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SNP polymorphisms of Y chromosome in the population of african fulani people
Bučková, Jana ; Černý, Viktor (advisor) ; Šimková, Halina (referee)
Markers on the non-recombining region of chromosome Y is a useful tool for study of diversity between populations. SNPs are the most commom polymorphisms in human genome. Mutation rate of SNPs is very low and so they may be used as genetic markers in evolutionary and population studies. We have analyzed 205 unrelated men from 11 Sub-Saharan Fulani's subpopulations. Fulani are an ethnic group of people spread over many countries, mainly in West Africa. Our samples are from Tindangou area, Banfora area (Burkina Faso), Bongor area, Linia area (Chad), Diafarabé area (Mali), Tcheboua area (Cameroon), Banfora area, Diffa area, Zinder area, Ader area and Abalak area (Niger). Using kit Signet Y-SNP Identification Systems and Luminex instrument with LabMAP Luminex Technology we detected particular Y chromosome's SNPs. LabMAP Luminex Technology is universal array platform, which as a probe using fluorescent polystyrene microspheres. We have observed 12 different haplogroups. Haplogroup E, which is typical African haplogroups, is determined with derivated allele in polymorfism M96. We have detected haplogroup E in maximum of 89,3% in the Fulani's subpopulations. In 7,8% we have detected haplogroup R, which is characteristic of populations in the Euroasia. Gene pool of Fulani's population is influenced with a...
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Molecular Genetic Applications in Archeological and Anthropological Context
Urbanová, Markéta ; Černý, Viktor (advisor) ; Brdička, Radim (referee) ; Brůžek, Jaroslav (referee)
6 Coxcr-usroN The aim of our studywas to establisha laboratoryprotocolfor isolationand analysisof aDNA. By studying three different skeletal collections answersabout sex, kinship and presenceof pathogenicbacteriawere searched. During the course of this thesisnew protocols for aDNA study were developedand continuously optimized'We wereableto evaluateinformationaboutsexof 37 subadultindividuals(.l8'7%)from Mikulčice settlementcemetery(9thcentury)andto confirmpÍesenceof Mycobacteriumlepraeon 2 skeletonsfromŽatec cemetery(l3th century).Subadult skeletonsexaminationbrought interestingresults of extremelyhigher presenceof maleindividuals. Unfortunately,notall aimswerefulťrlled.By establishedprotocolfor aDNA kinshipanalysisit wasnot possibleto retrievesufficientinťormationfor explanationof familial relationshipof individualsfrom thesame doubleburialsite. All acquiredexperienceand establishedprotocols are very valuable and in fururewe supposetheir full utilizationandimorovementin thefield of kinshioanalvsisof aDNA molecule. 28
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The mitochondrial genome in the ontogenesis
Töröková, Petra ; Brdička, Radim (advisor) ; Černý, Viktor (referee)
The main goal of this study is the comparison of sequences of the HVRII region of the mitochondrial genome in the cord blood sample and the saliva sample of the same individual, taken at average ten years from his/her birth. It is known that during ontogenesis the human genome changes. All the more the mitochondrial genome which shows a higher mutation rate, and moreover it is not taken care of it by repair mechanisms. In older individuals, there was found a distinctive amount of mitochondrial variations cumulated in different tissues in the process of the ontogenesis. This study is focused on the detection of these changes already in younger individuals. The tissue-specific variability which is created during ontogenesis might have an adverse influence on all sorts of the mtDNA based studies. The samples were taken in two regions (Teplice / Prachatice) that differ in the pollution of environment. With regard to that, the samples with discovered changes were compared from the standpoint of the region, which they had come from, with the aim to prove the influence of environment on the mutagenesis of the mitochondrial DNA. Samples were also compared from the point of view of sex. Furthermore the variability of the collection of Czech population was evaluated and the estimation of the genetic...
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The importance of Neolithic expansion in Central Europe - an assessment of phylogenetic age of mtDNA haplogroups in the Czech population.
Priehodová, Edita ; Černý, Viktor (advisor) ; Brdička, Radim (referee)
Agriculture, with different Neolithic cultures, starts in the Near East more than 10,000 years ago. This new way of life has very different archaeological manifestations that previous Mesolithic. After its Near Eastern emergence, the farming practices rapidly penetrated into southeastern Europe and the first signs of Neolithic in Central Europe are already 7,000 years old. It is being considered that the cultural innovations influenced demographic growth of the populations that have taken part in the Neolithic spread. In such situation, new mutations would have to fix and could form new specific haplogroups for Europe with ancestral ties to the Near East. Phylogeographic studies such as founder analysis of European and Near Eastern mtDNA sequences found that the European Neolithic component was enriched mainly by haplogroups J and T1, and that the genetic contribution of farming economy in European gene pool is about 10 - 20%. However, studies like these have not been yet realized in particular parts of Europe. The aim of this thesis is to disentangle the internal variability of Central European haplogroups J and T1 thought to be involved in the Neolithic demic diffusion. We classified these haplogroups from the HVS-I mtDNA sequences of 281 samples of the recent population of the Czech Republic. We...
