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G Kopsidas

Publications and source records attributed to G Kopsidas.

11 recordsLinked to original sources
PubMed2000

Preferential amplification is minimised in long-PCR systems.

The advent of long PCR (XL-PCR) has proven to be a major advance in PCR technology and is currently being utilised to investigate numerous biological systems. The analysis of mixed DNA populations is a particularly useful application for XL-PCR. For example, XL-PCR has been used to investigate the occurrence of heterogeneous mitochondrial DNA (mtDNA) rearrangement mutations. With XL-PCR it became possible to amplify the entire length of the mtDNA chromosome and detect any mtDNA deletion or insertion mutations based on a measurable change in overall sequence length. In the present communication, XL-PCR and conventional short-length PCR were used to amplify mitochondrial DNA sequences from several human vastus lateralis skeletal muscle samples. The experiments demonstrated that there was minimal preferential amplification of shorter DNA sequences with XL-PCR and was significantly less than the preferential amplification of shorter sequences observed with conventional PCR. Also, XL-PCR amplification of the complete mtDNA sequence from control DNA containing a single mtDNA template (leucocyte extracts) showed that the generation of PCR artefacts was not a predisposed failing of the system but was dependant on the standard rules that govern the set up and optimisation of any PCR reaction. In optimised systems, XL-PCR artefacts were not generated and a single PCR product was always recovered.

Aging↗
PubMed2000

Tissue mitochondrial DNA changes. A stochastic system.

Several lines of evidence support the view that the bioenergetic function of the mitochondria in postmitotic tissue deteriorates during normal aging. Skeletal muscle is one such tissue that undergoes age-related fiber loss and atrophy and an age-associated rise in the number of cytochrome c oxidase (COX) deficient fibers. With such metabolic pressure placed on skeletal muscle it would be an obvious advantage to supplement the cellular requirement for energy by up-regulating glycolysis, and alternative pathway for energy synthesis. Analysis of rat skeletal muscle utilizing antibodies directed against key enzymes involved in glycolysis has provided evidence of an age-associated increase in the enzymes involved in glycolysis. Fructose-6-phosphate kinase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, and pyruvate kinase protein levels appeared to increase in the soleus, gracilis, and quadriceps muscle from aged rats. The increase in the level of these proteins appeared to correlate to a corresponding decrease in the amount of cytochrome c oxidase protein measured in the same tissue. Together these results are interpreted to represent a general upregulation of glycolysis that occurs in response to the age-associated decrease in mitochondrial energy capacity. Mitochondrial DNA (mtDNA) damage and mutations may accumulate with advancing age until they reach a threshold level were they impinge on the bioenergy capacity of the cell or tissue. Evidence indicates that mtDNA from the skeletal muscle of both aged rats and humans not only undergoes changes at the nucleotide sequence level (mutations and DNA damage), but also undergoes modifications at the tertiary level to generate unique age-related conformational mtDNA species. One particular age-related conformational form was only detected in aged rat tissues with high demands on respiration, specifically in heart, kidney, soleus muscle, and, to a lesser extent, the quadriceps muscle. The age-related form was not detected in gracilis muscle which is predominantly dependent upon glycolysis with regard to its energy requirements. Finally, a comprehensive hypothesis is presented that features the stochastic nature of the mitochondrial system. The basis of the hypothesis is that a dynamic relationship exists between endogenous mutagen production, DNA repair, mtDNA turnover, and nuclear control of mtDNA copy number and that age-associated changes in the dynamics of this relationship lead to a loss of functional full-length mtDNA that eventually leads to bioenergy decline.

Aging↗
PubMed1998

Tissue-specific distribution of multiple mitochondrial DNA rearrangements during human aging.

