A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography

This dissertation explores the genetic histories of several populations living in the Altai Republic of Russia. It employs an approach combining methods from population genetics and phylogeography to characterize genetic diversity in these populations, and places the results in a molecular anthropological context. Previously, researchers used anthropological, historical, ethnographic and linguistic evidence to categorize the indigenous inhabitants of the Altai into two groups – northern and southern Altaians. Genetic data obtained in this study were therefore used to determine whether these anthropological groupings resulted from historical processes involving different source populations, and if the observed geographical and anthropological separation between northern and southern Altaians also represented a genetic boundary between them. These comparisons were made by examining mitochondrial DNA (mtDNA) coding region single nucleotide polymorphisms (SNPs), control region sequences (including HVS1), and several complete mitochondrial genomes. Variation in the non-recombining portion of the Y-chromosome (NRY) was characterized with biallelic markers and short tandem repeat (STR) haplotypes. Overall, this work provided a high-resolution data set for both unipaternally inherited genetic marker systems. The resulting data were analyzed using both population genetic and phylogeographic methods. Northern Altaians (Chelkan, Kumandin and Tubalar) were distinctive from the southern Altaians (Altai-kizhi) with both genetic systems, yet the Tubalar consistently showed evidence of admixture with southern Altaians, reflecting differences in the origin and population history of northern and southern groups as well as between ethnic northern Altaian populations. These results complement the observation of cultural differences as noted by anthropological/ethnographic research on Altaian populations. These differences likely reinforced and maintained the genetic differences between ethnic groups (i.e., a cultural barrier to genetic exchange). Therefore, biological and cultural lines of evidence suggest separate origins for northern and southern Altaians. Phylogeographic analysis of mtDNA and NRY haplotypes examined the impact of different historical events on genetic diversity in Altaians, including Neolithic expansions, the introduction of Kurgan cultures, the spread of Altaic-speakers, and the intrusion of the Mongol Empire. These insights also allowed for a greater understanding of the peopling of Siberia itself. The cultures of Altaian peoples ultimately helped to shape their current genetic variation

Morphological study and biochemical characterization of the Alveolate flagellate Colpodella sp. (Apicomplexa) in a diprotist culture with Bodo caudatus

Plasmodium falciparum, the causative agent of severe human malaria shares the presence of apical complex organelles with the free-living predatory alveolate, Colpodella sp. In this study we investigated morphological, biochemical and molecular characteristics of Colpodella sp. in a diprotist culture containing Bodo caudatus as prey. Colpodella attaches to its prey using the apical end. Attachment lasted for approximately 20 minutes while the cytoplasmic contents of the prey were aspirated into the posterior food vacuole of Colpodella in a process known as myzocytosis. Indirect immunofluorescence assay (IFA) using P. falciparum rhoptry specific antibodies showed intense reactivity with cytoplasmic vesicles of Colpodella but not Bodo caudatus. DNA isolated from a pellet of the diprotist culture was used in polymerase chain reaction (PCR) with oligonucleotide primers designed to target the P. falciparum (strains 3D7, DD2, FC27 and FCR8) rhoptry genes Rhop-3, Rhop-1 and RAMA. An approximately 2,906 bp single fragment was amplified from P. falciparum (strains 3D7 and FCR8) and diprotist DNA using RAMA primers. Similarly, DNA fragments of a similar size were amplified from the same DNA templates using primers targeting a highly conserved fragment of the18S rRNA used to identify a colpodellid associated with a human infection. Primers targeting conserved regions of the 18S rRNA of kinetoplastid species amplified a DNA fragment of 650 bp in P. falciparum (strains 3D7, DD2, FC27 and FCR8) and diprotist DNA. In addition, the kinetoplastid primers amplified a second fragment of approximately 2 kb from the diprotist DNA. Primers targeting the P. falciparum Rhop-1 gene amplified a 690 bp DNA fragment in all four P. falciparum strains but amplified a fragment of approximately 2 kb from diprotist DNA. Primers for the P. falciparum Rhop-3 gene target amplified a 660 bp DNA fragment in all four P. falciparum strains while DNA fragments of 2 kb, 800 bp and 500 bp were amplified from the diprotist DNA template. DNA sequence analysis of PCR amplified diprotist DNA identified the Rhop-3 gene demonstrating conservation of the Rhop-3 gene in Colpodella sp.https://engagedscholarship.csuohio.edu/u_poster_2017/1012/thumbnail.jp

