Abstract Fragile X syndrome, the most common inherited form of mental retardation syndrome, is caused by an expansion of the CGG trinucleotide repeat in the 5' UTR of the FMR1 gene, with concurrent hypermethylation of the region, which represses FMR1 expression. The syndrome is associated with the folate-sensitive chromosomal fragile site at Xq27.3 (FRAXA), where the gene responsible for the syndrome was first localized by linkage analysis using RFLP markers. In this study the linkage relationships of the RFLP markersat Xq27-28 and the characteristics of the CGG repeat expansion were investigated in northern Finnish fragile X families and molecular diagnostic methods were applied in order to improve diagnosis of the syndrome. Furthermore, the origin of fragile X mutations in the northern part of Finland was studied by haplotype analysis. Linkage studies were performed in 34 northern Finnish fragile X families/pedigrees using a total of 15 RFLPs (defining 11 loci). A refined genetic map around FRAXA including five RFLP markers having recombination fractions of 0.04 or less with FRAXA was obtained in an international study of 112 affected families, containing linkage data on twelve northern Finnish families. Linkage analysis significantly improved carrier detection in fragile X families compared with previous cytogenetic methods used in diagnosis. The most efficient RFLP-based protocol for carrier detection was proposed, which is based on use of the most adjacent markers and a minimum number of restriction enzymes. CGG repeat expansion of the FMR1 gene was investigated in original families collected for linkage studies and additional new ones. Large CGG repeat expansions (Δ > 500 bp) with concomitant methylation of the adjacent CpG island, i.e. full mutations, were found to be associated with mental retardation completely in males, but only 50% of the females having a full mutation were mentally impaired. Premutations (Δ < 700 bp) were found in healthy carriers. There was a size range of Δ = 500 to 700 bp, where the expansions could be either abnormally methylated or non-methylated, and it appeared that methylation is more important in determining the phenotype than the exact size of an expansion. Instability of the enlarged CGG repeats was detected, leading preferentially to size increases in successive generations. The instability of premutations was found to be stronger and the size increases larger in maternal than in paternal transmissions, and transition to a full mutation occurred only in female transmissions. In addition, the size of a maternal premutation was shown to have an important influence on the risk of its transition to a full mutation when transmitted. The critical premutation size leading invariably to full mutation in the offspring was found to be between Δ = 175 to 200 bp. In one of the studied families a rare contraction of a paternal premutation to a normal CGG repeat number in one of the daughters and further in her son was detected. Direct mutation analysis including measurement of the CGG repeat size and hypermethylation allowed unambiguous diagnosis of carriers and affected individuals in most cases. Haplotype analysis using two tightly linked microsatellite markers flanking the CGG repeat mutation was performed in 60 unrelated northern and eastern Finnish fragile X families. A significant difference was found in allelic and haplotypic distributions between normal X and fragile X chromosomes. A single haplotype, which was present only in 8% of the normal X chromosomes, accounted for 80% of the fragile X chromosomes. This enrichment of one fra(X) mutation in the Finnish population suggests founder effect.

Masters of Science / Genetic analysis for resistance to Woolly Apple Aphid in apple rootstock breeding populations MC Selala MSc Thesis, Department of Biotechnology, Faculty of Science, University of the WesternCape. The Woolly Apple Aphid (WAA) Eriosoma lanigerum (Hausm.) (Homoptera: Aphididae) is economically one of the most important pests in apple commercial production in the Western Cape province, South Africa. The apple cultivar Northern Spy possesses a single major gene (Er1) responsible for E. lanigerum resistance. This cultivar has been used as a commercial rootstock in apple breeding programmes. There are other genes also implicated in resistance to E. lanigerum from other cultivars. Manipulation and pyramiding of the E. lanigerum resistance genes (Er1, Er2 and Er3) might provide a necessary control for commercial apple production. The aim of this study was to construct a genetic linkage map for apple using microsatellite markers. The use of marker-assisted selection would greatly benefit local apple breeding programmes. Ninety six seedlings from a Northern Spy × Cox Orange Pippin mapping population were used for genetic linkage construction. Phenotypic data collection and analysis were performed to determine the E. lanigerum infestation patterns and the levels of resistance conferred by the Er1 gene from Northern Spy using 52 in vitro propagated seedlings in the greenhouse. Classification and quantification analysis showed association patterns between first assessments (30 days) to second assessment (60 days) in all replicate blocks. Roots and shoots data showed that it could be useful in quantitative trait loci (QTL) analysis, but may be used in different QTLs beingidentified due to the variations between roots and shoots data. A preliminary linkage map was constructed using a mapping population from Northern Spy × Cox Orange Pippin (96 seedlings).Fluorescently labelled published and predicted microsatellite markers were used in map construction. Primers were optimised using single apple cultivar and the detection of polymorphisms using nine apple cultivars. Optimised markers were multiplexed for high throughput data generation using the Polymerase Chain Reaction (PCR) technique. Multiplexed PCR products were pooled and analysed on an ABI 310 PRISM™ Genetic Analyser to determine allele fragment sizes, and the inherited segregation types in the seedlings. Computer software GenoTyper® 2.5.2 and JoinMap® 3.0 was used in data analysis from ABI 310 PRISM™Genetic Analyser and linkage map construction. Seventy two markers were used in linkage map construction, which produced nine linkage groups with some segments from the same linkage group. Twenty-one markers were aligned on the map 20 published and one predicted. Only one linkage group consisted of five markers while other linkage groups had two markers each. This study has proved that th preliminary linkage map could be used as the basis of a complete linkage map of Northern Spy × Cox Orange Pippin.

