Indonesia, a vast archipelago nation and home to a wide range of cultural, linguistic and genetic diversity, has been a navel of intercultural and interregional interaction between the Asian and the Pacific worlds since prehistoric times. By analyzing the genetic profile of Indonesian people across the archipelago, this dissertation aims to elucidate the colonization history of Indonesia and to assess the effect of social practices on the Indonesian gene pool. Genetic diversity has revealed the complex settlement history of the Indonesian archipelago, starting from the initial colonization of Indonesia ~50 kya, multiple migrations by hunter-gatherers from mainland Asia during the Paleolithic era, followed by a major Neolithic expansion of Austronesian-speaking farmers from a putative homeland of Taiwan, and historic era migrations that involved several foreign invasions via trading and the spread of major religions. The survival of older lineages in western and eastern Indonesia showed that these later expansions into the archipelago did not replace the gene pool of the previous inhabitants. Although most Indonesian communities today practice patrilocality, which is supported by genetic diversity and population structure analyses, matrilineal descent systems are thought to have dominated ancestral Austronesian societies. Preserving a rich Austronesian cultural heritage, such as matrilocal marriage practices, has particularly affected the genetic diversity and population structure of Timor. The dominance of Asian female lineages is apparent on the X chromosome compared to the autosomes, suggesting that female migrants played a leading role during the period of Asian immigration into Timor. Matrilocality may have been a driving force behind this admixture bias during the Austronesian expansion. This finding provides support for an Austronesian `house society' model in which the Austronesian expansion led to the dispersal of matrilocal societies with small numbers of neighboring non-Austronesian males marrying into Austronesian matrilocal, matrilineal houses. This study has revealed that the colonization history of Indonesia does not seem to comprise merely a Melanesian substratum with a single expansion of Austronesian speakers, yet rather involves multiple waves of human migration, coupled with an extensive admixture process.

Intraspecific relationships among the anchialine cave shrimp Typhlatya mitchelli were examined by sequencing a total of 1505 bp from portions of three mitochondrial DNA genes. Cytochrome b, cytochrome oxidase I, and 16S rRNA were partially sequenced and analyzed for specimens from six different cenotes (water-filled caves) across the Yucatan Peninsula, Mexico. The conspecific Typhlatya pearsei that is sympatric with T. mitchelli was also sequenced and used as the outgroup. Comparisons among specimens of T. mitchelli yielded low sequence divergence values (0-1.7%), with the majority being less than 0.4%. Phylogenetic tree topologies reconstructed with neighbor-joining, maximum likelihood, and maximum parsimony were in agreement in regards of the resolution of deep branches. Also, there was no obvious geographic differentiation among the majority of T. mitchelli samples, with the exception of specimens from Cenote San Antonio Chiich (Yokdzonot, Yucatan, Mexico) which all clustered into an extremely well supported monophyletic group. The level of differentiation of this group, together with the nearly total absence of differentiation among T. mitchelli from distant cave systems, suggests that this is an Evolutionary Significant Unit (ESU), which may correspond to a new species. This unidentified Typhlatya from Cenote San Antonio Chiich was helpful in establishing a period in which the epigean ancestor colonized the cenotes. Based on pairwise distance data and previously published shrimp molecular clocks (Baldwin et al., 1998), T. mitchelli and the putative new Typhlatya species last shared a common ancestor between 3-5 million years ago (mya), during the mid-Pliocene era, while T. mitchelli and T. pearsei was approximately 7-10 mya (middle to late Miocene). The ancestor to T. mitchelli and the unidentified Typhlatya species abandoned its shallow coastal water existence in the early Pliocene and eventually expanded its range across the peninsula. Approximately 4 mya, Cenote San Antonio Chiich became isolated from the remaining gene pool thereby halting gene flow. As the regional water table fluctuated in response to the rise and fall of Pleistocene sea levels, T. mitchelli actively colonized the peninsula. The discovery of a single, continuous subterranean freshwater system provides for a better understanding of anchialine biogeography within the Yucatan Peninsula.

Participation of metabolism in stem cell differentiation has been largely disregarded until recently. Here, functional proteomics and metabolomics were performed to unveil the mitochondrial and nuclear metabolism during dimethyl sulfoxide (DMSO)-induced differentiation of P19 cells. DMSO-treated cells were shown to exhibit increased glycolytic enzymes activities and fuel pyruvate into oxidative phosphorylation. Subsequently, enzymes of electron transport chain also had elevated activities upon differentiation. These changes in mitochondrial metabolism were concomitant with increased mitochondrial biogenesis as PGC-1α expression was higher in the differentiated cells. To study nuclear metabolism, particular focus was placed on delineating a potential role of nuclear lactate dehydrogenase (LDH). Nuclear LDH was found to exhibit higher expression in pluripotent cells. NAD+ generated from LDH reaction was discovered to promote histone deacetylation via sirtuin-1 (SIRT1). Drastic alterations in mitochondrial and nuclear metabolism during differentiation point to a pivotal role of metabolism in deciding the final destination of stem cells.

No description available.

No description available.

