Dissertations / Theses: 'Microsatellites'

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Jentzsch, Iris Miriam Vargas. "Comparative genomics of microsatellite abundance: a critical analysis of methods and definitions." Thesis, University of Canterbury. Biological Sciences, 2009. http://hdl.handle.net/10092/4282.

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This PhD dissertation is focused on short tandemly repeated nucleotide patterns which occur extremely often across DNA sequences, called microsatellites. The main characteristic of microsatellites, and probably the reason why they are so abundant across genomes, is the extremely high frequency of specific replication errors occurring within their sequences, which usually cause addition or deletion of one or more complete tandem repeat units. Due to these errors, frequent fluctuations in the number of repetitive units can be observed among cellular and organismal generations. The molecular mechanisms as well as the consequences of these microsatellite mutations, both, on a generational as well as on an evolutionary scale, have sparked debate and controversy among the scientific community. Furthermore, the bioinformatic approaches used to study microsatellites and the ways microsatellites are referred to in the general literature are often not rigurous, leading to misinterpretations and inconsistencies among studies. As an introduction to this complex topic, in Chapter I I present a review of the knowledge accumulated on microsatellites during the past two decades. A major part of this chapter has been published in the Encyclopedia of Life Sciences in a Chapter about microsatellite evolution (see Publication 1 in Appendix II). The ongoing controversy about the rates and patterns of microsatellite mutation was evident to me since before starting this PhD thesis. However, the subtler problems inherent to the computational analyses of microsatellites within genomes only became apparent when retrieving information on microsatellite distribution and abundance for the design of comparative genomic analyses. There are numerous publications analyzing the microsatellite content of genomes but, in most cases, the results presented can neither be reliably compared nor reproduced, mainly due to the lack of details on the microsatellite search process (particularly the program’s algorithm and the search parameters used) and because the results are expressed in terms that are relative to the search process (i.e. measures based on the absolute number of microsatellites). Therefore, in Chapter II I present a critical review of all available software tools designed to scan DNA sequences for microsatellites. My aim in undertaking this review was to assess the comparability of search results among microsatellite programs, and to identify the programs most suitable for the generation of microsatellite datasets for a thorough and reproducible comparative analysis of microsatellite content among genomic sequences. Using sequence data where the number and types of microsatellites were empirical know I compared the ability of 19 programs to accurately identify and report microsatellites. I then chose the two programs which, based on the algorithm and its parameters as well as the output informativity, offered the information most suitable for biological interpretation, while also reflecting as close as possible the microsatellite content of the test files. From the analysis of microsatellite search results generated by the various programs available, it became apparent that the program’s search parameters, which are specified by the user in order to define the microsatellite characteristics to the program, influence dramatically the resulting datasets. This is especially true for programs suited to allow imperfections within tandem repeats, because imperfect repetitions can not be defined accurately as is the case for perfect ones, and because several different algorithms have been proposed to address this problem. The detection of approximate microsatellites is, however, essential for the study of microsatellite evolution and for comparative analyses based on microsatellites. It is now well accepted that small deviations from perfect tandem repeat structure are common within microsatellites and larger repeats, and a number of different algorithms have been developed to confront the challenge of finding and registering microsatellites with all expectable kinds of imperfection. However, biologists have still to apply these tools to their full potential. In biological analyses single tandem repeat hits are consistently interpreted as isolated and independent repeats. This interpretation also depends on the search strategy used to report the microsatellites in DNA sequences and, therefore, I was particularly interested in the capacity of repeat finding programs to report imperfect microsatellites allowing interpretations that are useful in a biological sense. After analzying a series of tandem repeat finding programs I optimized my microsatellite searches to yield the best possible datasets for assessing and comparing the degree of imperfection of microsatellites among different genomes (Chapter III) During the program comparisons performed in Chapter II, I show that the most critical search parameter influencing microsatellite search results is the minimum length threshold. Biologically speaking, there is no consensus with respect to the minimum length, beyond which a short tandem repeat is expected to become prone to microsatellite-like mutations. Usually, a single absolute value of ~12 nucleotides is assigned irrespective of motif length.. In other cases thresholds are assigned in terms of number of repeat units (i.e. 3 to 5 repeats or more), which are better applied individually for each motif. The variation in these thresholds is considerable and not always justifiable. In addition, any current minimum length measures are likely naïve because it is clear that different microsatellite motifs undergo replication slippage at different length thresholds. Therefore, in Chapter III, I apply two probabilistic models to predict the minimum length at which microsatellites of varying motif types become overrepresented in different genomes based on the individual oligonucleotide frequency data of these genomes. Finally, after a range of optimizations and critical analyses, I performed a preliminary analysis of microsatellite abundance among 24 high quality complete eukaryotic genomes, including also 8 prokaryotic and 5 archaeal genomes for contrast. The availability of the methodologies and the microsatellite datasets generated in this project will allow informed formulation of questions for more specific genome research, either about microsatellites, or about other genomic features microsatellites could influence. These datasets are what I would have needed at the beginning of my PhD to support my experimental design, and are essential for the adequate data interpretation of microsatellite data in the context of the major evolutionary units; chromosomes and genomes.

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Rose, Owen Charles. "The evolution of microsatellites." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286155.

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Khayms, Vadim. "Advanced propulsion for microsatellites." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8824.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2000.
Includes bibliographical references (leaves 162-166).
Microsatellites have become increasingly popular in recent years as they offer significant cost savings, higher reliability, and are generally more affordable for a large variety of commercial applications. Since many microsatellite missions require considerable propulsion capabilities, miniaturization of the propulsion subsystem is critical in the design of most miniature spacecraft. A broad range of existing propulsion technologies have been considered for the purpose of identifying those devices which maintain high performance at small scale. Scaling laws were developed for each of the selected devices so as to preserve, whenever possible, the basic non-dimensional quantities which ultimately determine the performance of the individual thrusters at small scale. Hall thrusters were initially identified as most promising. In an effort to miniaturize the Hall thruster, a number of complications have been encountered. Some of the most troublesome were higher magnetic field requirements, larger internal heat fluxes and temperatures, and difficulties associated with the manufacturing of the various miniaturized components. In order to validate the proposed scaling laws, a 50 Watt Hall thruster has been designed, manufactured, and tested in a vacuum tank. Results of the experimental testing indicate that, although the maximum thrust levels obtained were on the order of 1.8 mN, about two thirds of the nominal design value, the propellant utilization efficiencies were unexpectedly low at approximately 40%. Close examination of the magnetic assembly has shown that the tip of the iron center pole was overheating during operation due to the insufficient heat conduction. The tip temperatures were estimated to reach 900°C, exceeding the Curie point of iron. As a consequence of the change in the magnetic field profile and the resultant leakage of electrons, the observed ionization fraction and, therefore, the utilization efficiency were lower than expected. Despite the low efficiencies, which were most likely caused by the design imperfections rather than physical limitations, the effort to miniaturize a Hall thruster has provided a number of useful insights for any such attempts in the future. Most importantly, this work has highlighted the generic difficulty, common to all plasma thrusters, associated with the increase of the plasma density as the scale of the device is reduced. The consequences of strict scaling, most notably the higher particle fluxes which cause an increase in the erosion rates and significant loss of operating life at small scale, created a strong incentive to search for propulsion schemes which avoid ionization by electron bombardment. In the quest for a more durable device that could operate at low power, yet provide sufficient operating life to be of practical interest, colloidal thrusters were considered for miniaturization. These are representatives of a technology of electrostatic accelerators which does not rely on ionization in the gas phase and, hence, their operating life is not compromised at small scale. In addition to their intrinsically small dimensions and extremely low operating power levels, eliminating the need for further "miniaturization", colloidal thrusters possess a number of desirable characteristics which make them ideal for many microsatellite missions. Although the physics of electrospray emitters has been studied for decades, many of the mechanisms responsible for the formation of charged jets are still poorly understood. In order to gain further insight, a semi-analytical fluid model was developed to predict the effects of fluid's viscosity on the flow pattern. Results of the analysis indicate that over a broad range of operating conditions viscous shear flow is insignificant in the vicinity of the jet irrespective of the fluid's viscosity. In an attempt to further understand the physics of colloidal thrusters, specifically the effects of internal pressure, electrode geometry, and the internal electrostatic fields on the processes involved in the formation of charged jets, a detailed electrohydrodynamic model was formulated. A numerical scheme was developed to solve for the shape of the fluid meniscus given a prescribed set of operating conditions, fluid properties, and electrode configurations. Intermediate solutions for the conical region have already been obtained, however, convergence in the vicinity of the jet requires further studies. A fully developed model promises to provide valuable information and guidance in the design of colloidal thrusters.
by Vadim Khayms.
Ph.D.

