An interpopulation study was done on the rodent species Otamys irroratus (Muridae:Otomyinae) using restriction fragment length Polymorphisms to examine the mitochondrial DNA (mtDNA) of 30 vlei rats (Otamys irroratus) from three South African locations and 12 Angoni vlei rats (O.angoniensis) from two locations which were included as an outgroup. The three O.irroratus Populations originated from Karkloof and Kamberg in the Natal midlands and from Rietvlei in the Southern Transvaal. Mitochondrial DNA was extracted and purified by cesium-chloride/ethidium-bromide ultracentrifugation and digested with 19 class 11 restriction endonucleases. The fragments were end-labelled with 32P-dCTP, separated by electrophoresis on horizontal 1% agarose gels and the bands detected by autoradiography. The resultant individual-specific fragment patterns were analysed using the Restsite analysis program (v 1.1; Nei and Miller, 1990) to obtain a measure of the percent sequence divergences between and within the 3 POpulations of O.irroratus as well as between this species and the outgroup. The 19 endonucleases detected 19 distinct O.irroratus mtDNA maternal lineages and 3 O.angoniensis lineages. The O.irroratus lineages were clearly geographical ly structured and most closely reflected the Avise et al. (1987) category I (phylogenetic discontinuity with spatial separation). The only exception was a possible ancestral lineage represented by single individuals from Kamberg and Karkloof. Phylogenetic affinities between the most diverse lineages found at Kamberg and most Karkloof clones appear to be consistent with the finding of Pillay et al. (1993) and Contrafatto et al. (1992b) that Kamberg O.irroratus is an incipient sibling species of Karkloof O.irroratus. The mtDNA data indicates that the O.irroratus Populations at Karkloof and Kamberg last shared a common ancestor approximately 365 000 years ago. By contrast, O.angoniensis showed no evidence of geographic mtDNA structuring and is best described by the Avise et al. (1987) category Ill, which reflects phylogenetic continuity with spatial separation. These classifications must be regarded with caution given the limited distributional range of each species covered by this investigation. The interspecific mtDNA sequence divergence between O.irroratus and O.angoniensis of 11.57% substaniates morphological, karyotypic and allozymic evidence that these two sympatric species are also sibling species and they appear to have last shared a common ancestor between 1.2 and 2.4 million years ago. / Thesis (M.Sc.)-University of Natal, Durban, 1993.

The contribution of yeast strain background, specifically auxotrophic markers, to stability and fidelity of mtDNA replication was investigated. In summary, the ade2, his3delta200, and hap1 mutations have complex effects on mitochondrial functions, the severity of which appears to depend on other components in the genetic background of the strain. These results are important as many commonly used laboratory strains are related to the respiratory hampered S288c strain and are used for studies of orthologous human mutations associated with various mitochondrial diseases. These observations have added to our understanding of fungal mtDNA replication and have informed the mitochondrial community of problematic strains that need to be considered when using this model organism. The function of the yeast mitochondrial DNA polymerase (Mip1p) carboxyl-terminal extension (CTE) was investigated both in vivo and in vitro by genetically engineering various truncations of the CTE. The respiratory competence of mip1delta175 and mip1delta205 cells, in which Mip1p lacks the C-terminal 175 and 205 residues respectively, are indistinguishable from that of wild-type. In contrast, strains harbouring Mip1pdelta351, Mip1pdelta279, Mip1pdelta241, and Mip1pdelta222 rapidly lose mtDNA. At a low frequency, mip1delta216 cells grow poorly on glycerol. Fluorescence microscopy and Southern blot analysis revealed lower levels of mtDNA in these cells, and rapid loss of mtDNA during fermentative growth. Therefore, only the polymerase-proximal segment of the Mip1p CTE is necessary for mitochondrial function. To determine more precisely the defects associated with polymerase truncation variants, these proteins were overexpressed in yeast and used in a novel non-radioactive mtDNA polymerase assay. The threonine-661 and alanine-661 variants, shown by others to be responsible for the increased mtDNA mutability of various laboratory yeast strains at increased temperature, were examined in combination with CTE-truncations. These experiments suggest that exonuclease function is not effected in the alanine-661 variant at 37 degrees Celsius whereas polymerase activity is, and this higher relative level of exonuclease activity could be a contributing factor to mtDNA instability in S288c-related strains. Lastly, isogenic CTE truncation variants all have less DNA polymerase activity than their parental wild-type. Based on these results, several possible roles for the function of the CTE in mtDNA replication are suggested.