The blood brain barrier (BBB), formed by endothelial cells lining the lumen of the brain capillaries, is a restrictively permeable interface that only allows transport of specific compounds into the brain. Cardiolipin (CL) is a mitochondrial- specific phospholipid known to be required for the activity and integrity of the respiratory chain. The current study examined the role of cardiolipin in maintaining an optimal mitochondrial function that may be necessary to support the barrier properties of the brain microvessel endothelial cells (BMECs). Endothelial cells have been suggested to obtain most of their energy through an-aerobic glycolysis based on studies of cells that were obtained from the peripheral vasculatures. However, here, we showed that the adult human brain capillary endothelial cell line (hCMEC/D3) appeared to produce ~60% of their basal ATP requirement through mitochondrial oxidative phosphorylation. In addition, RNAi mediated knockdown of the CL biosynthetic enzyme cardiolipin synthase (CLS), although did not grossly affect the mitochondrial coupling efficiency of the hCMEC/D3 cells, did seem to reduce their ability to increase their mitochondrial function under conditions of increased demand. Furthermore, the knockdown appeared to have acted as a metabolic switch causing the hCMEC/D3 cells to become more dependent on glycolysis. These cells also showed increase in [3H]-2-deoxyglucose uptake under a low glucose availability condition, which might have served as a mechanism to compensate for their reduced energy production efficiency. Interestingly, the increase in glucose uptake appeared correlated to an increase in [3H]-2-deoxyglucose glucose transport across the knockdown confluent hCMEC/D3 monolayers grown on Transwell® plates, which was used in our study as an in vitro model for the human BBB. This suggests that changes in the brain endothelial energy status may play a role in regulating glucose transport across the BBB. These observations, perhaps, also explain why the brain capillary endothelial cells were previously observed to possess higher mitochondrial content than those coming from non-BBB regions (Oldendorf et al. 1977).

Age-related neurodegenerative proteinophaties, including polyglutamine (polyQ) diseases such as Huntington’s disease, are a group of disorders in which a single protein or a set of proteins misfold and aggregate resulting in a progressive and selective loss of anatomically or physiologically related neuronal systems. Despite evidence showing a clear relationship between mitochondrial dysfunction, aging and neurodegenerative proteinophaties, the extent of the mitochondrial respiratory chain deficits, the involvement of mitochondrial dysfunction and the mechanisms responsible for these processes are largely unknown. Using yeast models of cellular aging and polyQ disorders we show that mitochondrial dysfunction is an important contributor to the process of aging and age-related neurodegenerative diseases. Preserving mitochondrial function is essential for standard wild-type aging. Enhancement of mitochondrial biogenesis ameliorates polyQ cytotoxicity and is a required component of interventions that retard the aging process.

In eukaryotic cells, energy is produced by the coordinated action of the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). Cytochrome c oxidase (COX) is the fourth enzyme of the MRC. COX catalytic activity is mediated by prosthetic groups located in subunits 1 (Cox1) and 2. More than twenty nuclear encoded factors are required for the assembly of the functional enzyme. Cox1 is the center of a regulatory mechanism in which its protein levels depend on the availability of its assembly partners. A key element in the regulatory pathway is the nuclear encoded factor Mss51, a protein essential for COX1 mRNA translation and Cox1 stability. In this thesis work, we show that Mss51 performs these two functions by dynamically interacting with several protein partners, including COX assembly chaperones and the Hsp70 general chaperone Ssc1. We have also characterized functional domains in Mss51. Specifically, we are reporting the presence of two conserved CPX (Val,Leu) heme-binding motifs, essential for in vivo Mss51 functions. Our data supports a system in which the efficiency of Mss51 as a translational activator is regulated by heme levels perhaps in a redox-sensitive manner. This study contributes to the current knowledge and understanding of the COX assembly process by disclosing new mechanisms involved in its intricate regulation.

Mulloway are a large native inshore marine fish that are currently being evaluated by NSW Fisheries for their potential in aquaculture. The current study developed and applied molecular genetic markers to assess the geographical scale at which future hatcheries should be developed for the species. In addition, it evaluated the impact that current breeding practices in NSW have had on genetic diversity in culture cohorts. The study showed that wild Australian populations of this species constitute a single management unit (genetic stock), but that current hatchery practices employed in NSW are eroding natural genetic diversity. Thus a single hatchery could provide cultures stock to the whole Australian industry without compromising wild populations but that hatchery management practices will need to be modified in the future, to minimise levels of inbreeding.

Studies in a number of human tissues have revealed that the activities of mitochondrial respiratory chain enzyme complexes decline during the aging process. Other studies have suggested that aging increases the frequency of mitochondrial DNA (mtDNA) mutation and leads to the accumulation of mutant mtDNA species, mainly those with large deletions and point mutations. Although the mitochondrial theory of aging may be more applicable to post mitotic tissues, abnormalities of mtDNA have also been reported in tissues which retain a mitotic capacity. Fresh tissues from elderly patients are difficult to obtain and only a limited number of studies on biochemical examination of respiratory chain enzyme complex activities have been carried out. Prostate tissue is readily available in elderly male subjects because of the high prevalence of benign prostatic hypertrophy in this sub-group of the population, and endoscopic surgery is routinely performed for excision of the diseased prostate. In this study, mitochondrial respiratory function and the mtDNA mutations in prostate tissues of elderly patients (aged from 56 to 92) were studied in 24 subjects. This included the measurement of the activities of the respiratory chain enzyme complexes and screening for mitochondrial point mutations and deletions at sites commonly affected in neurodegenerative diseases. (For complete summary open document)