No description available.

Dispersal of aquatic insects is difficult to measure with traditional direct trapping methodologies. However, genetic markers are an ideal surrogate to indirectly infer dispersal and gene flow. For this research, a portion of the cytochrome oxidase I gene was used to evaluate gene flow and dispersal of Epeorus pleuralis located in the northern Appalachian headwater streams of the Allegheny, Genesee, and Susquehanna watersheds. A total of 536 basepairs from 16 individual insects were used for analysis. Thirteen haplotypes were discovered, two of which were shared between the Allegheny and Genesee streams. Although no shared haplotypes were found in the Susquehanna, analysis of molecular variance results suggest that there is not a significant genetic difference between the three populations and attributes the majority of variation to within population differences.

The marsh rice rat (Oryzomys sp.) is a semiaquatic rodent native to wetlands in the southeastern United States. The northwestern-most part of the rice rat’s range extends to Illinois where rice rats are found in wetlands across the southern part of the state. Recent studies have shown that rice rats in the United States can be divided into two species: O. palustris and O. texensis, but the taxonomic status of rice rats in Southern Illinois is unclear. To resolve this, I sequenced cytochrome-b and the control region, two regions of mitochondrial DNA, for 16 rice rats and constructed a phylogeny using these new sequences and previously obtained O. palustris and O. texensis sequences. In contrast to previous morphological assessments, I found that rice rats in Southern Illinois should be classified as O. texensis. This would extend the range of O. texensis north and west from its current extent. Further investigation using nuclear loci will be needed to confirm this classification.

Bio-archaeology is the study of biological remains found at sites of archaeological interest. It is an interdisciplinary science employing different scientific fields including physical anthropology, geography, archaeology and genetics. Genetic analysis includes ancient DNA (aDNA) studies, now a specialised field in genetics. This approach was used to analyse human skeletal material of eight individuals from various Iron Age archaeological sites in southern Africa. Included in this sample is a naturally mummified individual from Tuli, in Botswana. The context of the specimens found in the Limpopo Province (Thulamela), as well as their cultural links with the Zimbabwe Culture Complex (which includes Mapungubwe and Khami) suggests that some gene exchange might have occurred. While this is not the first aDNA study on southern African samples, it is the first aDNA study based on southern African Iron Age human individuals and also included a naturally mummified individual. Morphometric and morphological analyses have indicated the age at death, sex and health status of the individuals, and the context in which they were found has helped in assessing their cultural affinity. Bone samples were analysed in a specialized aDNA laboratory at the Centre for Evolutionary Medicine in Switzerland. Following DNA extraction, ancestry-specific mitochondrial DNA was amplified from all samples and was compared to that of modern sub-Saharan Africans whose data were accessed from GenBank. Some individuals show (maternal) genetic similarities to present-day Sotho/Tswana groups. The male individual from Thulamela aligns somewhat more with the groups from the west and the female with the eastern peoples. Two Early Iron Age individuals from Happy Rest presented some similarities to the Khoesan peoples. Genetic-sex determination efforts were inconclusive for all individuals. The purpose of this study was to place the Thulamela individuals within the context of the genetic diversity in South Africa. It was noted that the introduction of genetic material from the early Sotho/Tswana was gradual in the case of Thulamela. Two other individuals from Happy Rest, who were contemporaries of each other, showed very little genetic variation and it can be said that their maternal DNA was of the same (possibly Khoesan) origin. Further resolution in haplotype assignment will be done in future. These temporally and spatially dispersed individuals can only provide a glimpse into the population interactions of the Iron Age that may have partially shaped the immense genetic diversity of present-day southern Africa. / Dissertation (MSc)--University of Pretoria, 2014. / tm2015 / Anatomy / MSc / Unrestricted

Polychaetes are among the most abundant and diverse groups in the benthic environment; however, the diversity of marine polychaetes remains underexplored. On coral reef ecosystems, scientists predict 80-90% of species are still undescribed due to low sampling efforts in certain regions and the understudied nature of smaller invertebrates, such as polychaetes. Sabellidae, a prominent family of polychaetes, are known for their widespread distribution and are recognized as an ornamental worm due to their feather-like appendages. Here, we detail the diversity of Sabellidae around the understudied Arabian Peninsula. The Arabian Peninsula is surrounded by diverse marine ecosystems (e.g., coral reefs, seagrass beds) occurring in extreme environmental conditions (e.g., higher seawater temperature and strong seasonal variation). Our samples included 178 sabellids from the Saudi Arabian Red Sea, the Arabian Sea, and the Arabian Gulf. Collected from February 2019 to February 2020, these sabellids were sampled from hard and soft substrate on coral reefs and their associated habitats. We used two molecular markers, the cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA alongside an array of morphological analyses, including widely used characters, meristic counts, and morphometric measurements, to identify seven morphotypes. Environmental and biological information was also recorded to understand more about the ecology of these relatively understudied polychaetes. Our combined morphological and genetic analyses acknowledge the presence of six species from the genera Sabellastarte, Bispira, Branchiomma, and Acromegalomma. Our study identified the existence of potential undescribed species in the region and proposed expanded geographic ranges for three accepted species, Sabellastarte sanctijosephi, Branchiomma luctuosum, and Acromegalomma nechamae. The present work increases the current knowledge about the overall systematics of marine polychaetes in the Arabian Peninsula and ultimately contributes to the reassessment of the family’s biogeography.

