Le développement du laser a ouvert la voix à l'exploration de nouveaux domaines scientifiques et industriels. Les impulsions laser à haute intensité sont un outil unique pour les études d'interaction lumière/matière et leurs applications. Mais elles sont générées par des systèmes laser reposant sur l'utilisation de milieux à gain en verre pompés par des lampes flashes et sont donc intrinsèquement limitées en termes de cadence et d'efficacité. Le développement, au cours de ces dernières années, des lasers semi-conducteurs a attiré l'attention sur une nouvelle classe de lasers, les « laser solides pompés par diodes » (DPSSL). Ils possèdent une grande efficacité et sont des candidats de choix pour les systèmes compacts à haute puissance moyenne requis pour des applications industrielles, mais aussi en tant que sources de pompe à haute puissance pour des lasers ultra-intenses. Les travaux décrits dans cette thèse s'inscrivent dans le cadre du système laser Lucia (1 kilowatt de puissance moyenne), actuellement en construction au «Laboratoire d'Utilisation des Intenses lasers» (LULI) à l'Ecole Polytechnique, France. La génération d'impulsions laser de durée sub-10 nanosecondes avec des énergies allant jusqu'à 100 joules et des taux de répétition de 10 hertz est principalement limitée par l'émission spontanée amplifiée (ASE) et les effets thermiques. L'étude de ces limitations est le thème central de ce travail. Leur impact est discuté dans le cadre d'un premier jalon énergétique fixé vers 10 joules. Le système laser mis au point est présenté en détails depuis l'oscillateur jusqu'à la fin de la chaine d'amplification. Une discussion complète de l'impact de l'ASE et des effets thermiques est complétée par des vérifications expérimentales. Les modèles de simulation informatique développés sont validés puis utilisés pour prédire les performances du système laser qui, lors d'une première activation, à atteint un niveau d'énergie de 7 joules en régime mono-coup et de 6,6 joules pour un taux de répétition de 2 hertz. Les limitations actuelles sont discutées ainsi que les approches envisagées pour des développements futurs.

This thesis describes three readout formats for molecular analyses. A common feature in all works is probing techniques that upon specific target recognition ideally results in equimolar amounts of DNA circles. These are then specifically amplified and detected using any of the techniques presented herein. The first paper presents a method that enables homogeneous digital detection and enumeration of biomolecules, represented as fluorescence-labelled DNA macromolecules. This method offers precise measurements to be performed with a wide linear dynamic range. As an application, two closely related bacterial species were selectively detected. The second paper further investigates and optimizes the properties of the technique presented in paper one. The third paper demonstrates a platform that enables simultaneous quantitative analysis of large numbers of biomolecules. The array format and decoding scheme together propose a digital strategy for decoding of biomolecules. The array and the decoding procedure were characterized and evaluated for gene copy-number measurements. The fourth paper examines a new strategy for non-optical measurements of biomolecules. Characteristics of this technique are investigated, and compared to its optical equivalent, fluorescence polarization.

Host-Associated Differentiation (HAD) is the formation of genetically divergent hostassociated lineages maintained by ecological isolation. HAD is potentially an important route to ecological speciation in parasites including many insects. While HAD case studies are accumulating, there is a dearth of negative results in the literature making it difficult to know how common the phenomenon really is or whether there are specific traits of parasites which promote HAD. To address these two problems, studies are needed which both publish negative results (i.e., parasites not showing HAD) and test for HAD in multiple parasite species on the same pair of host species (i.e., control for host plant effects). In this study, HAD was tested in three species of herbivorous insects and one parasitoid species on the same two host tree species: pecan and water hickory. The insects were selected based on the presence or absence of two traits, parthenogenesis and endophagy. A test for HAD was considered “positive” when population substructure was explained by host-association. To test for the presence of HAD, insects were sampled sympatrically to eliminate geographical isolation as a confounding factor, sampling was replicated spatially to assure that HAD persisted, and multiple loci were sampled from each individual. Genetic data was analyzed using cluster analyses. HAD was found in both pecan leaf phylloxera and yellow pecan aphid but not in pecan bud moth or in the parasitoid of the yellow pecan aphid, Aphelinus perpallidus. Interestingly, both taxa showing HAD are parthenogenetic and both taxa not showing HAD reproduce sexually. Species showing HAD were tested for the presence of a pre-mating reproductive isolating mechanism (RIM) which could be maintaining HAD despite the potential for gene flow. Selection against migrants to the alternative host was tested in yellow pecan aphid using a no-choice fitness experiment. The overall contribution of this RIM to total isolation was positive and ranged from 0.614 to 0.850. The RIM of “habitat preference” was tested in pecan leaf phylloxera using a dual-choice preference experiment. In this species, preference was only detected for phylloxera originating from water hickory suggesting that host discrimination ability may be a less important factor promoting differentiation in phylloxera.

