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Physical mapping of genome regions without linkage map using BAC clones in Xenopus tropicalis
Špirhanzlová, Petra ; Krylov, Vladimír (advisor) ; Marec, František (referee)
Xenopus leavis was a favorite model organism during the 20th. century, but nowadays it has been replaced by diploid Xenopus tropicalis, which has not only shorter generation time, but also smaller genom. One of the disadvantages of Xenopus tropicalis is the lack of full physical and linkage map. According to JGI genome database (assembly 4.1) there are unmapped regions on short arm of the chromosome 2 and 7 . Several BAC clones ( with a single or dual-end sequence) has been found to be located within this region, according to a recent assembly 7.1. However , it isn't clear whether 100bp length of BAC ends is enough to place entire BAC clone into the genom of Xenopus tropicalis. In order to prove correct inclusion of these BAC clones into JGI database, several BAC clones, which are supposed to be located on short arm of chromosome 2, were picked. Using fluorescence in situ hybridisation, the signal of these BAC clones was localised on the short arm of chromosome 1 instead of chromosome 2 and in most cases they had opposite orientation. It means that the 100bp lenght of BAC ends propably isn't sufficient to place entire BAC clone on chromosome. New working protocol of BAC DNA isolation and labeling was established.
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Physical mapping of genome regions without linkage map using BAC clones in Xenopus tropicalis
Špirhanzlová, Petra ; Krylov, Vladimír (advisor) ; Marec, František (referee)
Xenopus leavis was a favorite model organism during the 20th. century, but nowadays it has been replaced by diploid Xenopus tropicalis, which has not only shorter generation time, but also smaller genom. One of the disadvantages of Xenopus tropicalis is the lack of full physical and linkage map. According to JGI genome database (assembly 4.1) there are unmapped regions on short arm of the chromosome 2 and 7 . Several BAC clones ( with a single or dual-end sequence) has been found to be located within this region, according to a recent assembly 7.1. However , it isn't clear whether 100bp length of BAC ends is enough to place entire BAC clone into the genom of Xenopus tropicalis. In order to prove correct inclusion of these BAC clones into JGI database, several BAC clones, which are supposed to be located on short arm of chromosome 2, were picked. Using fluorescence in situ hybridisation, the signal of these BAC clones was localised on the short arm of chromosome 1 instead of chromosome 2 and in most cases they had opposite orientation. It means that the 100bp lenght of BAC ends propably isn't sufficient to place entire BAC clone on chromosome. New working protocol of BAC DNA isolation and labeling was established.
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Molecular basis of the Amphibian germ plasm
Špirhanzlová, Petra ; Krylov, Vladimír (advisor) ; Nedvídek, Josef (referee)
2. Abstract Xenopus germ plasm originates in previtellogenic oocytes in an area rich in mitochondria - the mitochondrial cloud. After its first appearance, the germ plasm localises to the vegetative pole of the egg and takes the form of small islands. After fertilization, the germ plasm aggregates at the apex of the vegetal pole of the embryo and then it separates into blastomers directly surrounding the vegetal pole. The germ plasm consists of mitochondria, germinal granules, ribozomes and various ribonucleic acids (RNAs). In Xenopus, the germ plasm RNAs are required for the formation of the primordial germ cell line. XDead end is fundamental for the migration, differentiation and survival of germ cells. Embryos depleted of fatvg are defective in primordial germ cell (PGC) formation and cortical rotation and organelle transport are inhibited in these embryos. Xdazl is required for early PGC differentiation and indirectly contributes to the migration of PGCs through the endoderm. Some germ plasm proteins, for example, Fatvg and Xcat-2, also play an important role in the determination of the dorsal/ventral axis.
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