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Chilakamarri, Sunita R. "Genetic differentiation in Alewife populations using microsatellite loci." Link to electronic thesis, 2005. http://www.wpi.edu/Pubs/ETD/Available/etd-053105-164623/.

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Bodnarik, Julia G., Dave Hamara, Michael Groza, Ashley C. Stowe, Arnold Burger, Keivan G. Stassun, Liviu Matei, Joanna C. Egner, Walter M. Harris, and Vladimir Buliga. "Neutron detector development for microsatellites." SPIE-INT SOC OPTICAL ENGINEERING, 2017. http://hdl.handle.net/10150/627176.

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We present a preliminary design for a novel neutron detection system that is compact, lightweight, and low power consuming, utilizing the CubeSat platform making it suitable for space-based applications. This is made possible using the scintillating crystal lithium indium diselenide ((LiInSe2)-Li-6), the first crystal to include Li-6 in the crystalline structure, and a silicon avalanche photodiode (Si-APD). The schematics of this instrument are presented as well as the response of the instrument to initial testing under alpha, gamma and neutron radiation. A principal aim of this work is to demonstrate the feasibility of such a neutron detection system within a CubeSat platform. The entire end-to-end system presented here is 10 cm x 10 cm x 15 cm, weighs 670 grams and requires 5 V direct current at 3 Watts.

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Sheikh, Sanea. "Microsatellites in the Flycatcher Genome." Thesis, Uppsala universitet, Systematisk biologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-191385.

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Harr, Bettina. "Evolution of microsatellites in Drosophila." [S.l. : s.n.], 2000. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB8845129.

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Marouillat-Védrine, Sylviane. "Etudes des variations structurales chromosomiques dans l'autisme et la déficience mentale." Thesis, Tours, 2011. http://www.theses.fr/2011TOUR3133/document.

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L’autisme et la déficience mentale sont deux syndromes neuro-développementaux impliquant des facteurs génétiques. Notre travail a consisté à rechercher de nouveaux gènes candidats ou facteurs de susceptibilité chez 106 patients atteints d’autisme et 68 de déficience mentale non syndromique sporadique.Nous avons observé une association entre l’allèle 4 d’un marqueur microsatellite GXAlu localisé en 17q11.2 dans l’intron 27b du gène NF1 et des patients atteints de déficience mentale non-syndromique.Nous avons contribué à la mise en évidence d’une augmentation d’expression du transcrit NLGN4X, chez un patient autiste avec un retard mental non-syndromique présentant une mutation dans le promoteur du gène NLGN4X.L’étude de la région 22q13 par MLPA, nous a permis de mettre en évidence une délétion de novo d’au moins 1Mb chez un patient autiste.Les variations de nombre de copies (CNV) ont été étudiées chez des autistes par QPCR. Nous avons identifié 27 variations réparties sur 17 gènes parmi les 36 explorés. Les CNV observés dans les gènes ITGA6, TAGLN3, HOXA1, DLG4 et UBE2C sont intéressants en raison de l’implication de ces gènes dans le développement cérébral ou la fonction neuronale.L’ensemble de ces résultats nécessite des expériences complémentaires de validation
Autism and mental retardation are two neurodevelopmental syndromes involving genetic factors. Our work consists in finding new candidate genes or susceptibility factors. 106 autistic patients and 68 sporadic non-syndromic mentally retardated patients were studied.We have shown an association between allele 4 of a microsatellite marker GXAlu locasized in 17q11.2, in intron 27b of the NF1 gene and patients with non-syndromic mental retardation.We contributed to the study on the NLGN4X gene. We demonstrated an increase of expression of NLGN4X transcript, in an autistic patient with non-syndromic mental retardation linked to a mutation in the NLGN4X gene promoter.We study the 22q13 region with MLPA method, we have demonstrated a deletion de novo of at least 1Mb in an autistic patient.The copy number variations (CNV) have been investigated in an autistic population by QPCR. We identified 27 variations on 17 genes among the 36 investigated. The CNV observed in ITGA6, TAGLN3, HOXA1, DLG4 and UBE2C genes are interesting because of the involvement of these genes in brain development or neuronal function.These results require further experiments for validation

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Karhu, A. (Auli). "Evolution and applications of pine microsatellites." Doctoral thesis, University of Oulu, 2001. http://urn.fi/urn:isbn:9514259246.

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Abstract The evolution of microsatellites was studied within and between the pine species. Sequences showed that microsatellites do not necessarily mutate in a stepwise fashion and that size homoplasy is common due to flanking sequence and repeat area changes within and between the species. Thus, some assumptions of statistical methods based on changes in repeat numbers may not hold. Sequences from cross-species amplifications revealed evidence of duplications of microsatellite loci in pines. On two independent occasions, the repeat area of the microsatellite had undergone a rapid expansion during the last 10-25 million of years. Microsatellite markers were used together with other molecular markers (allozymes, RFLPs, RAPDs, rDNA RFLPs) and an adaptive trait (date of bud set) to study patterns of genetic variation in Scots pine (Pinus sylvestris) in Finland. All molecular markers showed high level of within population variation, while differentiation among populations was low (FST = 0.02). Of the total variation in bud set, 36.4 % was found among the populations which experience a steep climatic gradient. Thus, the markers applied were poor predictors of population differentiation of the quantitative trait studied The distribution of genetic variation was studied in five natural populations of radiata pine (Pinus radiata), species which has gone through bottlenecks in the past. Null allele frequencies were estimated and used in later analyses. Microsatellites showed high level of variability within populations (He = 0.68-0.77). Allele length distributions and average number of alleles per locus showed some traces of bottlenecks. Instead, comparison of observed genetic diversities and expected diversities suggested post-bottleneck expansion of populations. Genetic differentiation (FST and RST) among populations was over 10 %, reflecting situation in the isolated radiata pine populations. Using microsatellites and a newly developed Bayesian method, individual inbreeding coefficients were estimated in five populations of radiata pine. Most individuals were outbred while some were selfed. Presumably, in ancestral radiata pine populations the recessive deleterious alleles have been eliminated after bottlenecks and the mating system has changed as a consequence.

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Taylor, Tiawanna. "The development of microsatellites for parrots (Psittaciformes)." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.288084.

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McLinko, Ryan (Ryan M. ). "Conceptual Phase Structural Design Tool for Microsatellites." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/67068.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2011.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references (p. 122-124).
Gaining traction or momentum in the conceptual design phase for a complex system can be an arduous and daunting process, whether the complex system being designed is a satellite, airplane, car, or one of countless other systems. The design of small satellites is particularly affected by the difficulties in gaining traction since most of the customized tools that exist are proprietary, a significant experience base is required to be able to perform system level design trades, and the issue that most satellites serve one-of-a-kind applications. Of the subsystems in a satellite, the structures subsystem (along with other "downstream" subsystems, such as power and thermal), tends to be less mature during the conceptual design phase since its design depends strongly on the particular designs and requirements of each of the other subsystems, which also take time to mature. The Conceptual Phase Structural Design Tool for Microsatellites (SDT) facilitates the development of potential small satellite structural architectures and the selection of an initial satellite architecture to use in the detailed design process. The tool is capable of evaluating the strength, stiffness, mass, and inertial properties of a satellite architecture and is customizable to a wide range of potential missions by allowing for a number of structural architectures and customizable component placement. Furthermore, the tool has been developed with two key niches in mind. First, it is available to students with little to no satellite design experience, thus enabling a greater number of people, including those who are unfamiliar with the process of structural design at the beginning of the program, to design higher quality spacecraft from the start. Second, it is open source and deployable in a state that is usable and customizable by members of the satellite design industry.
by Ryan McLinko.
S.M.

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Csilléry, Katalin. "Statistical inference in population genetics using microsatellites." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3865.