In order to identify organizational differences between sterile Polima (pol) and fertile Campestris (cam) mitochondrial genomes that could be linked to cytoplasmic male sterility (CMS), the physical map of the pol mitochondrial genome was constructed and compared to the physical map of the cam mitochondrial genome. The only structural differences between the two genomes are confined to a region encompassed by a 4.5 kb segment, present in pol mtDNA but absent in cam mtDNA. This 4.5 kb CMS-associated pol segment contains a chimeric gene called orf224 that is cotranscribed with atpG and comprises the single mtDNA region expressed differently in fertile, sterile and fertility restored plants which makes it a good candidate for specifying the sterility trait. Sequence analysis of the pol 4.5 kb segment has shown that orf224 was the only significant open reading frame (ORF) within the segment that gives rise to abundant transcripts, strengthening the view that the orf224/atp6 gene region is conferring pol male sterility. The pol 4.5 kb segment is also present and similarly organized in the common Brassica napus nap mtDNA but the sequences flanking the two segments are unrelated. Thus, the 4.5 kb segment appears to have transposed during the evolution of the pol and nap mitochondrial genomes and appears to have been lost in the cam mitochondrial genome. Sequence analysis of the nap segment revealed the presence of an ORF related to but divergent from orf224. This open reading frame (orf222) potentially encodes a protein of 222 amino-acids with 79% homology to the predicted product of orf224. orf222 is co-transcribed with the third exon of the trans-spliced gene, nad5, and another ORF of unknown function. Expression of the orf222 gene region is tightly associated with nap CMS since the levels of orf222 transcripts are significantly reduced upon restoration while the expression of 22 other mitochondrial genes do not consistently correlate with nap CMS. Antibodies were rai

Traumatic brain injury (TBI) is a prominent disease in developed countries, and age is an important factor in functional outcome. Although aged patients typically show diminished recovery compared to young patients, and have higher mortality and morbidity following TBI, the mechanism is not well understood. To date, there is no effective therapeutic for TBI. Previous studies indicate a secondary injury in TBI begins immediately after impact, and is likely the major contribution to delayed neuron dysfunction and loss. Studies also suggest mitochondrial dysfunction and increased free radical species (ROS) production following TBI may play a key role in the process. To evaluate oxidative damage following TBI, especially in aging, young (3 months), middle aged (12 months) and aged (22 months) Fisher-344 rats were subjected to a unilateral controlled cortical impact (CCI) injury, and tissue sparing, 4-hydroxynonenal (HNE) and acrolein levels, and antioxidant enzyme activities, and DNA oxidative damage were measured. In order to evaluate changes in mitochondria following TBI, mitochondrial protein levels were investigated using young adult animals. To evaluate a potential therapeutic for TBI, the effect of creatine on oxidative damage was evaluated. These studies show an age dependent increase of oxidative damage following TBI, demonstrated by increased levels of 4-HNE, acrolein and 8-hydroxyguanine. Middle aged and aged animals showed increased tissue loss compared to young animals 7 days post injury. Mitochondrial proteins involved in the respiratory chain, carrier proteins and channel proteins were significantly decreased 24 h post injury in ipsilateral cortex, but increased in both ipsilateral and contralateral hippocampus. To study potentially protective compounds in TBI, animals were fed with creatine two weeks before TBI and showed less oxidative damage and increased antioxidant capacity, which suggests creatine may be a potential drug for clinical treatment of TBI. The work described in this dissertation is the first to show increased oxidative damage and diminished antioxidant capacity in TBI in aging. The study of mitochondriafollowing TBI using quantitative proteomics is also the first time to show multiple mitochondrial proteins change following TBI. These data are also the first to show creatine can increase antioxidant defenses. These studies contribute to our understanding the mechanisms of secondary injury in TBI in aging.

