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Diversity of European freshwater cyclopoid species: phylogeny, morphology and ecology
Krajíček, Martin ; Černý, Martin (advisor) ; Brancelj, Anton (referee) ; Wyngaard, Grace (referee)
Cyclopoids are together with Calanoids and Harpacticoids a part of the largest, very diverse group of crustaceans and the most numerous aquatic metazoans of the world. The history of their research goes as far back as to the beginning of 19th century when the first cyclopoid copepods were described. The taxonomy of cyclopoids started to develop gradually since that time, adding new and more detailed methods and morphological characters, as well as a certain degree of taxonomical confusion. In last decades, the molecular-genetic techniques of DNA sequencing have become available offering a new independent tool for taxonomists. This work contains different studies concerning the morphology, taxonomy, ecology, distribution and colonisation of cyclopoid copepods, with the use of molecular tools as a uniting element. Chapter 1 of this thesis summarizes basic knowledge about the taxonomy, morphology and biology of cyclopoid copepods and introduces the following chapters containing four studies presented as single publications. The taxonomy of copepods of the genus Cyclops is based mainly on the morphology which is sometimes ambivalent and some of the most problematic species groups are presented here. Chapter 2 presents our unique results, the first reconstruction of phylogenetic relationships among 15...
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The analysis of immunoglobulin and T-cell receptor gene rearrangements using next generation sequencing
Hašek, Daniel ; Froňková, Eva (advisor) ; Javorková, Eliška (referee)
DNA sequencing is a molecular genetic method that results in data about sequence and type of nucleotides present in a given sample of deoxyribonucleic acid (DNA), a molecular carrier of genetic information. These data are frequently of a crucial value for many fields; research, medicine, industry, criminalistics or others. During a long period of time almost all the sequencing was performed using a method invented by Frederick Sanger in the 70's, a technique that uses modified nucleotides that once incorporated into a DNA strand prevent this from further elongation. DNA synthesis in presence of such nucleotides leads to a formation of a mixture of fragments of different lenght that are electrophoretically separated by lenght and the sequence is read from the resulting gel. Since the principle of this method entails some inherent drawbacks (e.g. low throughput and coverage) a significant effort is made lately to develop alternative sequencing approaches. These methods colectively refered to as next-generation sequencing (NGS) use several technologies in order to overcome the limitations of the Sanger sequencing. This thesis discusses the most important NGS methods and focuses on their possible application for sequencing of immunoglobulin and T-cell receptor gene rearrangements, an area of undisputable...
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Targeted next generation sequencing of candidate genes responsible for impaired spermatogenesis and male infertility
Daňková, Michaela ; Liška, František (advisor) ; Holá, Dana (referee)
Infertility is a widespread health problem, caused by the male factor in about half of all cases, and in about a half of the infertile men the cause is unknown. In a significant number of these men, genetic etiology is assumed. Current routine methods of laboratory diagnostics, which include karyotype examination, exclusion of mutations in the CFTR gene, and Y chromosome microdeletions, do not usually reveal the cause of infertility. That is why researchers' efforts aim at detecting mutations in other genes that are causing male infertility. In recent years, animal models have been used to identify many genes necessary for fertility. Based on these findings, 12 candidate genes have been selected (CAPZA3, CDC14B, CDC42, CNTROB, CSNK2A2, GOPC, HOOK1, HRB, OAZ3, ODF1, RIMBP3, SPATA16) that are essential for spermatogenesis. Mouse or rat mutants in these genes are primarily associated with oligoasthenoteratozoospermia, since they are involved in sperm morphogenesis. However, the phenotype spectrum may comprise also azoospermia. The purpose of the thesis was to determine the sequence of the afore mentioned genes in infertile men with impaired spermatogenesis and to reveal presence or absence of pathogenic mutations in these genes, using cDNA and genomic DNA from peripheral blood. The candidate genes were...
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Detection of Genome Variations
Beluský, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
An influence of variations in human genome is perceptible at a first glance on human itself to see differences between the individuals and entire populations. Also, behavior or probability of certain diseases are influenced in large way by differences at genome's level. This work presents methods for detecting variations in the human genome that were developed after an arose of the second-generation sequencing technologies. A new tool that combines read pair and split read methods, with information about a depth of coverage was also designed and implemented. The tool was tested on simulated and real data and compared with a reference outputs.
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DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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2 DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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DNA sequencing
Felsberg, Jürgen
Performance of scientific and technical work largely consisting of DNA sequencing according to client specification. In adition all DNA analysis necessery for DNA sequencing are carried out.
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