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PubMed2001

Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut.

We have shown that bacterial mutation rates change during the experimental colonization of the mouse gut. A high mutation rate was initially beneficial because it allowed faster adaptation, but this benefit disappeared once adaptation was achieved. Mutator bacteria accumulated mutations that, although neutral in the mouse gut, are often deleterious in secondary environments. Consistently, the competitiveness of mutator bacteria is reduced during transmission to and re-colonization of similar hosts. The short-term advantages and long-term disadvantages of mutator bacteria could account for their frequency in nature.

Adaptation, Physiological↗

PubMed2005

Aging and genome maintenance.

Genomic instability in somatic cells has been implicated as a major stochastic mechanism of aging. Using a transgenic mouse model with chromosomally integrated lacZ mutational target genes, we found mutations to accumulate with age at an organ- and tissue-specific rate. Also the spectrum of age-accumulated mutations was found to differ greatly from organ to organ; while initially similar, mutation spectra of different tissues diverged significantly over the lifetime. To explain how genomic instability, which is inherently stochastic, can be a causal factor in aging, it is proposed that randomly induced mutations may adversely affect normal patterns of gene regulation, resulting in a mosaic of cells at various stages on a trajectory of degeneration, eventually resulting in cell death or neoplastic transformation. To directly address this question we demonstrate that it is now possible to analyze single cells, isolated from old and young tissues, for specific alterations in gene expression.

Aging↗

PubMed1997

A new mtDNA mutation showing accumulation with time and restriction to skeletal muscle.

We have identified a new mutation in mtDNA, involving tRNALeu(CUN) in a patient manifesting an isolated skeletal myopathy. This heteroplasmic A-->G transition at position 12320 affects the T psi C loop at a conserved site and was not found in 120 controls. Analysis of cultured fibroblasts, white blood cells/platelets, and skeletal muscle showed that only skeletal muscle contained the mutation and that only this tissue demonstrated a biochemical defect of respiratory-chain activity. In a series of four muscle-biopsy specimens taken over a 12-year period, there was a gradual increase, from 70% to 90%, in the overall level of mutation, as well as a marked clinical deterioration. Single-fiber PCR confirmed that the proportion of mutant mtDNA was highest in cytochrome c oxidase-negative fibers. This study, which reports a mutation involving tRNALeu(CUN), demonstrates clearly that mtDNA point mutations can accumulate over time and may be restricted in their tissue distribution. Furthermore, clinical deterioration seemed to follow the increase in the level of mutation, although, interestingly, the appearance of fibers deficient in respiratory-chain activity showed a lag period.

Base Sequence↗

PubMed1998

p53 protein expression in non-Hodgkin's lymphomas is infrequently related to p53 gene mutations.

Accumulation of the p53 protein has been found in several types of lymphomas. However, p53 gene mutations have been infrequently demonstrated in some specific types of lymphomas. In the present study, a correlation between p53 immunoreactivity and p53 gene mutations in a large panel of non-Hodgkin's lymphoma (NHL) cases is attempted. A panel of 202 cases of NHL was evaluated by immunohistochemical staining for p53 protein. All cases that were immunohistochemically positive for p53 protein were analyzed by the polymerase chain reaction (PCR) single strand conformation polymorphism (SSCP) method to identify mutations within the p53 gene. In order to confirm the mutation, sequencing of PCR-amplified p53 gene segments was performed. Overexpression of p53 protein was found in 59 of the 202 cases of NHL, but only four of these 59 cases showed a shift on SSCP analysis, and point mutations were detected in three of them by the subsequent sequencing. p53 immunoreactivity was generally greater in high-grade lymphoma. The results of this study suggest that immunohistochemical reactivity for p53 protein is not a reliable indicator of the presence of their structural alterations of p53 gene exons 4-9 in NHL.

Amino Acid Sequence↗

PubMed2005

Hamilton's indicators of the force of selection.

To quantify the force of selection, Hamilton [Hamilton, W. D. (1966) J. Theor. Biol. 12, 12-45] derived expressions for the change in fitness with respect to age-specific mutations. Hamilton's indicators are decreasing functions of age. He concluded that senescence is inevitable: survival and fertility decline with age. I show that alternative parameterizations of mutational effects lead to indicators that can increase with age. I then consider the case of deleterious mutations with age-specific effects. In this case, it is the balance between mutation and selection pressure that determines the equilibrium number of mutations in a population. In this balance, the effects of different parameterizations cancel out, but only to a linear approximation. I show that mutation accumulation has little impact at ages when this linear approximation holds. When mutation accumulation matters, nonlinear effects become important, and the parameterizations of mutational effects make a difference. The results also suggest that mutation accumulation may be relatively unimportant over most of the reproductive lifespan of any species.