As two species diverge, much of their genomes begin to differentiate. In many lineages, however, the genomic structure remains remarkably intact, with orthologous gene content maintained across millions of years and significant changes to their biological characteristics. The maintenance of gene content is defined as conserved synteny while the preservation of gene order is defined as conserved linkage; the conservation of both can be incredibly informative when interrogating and comparing two genomes. In non-model organisms, linkage conservation to a well-developed model allows informed, cost-effective and rapid answers to fundamental biological questions without generation of equivalent resources. With the development of new model organisms, we can begin to discuss more fundamental evolutionary concepts, such as the maintenance of chromosomal gene content across larger evolutionary time-scales, or the reorganization that occurs in chromosomes following major genomic events such as whole-genome duplications. In this work, I utilized the rapid development of primary genomic resources in the non-model teleost sablefish (Anoplopoma fimbria) to demonstrate that conserved linkage to a model genomic reference can identify the gene most likely responsible for genetic sex-control. I then assembled the first genome for a non-duplicated member of the teleost lineage Protacanthopterygii, the northern pike (Esox lucius), and demonstrated the conservation of synteny between three major lineages of teleosts, the Protacanthopterygii, the Acanthopterygii and the Ostariophysi. I further showed that the genome of northern pike retains an ancestral teleost organization and pre-duplicated genome in comparison to the economically important Salmoniformes. Finally, with continued improvements of the genome to the chromosome level, I demonstrated the degree of conserved linkage maintained between Atlantic salmon and northern pike and explained how conserved linkage through both genomes could be used to improve the genome assembly of the other, even with over 125 million years of separation. As genomic technology continues to advance and new genomic resources become available, the continued refinement of genome re-organization post duplication will be revealed, and this pre-duplication outgroup will continue to push our understanding of the effects of genome duplication, as we transition from genome organization to functional modifications of gene duplicates following duplication. / Graduate / 2018-12-01

This dissertation analyzes the obstacles against further cooperation in international economic relations. The first essay explains the gradual nature of trade liberalization. I show that existence of asymmetric information between governments provides a sufficient reason for gradualism to exist. Governments prefer starting small to reduce the cost of partner’s betrayal when there is sufficient degree of information asymmetry regarding the partner’s type. Learning about partner’s incentive structure enhances expectations, encouraging governments to increase their current level of cooperation. Specifically, the uninformed government’s subjective belief for the trading partner being good is improved as the partner acts cooperatively. This updated belief, in turn, lowers the subjective probability of future betrayal, enabling further progress in cooperation. The second essay analyzes the relationship between two countries facing two policy dilemmas in an environment with two way goods and capital flows. When issues are independent and countries are symmetric, signing separate agreements for tariffs (Free Trade Agreements-FTA) and for taxes (Tax Treaties-TT) provides the identical level of enforcement as signing a linked agreement. However, linkage can still improve the joint welfare by transferring the slack enforcement power in a case of asymmetric issues or countries. I report non-results in two cases where the policy issues are interconnected due to technological spillover effect of FDI. Moreover, I show that linking the agreements actually reduces enforcement when agreements are linked under a limited punishment rule and policy variables are strategic substitutes. The third essay investigates the welfare/enforcement consequences of linking trade and environmental agreements. In the standard literature, linking the agreements generate non-trivial results only when there is structural relation between the issues. I focus on institutional design of the linkage and show that even if environmental aspects of international trade are negligible linking the agreements might still have some interesting welfare implications under current GATT Rules. Specifically, when traded goods are substitutes in consumption, linking the environmental agreement with trade agreement under the Withdrawal of Equivalent Concession Rule (Article XXVIII) will reduce the enforcement. However, enforcement in environmental issue increases when the same rule is implemented in the absence of linkage.