Blumeria graiminis f. sp. hordei (powdery mildew) is an obligate biotroph infecting hordeum vulgare (barley). It is one of the most devastating pathogens of barley, decreasing barley yield in great extent. In order to decrease barley loss, numerous studies are being conducted for overcoming the disease from the sides of both pathogen and host. However the pathogen is evolving very rapidly preventing the effective use of pesticides such as fungisides or development of resistant barley varieties by crossing race-specific resistance varieties, varieties having R genes, with susceptible but high yield producing varieties. In order to understand the mechanism of pathogen-host interactions, and producing enduring solutions for the problem of yield loss in barley molecular tools need to be used. In this thesis study, Amplified Fragment Length Polymorphism (AFLP) molecular marker method is used in order to reveal the molecular characterization of Turkish Blumeria graminis f. sp. hordei varieties collected from &Ccedil / ukurova region in Turkey. Thirty-nine samples were analyzed with eigth universal races, of which virulence genes are studied. AFLP studies were conducted on LI-COR 4300 DNA Analyzer system. Bioinformatics analysis was performed with NTSYS program. By the help of this Numerical Taxonomic System, similarity, dissimilarity, clustering, dendograms, two-dimensional scatter plots, and three-dimensional perspective plots were obtained. By the light of these analyses Turkish Blumeria graminis f. sp. hordei varieties together with universal races are grouped into three clusteres. In conclusion, studying Turkish Blumeria graminis f. sp. hordei isolates and comparing them with universal races is a unique study in terms of characterizing the Turkish Bgh isolates for the first time, and can be used as a frontier study for studying Resistance genes, by reverse genetic tools.

Šio darbo tikslas buvo ištirti atsitiktinai padaugintos polimorfinės DNR (APPD) metodu skirtingas Europinio bebro (Castor fiber) subpopuliacijas Lietuvoje. Buvo ištirtos Europinio bebro 4 subpopuliacijose: Mituvos, Vilkaraisčio, Giedraičių ir Rusnės salos. DNR atsitiktinai padaugintų fragmentų polimorfizmas buvo tirtas naudojant 10 pradmenų. Pagal Nei apskaičuotą genetinę distanciją tarp populiacijų, labiausiai genetiškai panašios buvo Giedraičių ir Vilkraisčio subpopuliacijos (0,936), didžiausia genetinė distancija nustatyta tarp Rusnės salos ir Vilkaraisčio subpopuliacijų (0,288). Ištirtos subpopuliacijos grupuojasi į du klasterius: vieną klasterį sudaro Rusnės salos ir Mituvos subpopuliacijos, kitą – Vilkaraisčio ir Giedraičių subpopuliacijos. Europinio bebro subpopuliacijų genetinei įvairovei nustatyti, Popgene programa buvo apskaičiuoti 4 parametrai. Shannon informacinis indeksas svyravo nuo 0,2527 (Rusnės sala) iki 0,3895 (Giedraičiai). Nei genetinė įvairovė svyravo nuo 0,1677 (Rusnės sala) iki 0,2589 (Mituva). Didžiausias nustatytas alelių skaičius buvo Mituvoje (1,8911), mažiausias Rusnės saloje (1,5050). Efektyvus alelių skaičius svyravo nuo 1,2864 (Rusnės sala) iki 1,444 (Giedraičiai). Didžiausia genetinė įvairovė buvo aptikta Mituvos subpopuliacijoje, o mažiausia genetine įvairove pasižymi Rusnės salos subpopuliacija. Daugiausia polimorfinių lokusų buvo aptikta Mituvos subpopuliacijoje (89,11%), o mažiausiai Rusnės salos subpopuliacijoje (50,5%). Nustatėmė, kad... [toliau žr. visą tekstą] / The aim of this study is to evaluate genetic structure of European beavers (Castor fiber) subpopulations from Lithuania using RAPD (Random Amplified Polymorphic DNA) method. We investigated genetic variability of 4 subpopulations from Rusne, Mituva, Giedraiciai and Vilkaraistis. 