Thesis (Ph. D.)--University of California, San Diego, 2003. / Vita. Includes bibliographical references (leaves 353-374).

Hypervariable minisatellite regions of human DNA are of considerable interest, not only as highly informative genetic systems, but also as intermediately sized regions of tandem repetition. Methods for the isolation of minisatellite loci from the human genome have been investigated, and 23 new hypervariable loci cloned from an ordered array Charomid library. This method not only allows very efficient isolation of human minisatellites, but can also be used to observe the degree of overlap between multi-locus DNA fingerprinting probes. The 23 new loci have a mean heterozygosity level of 71%, and have been characterized and mapped in the genome. The genomic disposition of human minisatellites has been analysed by investigation of cloned examples. The minisatellites studied show a strong tendency to cluster near the ends of chromosomes, and sequence analysis demonstrates a significant excess of dispersed repeat elements in the DNA flanking human minisatellites. Minisatellite variant repeat (MVR) mapping has also been used to investigate the internal structure of minisatellite alleles. Somatic allele length mutation events have been demonstrated in DNA from colorectal adenocarcinomas, and the mutations observed show many features of general similarity to germline mutation events. A series of human breast tumours has been screened for somatic change, using both multi-locus DNA fingerprinting probes and single-locus minisatellite probes. Somatic change in breast cancers is much less frequent than in colorectal tumours, but some allele losses and mutations have been defined, including a highly unusual mutation, which may be the result of a minisatellite transposition event. Finally, evolution at minisatellite loci has been studied, both by examination of allelic states in current human populations, as well as comparison with non-human primates.

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A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science / There are a number of recorded difficulties in classing lithop species according to their phenotype alone. DNA profiling, which can provide a quantitative measure of the degree of sequence similarity between any two genomic DNA's, is the method of choice for establishing phylogenetic relationships between species. (Abbreviation abstract} / Andrew Chakane 2018

La popularité des réseaux informatiques et d'Internet s'accompagne d'un essor des applications communicantes et de la multiplication des protocoles dont le fonctionnement est plus ou moins compliqué, ce qui implique également des performances différentes en termes de robustesse. Un premier objectif de cette thèse est d'approfondir plus en détails la robustesse de protocoles s'illustrant par d'extraordinaires performances empiriques tels que les botnets. De plus, l'essor et la diversité des protocoles peut s'accompagnee d'un manque de spécification que la rétro-ingénierie tente de retrouver. Une première phase essentielle est de découvrir les types de messages. La technique mise en oeuvre dans cette étude s'appuie sur les machines à vecteurs de supports tout en ayant au préalable spécifié de nouvelles représentations des messages dont la complexité de calcul est très réduite par rapport aux autres techniques existantes. Enfin, il existe généralement un grand nombre d'applications distinctes pour un même protocole et identifier précisément le logiciel ou le type d'équipement utilisé est un atout essentiel dans plusieurs domaines tels que la supervision ou la sécurité des réseaux. S'appuyant uniquement sur les types de messages, le comportement d'un équipement, c'est-à-dire la manière dont il interagit avec les autres, est une information très avantageuse lorsqu'elle est couplée avec les délais entre les messages. Enfin, la grammaire d'un protocole connu permet de construire les arbres syntaxiques des messages, dont le contenu et la structure sémantiquement riche, avaient peu été étudiés jusqu'à maintenant dans le cadre de l'identification des équipements. / The growth of computer networks like the Internet entailed a huge increase of networked applications and the apparition of multiple, various protocols. Their functioning complexity is very variable implying diverse performances. The first objective of this PhD thesis is to evaluate precisely the robustness of those networked applications, which are known to be very efficient and seem scalable, like for instance, the botnets. Hence, several botnets protocols are imitated. Furthermore, protocol reverse engineering has skyrocketed because many protocols are not always well documented. In this domain, the first necessary step is to discover the message types and this work introduces a novel technique based on support vector machines and new simple message representations in order to reduce the complexity. Finally, there are many distinct applications for a single protocol which can be identified thanks to device fingerprinting techniques whose the domain of application is related to security and network management. The first technique proposed in this PhD thesis can work with the previous contribution about reverse engineering because the devices could be identified only based on the types of messages exchanged which are aggregated into a temporal behavioral tree including message delays. Besides, the syntactic tree structure of a message is also a good discriminative feature to distinguish the different devices but was very little considered until now.

The central theme in this thesis is Empirical Bayes. It starts off with application of Bayes and Empirical Bayes methods to deoxyribonucleic acid fingerprinting. Different Bayes factors are obtained and an alternative Bayes factor using the method of Savage is studied both for normal and non- normal priors. It then moves on to deeper methodological aspects of Empirical Bayes theory. A 1983 conjecture by Carl Morris on the parametric empirical Bayes prediction intervals for the normal regression model is studied and an improvement suggested. Carlin and Louis’ (1996) parametric empirical Bayes prediction interval for the same model is also dealt with analytically while their approach had been primarily numerical. It is seen that both of these intervals have the same coverage probability up to a certain order of approximation and they have the same expected length up to the same order of approximation. Both the intervals are equal tailed up to the same order of approximation. Then the corrected proof of an important published result by Datta, Ghosh and Mukerjee (2000) is provided using first principles of probability matching. This result is relevant to our work on parametric empirical Bayes prediction intervals.

Random amplified polymorphic DNA (RAPD) was tested for the identification and classification of Leishmania. RAPD was found to be useful for the identification of species of L. (Leishmania) and L. (Yiannia) and for the classification of L. (Yiannia) species. The polymerase chain reaction (PCR) was tested for the identification of Leishmania from mammals and lizards, using both published primers and new primers which amplify kinetoplast minicircle DNA. The size of the PCR product was found to be useful for discriminating between some sympatric pairs of species such as L. braziliensis and L. mexicana. Isotopically labelled probes prepared from the variable region of the kinetoplast minicircle were tested for specificity for the identification of New and Old World species of Leishmania. The specificity was dependent on the concentration of target DNA and was manipulated to investigate relationships between Leishmania species. Restriction digests of kinetoplast DNA (schizodemes) prepared by PCR and by centrifugation through 20% sucrose were compared for the identification of strains of L. infantum and L. chagasi. Twenty three strains of L. chagasi from cases of visceral and cutaneous leishmaniasis in Honduras were examined by RAPD, schizodemes, differential display, isoenzyrnes, RFLPs and PFGE to discover whether genetic differences existed between parasites causing the two different pathologies. The parasites were found to be unusually homogeneous and no differences were found which correlated with pathology by any of these methods. Restriction digests of PCR amplified small subunit ribosomal DNA (SSU rDNA) (ribodemes) were tested to find markers specific for the genus Leishmania. A classification of the Leishmania based on the restriction fragments indicated that L. hertigi and L. herreri were more closely related to Endotrypanum than to Leishmania, and that the lizard Leishmania could not be placed in separate genus from the Leishmania. Ribodemes were used to identify two strains of parasites supplied by colleagues in Central America that could not be identified by existing methods for the identification of Leishmania. One of these strains appeared to be identical to a C. luciliae reference strain. The other strain produced a fingerprint unlike any of the available reference strains. A variable region of the SSU rRNA gene was identified that was suitable for classifying trypanosomatids and the sequence of this region was used to classify the strain that could not be identified by fingerprinting.

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 1994. / Vita. Abstract. Includes bibliographical references (leaves 105-111). Also available via the Internet.