current tools even with half the genome coverage than accepted protocol and provides an important first step for novel translocation discovery in cancer genome. / Dissertation/Thesis / Ph.D. Biomedical Informatics 2014

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Syftet med den här studien är att se hur matematikundervisningen kan planeras och genomföras för att variera och individualisera undervisningen. Undervisningen som kommer att granskas är den dagliga verksamheten som bedrivs i klassrummen med elever i årskurserna 4-6. Studien fokuserar på delarna problemlösning och räknesätten inom matematiken och hur den individualiserade undervisningen uttrycks inom dessa utvalda delar.   Metoderna som använts för att genomföra studien är intervjuer och observationer. Dessa metoder är båda av kvalitativ art.   De resultat som studien visar är att även om lärare har en vilja att variera och individualisera sin undervisning är det i praktiken svårt att genomföra. Det beror bland annat på tidsbrist, i klassrummet finns många elever och som ensam lärare är det svårt att se varje elev och ge den tid och stöd som behövs. En lärare hinner inte fundera igenom vad elever egentligen behöver hjälp med och vad det är som hindrar dem från att komma vidare i sitt skolarbete. Istället för att ta sig tiden till att fundera på detta och hitta ett annat sätt att hjälpa och förklara blir det att läraren förklarar på samma sätt hela tiden.

Spin transfer torque magnetic random access memory (STT-MRAM) is a competitive, future memory technology that has gained immense interest in recent years due to its small cell size, voltage and process compatibility with CMOS and nano-second read/write speeds. It exhibits high density (3-4x of SRAM), non-volatility and process scalability and hence is widely being considered as a viable alternative for SRAM in last-level caches. As the design and fabrication process matures for the STT-MRAM, there is a need to study the various fault models that can affect this novel memory technology. This work presents a comprehensive analysis of fault models in STT-MRAM under both parametric variations as well as resistive defects (opens and shorts). Sensitivity of read, write and retention to process parameter variations such as lithographic and material variations are studied. In addition, defects (both intra-cell and inter-cell) and the corresponding fault models have been studied and data patterns which excite these faults are explored.

No description available.