Mitochondria are dynamic organelles known primarily for their roles in oxidative metabolism and programmed cell death. Both of these processes are regulated by the mitochondrial matrix calcium concentration. Little is known about how mitochondrial calcium is regulated: no plant mitochondrial Ca2+-ATPase pumps or no mitochondrial Ca2+ channels have been identified to date. In addition, little is known concerning any physical interactions between mitochondria and endoplasmic reticulum (ER), an important cellular calcium store, and how these modulate cellular calcium fluxes. In this work stable transgenic Arabidopsis lines expressing fluorescent marker proteins were generated to allow visualisation of mitochondria and the ER in the same cells, and to measure mitochondrial calcium fluxes using aequorin. According to my results, there is a physical association between mitochondria and ER and this association cannot be disrupted by chemical treatments (latrunculin B, methyl viologen and antimycin A). As part of this work I identified an Arabidopsis gene, Mitochondrial Calcium Uptake 1 (MCU1), which encodes a protein with features that suggest a role in mitochondrial calcium dynamics. Fluorescent protein fusions of this protein demonstrated that it localizes to mitochondria. An Arabidopsis T-DNA line was identified with an insertion in MCU1. However, little effect of the insertion on transcript abundance of MCU1 was observed.

Ozone therapy is an alternative form of therapy that has gained attention in the last couple of years. It is believed that O3 may exert a stimulatory effect on the antioxidant defence and immune systems and may therefore be effective in the treatment of ischemic disorders. diabetes mellitus. AIDS and other diseases. On the other hand. it is well known that O3 is a reactive molecule that is toxic to the pulmonary system. Therefore. there remains scepticism regarding its use as a form of therapy. In order to shed some light on this. the effects of ozone autohemotherapy (O3-AHT) on the energy homeostasis of white blood cells were investigated. The possible protective effects of the plasma antioxidant defence system during O3-AHT, were also investigated. Venous blood from six apparently healthy human donors was collected in heparin. In one aliquot a precise volume of blood was mixed with an equal volume of O2/O3 gas mixture containing 20 or 80 μg/ml O3 for 20 minutes. In the other aliquot, the plasma was washed out and the cells resuspended in a buffered phosphate solution. The buffered blood cells were treated with the same concentrations of O3. Control samples was either not treated or treated with a corresponding volume of O2 . Various biochemical analyses were done on the whole blood and buffered cells to determine the oxidant/antioxidant status, cell viability, apoptosis and mitochondrial function. The higher concentration of O3 increased oxidative stress and caused death of white blood cells. Antioxidant enzyme (catalase, glutathione reductase and glutathione peroxidase) activity and the plasma antioxidant capacity decreased, whereas superoxide dismutase levels increased slightly. Exposure to O3 also increased caspase 3/7 activity. A decrease in mitochondrial function was measured by a decrease in ATP levels and an increase in NADH/NAD+ ratio. Complex IV of the respiratory chain was almost completely inhibited by both O3 concentrations. These results indicated that the death of white blood cells was probably through apoptosis. These effects were more evident in the absence of plasma antioxidants. Therefore. high concentrations of O3 were damaging to the cells, but this effect was lessened by antioxidants present in plasma. In view of the results, the use of O3 as a therapy needs to be reconsidered. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2007.

