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Co-evolutionary aspects of genetic diversity: milk production and lactase persistence
Priehodová, Edita ; Černý, Viktor (advisor) ; Brůžek, Jaroslav (referee) ; Macholán, Miloš (referee)
Lactase persistence (LP) is genetically determined ability to digest lactose (milk sugar) in adulthood. Lactose is digested by the intestinal enzyme - lactase. In mammals, production of lactase declines after the weaning period. In case of the LP, the lactase is produced during whole life and thus it is possible to drink larger amounts of fresh milk without digestive problems. However, LP is documented only in some human populations. Its worldwide distribution is unequal, the highest rates are found in northern Europe and in pastoralists living in arid regions of Africa and Arabia. The origin of this trait is related to the emergence of agriculture 10,000 years ago, and the beginnings of milk production. In some populations, there is a strong signal of positive selection for the LP caused by various factors depending on various living conditions. The LP is associated with single nucleotide polymorphisms (SNPs) located approximately 14 kb upstream from lactase gene. Nowadays we know five different SNPs which cause the LP and they have probably different origin and have expanded independently. One of the possible centres of the LP origin is the Arabian Peninsula, where the LP variant -13,915*G probably first appeared and spread. In this thesis, occurrences of different LP mutations were investigated...
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Biological characteristics of individuals from the baroque level of St. Benedict cemetery in Prague - an analysis of the demographical crisis
Pinkr, Tomáš ; Brůžek, Jaroslav (advisor) ; Černý, Viktor (referee)
The target of this thesis was to identify mass graves of the burial phase V. in the cemetery around the former St. Benedict Church in Prague and to determine, by means of dental epigenetic traits, if there is a biological relation among selected groups of mass graves and if they belong to one demographic crisis. The analysis of the archaeology-anthropologic documentation was the essential part of this thesis. By this analysis the identification of mass graves and their combination to higher groups according to the following criteria: a locating the mass grave at the cemetery, a position of individual burials in the mass graves, the burial way and artefacts found was possible. The previous research made by the French- Czech team, namely radiocarbon dating of several graves, was also supportive. The actual investigation of the biological relation (similarity) of individuals from mass graves was carried out by means of dental epigenetic traits. These traits were evaluated according to verbal description and plaster casts of teeth (Turner at al. 1991). The following statistical methods were used for the evaluation: a measure of divergence and the mean measure of divergence stating the unlikeness of probability occurrence of corresponding features. The result of this work was the identification of 19 mass graves...
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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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