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Statistical inference from molecular population genetic data is currently a very active area of research for two main reasons. First, in the past two decades an enormous amount of molecular genetic data have been produced and the amount of data is expected to grow even more in the future. Second, drawing inferences about complex population genetics problems, for example understanding the demographic and genetic factors that shaped modern populations, poses a serious statistical challenge. Amongst the many different kinds of genetic data that have appeared in the past two decades, the highly polymorphic microsatellites have played an important role. Microsatellites revolutionized the population genetics of natural populations, and were the initial tool for linkage mapping in humans and other model organisms. Despite their important role, and extensive use, the evolutionary dynamics of microsatellites are still not fully understood, and their statistical methods are often underdeveloped and do not adequately model microsatellite evolution. In this thesis, I address some aspects of this problem by assessing the performance of existing statistical tools, and developing some new ones. My work encompasses a range of statistical methods from simple hypothesis testing to more recent, complex computational statistical tools. This thesis consists of four main topics. First, I review the statistical methods that have been developed for microsatellites in population genetics applications. I review the different models of the microsatellite mutation process, and ask which models are the most supported by data, and how models were incorporated into statistical methods. I also present estimates of mutation parameters for several species based on published data. Second, I evaluate the performance of estimators of genetic relatedness using real data from five vertebrate populations. I demonstrate that the overall performance of marker-based pairwise relatedness estimators mainly depends on the population relatedness composition and may only be improved by the marker data quality within the limits of the population relatedness composition. Third, I investigate the different null hypotheses that may be used to test for independence between loci. Using simulations I show that testing for statistical independence (i.e. zero linkage disequilibrium, LD) is difficult to interpret in most cases, and instead a null hypothesis should be tested, which accounts for the “background LD” due to finite population size. I investigate the utility of a novel approximate testing procedure to circumvent this problem, and illustrate its use on a real data set from red deer. Fourth, I explore the utility of Approximate Bayesian Computation, inference based on summary statistics, to estimate demographic parameters from admixed populations. Assuming a simple demographic model, I show that the choice of summary statistics greatly influences the quality of the estimation, and that different parameters are better estimated with different summary statistics. Most importantly, I show how the estimation of most admixture parameters can be considerably improved via the use of linkage disequilibrium statistics from microsatellite data.

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Loire, Etienne. "Evolution des microsatellites codants chez les primates." Paris 6, 2009. http://www.theses.fr/2009PA066495.

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Les microsatellites sont des séquences qui présentent des mécanismes mutationnels propres à leur nature répétée et qui aboutissent à de fréquents changements du nombre d’unité qui les composent. Cette nature hypermutable des microsatellites, extrêmement abondants dans les génomes eucaryotes, est responsable de leur polymorphisme élevé au sein des populations. Ces répétitions sont soumises à une force de sélection qui tend à les purger hors des gènes, en raison de l’instabilité qu’ils confèrent à ces derniers. Nous avons caractérisé les gènes humains qui contiennent un microsatellite codant instable et sont pour cette raison qualifiés d’hypermutables. Ces gènes hypermutables sont spécifiquement impliqués dans un nombre restreint de fonctions cellulaires. La pression de sélection négative qui s’exerce à l’encontre des répétitions n’est pas homogène selon les groupes fonctionnels considérés. Au sein du phylum des primates, les microsatellites codants évoluent par insertion et délétion, mais également par substitution et ce à un rythme deux fois élevé que celui du reste des séquences codantes. Ces substitutions créent ou interrompent les répétitions. La distribution des effectifs reste à l’équilibre dans toutes les espèces considérées. En nous penchant sur un type particulier de microsatellite, nous avons pu estimer le coefficient de sélection. L’effet d’un microsatellite sur la valeur adaptative d’un individu est relativement faible, mais suffisant pour biaiser la distribution de ces répétitions.

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Buschiazzo, Emmanuel. "Conservation and Evolution of Microsatellites in Vertebrate Genomes." Thesis, University of Canterbury. Biological Sciences, 2008. http://hdl.handle.net/10092/1595.

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Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

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Vowles, Edward Joseph. "The evolution of microsatellites and their flanking sequences." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439035.

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Khayms, Vadim. "Design of a miniaturized Hall thruster for microsatellites." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/50313.

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Ross-Adams, Helen Esther. "The characterisation of selected grapevine cultivars using microsatellites." Thesis, Stellenbosch : Stellenbosch University, 2002. http://hdl.handle.net/10019.1/53092.

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Thesis (MScAgric)--Stellenbosch University, 2002.
ENGLISH ABSTRACT: Grapevine supports one of the oldest industries in South Africa today, and is also of significant international importance. With increasing international trade and the transport of fruit and other grapevine-derived products between borders, it has become increasingly important for South African farmers and viticulturalists to ensure their products conform to strict international market requirements if they are to remain competitive. Such requirements include the correct and accurate identification of berries and wines according to cultivar. In light of this, 26 different wine, table grape and rootstock cultivars, as well as a number of clones from KWV's core germplasm collection were characterised at 16 microsatellite marker loci. Microsatellite markers are known for their high level of informativeness, reliability and reproducibility, and are widely used in the identification and characterisation of plant varieties, population analyses and forensic applications. Unique allelic profiles were obtained for all but two plants, which proved to be identical at all loci considered, and thus 'clones'. These profiles were collated to form a database, containing the DNA fingerprints of each sample at each locus. The relative levels of informativeness of each marker used were also determined, and compared with those found in the literature. Six markers proved to be highly informative, and are promising in the potential application of this technology to other cultivars. The applicability of microsatellite markers to such studies is confirmed; this approach could easily be extended to include any number of cultivars of national and international interest. The results of such an investigation would have important implications for both the farming and commercial industries alike.
AFRIKAANSE OPSOMMING: Wingerd ondersteun een van die oudste industriee in Suid-Afrika vandag, en is ook van groat intemasionale belang. Met die toenemende intemasionale ruilhandel en die vervoer van vrugte en ander wingerd produkte tussen grense, het dit toenemend belangrik geword vir SuidAfrikaanse wingerdboere om te. verseker dat hulle produkte voldoen aan die streng vereistes van die intemasional mark, indien hulle kompeterend wil bly. Hierdie vereistes sluit in die korrekte en akkurate identifisering van druiwe en wyn volgens kultivar. Met hierdie vereistes in ag geneem, is 26 verskillende wyn, tafeldruif en wortelstok kultivars, asook 'n aantal klone van die KWV se kern kiemplasma versameling, gekarakteriseer by 16 mikrosatelliet merker loki. Mikrosatelliet merkers word gekenmerk deur 'n hoe vlak van informatiwiteit, betroubaarheid en herhaalbaarheid en word wydverspreid gebruik in die identifisering en karakterisering van plant varieteite, populasie analises en forensiese toepassings. Unieke alleliese profiele is vir a1 die plante verkry, behalwe vir twee plante wat identiese resultate by alle loki opgelewer het en dus as "klone" beskou kan word. Hierdie profiele is bymekaar gevoeg om 'n databasis te vorm wat die DNA vingerafdrukke van elke monster by elke lokus bevat. Die relatiewe vlak van informatiwiteit van al die merkers is ook bepaal en vergelyk met merkers in die literatuur. Ses van die merkers blyk om hoogs informatief te wees en lyk belowend in die potensiele toepassing van hierdie tegnologie op ander kultivars. Die toepaslikheid van mikrosatelliet merkers op sulke studies is bevestig; hierdie benadering kan maklik aangepas word om enige aantal kultivars van nasionale en intemasionale belang in te sluit. Die resultate van s6 'n ondersoek sal belangrike implikasies inhou vir beide die boerdery en kommersiele industriee.

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Leclercq, Sébastien. "Origines des séquences microsatellites dans les génomes eucaryotes." Phd thesis, Montpellier 2, 2007. http://www.theses.fr/2007MON20190.

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Les microsatellites sont des entités génomiques présentes dans tous les organismes vivants. Nous nous intéressons dans cette thèse à leur apparition, en se basant sur l'analyse de la séquence du génome humain. Il a tout d'abord fallu extraire les microsatellites, et il existe plusieurs algorithmes de fonctionnement différents pour cela. La première partie de cette thèse se concentre sur la comparaison de quelques-uns des algorithmes de recherche de répétitions en tandem, et dresse un portait de chacun des algorithmes. Deux possibilités majeures d'apparition des microsatellites sont détaillées. Dans le premier cas, l'étude est focalisée sur le rôle des séquences Alu. La deuxième étude cherche à établir l'impact de trois mécanismes différents : la mutation ponctuelle, le glissement de polymérase et la micro-duplication. Un modèle général d'apparition des microsatellites est enfin proposé, suggérant une dynamique d'apparition plus complexe que ce qui était précédemment supposé
Microsatellites, are genomic elements found in the genomes of all living species. This thesis focuses on the microsatellite apparition, by analysing the complete human genome sequence. This requires extracting microsatellite loci from the sequence, using specific algorithms. However these available algorithms differs in detection method. The first part of this thesis is dedicated to the comparison of some algorithms of tandem repeats detection, and present an overview of their qualities and limitations. Microsatellite birth essentially derived from transposable elements (TEs) or from mutation from any DNA sequence. The analysis of TE-mediated birth focuses on the role of Alu elements. Mutation mediated birth is analysed though three different mechanisms: point mutation, DNA slippage and adjacent micro-duplication of a small number of nucleotides. A general model of microsatellite apparition is then proposed, suggesting a more complex apparition dynamic than was previously thought

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Leclercq, Sébastien. "Origines des séquences microsatellites dans les génomes eucaryotes." Phd thesis, Université Montpellier II - Sciences et Techniques du Languedoc, 2007. http://tel.archives-ouvertes.fr/tel-00261560.