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The genetic links around the Red Sea as revealed by the mtDNA
Čížková, Martina ; Černý, Viktor (advisor) ; Rídl, Jakub (referee)
The Red Sea region is one of the important places that allow us to uncover traces of the evolution of anatomically modern humans. Besides the questions related to its expansion out of Africa, this region is also important in terms of the mutual influence between populations of Africa and Arabia that after a long period of isolation and genetic differentiation related to climate change in the Pleistocene and subsequent development of seaways and land routes in the Holocene began to contact with each other more frequently. Number of genetic analyzes has been done but some issues concerning on the later development still remain inadequately answered, mainly because of insufficient material. This work is focused on the analysis of 200 mtDNA sequences of four Sudanese populations - two populations of nomadic herdsmen Rashaida and Beja living in the close neighborhood around the city of Kassala and speaking different languages and two populations of the Nile Valley with settled way of life. Analysis of the intrapopulation level revealed much higher diversity of the sedentary populations (in this work the sedentary populations are represented by the Nubians and Arabs). Interpopulation variability and genetic distances within other 46 populations of the Red Sea showed that although Rashaida and Beja people...
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The impact of geography and subsistence on distribution of NRY haplogroups in Europe and Africa
Nováčková, Jana ; Černý, Viktor (advisor) ; Munclinger, Pavel (referee) ; Macholán, Miloš (referee)
Y chromosome is due to its special characteristics the ideal tool of archaeogenetic studies. Its diversity is influenced by several factors and I analysed two of them (geographical location and subsistence). I generated SNPs and STRs data from several loci of samples from Slovakia (156 samples, 5 regions) and sub-Saharan Africa, where I analysed samples of sedentary farmers (481 samples, 18 regions) and nomadic pastorals (405 samples, 16 regions). Slovakia is situated at the meeting point of two migration ways. First of them was spread from the east to the west and is associated with enlargement of haplogroup R1a in Europe. The second came from the Iberian Peninsula eastward and is associated with enlargement of haplogroup R1b. Results of MDS graphs replicate the geographical map of Europe. Slovakia is situated in the middle of Russian, Balkanian and Iberian samples. Correlation between genetics and geographic distances is indicated by hierarchical AMOVA analysis and Mantel tests. Populations in sub-Saharan Africa differ from each other by the subsistence pattern. Different life style influence the diversity of the Y chromosome. Nomadic pastoralists and sedentary farmers share different haplogroups, for example, while haplogroup R1b was detected only in nomadic pastoral groups, sedentary farmers...
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Population Structure of African Populations Inferred from Alu Insertions.
Fajkošová, Zuzana ; Černý, Viktor (advisor) ; Frynta, Daniel (referee)
The population genetic study was carried out on 188 unrelated individuals from 5 populations of the Sahel. Relationships of nomadic Fulani to sedentary populations of different linguistic backgrounds and geographic origins were inferred from 16 polymorphic Alu insertions. Bayesian clustering approaches could be applied due to biallelic multilocus nature of the data. Fulani were shown to be divergent from neighbouring sedentary populations (Kassena and Mossi) and similar to Somali of East Africa. In context of already published genetic data, these results could be interpreted as Saharan origin of Fulani diaspora that was caused by Sahara drying out around 6 000 BP. After this initial migration of nomads to West Africa, a primarily female gene flow (integration of females) must have influenced the Fulani population. In contrast to Fulani, Songhai have shown a signal of recent admixture in concordance with historical and linguistic assumptions. KEY WORDS Alu insertions, Fulani, population genetics, Sahel
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Immunoregulatory characteristics of immune cells of children of allergic and non-allergic mothers and the possibility of their modulation with probiotic E.coli strain O83:K24:H31
Černý, Viktor
Due to high incidence, medical and socioeconomic burden and impact on individual quality of life and productivity, allergic disorders are a crucial issue for 21st century immunology. Much still remains to be elucidated, particularly regarding the very early processes in allergy development. In order to introduce timely, effective preventive measures, novel, more reliable predictive factors of allergy risk also need to be established. Dysregulation of proper balance between the branches of immune response, particularly unwarranted dominance of Th2, is the underlying cause of allergy. After birth, new immune balance needs to be established to prepare the neonate for adequate reactivity towards newly encountered environmental stimuli. Regulatory T cells (Treg) play a central role in finely setting this balance and inducing tolerance towards harmless environmental antigens, including allergens. Interactions with external factors, most importantly microbiota, modulate this process during the early postnatal "window of opportunity." Analysis of cord blood Treg of children of allergic mothers uncovered decreased presence of function-associated surface markers and lower production of IL-10. Furthermore, decreased proportion of Helios- induced Treg was observed in children with higher risk of allergy....
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Population structure, migration and dynamics in Africa and Arabia
Čížková, Martina ; Černý, Viktor (advisor) ; Frynta, Daniel (referee) ; Zrzavý, Jan (referee)
In addition to the interaction of evolutionary forces, the population history of the African Sahel and Arabia has been influenced by the spread of Neolithic cultural innovations. The reflection of these processes today is a very complex structured diversity of the current populations, which is presented here through the analysis of several genetic markers. The aim is to provide a comprehensive view of the history of demographic processes in the Sahel and Arabia, by combining genetic, linguistic, subsistence and geographical data obtained from local populations. A study of a large dataset of mtDNA sequences showed that Arabia was a major crossroads in gene flow, and although it was colonized by anatomically modern humans from East Africa, today's differentiation from Africa is greater than the differentiation between local populations in these regions. Even the Sahel was an important biocorridor in the past. Today, we encounter populations of various subsistence strategies (nomadic pastoralists and settled farmers), between which gene flow has been severely restricted. A comparison of uniparently inherited loci in both groups points to different migratory activity in the eastern and western parts of the Sahel. Analyzes of Alu elements, which indicated the inclination of West African herders (Fulbs)...
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