Mitochondria, according to the free radical theory of aging, are the major source of reactive oxygen species (ROS). The results, presented in this paper, question the role of reactive oxygen species in contributing significantly to the extent of mitochondrial bioenergy degradation of the tissues, which can be correlated with mtDNA rearrangements. We report here that mtDNA rearrangements, including deletions and duplications, in tissues from human aged subjects, occur in levels ranging from very low in liver, to considerable in cardiac muscle, to almost total in skeletal muscle. The extent of mtDNA rearrangements is correlated at both the individual tissue and cell level with cytochrome oxidase (COX) activity as the exemplifier of cellular bioenergy capacity. Thus, the ROS proposal in its simplest form as it affects mtDNA and mitochondrial electron transport system is not supported by the available data.

Aged↗
PubMed1998

An age-associated correlation between cellular bioenergy decline and mtDNA rearrangements in human skeletal muscle.

Post-mitotic tissues such as skeletal muscle develop a tissue bioenergy mosaic during the process of normal aging that eventually culminates into a bioenergetically diverse tissue containing cells ranging in their oxidative phosphorylation capacity from normal to grossly defective. The mosaic is postulated to develop continuously from birth with the relative proportions of cytochrome c oxidase (COX) proficient (positive) and COX deficient (negative) muscle fibers differing dramatically as a function of age. Generally, young individuals only display the rare fiber deficient in COX activity while aged individuals show a significantly higher proportion of negative fibers. There appears to be a random element governing which cells will be affected. Consequently, adjacent cells within a given tissue may exhibit vastly differing COX activities. Multiple mitochondrial DNA (mtDNA) deletions also appear to accumulate in skeletal muscle, similarly displaying a dramatic disparity as a function of age. Our previous findings have indicated that the accumulation of multiple mtDNA deletions, along with a concurrent decrease in wild-type mtDNA, strongly correlates with the age-associated decrease in COX activity observed in skeletal muscle. Although no definitive associations were established at the cellular level, an important prediction arose from this study. Cells that accumulate large numbers of mitochondrial mutations and have reduced levels of full-length mtDNA would be expected to be severely affected and show reduced COX activity as a consequence. Cells that accumulate fewer mutations or retain adequate amounts of wild-type mtDNA would be predicted to be less affected or even retain normal oxidative metabolism. In order to establish a link associating COX activity to the status of mtDNA within individual fibers, we developed single cell extra-long PCR (XL-PCR). The procedure was used to assess the relative concentration of full-length mtDNA with respect to any mtDNA deletions detected in individual human skeletal muscle fibers of 'pre-established' COX activity. Single cell XL-PCR analysis of COX positive fibers dissected from a 5-year old and 90-year old individual showed that 80% or more of the fibers contained full length mtDNA and few, if any, mtDNA rearrangements. COX deficient or COX intermediate fibers taken from the same individuals, by contrast, depicted a heterogeneous population of rearranged mtDNA species with no detectable full-length mtDNA. The data presented here indicates that COX deficient muscle fibers extracted from individuals, regardless of age, were accompanied by extensive mtDNA rearrangements and reduced levels of full-length mtDNA. This provides compelling evidence linking mtDNA mutations to COX activity decline in skeletal muscle and has important implications when considering the molecular basis of the aging process.

Aged↗
PubMed1998

The age-associated decrease in the amount of amplifiable full-length mitochondrial DNA in human skeletal muscle.

There has been a continuous evolution in our concept [1] that mtDNA undergoes a range of mutations with age and that such alterations lead to a decline in mitochondrial bioenergy capacity. Here we report that a wide range of deletion mutations accumulate with age and the amount of full-length mtDNA (FLmtDNA) amplifiable by extra-long PCR (XL-PCR) markedly decreases with age. An analysis of single human quadriceps muscle fibres reveals a close correlation between the decrease in FLmtDNA and the decline in cytochrome c oxidase activity, an exemplifier of mitochondrial bioenergy. However, Southern blotting analysis of unamplified genomic DNA shows that there is little decrease in FLmtDNA in aged quadriceps. The results are interpreted to indicate that while there is little change in the total mtDNA with age, nonetheless a significant proportion of this mtDNA is extensively damaged such that it cannot be amplified by XL-PCR. The amplifiable FLmtDNA, which putatively represents the functional component of the mtDNA, decreases markedly with age.