10 primers were used in this analysis. Acording to Nei‘s genetic identity, the most similar were subpopulations from Giedraiciai and Vilkaraistis (0,936), the highest genetic distance was observed between subpopulations from Rusnes island and Vilkaraistis (0,288). These subpopulations form two clusters: Mituva and Rusnes island forms one cluster and Vilkaraistis and Giedraiciai – another. To evaluate the genetic variation in subpopulations we analysed four parameters. Shannon’s informations index was from 0,2527 in Rusnes island to 0,3895 in Giedraiciai.The highest Nei‘s genetic variaty was observed in subpopulation from Mituva and the smallest in Rusnes island (0,1677).The highest number of alleles was detected in Mituva (1,8911) and the smalest in Rusnes island (1,5050). The efective number of alleles was from 1,2864 in Rusnes island to 1,444 in Giedraiciai. From these parametres we can see that the most genetic diversity is observed in subpopulation from Mituva and the smallest in subpopulation from Rusnes island. We detected that the in Rusnes island 50,5 % of loci were polimorphic, and in subpopulation from Mituva even 89,11% of loci were polimorphic. We found out that molecular diversity is... [to full text]

The characterization of the banana germplasm collection from Rubona - Rwanda was investigated using morphological and cytological characteristics of the genomic groups. Genetic diversity was assessed using Random Amplified Polymorphic DNA analysis. The survey was conducted to evaluate the distribution of banana cultivars in the four major growing regions of Rwanda. A total of 90 accessions from the National Banana Germplasm Collection at Rubona Rwanda were characterized and six characters of the fingers (length, width, weight, green life, post green life and length/width ratio) were subjected to principal component analysis (PCA). The cooking and beer clones were separated. The cooking clones were further grouped into three clone sets: Musakala, Nakabululu, and one that constitutes Nakitembe and Nfuuka clone sets. The AAB genomic group was separated from AAA, AB and ABB genomic groups. The results from the survey showed that East African Highland bananas are the most important genotype group in the four major banana growing regions of Rwanda ranging between 60 - 90% of banana mats counted. Several new Highland banana cultivars were recorded, such as 'Intokatoke', 'Igihuna', 'Ingenge', 'Ingaju', 'Icyerwa', 'Mitoki', 'Madamu', 'Inkokobora', 'Intokekazi', 'Bugoyi', 'Ishoki'. Amongst these cultivars, some were classified as cooking and others as brewing bananas. However, in the National Banana Germplasm Collection at Rubona - Rwanda, the uses of these cultivars are recorded differently therefore increasing the need for agro-morphological characterization. The assessment of ploidy level of accessions from the National Banana Germplasm Collection at Rubona - Rwanda, by flow cytometry showed misclassification of some accessions such as 'Pomme', 'Kamaramasenge', 'Gisubi kayinja', 'Gisubi kagongo', and 'Dibis' which were classified as diploid, diploid, triploid, and tetraploid respectively. They IV were found to be triploid, triploid, triploid, diploid and triploid. All these bananas were recently introduced into Rwanda, while the endemic Highland bananas were triploid. The genomic group and genetic similarities of 49 accessions were investigated using Random Amplified Polymorphic DNA markers. The genomic group of bananas assessed were established using OPA-18 (PILLAY et al., 2000) and OPG-17 primers. These primers showed bands 441 and 443 base pairs (bp) respectively for the accessions having only the B genome. Whilst they were absent