Morphological study and biochemical characterization of the Alveolate flagellate Colpodella sp. (Apicomplexa) in a diprotist culture with Bodo caudatus

Plasmodium falciparum, the causative agent of severe human malaria shares the presence of apical complex organelles with the free-living predatory alveolate, Colpodella sp. In this study we investigated morphological, biochemical and molecular characteristics of Colpodella sp. in a diprotist culture containing Bodo caudatus as prey. Colpodella attaches to its prey using the apical end. Attachment lasted for approximately 20 minutes while the cytoplasmic contents of the prey were aspirated into the posterior food vacuole of Colpodella in a process known as myzocytosis. Indirect immunofluorescence assay (IFA) using P. falciparum rhoptry specific antibodies showed intense reactivity with cytoplasmic vesicles of Colpodella but not Bodo caudatus. DNA isolated from a pellet of the diprotist culture was used in polymerase chain reaction (PCR) with oligonucleotide primers designed to target the P. falciparum (strains 3D7, DD2, FC27 and FCR8) rhoptry genes Rhop-3, Rhop-1 and RAMA. An approximately 2,906 bp single fragment was amplified from P. falciparum (strains 3D7 and FCR8) and diprotist DNA using RAMA primers. Similarly, DNA fragments of a similar size were amplified from the same DNA templates using primers targeting a highly conserved fragment of the18S rRNA used to identify a colpodellid associated with a human infection. Primers targeting conserved regions of the 18S rRNA of kinetoplastid species amplified a DNA fragment of 650 bp in P. falciparum (strains 3D7, DD2, FC27 and FCR8) and diprotist DNA. In addition, the kinetoplastid primers amplified a second fragment of approximately 2 kb from the diprotist DNA. Primers targeting the P. falciparum Rhop-1 gene amplified a 690 bp DNA fragment in all four P. falciparum strains but amplified a fragment of approximately 2 kb from diprotist DNA. Primers for the P. falciparum Rhop-3 gene target amplified a 660 bp DNA fragment in all four P. falciparum strains while DNA fragments of 2 kb, 800 bp and 500 bp were amplified from the diprotist DNA template. DNA sequence analysis of PCR amplified diprotist DNA identified the Rhop-3 gene demonstrating conservation of the Rhop-3 gene in Colpodella sp.https://engagedscholarship.csuohio.edu/u_poster_2017/1012/thumbnail.jp

Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions

Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation

Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans

In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1vG542A, which has been shown to be shared among Native Americans but is rare in other populations. O1vG542A was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1vG542A is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1vG542A is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1vG542A, which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population. Am J Phys Anthropol 151:649–657, 2013. © 2013 Wiley Periodicals, Inc

Rocky Flats Neutron Detector Testing at Valduc, France

Recent program requirements of the US Department of Energy/NNSA have led to a need for a criticality accident alarm system to be installed at a newly activated facility. The Criticality Safety Group of the Lawrence Livermore National Laboratory (LLNL) was able to recover and store for possible future use approximately 200 neutron criticality detectors and 20 master alarm panels from the former Rocky Flats Plant in Golden, Colorado when the plant was closed. The Criticality Safety Group participated in a facility analysis and evaluation, the engineering design and review process, as well as the refurbishment, testing, and recalibration of the Rocky Flats criticality alarm system equipment to be used in the new facility. In order to demonstrate the functionality and survivability of the neutron detectors to the effects of an actual criticality accident, neutron detector testing was performed at the French CEA Valduc SILENE reactor from October 7 to October 19, 2010. The neutron detectors were exposed to three criticality events or pulses generated by the SILENE reactor. The first excursion was performed with a bare or unshielded reactor, and the second excursion was made with a lead shielded/reflected reactor, and the third excursion with a polyethylene reflected core. These tests of the Rocky Flats neutron detectors were performed as a part of the 2010 Criticality Accident Alarm System Benchmark Measurements at the SILENE Reactor. The principal investigators for this series of experiments were Thomas M. Miller and John C. Wagner of the Oak Ridge National Laboratory, with Nicolas Authier and Nathalie Baclet of CEA Valduc. Several other organizations were also represented, including the Y-12 National Security Complex, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, CEA Saclay, and Babcock International Group