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010

Deficiencies of the oxidative phosphorylation system (OXPHOS) that consists of five enzyme complexes (I-IV) lead to a diversity of cellular consequences. This includes altered Ca2+ homeostasis, reduced ATP production and increased ROS (reactive oxygen species) production. One of the secondary consequences of such deficiencies is the adaptive transcriptional responses of several mitochondrial- and nuclear-encoded genes involved in OXPHOS biogenesis. Additionally, several other genes that are involved in several other functions, such as metallothioneins (MTs), are differentially expressed. In this study we investigated two hypotheses: firstly, that in complex I deficient cells the increased expression of MTs, specifically MT1B and MT2A, has a protective effect against ROS-related consequences of a complex I deficiency. The second hypothesis stated that genes involved in mitochondrial replication and transcription are differentially expressed in OXPHOS deficient cell lines. Firstly, the expression and role of metallothioneins (MTs) in an in vitro complex I deficient model was investigated. The increased expression of different MT isoforms in the presence of the complex I inhibitor rotenone in HeLa cells was confirmed. In this complex I deficient model overexpression of MT1B and especially MT2A isoforms also protected against ROS, mtPTP opening, apoptosis and ROS-induced necrosis. This data supports the hypothesis that increased expression of MT2A has a protective effect against the death-causing cellular consequences of rotenonetreated HeLa cells. Secondly, we investigated the differential expression of selected mitochondrial- and nuclear genes involved in OXPHOS function and regulation. Two experimental in vitro models were developed and utilized in the study. Firstly, a transient siRNA knockdown model of the NDUFS3 subunit of complex I in 143B cells was developed, characterized and introduced. Then the effect of the knockdown on several biochemical parameters (ROS and ATP levels), mtDNA copy number, total mtRNA levels, and RNA levels of several nuclear- and mitochondrial-encoded transcripts encoding structural as well as functional proteins was determined. Additionally, to investigate the effect of stable OXPHOS deficiency, stable shRNA knockdown models of the NDUFS3 subunit of complex I, as well as the Rieske subunit of complex III were introduced and characterized. The second hypothesis about the effect of OXPHOS deficiencies on mtDNA replication and transcription could not, without a doubt, be supported or contradicted by the data. It was determined from the data that an OXPHOS deficiency, which does not result in increased ROS levels, does not significantly affect the regulation of mtDNA replication/transcription or nuclear OXPHOS gene transcription. However, when OXPHOS deficiency was accompanied by increased ROS levels, some structural mitochondrial-encoded transcripts and regulatory nuclear-encoded transcripts were up-regulated, specifically ND6, D-loop, DNApol and TFB2M. Nonetheless, increased ROS production in the presence of OXPHOS deficiency is probably not exclusively responsible for responses of all regulatory proteins involved in mtDNA replication/transcription in vitro. Additionally, this compensatory regulation might be more dependent on mtDNA transcription than mtDNA copy number, and the data showed that TFB2M might be a key regulatory protein involved early in this mechanism before any other regulatory proteins are affected. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010.

The contribution of yeast strain background, specifically auxotrophic markers, to stability and fidelity of mtDNA replication was investigated. In summary, the ade2, his3delta200, and hap1 mutations have complex effects on mitochondrial functions, the severity of which appears to depend on other components in the genetic background of the strain. These results are important as many commonly used laboratory strains are related to the respiratory hampered S288c strain and are used for studies of orthologous human mutations associated with various mitochondrial diseases. These observations have added to our understanding of fungal mtDNA replication and have informed the mitochondrial community of problematic strains that need to be considered when using this model organism. The function of the yeast mitochondrial DNA polymerase (Mip1p) carboxyl-terminal extension (CTE) was investigated both in vivo and in vitro by genetically engineering various truncations of the CTE. The respiratory competence of mip1delta175 and mip1delta205 cells, in which Mip1p lacks the C-terminal 175 and 205 residues respectively, are indistinguishable from that of wild-type. In contrast, strains harbouring Mip1pdelta351, Mip1pdelta279, Mip1pdelta241, and Mip1pdelta222 rapidly lose mtDNA. At a low frequency, mip1delta216 cells grow poorly on glycerol. Fluorescence microscopy and Southern blot analysis revealed lower levels of mtDNA in these cells, and rapid loss of mtDNA during fermentative growth. Therefore, only the polymerase-proximal segment of the Mip1p CTE is necessary for mitochondrial function. To determine more precisely the defects associated with polymerase truncation variants, these proteins were overexpressed in yeast and used in a novel non-radioactive mtDNA polymerase assay. The threonine-661 and alanine-661 variants, shown by others to be responsible for the increased mtDNA mutability of various laboratory yeast strains at increased temperature, were examined in combination with CTE-truncations. These experiments suggest that exonuclease function is not effected in the alanine-661 variant at 37 degrees Celsius whereas polymerase activity is, and this higher relative level of exonuclease activity could be a contributing factor to mtDNA instability in S288c-related strains. Lastly, isogenic CTE truncation variants all have less DNA polymerase activity than their parental wild-type. Based on these results, several possible roles for the function of the CTE in mtDNA replication are suggested.

The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. / Thesis (Ph.D. (Biochemistry))--North-West University, Potchefstroom Campus, 2010