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Les microsatellites, séquences répétées en tandem de période une à six paires de bases, sont des entités génomiques présentes dans tous les organismes qu'ils soient animaux, végétaux ou microbiens. Ils présentent un cycle de vie caractérisé par trois phases principales : une apparition et une maturation, une dynamique à l'état mature, puis une dégénérescence. Nous nous intéressons dans cette thèse à la première phase, l'apparition des microsatellites.
Pour traiter ces questions, nous nous sommes basés sur l'analyse de la séquence du génome humain. L'une des lacunes de ce type d'analyse est qu'il faut d'abord extraire les microsatellites du génome, et qu'il existe plusieurs algorithmes de nature et fonctionnement différents. La première partie de cette thèse se concentre donc sur la comparaison de quelques-uns des principaux algorithmes de recherche de répétitions en tandem, et dresse un portait des différentes qualités et limitations de chacun des algorithmes.
Deux possibilités majeures sont détaillées, l'apparition par l'intermédiaire d'éléments transposables (ETs), et l'apparition spontanée à partir d'une séquence quelconque. Dans le premier cas, l'étude est focalisée sur le rôle des queues polyA des séquences Alu chez les primates. La question de l'apparition à partir d'une séquence quelconque cherche à établir l'impact de trois mécanismes mutationnels différents sur la création et le développement primordial des microsatellites : la mutation ponctuelle, le glissement de polymérase et la micro-duplication adjacente de quelques nucléotides. Un modèle général d'apparition des microsatellites est aussi proposé, suggérant une dynamique d'apparition plus complexe que ce qui était précédemment supposé.

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Bodur, Cagri. "Genetic Structure Analysis Of Honeybee Populations Based On Microsatellites." Phd thesis, METU, 2005. http://etd.lib.metu.edu.tr/upload/12606592/index.pdf.

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We analyzed the genetic structures of 11 honeybee (Apis mellifera) populations from Tü
rkiye and one population from Cyprus using 9 microsatellite loci. Average gene diversity levels were found to change between 0,542 and 0,681. Heterozygosity levels, mean number of alleles per population, presence of diagnostic alleles and pairwise FST values confirmed the mitochondrial DNA finding that Anatolian honeybees belong to north Mediterranean (C) lineage. We detected a very high level of genetic divergence among populations of Tü
rkiye and Cyprus based on pairwise FST levels (between 0,0 and 0,2). Out of 66 population pairs 52 were found to be genetically different significantly. This level of significant differentiation has not been reported yet in any other study conducted on European and African honeybee populations. High allelic ranges, and high divergence indicate that Anatolia is a genetic centre for C lineage honeybees. We suggest that certain precautions should be taken to limit or forbid introduction and trade of Italian and Carniolan honeybees to Tü
rkiye and Cyprus in order to preserve genetic resources formed in these territories in thousands of years. Effectivity at previously isolated regions in Artvin, Ardahan and Kirklareli was confirmed by the high genetic differentiation in honeybees of these regions. Genetically differentiated Karaburun and Cyprus honeybees v and geographical positions of the regions make these zones first candidates as new isolation areas.

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Paetkau, David Henry. "Genetic studies of North American bear populations using microsatellites." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq23052.pdf.

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Duncan, Stuart. "Development and exploitation of GPS attitude determination for microsatellites." Thesis, University of Surrey, 2010. http://epubs.surrey.ac.uk/804951/.

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Fernandez-Salivar, Juan A. "Miniaturised UV imaging spectrometer for atmospheric monitoring from microsatellites." Thesis, University of Surrey, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.502648.

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Bodo, Sahra. "Induction d'un processus d'instabilité des microsatellites du génome dans des modèles murin et cellulaire : intérêt physiopathologique et clinique." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066565/document.

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L'inactivation du système MMR (mismatch repair) favorise un processus oncogénique d'instabilité des microsatellites du génome (MSI). Au cours de ma thèse, j'ai étudié d'une part le rôle de l'azathioprine (Aza) dans l'induction de tumeurs MSI chez la souris. Des études épidémiologiques avaient rapporté une corrélation entre l'émergence de cancers MSI tardifs chez l'homme, et la prise au long cours de cet immunosuppresseur dont la cytotoxicité in vitro est médiée par l'activité MMR. Dans une étude dose-réponse, j'ai observé l'émergence de rares lymphomes MSI de survenue tardive chez la souris de génotype sauvage traitée par l'Aza, mais pas par la ciclosporine (autre immunosuppresseur utilisé en comparaison). Ces résultats permettent d'établir in vivo que l'Aza est un facteur de risque pour l'émergence de tumeurs MSI lors d'une exposition prolongée. D'autre part, je me suis intéressée au syndrome CMMRD (constitutional MMR deficiency), une prédisposition majeure et rare, aux cancers MSI. Les patients atteints étant porteurs de mutations germinales bialléliques d'un gène MMR, le diagnostic repose sur le génotypage constitutionnel, une méthode non-contributive quand un variant de signification inconnue est détecté (30% patients). Dans ce contexte, j'ai développé une méthode d'aide au dépistage de ce syndrome chez les sujets à risque, l'hypothèse étant que 2 caractéristiques fonctionnelles des cellules tumorales MMR-déficientes, le phénotype MSI et la tolérance aux agents génotoxiques tels que l'Aza, pouvaient être objectivées dans les tissus sains des patients CMMRD. Mes travaux proposent un test diagnostique sensible et spécifique qui répond aux limites de l'analyse génétique
Inactivation of the MMR (mismatch repair) system promotes the oncogenic process of microsatellite instability (MSI). During my PhD, I firstly investigated the role of azathioprine (Aza) in the induction of MSI tumors in mice. Epidemiological studies reported a correlation between the occurrence of late MSI cancers in humans and long-term treatment with this immunosuppressant whose cytotoxicity was shown in vitro to be mediated by MMR activity. Using a dose-response study, I observed the occurrence of rare late-onset MSI lymphomas in wild-type mice treated with Aza, but not with ciclosporin (another immunosuppressant used for comparison). These results established in vivo that long-term Aza exposure is a risk factor for the emergence of MSI tumors. Secondly, I was interested in the CMMRD syndrome (constitutional MMR deficiency), a major and rare predisposition to MSI cancers. Since CMMRD patients are carriers of biallelic germline mutations of a MMR gene, diagnosis is based on constitutional genotyping, a method that was found non-contributory when a variant of unknown significance is detected (30% patients). In this context, I developed a complementary approach for the detection of this syndrome in at-risk patients, based on the hypothesis that two functional features of MMR-deficient tumor cells, i.e. the MSI phenotype and the tolerance to genotoxic agents such as Aza, can be demonstrated in non-neoplastic tissues of CMMRD patients. We provided a sensitive and specific method that may constitute a valuable tool when diagnosis of CMMRD could not be confirmed by genetic testing

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Fouquet, Marc. "Earth imaging with microsatellites : an investigation, design, implementation and in-orbit demonstration of electronic imaging systems for Earth observation on-board low-cost microsatellites." Thesis, University of Surrey, 1995. http://epubs.surrey.ac.uk/844455/.

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This research programme has studied the possibilities and difficulties of using 50 kg microsatellites to perform remote imaging of the Earth. The design constraints of these missions are quite different to those encountered in larger, conventional spacecraft. While the main attractions of microsatellites are low cost and fast response times, they present the following key limitations: Payload mass under 5 kg, Continuous payload power under 5 Watts, peak power up to 15 Watts, Narrow communications bandwidths (9.6 / 38.4 kbps), Attitude control to within 5°, No moving mechanics. The most significant factor is the limited attitude stability. Without sub-degree attitude control, conventional scanning imaging systems cannot preserve scene geometry, and are therefore poorly suited to current microsatellite capabilities. The foremost conclusion of this thesis is that electronic cameras, which capture entire scenes in a single operation, must be used to overcome the effects of the satellite's motion. The potential applications of electronic cameras, including microsatellite remote sensing, have erupted with the recent availability of high sensitivity field-array CCD (charge-coupled device) image sensors. The research programme has established suitable techniques and architectures necessary for CCD sensors, cameras and entire imaging systems to fulfil scientific/commercial remote sensing despite the difficult conditions on microsatellites. The author has refined these theories by designing, building and exploiting in-orbit five generations of electronic cameras. The major objective of meteorological scale imaging was conclusively demonstrated by the Earth imaging camera flown on the UoSAT-5 spacecraft in 1991. Improved cameras have since been carried by the KITSAT-1 (1992) and PoSAT-1 (1993) microsatellites. PoSAT-1 also flies a medium resolution camera (200 metres) which (despite complete success) has highlighted certain limitations of microsatellites for high resolution remote sensing. A reworked, and extensively modularised, design has been developed for the four camera systems deployed on the FASat-Alfa mission (1995). Based on the success of these missions, this thesis presents many recommendations for the design of microsatellite imaging systems. The novelty of this research programme has been the principle of designing practical camera systems to fit on an existing, highly restrictive, satellite platform, rather than conceiving a fictitious small satellite to support a high performance scanning imager. This pragmatic approach has resulted in the first incontestable demonstrations of the feasibility of remote sensing of the Earth from inexpensive microsatellites.