Adolescent↗
PubMed1997

Deltoid human muscle mtDNA is extensively rearranged in old age subjects.

Extra long PCR analysis of mitochondrial DNA (mtDNA) isolated from skeletal muscle of humans of different ages revealed three phenomena: (i) the amount of normal length mtDNA (16.5 kb) was progressively reduced with age, such that the cells of old age individuals (about 90 years) contained little, or undetectable amounts of normal length mtDNA; (ii) the total amount of mtDNA did not appear to be greatly decreased rather the extent of mtDNA deletions greatly increased; (iii) in old age subjects, considerable amounts of over-sized mtDNA (more than 16.5 kb) was observed. Enzyme histochemical analysis of cytochrome-c oxidase (COX) activity in the muscle tissue of all subjects evidenced a cellular bioenergy mosaic with cells ranging from high to zero detectable enzyme activity in the muscle samples. The frequency of COX deficient muscle fibres was highly dependent on the age of the subject. We have found that the extent of the mtDNA mutational changes strongly correlate with the observed progressive decrease in COX activity. Therefore, it was suggested that the total extent of mtDNA mutation is very large in old age subjects and is sufficient to account for the decline in cellular COX activity with age and for a progressive decrease of overall mitochondrial bioenergetic capacity.

Adult↗
PubMed1996

Frameshift mutagenesis by 9-aminoacridine: antimutagenic effects of adenosine compounds.

It has been shown that frameshift mutagenesis by 9-aminoacridine (9AA) in Salmonella typhimurium is significantly inhibited if glucose is present while cells are being treated in liquid defined medium. We suggested that this effect might be a result of glucose-provoked alterations of cAMP levels within the cell. We therefore sought to investigate the effects of exogenous cAMP on mutagenesis by 9-aminoacridine in both Salmonella typhimurium and Escherichia coli. Contrary to expectation, we found that frameshift mutagenesis was significantly depressed when high concentrations of cAMP were added to the defined medium during liquid treatment with 9AA. Other adenosine 5'-phosphates such as adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP) and adenosine 5'-monophosphate (AMP) added to the liquid medium during 9AA treatment also substantially decreased the reversion rate to prototrophy in both S. typhimurium and E. coli, as did adenosine itself. Further experiments showed that neither influx nor efflux of 9-aminoacridine molecules were greatly affected by adenosine compounds, and that although cAMP and adenosine exerted similar antimutagenic effects on 9AA-treated stationary phase cells, their effects on log phase cells were quite different. The antimutagenic effect of a representative adenosine compound (ATP) was found to persist for some time after stationary phase cells had been washed, with maximal mutability being regained only after about 3 h.

Adenine Nucleotides↗
PubMed1996

Analysis of chimeric UmuC proteins: identification of regions in Salmonella typhimurium UmuC important for mutagenic activity.

Unlike Escherichia coli, the closely related bacterium Salmonella typhimurium is relatively unresponsive to the mutagenic effects of DNA-damaging agents. Previous experiments have suggested that these phenotypic differences might result from reduced activity of the S. typhimurium UmuC protein. To investigate this possibility, we have taken advantage of the high degree of homology between the UmuC proteins of E. coli and S. typhimurium and have constructed a series of plasmid-encoded chimeric proteins. The possibility that the phenotypic differences might be due to differential expression of the respective UmuC proteins was eliminated by constructing chimeric proteins that retained the first 25 N-terminal amino acids of either of the UmuC proteins (and presumably the same translational signals), but substituting the remaining 397 C-terminal amino acids with the corresponding segments from the reciprocal operon. Constructs expressing mostly E. coli UmuC were moderately proficient for mutagenesis whereas those expressing mostly S. typhimurium UmuC exhibited much lower frequencies of mutation, indicating that the activity of the UmuC protein of S. typhimurium is indeed curtailed. The regions responsible for this phenotype were more precisely localized by introducing smaller segments of the S. typhimurium UmuC protein into the UmuC protein of E. coli. While some regions could be interchanged with few or no phenotypic effects, substitution of residues 212-395 and 396-422 of E. coli UmuC with those from S. typhimurium resulted in reduced mutability, while substitution of residues 26-59 caused a dramatic loss of activity. We suggest, therefore, that the primary cause for the poor mutability of S. typhimurium can be attributed to mutations located within residues 26-59 of the S. typhimurium UmuC protein.