Aging↗

PubMed2001

Soluble model for the accumulation of mutations in asexual populations.

Finite asexual populations can accumulate an increasing number of deleterious mutations by a process known as Muller's ratchet, which consists of successive losses of the fittest or least-loaded classes of individuals in the population. We present here a simplified theoretical framework to describe the serial bottleneck passages setup used in experiments to demonstrate the decrease of the population mean fitness due to the operation of ratchet. In particular, we calculate the expected time between consecutive clicks of the ratchet and derive expressions relating the moments of the mean fitness distribution to the mutation and selection parameters.

Models, Genetic↗

PubMed2000

Bladder cancer genotype stability during clinical progression.

Genomic instability is manifested by the accumulation of large numbers of mutations. The rate at which mutations accumulate has been difficult to estimate because serial comparisons are required. For further insight into how quickly mutations accumulate during clinical progression, cell lines sequentially isolated 6 or 11 months apart from two patients with metastatic bladder cancer were compared for loss of heterozygosity (LOH). The genomes were scanned at approximately 200 polymorphic microsatellite loci to increase the resolution and sensitivity for losses. The cell lines from both patients had evidence of genomic instability, with aneuploidy, chromosomal instability, and fractional allelic losses of 0.15 and 0. 48, respectively. However, additional changes were relatively infrequent, with more than 90% identity between the initial and recurrent cell lines. Allelic losses were not randomly scattered, but clustered on specific chromosomes. Therefore, the numbers of loci with further LOH during the clinical progression of some bladder cancers are small relative to the total number of loci with LOH, suggesting that most allelic losses accumulate before clinical presentation.

Alleles↗

PubMed1997

Mutations, tissue accumulations, and serum levels of p53 in patients with occupational cancers from asbestos and silica exposure.

In order to determine the relationship between mutations, tissue accumulations, and serum levels of p53 in occupational cancers, we used denaturing gradient gel electrophoresis and DNA sequencing of exons 5-9 of the p53 gene, immunohistochemical analysis for tissue identification of mutant p53 protein, and enzyme-linked immunosorbent assay for serum levels of mutant p53 protein to examine for such alteration in a cohort of individuals with workplace exposure to asbestos or silica, and resultant lung cancers or mesotheliomas. DNA analysis detected mutations in 5 of 18 (28%) tumors, and tissue accumulations of protein were detected in 7 of 20 (35%) tumors; the agreement between mutational and immunohistochemical analyses was significant (kappa = 0.62, P = 0.002). Serum elevations of protein were detected in 4 of 11 (36%) cases with available serum samples; the agreement between tissue alterations and serum elevations was also significant (kappa = 0.71, P = 0.017). In addition, based on the analysis of banked samples, serum results tended to be consistent over time prior to the diagnosis of disease (positive predictive value = 0.67, negative predictive value = 0.83). These results suggest that serum levels of p53 are reasonably accurate in reflecting tissue alterations in p53 at the gene and/ or protein level and may be early biomarkers of disease risk.

Adult↗

PubMedDate not supplied

[Enzymatic DNA methylation as an aging mechanism].

By analysis of 70 functional parameters of organism it has been shown that the senescence of human organs starts from the age of 20 +/- 10 years and it has more or less a linear character in the most cases. Judging by the averaged aging rate, human maximal lifespan can be equal to about 145 years. An aging model has been proposed according to it the functional involution is caused by cells destructing and is a result of gradual accumulation of special mutations in genome. The evidences has been obtained that enzymatic DNA methylation is a powerful generator for the 5mC-->T+C transition, constantly occurring with each cell division. It has been found that the age-related loss of the most part or all 5mC residues from DNA coincides with both the Hayflick limit in cell lines and the maximal lifespan of different animal species studied. The rate of DNA hypomethylation is proportional to the cell aging rate in vitro and in vivo. The 5mC-->T transitions contribute more than half of all point mutations, accumulated in genome of vertebrates during evolution. These substitutions occur ten times more often in the methylated sites than in other positions of DNA and they disproportional contribute to the general mutagenesis and to the hereditary human diseases. The conclusion has been made that DNA methylation meet the requirements of the main criterions of an aging biomarker and it can be considered as a mechanism for genetically programmed accumulation of mutations with aging. In immortal cell lines this mechanism starts working in the reverse direction, increasing the 5mC content in DNA.

Aging↗

PubMed2003

Increased mitochondrial processing intermediates associated with three tRNA(Leu(UUR)) gene mutations.