It has been postulated that the differences in longevity observed between organisms of different sexes within a species can be attributed to differences in oxidative stress. It is generally accepted that differences are due to the higher female estrogen levels. However, in some species males live the same or longer despite their lower estrogen values. Therefore, in the present study, we analyze key parameters of mitochondrial bioenergetics, oxidative stress and apoptosis in the B6 (C57Bl/6J) mouse strain. There are no differences in longevity between males and females in this mouse strain, although estrogen levels are higher in females. We did not find any differences in heart, skeletal muscle and liver mitochondrial oxygen consumption (State 3 and State 4) and ATP content between male and female mice. Moreover, mitochondrial H2O2 generation and oxidative stress levels determined by cytosolic protein carbonyls and concentration of 8-hydroxy-2′-deoxyguanosine in mitochondrial DNA were similar in both sexes. In addition, markers of apoptosis (caspase-3, caspase-9 and mono- and oligonucleosomes: the apoptosis index) were not different between male and female mice. These data show that there are no differences in mitochondrial bioenergetics, oxidative stress and apoptosis due to gender in this mouse strain according with the lack of differences in longevity. These results support the Mitochondrial Free Radical Theory of Aging, and indicate that oxidative stress generation independent of estrogen levels determines aging rate.

Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis briggsae natural isolates and mutation-accumulation (MA) lines of both C. briggsae and Caenorhabditis elegans. Substantial natural variation was discovered for most mitochondrial form and function traits measured for a set of C. briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5δ) that correlates negatively with organismal fitness. Most among-isolate phenotypic variation could be accounted for by phylogeographic clade membership rather than nad5δ level. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. An MA experimental approach revealed that average levels of both ROS and nad5δ heteroplasmy evolved in remarkably linear ways in C. briggsae maintained under extreme inbreeding. In particular, among C. briggsae isolates prone to acquiring the nad5δ deletion, nad5δ level increased to a plateau of ~50% during successive generations of MA treatment. Conversely, mitochondrial ROS level increased or declined in a strain-specific fashion, which also meant that the relationship between ROS and nad5δ was strain-specific. Further, all lines generated from the isolate with the highest starting level of nad5δ heteroplasmy went extinct prior to generation 20 of MA treatment. Patterns of among-line variance in ROS level were also strain-specific but generally did not conform to the canonical pattern of increasing among-line variance expected for MA experiments. MA lines of C. elegans that had previously been subjected to whole-genome sequencing were found to vary significantly in ROS levels but not in 8-oxo-dG content. Despite a significant positive correlation between 8-oxo-dG and ROS levels, no relationship between oxidative stress measures and base substitution rate or G-to-T transversion rate was revealed. Finally, analysis of patterns of phenotypic correlation for a suite of 24 mitochondrial traits measured in C. briggsae natural isolates support a role for ΔΨM in shaping mitochondrial dynamics, but no such role for mitochondrial ROS. Further, our study suggests a novel model of mitochondrial population dynamics dependent upon cellular environmental context and with implications for mitochondrial genome integrity. This work identifies extensive natural variation and capacity for evolution in organellar traits within multicellular eukaryotic species, with a central role for δΨM in mitochondrial dynamics that may have implications for evolutionary adaptation to thermal niches.

京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第18401号 / 情博第516号 / 新制||情||91(附属図書館) / 31259 / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 守屋 和幸, 教授 松田 哲也, 教授 荒井 修亮 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DGAM

No description available.

Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. First, I present a systematic review of the literature that shows cf-mtDNA levels respond to common real-world stressors. The review discusses current knowledge on the mechanisms of cf-mtDNA release, its molecular forms of transport, potential physiological functions, cellular and neuroendocrine triggers, and factors that may contribute to cf-mtDNA removal from the circulation. Second, to evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. I describe the development of MitoQuicLy: Mitochondrial DNA Quantification in cell-free samples by Lysis. I demonstrate high agreement between MitoQuicLy and a commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. I find that cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Finally, I deploy MitoQuicLy in a highly phenotyped cohort of participants with mitochondrial disease and healthy controls to quantify the impact of a brief psychological stressor on cf-mtDNA levels in three biofluids and evaluate how cf-mtDNA release varies between individuals, biofluids, and mitochondrial disease status. These studies set the stage for a research agenda identifying novel links between psychological stress and physiological response, which may improve our understanding of how stressful experiences increase disease risk. In the future, cf-mtDNA release or its downstream effects may be targeted to modulate the impact of psychological stress on human health.