Amino Acid Sequence↗
PubMed1994

Mutagenesis by 9-aminoacridine in Salmonella typhimurium: inhibition by glucose and other PTS class A carbon sources.

Reversion of the hisC3076 frameshift marker of Salmonella typhimurium has been measured following treatment of cells in growth and non-growth media with 9-aminoacridine (9AA). By varying the carbon source present in a defined medium, it has been shown that mutagenesis is reduced close to the spontaneous level in the presence of glucose whilst significant reductions are also observed with glucosamine, mannose, mannitol, fructose or glucose 6-phosphate. Intermediate mutant yields are observed when lactic acid or glycerol are present, whereas any one of a further group of carbon sources (gluconate, arabinose, ribose, succinate or casein hydrolysate) permit relatively large numbers of mutants to be recovered. Interestingly, when any one of these "high yield" carbon sources is supplemented with glucose the strong inhibitory effect characteristic of glucose is again observed. On the basis of these results, it can be concluded that inhibition of 9AA-induced reversion by a carbon source is not an exclusive property of glucose, although when more than one carbon source is present the inhibitory effect of glucose predominates. Possible explanations for these findings include the active exclusion of 9AA from cells as a direct consequence of glucose transport across the cell membrane. To address this possibility, cells were pre-grown in verapamil, a calcium channel antagonist which is known to increase the mutagenicity of various 9-anilinoacridine derivatives in S. typhimurium. We found that glucose inhibition of 9AA-induced mutagenesis was not relaxed to any significant extent following treatment with verapamil. In a further experiment, two glucose analogues (2'-deoxyglucose and methyl-D-glucoside) known to be actively transported into the cell but not metabolised past the first phosphorylation step were used. These analogues inhibit the transport into the cell of several types of molecules, but since they do not significantly depress 9AA mutagenesis it seems unlikely that blockage of 9AA transport across the cell membrane can be invoked to explain the inhibitory effect of glucose on 9AA mutagenesis. An alternative explanation based on glucose-mediated repression of an error-prone, mutation-generating, DNA-repair process is presented.

Aminacrine↗
PubMed1993

Glucose inhibition of mutagenesis by 9-aminoacridine in Salmonella typhimurium.

Back mutation to prototrophy of the hisC3076 marker of Salmonella typhimurium has been measured following treatment with 9-aminoacridine (9AA) under conditions in which growth is either permitted or not permitted. Cells treated with 9AA in buffer (i.e. under conditions in which little or no replication was possible) were found to respond well to 9AA-induced mutagenesis. This remained true whether or not the plating medium contained trace amounts of histidine to allow residual replication of His- cells (as for example in the Ames test); yields of His+ mutants were also about the same regardless of whether the plating medium contained glucose or glycerol as the sole carbon source. By contrast, 9AA-induced mutagenesis was essentially abolished when cells were treated in buffer containing 1% glucose (i.e. under conditions which strongly favoured replication). Glucose inhibition of 9AA-induced mutagenesis began to be apparent at glucose concentrations of about 0.02%, whilst total abolition was observed at about 0.2%. In addition, glucose inhibition was found to be dependent on the concentration of 9AA, the induced mutation rate increasing at levels of up to 100-150 micrograms/ml of 9AA and then declining steeply at higher levels. Further kinetic studies indicated that glucose could depress the 9AA-induced mutation rate significantly even in cells exposed to the mutagen for up to 18 min prior to the addition of glucose, whilst inhibition of 9AA mutagenesis by glucose was both temporary and reversible.

Aminacrine↗