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Bond, Joanna Margaret. "Genetic analysis of the sperm whale (Physeter macrocephalus) using microsatellites." Thesis, University of Cambridge, 1999. https://www.repository.cam.ac.uk/handle/1810/265611.

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The sperm whale is the largest of the toothed whales (Odontoceti), and inhabits deep waters from equatorial to Polar Regions. Sperm whales are social and commonly l r . found in small groups. However, sociality varies according to sex and age. Immature males form bachelor groups that disperse as they mature, mature males are frequently encountered alone. Sperm whales are renowned for their diving capabilities. Therefore, surface observations are only possible for 10 to 15 minutes every hour. Consequently, the sperm whale is an ideal candidate for investigation using genetic markers. Genetic variation can reveal information on geographical structuring of populations and, on a finer scale, the social organisation within these groups. The focus of this thesis is an investigation into the structure of populations around the Azores. To date, this work represents the most comprehensive molecular investigation into North Atlantic sperm whales. Since 1988 sloughed skin samples have been collected from the Azores but, to facilitate the comparison between local and global structuring, samples were also obtained from a number of geographically distinct regions. Twelve microsatellite loci and a marker to indicate sex were selected for screening. Genetic variation was sufficient to allow identification of individuals with a high degree of accuracy. A system of scoring the amplification quality was found to be both a simple and accurate method of determining the reliability of a genotype. Errors were found to arise infrequently, hence their influence in the final dataset was considered negligible. Of the 467 sloughed skin samples collected from the Azores, 102 individuals were identified. The majority of these samples had been collected from groups. As groups are presumed to be matrilineal, the identification of mother calf pairs was anticipated. However the samples revealed few parent offspring combinations. Within a group the majority of whales were related at the level of half )siblings. This indicates that I I Azorean groups comprise of individuals related through either the maternal or paternal lineage. Full siblings were also identified, which suggests that a degree of mate choice can occur. The first insight into the relationships within bachelor groups arose when two such groups, stranded off the coast of Scotland, were examined. Individuals within the groups were predominantly unrelated to each other. However, potential half/sibling relationships within the groups were identified. A mother offspring pair was identified between an Azorean whale and one of the stranded whales. Microsatellite data from Atlantic (n=I32) and Pacific (n=I59) sperm whales revealed low, but significant, inter-ocean variation. However, examinations of populations structuring on a finer scale (geographic regions) failed to reveal any consistent pattern of differentiation. This lack of differentiation is surprising when compared with other cetaceans, all of which show increased genetic differentiation with distance.

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Valsecchi, Elena. "Genetic analysis of the humpback whale (Megaptera novaeangliae) using microsatellites." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.242544.

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Fretwell, Neale. "A search for human Y-chromosome-specific minisatellites and microsatellites." Thesis, University of Leicester, 1996. http://hdl.handle.net/2381/34411.

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This thesis describes an attempt to isolate polymorphic minisatellite and microsatellite loci from the male-specific region of the human Y chromosome. Y chromosome polymorphisms are useful in the study of human evolution, since the majority of the chromosome is exempt from meiotic recombination and is passed down intact in paternal lineages. Y-specific polymorphisms can be used to identify males that are related by descent. Base substitutions and sequence insertions are ideal for such analysis, because they represent very rare events and are unlikely to recur. However, these mutations are often highly population-specific, making them of little use in the investigation of inter-population relationships, or of intra-population studies in many cases. Minisatellite and microsatellite loci, on the other hand, show variability in all populations and complement the 'unique event' markers. A systematic search of a human Y-specific cosmid library for G+C-rich minisatellites identified many repetitive sequences, including 14 minisatellites from the Yp pseudoautosomal region. However no Y-specific minisatellites were found. Such sequences must be very rare, and may not be present at all in the Y-specific euchromatin, perhaps because inter-allelic exchange events are precluded in this region. Six novel Y-specific microsatellites were cloned using hybridisation selection from a degenerate PCR library. One multi-locus and two single-locus trinucleotide microsatellites were shown to be polymorphic and were used with two other microsatellites in a survey of diversity in 340 males, and to investigate the relationships between males in different haplotypic groups. No evidence for increased African diversity of Y chromosomes was found in an intercontinental comparison. These markers were also used to classify deletion and duplication events at the 50f2/C locus in 66 males from various populations. This analysis allowed the identification of novel deletion events that had not been distinguished by previous haplotyping analysis with base substitution and other polymorphisms.

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Delaugerre, Constance. "Diagnostic moléculaire de l'hémophilie A : évaluation de l'informativité des microsatellites." Paris 5, 1997. http://www.theses.fr/1997PA05P221.

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Wallace, Aaron L. "The taxonomic and systematic relationships of several salt marsh Fucus taxa (heterokontophyta, phaeophyceae) within the Gulf of Maine and Ireland examined using microsatellite markers." View this thesis online, 2005. http://libraries.maine.edu/gateway/oroauth.asp?file=orono/etheses/37803141.pdf.

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Thesis (Ph.D.)--University of New Hampshire (Dept. of Biochemistry and Molecular Biology), 2005.
Title from PDF title page. Available through UMI ProQuest Digital Dissertations. Includes bibliographical references. Also issued in print.

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Ramakrishna, W. "DNA fingerprinting and molecular characterization of microsatellites and minisatellites in rice." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 1994. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2817.

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Prudhomme, Jorian. "Phlébotomes et écosystèmes : impact des facteurs biotiques et abiotiques sur la structure génétique et phénotypique des populations." Thesis, Montpellier, 2015. http://www.theses.fr/2015MONTS027/document.