Accumulation of RNA 19 has been associated with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes. We analyzed total RNA in muscle specimens from six patients who had one of three pathogenetic point mutations in the mitochondrial tRNA(Leu(UUR)) gene, including A3243G, T3271C, and T3303C. Mitochondrial processing intermediates were identified and quantitated by Northern blotting. The percentage of DNA with the mutation also was determined in each patient. The intermediate (RNA 19) was significantly increased in all patients. The proportion of mutation-carrying RNA in processing intermediates was always higher than in the DNA fraction, suggesting that these mutations may have dominant-negative effects on mitochondrial RNA processing events at the tRNA(Leu(UUR)) gene boundary.

Blotting, Northern↗

PubMed2004

Twinkle and POLG defects enhance age-dependent accumulation of mutations in the control region of mtDNA.

Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes result in progressive accumulation of multiple mtDNA deletions in post- mitotic tissues is still unclear. A recent hypothesis suggested that mtDNA replication infidelity could promote slipped mispairing, thereby stimulating deletion formation. This hypothesis predicts that mtDNA of ad/arPEO patients will contain frequent mutations throughout; in fact, our analysis of muscle from ad/arPEO patients revealed an age-dependent, enhanced accumulation of point mutations in addition to deletions, but specifically in the mtDNA control region. Both deleted and non-deleted mtDNA molecules showed increased point mutation levels, as did mtDNAs of patients with a single mtDNA deletion, suggesting that point mutations do not cause multiple deletions. Deletion breakpoint analysis showed frequent breakpoints around homopolymeric runs, which could be a signature of replication stalling. Therefore, we propose replication stalling as the principal cause of deletion formation.

Adult↗

PubMed2004

Accumulation of mutations and somatic selection in aging neural stem/progenitor cells.

Genomic instability within somatic stem cells may lead to the accumulation of mutations and contribute to cancer or other age-related phenotypes. However, determining the frequency of mutations that differ among individual stem cells is difficult from whole tissue samples because each event is diluted in the total population of both stem cells and differentiated tissue. Here the ability to expand neural stem/progenitor cells clonally permitted measurement of genomic alterations derived from a single initial cell. C57Bl/6 x DBA/2 hybrid mice were used and PCR analysis with strain-specific primers was performed to detect loss of heterozygosity on nine different chromosomes for each neurosphere. The frequency with which changes occurred in neurospheres derived from 2-month- and 2-year-old mice was compared. In 15 neurospheres derived from young animals both parental chromosomes were present for all nine chromosome pairs. In contrast, 16/17 neurospheres from old animals demonstrated loss of heterozygosity (LOH) on one or more chromosomes and seven exhibited a complete deletion of at least one chromosomal region. For chromosomes 9 and 19 there is a significant bias in the allele that is lost where in each case the C57Bl/6 allele is retained in 6/6 neurospheres exhibiting LOH. These data suggest that aging leads to a substantial mutational load within the neural stem cell compartment which can be expected to affect the normal function of these cells. Furthermore, the retention of specific alleles for chromosomes 9 and 19 suggests that a subset of mutational events lead to an allele-specific survival advantage within the neural stem cell compartment.

Alleles↗

PubMed2006

Accumulation of deleterious mutations in small abiotic populations of RNA.

The accumulation of slightly deleterious mutations in populations leads to the buildup of a genetic load and can cause the extinction of populations of small size. Mutation-accumulation experiments have been used to study this process in a wide variety of organisms, yet the exact mutational underpinnings of genetic loads and their fitness consequences remain poorly characterized. Here, we use an abiotic system of RNA populations evolving continuously in vitro to examine the molecular events that can instigate a genetic load. By tracking the fitness decline of ligase ribozyme populations with bottleneck sizes between 100 and 3000 molecules, we detected the appearance and subsequent fixation of both slightly deleterious mutations and advantageous mutations. Smaller populations went extinct in significantly fewer generations than did larger ones, supporting the notion of a mutational meltdown. These data suggest that mutation accumulation was an important evolutionary force in the prebiotic RNA world and that mechanisms such as recombination to ameliorate genetic loads may have been in place early in the history of life.

Base Sequence↗

PubMed1960

The error hypothesis of mutation.

Accumulation of mutants in glucose-limited chemostats is proportional to growth rate, while in tryptophan-limited chemostats it is independent of growth rate. This behavior, which implies the failure of the error hypothesis, may be explainable on the basis of a unitary hypothesis: the results with glucose may be due to reversion or loss of latent mutants.

Genetics↗

PubMed1996

p53 accumulation and mutation are prognostic indicators of poor survival in human gastric carcinoma.