for the accessions " having an A genome. The genetic similarity was estimated via a Simple Matching coefficient which showed the lowest value 0.46 measured between 'Ingumba' and 'Ishika 'and the highest value of 0.85 between 'Kirayenda' and 'Inyabukuwe'. The data of matrix of coefficient of similarity was subjected to cluster analysis with unweighted pair group method with arithmetic average (UPGMA). Each accession was clearly separated demonstrating the usefulness of RAPDs in analysis of genetic diversity. The results of this study are very important to the Curator of the banana germplasm collection in Eastern Central Africa and for the future breeding of this crop. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Improved analytical methods provide new opportunities for both biological research and medical applications. This thesis describes several novel molecular techniques for nucleic acid and protein analysis based on detection or sequencing of amplified single molecules (ASMs). ASMs were generated from padlock probe assay and proximity ligation assay (PLA) through a series of molecular processes. In Paper I, a simple colorimetric readout strategy for detection of ASMs generated from padlock probe assay was used for highly sensitive detection of RNA virus, showing the potential of using padlock probes in the point-of-care diagnostics. In Paper II, digital quantification of ASMs, which were generated from padlock probe assay and PLA through circle-to-circle amplification (C2CA), was used for rapid and sensitive detection of nucleic acids and proteins, aiming for applications in biodefense. In Paper III, digital quantification of ASMs that were generated from PLA without C2CA was shown to be able to improve the precision and sensitivity of PLA when compared to the conventional real-time PCR readout. In Paper IV, a non-optical approach for detection of ASMs generated from PLA was used for sensitive detection of bacterial spores. ASMs were detected through sensing oligonucleotide-functionalized magnetic nanobeads that were trapped within them. Finally, based on in situ sequencing of ASMs generated via padlock probe assay, a novel method that enabled sequencing of individual mRNA molecules in their natural context was established and presented in Paper V. Highly multiplex detection of mRNA molecules was also achieved based on in situ sequencing. In situ sequencing allows studies of mRNA molecules from different aspects that cannot be accessed by current in situ hybridization techniques, providing possibilities for discovery of new information from the complexity of transcriptome. Therefore, it has a great potential to become a useful tool for gene expression research and disease diagnostics.

Backscatter communication enables wireless communication at a power consumption orders of magnitude lower than conventional wireless communication. Instead of generating new RF-signals backscatter communication leverages ambient signals, such as WiFi-, Bluetooth- or TV-signals, and reflects them by changing the impedance of the antenna. Backscatter communication is known as a short-range communication technique achieving ranges in the order of meters. To improve the communication range, we explore the use of a tunnel diode as an amplifier of the backscattered RF-signal. We developed the amplifier on a PCB-board together with a matching network tuned to give maximum gain at 868 MHz. Our work demonstrates that the 1N3712 tunnel diode can achieve gains up to 35 dB compared to a tag without amplification while having a peak power consumption of 48 μW. With this amplifier the communication distance can be increased by up to two orders of magnitude.