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Les phlébotomes sont des insectes hématophages appartenant à la famille des Psychodidae et à la sous-famille des Phlebotominae. Cet insecte diptère, jaunâtre, relativement petit (2 à 3 mm) compte environ 800 espèces. 70 de ces espèces ont été identifiées comme vecteurs potentiels dont une quarantaine sont des vecteurs prouvés. Ils peuvent transmettre différents pathogènes dont les principaux sont les leishmanies et les phlébovirus. Ce travail de thèse est focalisé sur les phlébotomes vecteurs de la leishmaniose. Les leishmanioses sont des maladies parasitaires causées par un protozoaire du genre Leishmania. Elles touchent un large panel d’hôtes vertébrés, dont l’homme et le chien. Elles sont toujours un problème de santé publique majeur dans de nombreux pays et sont actuellement en expansion. Bien que cette maladie soit largement étudiée, nous avons encore beaucoup apprendre sur son vecteur : le phlébotome. Par exemple, l’organisation des populations dans les écosystèmes et les paramètres qui les structurent, sont à l’heure actuelle très peu étudiés. Il est pourtant primordial de bien connaitre la biologie des différents acteurs d’un cycle parasitaire pour mieux comprendre la transmission du pathogène, évaluer les risques et enfin être capable de lutter efficacement contre la maladie. Dans ce contexte, le but de cette thèse est d’étudier l’écologie et la structure des populations de phlébotomes dans un foyer connu de leishmaniose et l’impact des facteurs biotiques et abiotiques sur leur organisation. Pour atteindre cet objectif, nous avons réalisé une collecte de phlébotomes le long d’un transect de 14km localisé dans la région de Montpellier, présentant une diversité altitudinale, climatique et environnementale. Les populations de phlébotomes ont été caractérisées d’un point de vue taxonomique, spatio-temporel, génétique (microsatellites), et morphométrique (géométrie morphométrie). Les résultats génétiques, morphométriques et de distribution des espèces ont été ensuite confrontés à des paramètres climatiques (température, humidité) ou environnementaux (altitude, versant, station, microhabitat).Durant ce travail, 4 espèces ont été capturées : Phlebotomus ariasi (93,23%), P. perniciosus (0,48%), P. mascittii (0,11%) et S. minuta (6,18%). Elles ont une activité saisonnière de Mai à Octobre avec un pic d’abondance en Juillet-Août quand les températures moyennes sont optimales pour les phlébotomes (20-30°C). Bien que l'environnement ait été considérablement transformé dans notre zone d'étude en 30 ans, l'abondance des phlébotomes ne semble pas avoir changé de façon significative, soulignant leur capacité d'adaptation aux modifications de l'écosystème à court et long terme. La présence et l’abondance des deux espèces prédominantes (P. ariasi et S. minuta) sont significativement influencées par l’altitude, la température, l’humidité relative, le versant ainsi que l’orientation des murs. Les analyses génétiques montrent que la diversité est conservée à toutes les échelles d’études et qu’il existe une structuration des phlébotomes en micropopulations. Les données de géométrie morphométrie révèlent un dimorphisme sexuel bien connu chez les insectes mais également une structuration phénotypique en fonction des facteurs environnementaux ou temporels (mois, versant, altitude et station). Ces deux types d’approches permettent grâce à leur complémentarité d’apporter des informations sur l’écologie et l’organisation des populations de phlébotomes et de discuter des conséquences sur la transmission de la leishmaniose
Sandflies are hematophagous insects belonging to the family Psychodidae and the subfamily phlebotominae. This diptera, yellowish, relatively small (2-3 mm) has about 800 species. 70 of these species have been identified as potential vectors of which forty are proven ones. They can transmit different pathogens; the main ones are Leishmania and phlebovirus.This thesis focused on sandflies, vectors of leishmaniasis. Leishmaniases are parasitic diseases caused by protozoa of the genus Leishmania. They affect a wide range of vertebrate hosts, including humans and dogs. They are still a major problem of public health in many countries and are currently in expansion. Although this disease is widely studied, we still have a lot to learn about its vector: the sandfly. For example, the organization of populations in ecosystems and the parameters which structure them are very little studied up to now. It is therefore essential to know the biology of the different actors of a parasite cycle to better understand the transmission of pathogens, to assess risks of transmission, and finally to be able to effectively fight against the disease.In this context, the aim of this thesis is to study the ecology and the structuring of sandfly populations in a known endemic area of leishmaniasis and the impact of biotic and abiotic factors on their organization. To reach this objective, we performed captures of sandflies along a 14km transect located in the Montpellier region which presents an altitudinal, climate and environmental diversity. Sandfly populations have been characterized by taxonomic, spatio-temporal, genetic (microsatellites) and morphometric (geometry morphometry) approaches. The genetic, morphometric and species distribution results were then confronted with climatic (temperature, relative humidity) or environmental parameters (altitude, slope, station, microhabitat).During this work, four species were captured: Phlebotomus ariasi (93.23%), P. perniciosus (0.48%), P. mascittii (0.11%) and S. minuta (6.18%). They have a seasonal activity from May to October with an abundance peak in July-August when average temperatures are optimal for sandflies (20-30°C). Although the environment has been considerably transformed in our study area in 30 years, the abundance of sandflies does not seem to have changed significantly, highlighting their ability to adapt to ecosystem modifications in short and long-term. The presence and abundance of the two predominant species (P. ariasi and S. minuta) are significantly influenced by altitude, temperature, relative humidity, slope and wall orientation.The genetic analyses show that diversity is maintained at all scales of study and that sandflies are organized in micropopulations. The morphometric geometry data reveal a sexual dimorphism, well known in insects but also a phenotypic structuring correlated to environmental or temporal factors (month, slope, altitude and station).Both of these approaches, because of their complementarity, help provide information on the ecology and organization of sandfly populations and to discuss about the consequences in terms of leishmaniasis transmission

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Santani, Avni Bhawan. "Genomic analysis of the horse Y chromosome." Texas A&M University, 2004. http://hdl.handle.net/1969.1/1494.

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Stallion fertility is of significant economic importance in the multibillion dollar equine industry. Presently, the underlying genetic causes of infertility in stallions are unknown. Analysis of the human genome has shown that in more than 25% of cases, male infertility is associated with deletions/rearrangements in the Y chromosome. Presently there is no gene map for the Y chromosome in the horse. Therefore, the primary aim of this study is to build a detailed physical map of the chromosome with a long-term aim to identify and analyze Y-specific factors affecting fertility in stallions. To materialize this, we constructed the first radiation hybrid and FISH map of the euchromatic region of the horse Y chromosome. This basic map was used to obtain Y-specific BAC clones that provided new STS markers from the end sequences. Chromosome walking provided 73 BACs comprising 7 contigs that were built across the euchromatic region using 124 markers for content mapping. The results were validated by restriction fingerprinting and Fiber FISH. The map is presently the most informative among the domestic species and second to only human and mouse Y chromosome maps. The construction of this map will pave the way for isolation and functional characterization of genes critical for normal male fertility and reproduction and will in the future lead to the development of a diagnostic test to facilitate early identification of deletions/rearrangements on the Y chromosome of potentially affected foals/stallions. The second part of the study comprised the first extended investigation to assess genetic variation in the horse Y chromosome. Approximately 4.5Mb of the euchromatic region was screened for polymorphic microsatellite markers. Of the 27 markers that were characterized and screened for polymorphism in 14 breeds of the domestic horse and eight extant equids, only one was polymorphic in the domestic horse, suggesting a low level of genetic variation on the chromosome. However, 21 of the markers showed noteworthy variation (on average four alleles/marker) among the eight equids. These markers will be vital in future studies aimed at elucidating the genetic relationships between the various equids through phylogenetic analysis.

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Gunn, Melissa Rose School of Biological Earth &amp Environmental Science UNSW. "The use of microsatellites as a surrogate for quantitative trait variation in conservation." Awarded by:University of New South Wales. School of Biological, Earth and Environmental Science, 2003. http://handle.unsw.edu.au/1959.4/22457.

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Conservation biologists are interested in maintaining genetic variation in small populations, with a view to maintaining fitness and the ability of the species to adapt to changing environmental conditions. The most important type of genetic variation is therefore that which affects fitness and reproduction, and is therefore subject to natural selection. Such fitness traits are often quantitative, i.e. are the result of a suite of loci, and are continuously variable. Microsatellite markers are a popular method of determining the level of variation present in a species??? genome. The assumption is made that microsatellites, which are neutral markers, behave in the same manner as quantitative traits. If this assumption were proved incorrect, then the use of neutral markers in conservation monitoring would have to be re-evaluated. In this study, experiments have been conducted using Drosophila melanogaster to test the assumption that variation in quantitative traits under stabilising selection declines at the same rate as heterozygosity in microsatellite markers, during a population bottleneck. Experimental population bottlenecks were of two effective population sizes (Ne), Ne=2 for one generation and Ne=60 for 35 generations. Based on the effective population size, we expected both types of bottlenecks to lose 25% of neutral genetic variation. Ten replicates of each bottleneck were maintained, along with four large control populations with Ne=320. In each population, heterozygosity (He) for eight microsatellite loci was compared with the heritability and additive genetic variance of two quantitative traits subject to balancing selection: fecundity and sternopleural bristle number. Microsatellite heterozygosity decreased in accordance with neutral predictions, whereas additive genetic variation in quantitative traits altered more than expected in both large and in bottlenecked populations relative to the initial sampling values, indicating that variation in quantitative traits was not being lost at the same rate as predicted by neutral theory. For most traits, the changes in additive genetic variance were congruent in all populations, large or bottlenecked. This congruence suggests that a common process was affecting all populations, such as adaptation. A mite infestation in early generations is a possible source of selective pressure. When bottlenecked populations were compared to the contemporaneous large populations (Ne = 320), the additive genetic variance of most traits was seen to have been lost in accordance with predictions from the loss of microsatellite heterozygosity. Loss of variation in microsatellites can thus be used to predict the loss of variation in quantitative traits due to bottlenecks, but not to predict the potentially much larger changes due to other processes such as adaptation. The effects of concurrent environmental stress and reduced population size were also evaluated. Endangered populations are often subject to environmental stress in addition to reduced population size, but the effect of stress on the additive genetic variance of fitness traits in organisms undergoing population bottlenecks is unknown. If the presence of stress alters the level of additive genetic variance in fitness traits, the viability of such populations could be substantially affected. The loss of microsatellite heterozygosity was not affected by the presence of a stress agent during a bottleneck. I found some significant effects of stress on the additive genetic variance of sternopleural bristles and fecundity; there was also a significant interaction between stress and the response to directional selection in sternopleural bristles. There was also an increase in the coefficient of variation of VA for sternopleural bristles. Stress may therefore affect the manner in which populations respond to selective pressures.