A suposta ubiquidade de sistemas decomponíveis foi interpretada por Holland (1975) como o principal motivo para o desempenho dos algoritmos genéticos (Genetic Algorithms (GAs)). A hipótese de Building Blocks (BBs) sugere que algoritmos genéticos mais eficientes poderiam ser implementados, contudo, apenas anos depois essas ideias puderam ser avaliadas experimentalmente no contexto de algoritmos de estimação de distribuição (Estimation of Distribution Algorithms (EDAs)). EDAs utilizam modelos probabilísticos, estimados a partir da população, para inferir características do espaço de busca que poderiam ser utilizadas para implementar operadores de reprodução mais eficazes. Tanto em problemas mono- quanto multi-objetivo, EDAs emergiram sob a premissa de que a eficácia dos operadores de reprodução seria proporcional à representatividade dos modelos probabilísticos utilizados. No entanto, estudos recentes tem demonstrado que a dificuldade em se construir modelos confiáveis pode tornar essa premissa inviável. Ou seja, para certos problemas de otimização os modelos probabilísticos utilizados seriam, em geral, de baixa qualidade e, portanto, não produziriam operadores eficazes. Esta tese trata das limitações encontradas na construção de modelos probabilísticos (linkage learning) sob a perspectiva da multimodalidade dos problemas em questão. A análise teórica considerou problemas aditivamente separáveis, enquanto a generalização das conclusões foi investigada em instâncias do modelo NK-landscapes e do problema da mochila multidimensional (Multidimensional Knapsack Problem (MKP)). Os resultados indicaram que a acurácia dos modelos probabilísticos é se relaciona inversamente ao grau de multimodalidade da função objetivo e que, em casos de extrema multimodalidade a construção de modelos probabilísticos confiáveis pode ser tornar infactível. Este resultado poderia inviabilizar o uso de EDAs no contexto multiobjetivo, devido a intrínseca multimodalidade de tais problemas. No entanto, observou-se que apesar da ausência de estatísticas confiáveis sobre cada uma das funções objetivo, a correlação entre elas se torna estatisticamente observável e útil aos operadores de reprodução na manutenção da diversidade e controle convergência da população. / The supposed ubiquity of nearly-decomposable systems was interpreted by Holland (1975) as the rationale for the performance of Genetic Algorithms (GAs), the Building Block (BB) hypothesis. His seminal studies suggest more efficient GAs as viable, but only later on his ideas have become practically tangible in the context of Estimation of Distribution Algorithms (EDAs). EDAs employ probabilistic modeling so as to infer properties of the search space (BBs) that could be useful for the effectiveness of reproduction operators. In both, single- and multi-objective contexts, EDAs have emerged on the assumption there is a correlation between how much information a model can conceive and how effective reproduction operators can be. However, more recent results suggest the difficulties in producing accurate linkage models can prevent such a relation to be true. In other words, for some optimization problems linkage learning might not be able to produce accurate linkage models, hence EDAs would not outperform GAs. This thesis addresses the limits of linkage learning in the context of single- and bi-objective problems, regarding the influence of multimodality on the accuracy of the linkage models and the efficiency of EDAs. A theoretical analysis was performed in terms of additively separable functions and general conclusions are assessed through experimentation with instances of the NK-model and the Multidimensional Knapsack Problem (MKP). The results indicated that the accuracy of the linkage models tends to decrease as a result of increasing multimodality, which weakens pairwise dependencies and might lead to pairwise independence in extreme cases. Since most EDAs rely on bivariate statistics to estimate multivariate distributions, their applicability is limited to optimization problems within a certain range of multimodality. In multi-objective problems, on the other hand, some EDAs have shown better performance than GAs, which seemed as a contradiction since multi-objective problems are inherently multimodal. Our results suggest that in such cases the correlation among the objective functions becomes statistically evident, as a consequence, linkage learning models such correlation instead of problems substructures, which is useful to obtain a better exploration of extreme regions of the objective space.