Made available in DSpace on 2015-03-26T13:51:59Z (GMT). No. of bitstreams: 1 texto completo.pdf: 536332 bytes, checksum: 5951891794c17e210fb52fda2d6fa297 (MD5) Previous issue date: 2013-03-22 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Devido à ausência de estudo de caracterização da variabilidade genética das populações de Pseudocercospora fijiensis recentemente introduzidas no Brasil, o objetivo desse trabalho foi avaliar a adequabilidade do marcador IRAP para estudar variações genéticas entre indivíduos, bem como determinar a estrutura genética da população brasileira de P. fijiensis com base no fingerprinting gerado por amplificação de polimorfismo entre retrotransposons (IRAP). Um total de 22 locos foi amplificado, sendo 77.3 % polimórficos. A análise de agrupamento revelou dois principais grupos no Brasil. A diversidade gênica (HE) foi de 0.22 e pela análise de variância molecular verificou-se que a maior variabilidade genética está dentro das populações. A Análise Discriminante de Componente Principal (DAPC) revelou que não há nenhuma estruturação relacionada com as origens geográficas e cultiva hospedeiro. O sistema de marcador baseado em retrotransposon IRAP é ferramenta apropriada para estudar a variabilidade genética em P. fijiensis. / Due to the lack of characterization study of genetic variability in populations of Pseudocercospora fijiensis recently introduced in Brazil, the objective of this study was to evaluate the suitability of IRAP marker for studying genetic variations between individuals, and to determine the genetic structure of the population of P. fijiensis based on fingerprinting generated by inter-retrotransposons amplified polymorphism (IRAP). A total of 22 loci were amplified and 77.3% showed a polymorphism. Cluster analysis revealed two major groups in Brazil. The observed genetic diversity (HE) was 0.22, and through molecular analysis of variance, it was determined that the greatest genetic variability occurs within populations. The Discriminant Analysis of Principal Components (DAPC) revealed no structuring related to the geographical origin of culture of the host. The IRAP-based marker system is a suitable tool for the study of genetic variability in P. fijiensis.

Made available in DSpace on 2014-06-12T15:04:58Z (GMT). No. of bitstreams: 2 arquivo1766_1.pdf: 916614 bytes, checksum: d16125fdbdb2b99a4f6d33952c69a16b (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2006 / O bicudo do algodoeiro, Anthonomus grandis Boheman, é considerado a maior praga da cotonicultura mundial, ocasionando danos que repercutem principalmente na produtividade, qualidade do algodão colhido e gasto com medidas de controle. Neste estudo foi realizada pela primeira vez, uma análise da diversidade e estrutura genética das populações naturais de A. grandis do Brasil. Doze populações coletadas em seis estados brasileiros (Paraíba, Ceará, Bahia, Pará, Mato Grosso e Goiás) em áreas onde são praticadas a agricultura em escala empresarial e agricultura familiar, foram avaliadas pelas técnicas de Polimorfismo do DNA Amplificado Randomicamente (RAPD), Isoenzimas e Microssatélite. Os resultados obtidos em seis populações pela técnica de RAPD baseados em 25 loci, revelaram uma heterozigosidade média de 0,262, com polimorfismo (P) variando de 52 a 84%. A diferenciação genética entre as populações foi extremamente elevada e significativa (GST = 0,258; p < 0,05), refletindo a existência de baixo fluxo gênico entre as mesmas (Nm = 0,72). A análise de cinco populações com 6 loci alozímicos mostrou uma heterozigosidade média de 0,212 e polimorfismo (P) variando entre 25 e 100%. O índice de diferenciação genética FST obtido por este marcador entre as populações correspondeu a 0,544 (p < 0,05), sugerindo a ocorrência de baixo fluxo gênico (Nm = 0,210) entre as populações. A heterozigosidade e o polimorfismo (P) observados em onze populações pela análise de 8 loci de microssatélites variaram entre 0,038 e 0,224 e de 37,5 a 75%, respectivamente. O FST entre as populações correspondeu a 0,220, produzindo um Nm de 0,8. Os três marcadores moleculares utilizados revelaram que as populações de A. grandis dos estados brasileiros avaliados apresentam baixa diversidade genética, em comparação às populações dos Estados Unidos, México e demais países da América do Sul, sugerindo que a colonização deste inseto ocorreu em uma ou poucas áreas. Os resultados obtidos relativos à diversidade genética também permitiram distinguir populações oriundas de regiões onde é praticada a agricultura em escala empresarial das áreas de agricultura familiar, assim como mostrou que as populações do nordeste podem estar servindo de fonte para colonização de novas áreas e de áreas já tratadas