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Lai, Yau-lin Caroline. "Genotyping of gestational trophoblastic disease." Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B23427383.

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Duffy, Andrew J. "Genetic variability and population differentiation in Scandinavian wolverines." Connect to this title online, 1997. http://www.nlc-bnc.ca/obj/s4/f2/dsk2/ftp01/MQ36353.pdf.

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Long, Qiaoming. "Molecular cloning of chicken transforming growth factor β1 and isolation of microsatellites." Thesis, University of Edinburgh, 1995. http://hdl.handle.net/1842/29227.

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LORIDON, KARINE. "Analyse de la variabilite genetique de sequences microsatellites trinucleotidiques chez arabidopsis thaliana." Clermont-Ferrand 2, 1998. http://www.theses.fr/1998CLF22066.

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Les microsatellites sont de petites sequences repetees en tandem presentes en un grand nombre de loci dans les genomes eucaryotes. Ils se caracterisent par une hypervariabilite de taille due a des variations de leur nombre de repetitions. Notre analyse porte sur la variabilite genetique des microsatellites trinucleotidiques chez la plante modele arabidopsis thaliana. L'amplification pcr de 12 loci microsatellites a ete realisee pour 49 ecotypes d'arabidopsis thaliana. Ces microsatellites presentent un niveau de polymorphisme intraspecifique modere, avec un nombre moyen d'alleles par locus egal a 4 (chaque locus possede entre 1 et 8 alleles) et un indice moyen de diversite genetique de 0,43. Le sequencage de nombreux alleles montre que 1) pour la plupart des loci microsatellites, les ecarts de taille entre alleles sont bien dus a des variations du nombre de repetitions trinucleotidiques, 2) pour les loci microsatellites imparfaits et composes formes de 2 blocs de triplets, les variations interalleliques affectent preferentiellement le bloc repete le plus long. Nos resultats font apparaitre une correlation entre le nombre moyen de repetitions et le nombre d'alleles observes pour un meme locus microsatellite. L'analyse de plantes individuelles revele une heterogeneite a l'interieur de certains ecotypes. Six ecotypes sont composes de 2 a 3 lignees. Les plantes heterozygotes observees dans 2 autres ecotypes temoignent vraisemblablement de croisements recents. Ces observations montrent qu'arabidopsis thaliana n'est pas une espece strictement autogame. Par ailleurs, les microsatellites trinucleotidiques apparaissent tres stables sur quelques generations ainsi que dans certaines situations de stress (regeneration, choc thermique).

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39

Pomares, Christelle. "Epidémiologie et formes cliniques atypiques de la leishmaniose à Leishmania infantum. : Apport du génotypage parasitaire." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5055/document.

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La leishmaniose à Leishmania infantum est une zoonose transmise de mammifère à mammifère par la piqûre d'un insecte vecteur, le phlébotome femelle. S'il est classiquement décrit la leishmaniose viscérale avec la triade classique fièvre, pâleur et splénomégalie, de nombreuses formes cliniques peuvent être associées à ce parasite. Le portage asymptomatique est la forme la plus fréquente et la plus répandue dans l'Ancien Monde ou le Nouveau Monde. Entre la leishmaniose viscérale et le portage asymptomatique, plusieurs formes cliniques sont présentes. Ainsi certains sujets vont exprimer la leishmaniose sous forme d'adénopathies isolées. Ces formes sont intermédiaires entre une expression pauci symptomatique et une leishmaniose viscérale larvée. Alors que L. infantum n'est pas classiquement retrouvé dans des formes muqueuses, des cas ont été récemment décrits. Ces formes muqueuses isolées ne sont pas rares puisque sur les 3 CHU Marseille, Montpellier et Nice, entre 1997 et 2009, 10 cas de leishmaniose muqueuse à L. infantum ont été diagnostiquées principalement chez des sujets immunodéprimés. Il est important de faire le diagnostic de ces formes cliniques particulières puisqu'elles ont pour diagnostic différentiel des néoplasies (lymphome pour la première et néoplasie de la sphère ORL pour la seconde). Afin d'appréhender le rôle du parasite dans l'expression clinique, il a été réalisé le typage par les microsatellites de neuf souches isolées de sujets porteurs asymptomatiques. Il s'avère que ces neuf souches sont très peu polymorphes et que sept d'entre elles possèdent un génotype unique
Leishmaniasis due to Leishmania infantum is a zoonotic disease transmitted from mammal to mammal through the bite of an insect vector the sandfly female. Beside the classical triad of visceral leishmaniasis symptoms: fever, pallor and splenomegaly, many clinical forms could be associated with this parasite infection. Asymptomatic carriage of L. infantum is the most common and the most widespread in the Old World and New World. Many other clinical forms are present and some subjects will develop only isolated lymphadenopathy. These forms are intermediate between pauci symptomatic and visceral leishmaniasis forms. Whereas L. infantum is not typically associated with mucosal forms, several cases have been described. Indeed, in the 3 academic hospitals of Marseille, Montpellier and Nice from 1997 to 2009, 10 cases were revealed mainly in immunocompromised patients. To understand the role of parasite in clinical expression, nine strains isolated from asymptomatic carriers were genotyped using microsatellite. The nine strains have few polymorphisms and seven of them are identical with a unique genotype. In addition, those strains are very different from strains of HIV-positive subjects. If the strains genetic appears to have a role in the clinical expression of the disease, the environment in which individuals live in endemic areas is associated with an excess of risk to develop visceral leishmaniasis. While in Marseille, cases of visceral leishmaniasis occur in an urban environment, they take place in Nice in a rural environment, as it is classically described. To investigate differences between parasite strains form Nice and Marseille studies with microsatellites are ongoing

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Beveridge, Maxine. "Molecular ecology of Dawson's burrowing bee Amegilla dawsoni (Hymenoptera: Anthophorini)." University of Western Australia. School of Animal Biology, 2006. http://theses.library.uwa.edu.au/adt-WU2006.0091.

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[Truncated abstract] In the last two decades, the use of microsatellites has revolutionized the study of ecology and evolution. Microsatellites, or short tandem repeats (STRs), are stretches of DNA repeats, 1 to 5 nucleotides long, where the number of repeats varies between individuals. They are co-dominant, highly variable, neutral markers, and are inherited in a Mendelian fashion. Microsatellite loci were isolated from Dawson’s burrowing bee, Amegilla dawsoni, a large, fast-flying solitary nesting bee endemic to the arid zone of Western Australia. Twelve polymorphic loci were found with an observed number of alleles ranging from two to 24 and observed heterozygosities between 0.17 and 0.85. These loci were used to examine two aspects of this bee’s molecular ecology; its population structure and mating system ... The molecular data were also used to show that the nesting female is the mother of all her offspring and that brood parasitism is unlikely in this species. The data indicate that females make daughters at the beginning of the season followed by large sons in the middle, and then small sons at the end. Females often place one brood cell directly above another. The distribution of sex and morph in these doublets follows a pattern with most containing a female on the bottom and a minor male on the top, followed by almost equal numbers of female on top of female and minor male on top of major male. This pattern is likely favoured by emergence patterns, with males emerging before females and minor males emerging before major males. I suggest that although minor males have low reproductive success, their production may nonetheless be beneficial in that minor males open up emergence tunnels for their larger and reproductively more valuable siblings. In addition, minor males may represent the ‘best of a bad job’ provisioning tactic arising from changes in the costs to nesting females of gathering brood provisions over the course of the flight season. This thesis demonstrates that microsatellites can be used to answer many questions regarding the molecular ecology of a species from the behaviour of the bees on a population scale to the mating behaviour of individual bees and how they allocate resources for the next generation. Many other aspects of the bee’s ecology could also be examined now that suitable molecular markers exist.

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Mallory, Melanie Ann. "Development and Characterization of Microsatellite Markers for the Grain Amaranths (Amaranthus spp. L.)." Diss., CLICK HERE for online access, 2007. http://contentdm.lib.byu.edu/ETD/image/etd1988.pdf.

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Choudhury, Arpita. "The use of microsatellite DNA fingerprinting for aquaculture and fisheries science /." View online ; access limited to URI, 2005. http://0-wwwlib.umi.com.helin.uri.edu/dissertations/dlnow/3186898.

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Chirhart, Scott Edward. "Evolutionary implications of microsatellite variation in the Peromyscus maniculatus species group." Texas A&M University, 2003. http://hdl.handle.net/1969.1/1279.