The aim of our study was to examine the prognostic significance of p53 protein accumulation and gene mutation in a series of 116 gastric carcinomas from a low incidence population. Formalin-fixed, paraffin-embedded tumour sections were used to investigate p53 protein accumulation by immunostaining with monoclonal antibody (MAb) DO-7 and p53 gene mutation by single-strand conformation polymorphism analysis of exons 5-8. Nuclear p53 accumulation was detected in 23% of tumours and mutation in 28%. Concordance between the 2 alterations was observed in 73% of cases. p53 protein accumulation was more frequent in tumours with lymph node metastasis, while p53 mutations were more frequent in tumours from older patients. The histopathological parameters of depth of invasion, grade and histological type showed no significant associations with either p53 alteration. In univariate analysis, both alterations were associated with significantly shortened patient survival. The 5-year survival rate for patients with a p53 mutation was 9% compared to 42% for those without a mutation. In multivariate analysis adjusted for the other histopathological parameters, p53 gene mutation but not immunohistochemically-detected p53 protein accumulation was an independent prognostic indicator of poor survival in gastric carcinoma.

Adult↗

PubMed2002

High molecular weight complexes of mutant superoxide dismutase 1: age-dependent and tissue-specific accumulation.

Mutations in the cytosolic enzyme, superoxide dismutase 1, have been identified as the cause of motor neuron disease in a subset of cases of familial amyotrophic lateral sclerosis. It has been postulated that the injurious property of mutant enzyme resides in its propensity to aggregate or its propensity to catalyze deleterious, copper-mediated, chemistries. Aggregates of SOD1 have been identified, histologically, in neurons and astroglia of the spinal cords of SOD1-linked FALS patients and in transgenic mice that express these mutant proteins. In the present study, we have employed a technique used in detecting and quantifying aggregates of mutant huntingtin (cellulose acetate filtration) to examine the molecular characteristics of mutant SOD1 in three previously characterized transgenic mouse models of FALS. We show that the brains and spinal cords of these mice accumulate mutant SOD1 complexes that can be trapped by cellulose acetate filtration. The relative abundance of these structures increases dramatically with age. Although expressed to the same level in nonnervous tissues, mutant SOD1 was not found in high molecular weight structures. We conclude that some aspect of the biology of neural tissues (in a setting of declining motor neuron function) predisposes to the accumulation of high molecular weight complexes of mutant SOD1.

Aging↗

PubMed2000

Identification of ubiquilin, a novel presenilin interactor that increases presenilin protein accumulation.

Mutations in the highly homologous presenilin genes encoding presenilin-1 and presenilin-2 (PS1 and PS2) are linked to early-onset Alzheimer's disease (AD). However, apart from a role in early development, neither the normal function of the presenilins nor the mechanisms by which mutant proteins cause AD are well understood. We describe here the properties of a novel human interactor of the presenilins named ubiquilin. Yeast two-hybrid (Y2H) interaction, glutathione S-transferase pull-down experiments, and colocalization of the proteins expressed in vivo, together with coimmunoprecipitation and cell fractionation studies, provide compelling evidence that ubiquilin interacts with both PS1 and PS2. Ubiquilin is noteworthy since it contains multiple ubiquitin-related domains typically thought to be involved in targeting proteins for degradation. However, we show that ubiquilin promotes presenilin protein accumulation. Pulse-labeling experiments indicate that ubiquilin facilitates increased presenilin synthesis without substantially changing presenilin protein half-life. Immunohistochemistry of human brain tissue with ubiquilin-specific antibodies revealed prominent staining of neurons. Moreover, the anti-ubiquilin antibodies robustly stained neurofibrillary tangles and Lewy bodies in AD and Parkinson's disease affected brains, respectively. Our results indicate that ubiquilin may be an important modulator of presenilin protein accumulation and that ubiquilin protein is associated with neuropathological neurofibrillary tangles and Lewy body inclusions in diseased brain.

Adaptor Proteins, Signal Transducing↗

PubMed2001

Evolution of thermal dependence of growth rate of Escherichia coli populations during 20,000 generations in a constant environment.

Twelve experimental populations of the bacterium Escherichia coli evolved for 20,000 generations in a defined medium at 37 degrees C. We measured their maximum growth rates across a broad range of temperatures and at several evolutionary time points to quantify the extent to which they became thermal specialists with diminished performance at other temperatures. We also sought to determine whether antagonistic pleiotropy (genetic trade-offs) or mutation accumulation (drift decay) was primarily responsible for any thermal specialization. Populations showed consistent improvement in growth rate at moderate temperatures (27-39 degrees C), but tended to have decreased growth rate at both low (20 degrees C) and high (41-42 degrees C) temperatures. Most loss occurred early in the experiment, when adaptation was most rapid. This dynamic is predicted by antagonistic pleiotropy but not by mutation accumulation. Several populations evolved high mutation rates due to defects in their DNA repair, but they did not subsequently undergo a greater decrease in growth rate at thermal extremes than populations that retained low mutation rates, contrary to the acceleration of decay predicted by mutation accumulation. Antagonistic pleiotropy therefore is more likely to be responsible for the evolution of thermal specialization observed in maximum growth rate.

Adaptation, Physiological↗