This thesis analyze the democratization process of Mongolia and Ghana by applying a comparative case study. The study use Steven Levitsky and Lucan Ways theory of Western linkage and leverage to analyze the Mongolian and Ghanaian transition process, from being an non-democratic state to an consolidated democracy, through looking at the development of Western linkage and leverage and if there is any correlation between this development and the progress of democracy in respective state.The findings are that Western linkage in Mongolia never has been high but that the levels of Western linkage has developed positive in 1991 and 1995. The levels of Western leverage has been high in Mongolia since 1991. In Ghana the levels of Western linkage has been high and developed positive since at least 1996, but the levels of Western leverage has been low since 1996. Thus, the correlation between high levels of Western linkage and leverage and the democratization progress in respective state is weak, but there is some correlation between a positive development of Western linkage and the progress of democracy.

We study the Cohen-Macaulay property of Rees algebras of modules of Kähler differentials. When the module of differentials has projective dimension one, it is known that condition $F_1$ is sufficient for the Rees algebra to be Cohen-Macaulay. The converse was proved if the module of differentials is already $F_0$. We weaken the condition $F_0$ globally by assuming some homogeneity condition.<br> <br> We are also interested in the defining ideal of the Rees algebra of a Jacobian module. If the Jacobian module is an ideal, we prove a formula for computing the defining ideal. Using the formula, we give an explicit description of the defining ideal in the monomial case. From there, we characterize the Cohen-Macaulay property of the Rees algebra.<br> <br> In the last chapter, we study Gorenstein linkage mostly in the graded case. In particular, we give an explicit example of a class of monomial ideals that are in the homogeneous Gorenstein linkage class of a complete intersection. To do so, we prove a Gorenstein double linkage construction that is analogous to Gorenstein biliaison.

Three cluster analysis programs were used to group the same 64 individuals, generated so as to represent eight populations of eight individuals each. Each individual had quantitative values for seven attributes. All eight populations shared a common attribute variance-covariance matrix. The first program, from F. J. Rohlf's MINT package, implemented single linkage. Correlation was used as the basis for similarity. The results were not satisfactory, and the further use of correlation is in question. The second program, MDISP, bases similarity on Euclidean distance. It was found to give excellent results, in that it clustered individuals into the exact populations from which they were generated. It is the recommended program of the three used here. The last program, MINFO, uses similarity based on mutual information. It also gave very satisfactory results, but, due to visualization reasons, it was found to be less favorable than the MDISP program.

Barley has had wide acceptance not only as a cultivated crop but also as an excellent source of genetic material. Barley was being used in inheritance studies by Tschermak when he rediscovered Mendel's laws of heredity. Since then barley has become one of the most widely used plants for genetic studies known today. More than 100 characters have been investigated indicating the relative ease of classification. There are 7 linkage groups corresponding to the 7 chromosomes in which 2 or more characters have been located as reported by Robertson (1939). But Kramer, Veyl, and Hanson (1954), from translocation experiments, suggest that linkage group III and VII should be combined in separate arms of the same chromosome. The present work is a study of character inheritance and linkage relationships aimed toward identifying the number of genes conditioning individual characters and associating them with linkage groups. When barley genes are more completely placed in their respective linkage groups, breeding for various good characteristics can be enhanced materially. This is readily accomplished when linkages are found between desirable characters for which selection is difficult or time-consuming.

The assignment of genetic factors to definite loci in the hereditary mechanism has been a great step in the progress of biology. Of the cereal crops, barley (Hordeum sp.), a crop of economic importance, offers a superior opportunity for genetic studies. Its adaptation to wide varieties of conditions, with a wealth of easily differentiated characters and only seven pairs of chromosomes, the barley plant provides excellent material for linkage studies. Although there is a vast amount of literature dealing with inheritance in barley, yet knowledge of the subject is still very limited. The mode of inheritance of about one hundred characters has been studied and linkage relations of nearly thirty-five characters have been made. The location of a relatively large number of them is still unknown. All the seven linkage groups are established and distinct viable characters are available in six of them, although but few in some cases. The desirability of making further studies in this crop is quite apparent. This manuscript contains the results of observations and experiments with sixteen characters which include three new characters not reported in the literature. All character pairs in each cross studied were checked for possible linkages or independence. The importance of such a study in the future improvement of the barley crop needs no emphasis.