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Given the distribution and probable evolutionary history of the Peromyscus maniculatus species group, an interspecific comparison of microsatellite variation among these species would be logically based (at least initially) on primers isolated from the genome of a geographically central population of P. maniculatus. Additionally, as the species in the group are recently diverged, reasonably informative microsatellite data are likely to require analysis of a rapid evolving category of microsatellite loci. The initial phase of this research involved the isolation, characterization and assessment of variation for a panel of DNA microsatellites containing perfect dinucleotide repeats from a geographically central population of P. maniculatus. Theoretical predictions and empirical studies indicate that phylogenetic analyses based on microsatellite primers isolated from a focal species may be subject to ascertainment biases that can be expected to degrade the efficacy of this approach with increasing phylogenetic depth between the species from which the microsatellites were isolated and those to which these loci are being compared. Results of an analysis of allelic variation at 12 pure, dinucleotide microsatellite loci (isolated from P. maniculatus) are reported for samples of all species in the P. maniculatus species group and the sister taxon P. leucopus. Examined for the species in the P. maniculatus species group for which there is an a priori highly corroborated phylogeny, evidence of ascertainment bias was apparent only for one locus that was unique to P. maniculatus. Genealogical analyses of the data over all loci yielded inferred relationships that were entirely concordant with the a priori corroborated phylogeny for P. maniculatus, P. keeni, P. polionotus, P. melanotis and P. leucopus. Genealogical analyses of the previously unresolved relationships of P. keeni and P. sejugis consistently placed these as an independent sister-group between P. maniculatus and P. polionotus. The geographically improbable sister-group association of P. keeni and P. sejugis may be the result of an historical ancestral continuity or may reflect large-scale lineage sorting rather than true phylogenetic propinquity. These data suggest that, given the choice of an appropriate focal species, even relatively small sets of pure dinucleotide microsatellites can provide reliable population genetic and systematic implications for taxa with divergence times dating to the Pleistocene.

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Martins, Aline Fernandes Angêlla [UNESP]. "Estrutura populacional de Anopheles darlingi em diferentes localidades de Rondônia ao longo do Rio Madeira através da genotipagem de microssatélites." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/102683.

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Made available in DSpace on 2014-06-11T19:32:13Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-01-28Bitstream added on 2014-06-13T20:23:14Z : No. of bitstreams: 1 martins_afa_dr_botib.pdf: 1302290 bytes, checksum: f4a20eda14cf780d998f0e02bf28f074 (MD5)
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
A malária é uma das principais parasitoses humanas do mundo, causando mais de um milhão de mortes, e quase 500 milhões de casos agudos da doença por ano. No Brasil, esta doença continua sendo uma das mais importantes do país, tendo sido registrados no ano de 2009 mais de 300 mil casos. O mosquito Anopheles darlingi é o principal vetor desta doença no Brasil e outros países da América do Sul. Devido à sua importância como vetor da malária humana, estudos sobre a estrutura populacional de An. darlingi tem sido objeto de vários estudos. A sua distribuição na Região Amazônica é ampla e dados recentes mostram alto grau de heterogeneidade, tanto genética como de comportamento. Grande parte desta variabilidade observada em An. darlingi pode estar relacionada com estratégias adaptativas para explorar nichos ecológicos distintos enquanto que a estrutura populacional e a diferenciação pode ser explicada por diferenças no tamanho efetivo da população, padrões de fluxo gênico e acontecimentos históricos e de colonização recente. De igual modo, alterações ambientais efetuadas pelo homem podem ter um impacto significativo na dinâmica de populações de vetores e, consequentemente, na transmissão da malária. Este projeto utilizou a genotipagem de 10 microssatélites para o estudo populacional de Anopheles darlingi coletados em sete localidades ao longo da extensão das Hidrelétricas de Jirau e Santo Antônio, às margens do Rio Madeira, em Porto Velho – RO. Estes métodos foram aplicados na caracterização de amostras coletadas nestas regiões no 1º e 2° semestres de 2007. O objetivo do trabalho foi analisar a estrutura populacional de An. darlingi ao longo do Rio Madeira, na área de influência das Hidrelétricas de Jirau e Santo Antônio. Os resultados mostraram alto fluxo gênico entre as populações, mesmo distando de 70 km. Foram encontradas diferenças...
Malaria is the major human parasitic diseases in the world, causing more than a million deaths and almost 500 million acute cases of disease per year. In Brazil, this disease remains one of the most important, having been recorded in the year of 2009 more than 300.000 cases. The mosquito Anopheles darlingi is the principal malaria vector in Brazil and other countries in South America. Due to its importance as a vector of human malaria, population structure of Anopheles darlingi has been the subject of several studies. Its distribution in the Amazon region is large and recent data show a high degree of heterogeneity, regarding genetic and behavioral aspects. Much of this observed variability may be related to adaptive strategies to exploit different ecological niches, while the population structure and differentiation can be explained by differences in effective population size, patterns of gene flow and historical events and recent colonization. Similarly, environmental changes made by man can take a significant impact on population dynamics of vectors and hence the transmission of malaria. This project genotyping 10 microsatellites for population-based study of Anopheles darlingi collected at seven locations along Rio Madeira at Porto Velho - RO. These methods were applied in the characterization of samples collected in these regions in the 1st and 2nd semesters of 2007. The objective was to analyze the population structure of Anopheles darlingi along the Madeira River, the area of influence of Hydroelectric of Jirau and San Antonio. The results showed high gene flow among populations, even at 70 km apart. We found significant genetic differences among populations when samples were compared seasonally. The samples collected in the first half of the year showed effective population size 10x greater than those collected in the second half. These differences may represent differences... (Complete abstract click electronic access below)

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Boley, Ryan Michael. "Relative species abundance and microhabitat preferences of larval Scaphirhynchus sturgeon in the middle Mississippi River." OpenSIUC, 2010. https://opensiuc.lib.siu.edu/theses/195.

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The pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (S. platorynchus) are benthic freshwater fishes that are sympatric throughout the range of the pallid sturgeon. Pallid sturgeon was listed as endangered under the Endangered Species Act in 1990, while shovelnose is common throughout the range. Previous abundance studies estimate the ratio of adult pallid to shovelnose sturgeon to be on the order of 1:82 in the middle Mississippi River, respectively. Despite adult abundances, reproduction and/or recruitment of pallid sturgeon larvae is undocumented in the middle Mississippi River. The current study aims to confirm the presence of pallid sturgeon reproduction and estimate the relative species abundances of larval pallid, shovelnose and hybrid sturgeon in the middle Mississippi River. Since larval pallid, shovelnose and hybrid sturgeon are virtually identical morphologically, the use of DNA markers was required for species designations; sixteen previously developed microsatellite loci were used in this study. Of the 583 larval Scaphirhynchus sturgeon collected from the middle Mississippi River, 581 were shovelnose, one was a hybrid and one was a pallid. This study was the first to genetically confirm the presence of pallid sturgeon reproduction in the middle Mississippi River. Differences in species ratios between adult and larval Scaphirhynchus sturgeon could be explained by three potential hypotheses; life history characteristics accentuate species ratios between adult and larval stages, pallid are experiencing low reproduction and/or low recruitment, or pallid larvae reside in different microhabitat locations compared to shovelnose.

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Schwartz, Tonia S. "Population structure of the gopher tortise (sic) (Gopherus polyphemus) in Florida, using microsatellites." [Tampa, Fla.] : University of South Florida, 2003. http://purl.fcla.edu/fcla/etd/SFE0000607.

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Batley, Jacqueline. "A study of the population ecology of willow beetles (Phyllodecta spp.) using microsatellites." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343295.

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Johnson, Kirsten M. "Characterization of length-dependent GGAA-microsatellites in EWS/FLI mediated Ewing sarcoma oncogenesis." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1523384027382108.

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Croteau, Emily Katherine. "Population genetics and phylogeography of bobcats (Lynx rufus) using microsatellites and mitochondrial DNA." Available to subscribers only, 2009. http://proquest.umi.com/pqdweb?did=1791777601&sid=3&Fmt=2&clientId=1509&RQT=309&VName=PQD.

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Thesis (Ph. D.)--Southern Illinois University Carbondale, 2009.
"Department of Zoology." Keywords: Bobcats, Microsatellite, Mitochondrial DNA, Phylogeography, Population genetics, Lynx rufus. Includes bibliographical references (p. 98-111). Also available online.

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Brockhurst, Veronica. "Development of novel DNA-based methods for the measurement of length polymorphisms (microsatellites)." Thesis, Queensland University of Technology, 2001.

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Dissertations / Theses on the topic 'Microsatellites'

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