Use of performance-monitoring to improve reliability of emergency diesel generators

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1998.Includes bibliographical references (p. 149-151).Emergency diesel generators are one of the most important contributors to the core damage failure rate of nuclear power plants. Current required testing and maintenance procedures are excessively strict and expensive without any real justification. Probabilistic risk assessment is used to propose a monitoring system and Technical Specification changes to reduce EDG unavailability without jeopardizing safety, and to ease the excessive deterministic requirements. The EDG fault tree is analyzed to identify the critical failure modes of the EDG, the failure of service water pumps, the failure of EDG building ventilation dampers, and the failure of the EDG "supercomponent," which includes the fuel oil, lubricating oil, cooling water, and starting air systems. We use data from the nuclear industry and the U.S. Navy to identify the most significant EDG supercomponent failure modes, including system fluid leakages, instrumentation & controls failures, electrical power output failures, and the fuel system governors. The monitoring system proposed includes instrumentation for twenty-one of the 121 basic events in the fault tree, for a total of 94.9% of EDG failure contributions. The failure modes identified with industry data are monitored, as are diesel engine mechanical failures currently assessed with teardown inspections. With a 50% reduction in these twenty-one basic event failure rates, the EDG system failure rate is reduced by 41.6%, from 0.097 per year to 0.059 per year. With this reduced failure rate, we propose to extend the EDG surveillance interval from one month to twelve months, to lengthen the running tests from one hour to twenty-four hours, and to eliminate the tear-down inspections conducted during refueling outages. To fully assess the benefits of these proposed changes, the monitoring system should be installed on an EDG on a trial basis. The work reported here demonstrates the feasible gains which can be realized, and proposes, a method for evaluating the efficacy of the system as realized through experimentation.by Jeffrey D. Dulik.S.M

Genetic Background and Climatic Droplet Keratopathy Incidence in a Mapuche Population From Argentina

Purpose To determine whether the incidence of and susceptibility to climatic droplet keratopathy (CDK), an acquired, often bilateral degenerative corneal disease, is influenced by the genetic background of the individuals who exhibit the disorder. Methods To determine whether the disease expression was influenced by the genetic ancestry of CDK cases in native Mapuche of the northwest area of Patagonia in Argentina, we examined mitochondrial DNA and Y-chromosome variation in 53 unrelated individuals. Twenty-nine of them were part of the CDK (patient) population, while 24 were part of the control group. The analysis revealed the maternal and paternal lineages that were present in the two study groups. Results This analysis demonstrated that nearly all persons had a Native American mtDNA background, whereas 50% of the CDK group and 37% of the control group had Native American paternal ancestry, respectively. There was no significant difference in the frequencies of mtDNA haplogroups between the CDK patient and control groups. Although the Y-chromosome data revealed differences in specific haplogroup frequencies between these two groups, there was no statistically significant relationship between individual paternal genetic backgrounds and the incidence or stage of disease. Conclusions These results indicate a lack of correlation between genetic ancestry as represented by haploid genetic systems and the incidence of CDK in Mapuche populations. In addition, the mtDNA appears to play less of a role in CDK expression than for other complex diseases linked to bioenergetic processes. However, further analysis of the mtDNA genome sequence and other genes involved in corneal function may reveal the more precise role that mitochondria play in the expression of CDK

Fire Detection in Video Stream by Using Simple Artificial Neural Network

This paper deals with the preliminary research of the fire detection in a video stream. Early fire detection can save lives and properties from huge losses and damages. Therefore the surveillance of the areas is necessary. Early fire discovery with high accuracy, i.e. a low number of false positive or false negative cases, is essential in any environment, especially in places with the high motion of people. The traditional fire detection sensors have some drawbacks: they need separate systems and infrastructure to be implemented, to use sensors in the case of the industrial environment with open fire technologies is often impossible, and others. The fire detection in a video stream is one of the possible and feasible solutions suitable for replacement or supplement of conventional fire detection sensors without a need for installation a huge infrastructure. The paper provides the state of the art in the fire detection. The following part of the paper proposes the new system of feature extraction and describes the feedforward neural network which was used for the training and testing of the proposed idea. The promising results are presented with over 93% accuracy on a selected dataset of movies which consist of more and highly varied instances than published by other researchers involved in the fire detection field. The structure of the neural networks promises higher computational speed than currently implemented deep learning systems