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PubMed1996

Analysis of liver development, regeneration, and carcinogenesis by genetic marking studies.

The mechanism of generating new hepatocytes and bile ductule cells in the liver has been controversial. Oval cells are found in the periportal region under some circumstances and may represent multipotent stem cells. The role of stem cells in generating new liver cells in normal and pathological conditions is unclear, however. Genetic marking can be used to determine the ability of a particular cell to replicate and to migrate. Cells of known lineage are marked at an initial time point, and their developmental potential determined by the cluster size, position, and phenotype of marked cells at a later time point. Recently, genetic marking studies have demonstrated that the hepatocyte itself is the source of new hepatocytes in the normal postnatal liver and that daughter cells do not migrate. These studies have also demonstrated that the hepatocyte can replicate extensively when stimulated. Finally, genetic marking studies suggest that either hepatocytes or oval cells can develop into a hepatocellular carcinoma or cholangiocarcinoma if a sufficient number of genetic mutations accumulate. The implications of these results for hepatic gene therapy, treatment of liver insufficiency states, and liver cancer are discussed. Future genetic marking studies may help to address some remaining questions in liver biology.

Animals↗
PubMed2007

Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients.

PURPOSE OF REVIEW: Chronic infection with Pseudomonas aeruginosa is a leading cause of morbidity and mortality in individuals with cystic fibrosis despite the aggressive use of antibiotics. P. aeruginosa employs a number of strategies that promote chronic pulmonary colonization instead of acute infection. These include biofilm formation, evasion of the host immune system, and conversion to a mucoid phenotype. This review discusses recent advances regarding P. aeruginosa pathogenesis and biofilm behavior in the setting of chronic pulmonary disease. RECENT FINDINGS: Biofilm formation in the cystic fibrosis lung likely occurs under anaerobic conditions, is controlled by bacterial quorum-sensing mechanisms, and is enhanced by environmental components in the cystic fibrosis airway. P. aeruginosa possesses regulatory pathways that recognize environmental cues to favor either acute infection or chronic colonization. P. aeruginosa that inhabit the respiratory tract accumulate mutations favoring chronic colonization. Azithromycin, a macrolide with clinical benefit in cystic fibrosis, alters P. aeruginosa biofilm formation. Promising new therapies that target biofilm formation include molecules that disrupt quorum sensing. SUMMARY: Eradication of P. aeruginosa in cystic fibrosis patients remains problematic. As more information emerges about P. aeruginosa behavior in vivo, potential therapeutics directed against biofilms and mucoid P. aeruginosa are being developed.

Anti-Bacterial Agents↗
PubMed1997

Genetic variation for total fitness in Drosophila melanogaster.

We measured the heterozygous effects on net fitness of a sample of 12 wild-type third chromosomes in D. melanogaster. Effects on fitness were assessed by competing the wild-type chromosomes against balancer chromosomes, to prevent the production of recombinants. The measurements were carried out in the population cage environment in which the life history had been evolving, in an undisturbed population with overlapping generations, and replicated measurements were made on each chromosome to control for confounding effects such as mutation accumulation. We found significant variation among the wild type chromosomes in their additive genetic effect on net fitness. The system provides an opportunity to obtain an accurate estimate of the distribution of heterozygous effects on net fitness, the contribution of different fitness components including male mating success, and the role of intra-chromosomal epistasis in fitness variation.

Animals↗
PubMed1999

Another set of responses and correlated responses to selection on age at reproduction in Drosophila melanogaster.

Ageing is the decline in survival probability and fertility later in adult life. It can evolve through mutation accumulation and pleiotropy. Artificial selection by age at reproduction is a useful method for detecting the effects of pleiotropy, and for producing lines that differ in their rate of ageing for further analysis. However, the approach has encountered difficulties from gene-environment interaction and inadvertent selection. We have produced a new set of selection lines in Drosophila melanogaster, breeding from either 'young' or 'old' adults, and avoiding some of the difficulties present in previous studies. Breeding from older adults resulted in an evolutionary increase in survival but, contrary to all previous studies using this method, in no increase in late-life fertility. The increase in survival was accompanied by an evolutionary decline in fertility early in adult life, confirming the importance of pleiotropy in the evolution of ageing. Contrary to previous studies, there were no correlated responses to selection in the pre-adult period; development time, larval competitive ability and adult size achieved did not differ between the lines from the two selection regimes.

Aging↗
PubMed1999

Microsatellite evolution: polarity of substitutions within repeats and neutrality of flanking sequences.

Though extensively used in a variety of disciplines, the evolutionary pattern of microsatellite sequences is still unclear. We addressed several questions relating to microsatellite evolution by analysing historically accumulated mutation events in a large set of artiodactyl (CA)n repeats, through sequence analysis of orthologous bovine and ovine loci. The substitution rate in microsatellite flanking sequences was not different from that in intron sequences, suggesting that if intron sequences in general are selectively neutral, sequences close to microsatellites are similarly so. This observation thus does not support the idea that successful heterologous amplification of microsatellites across distantly related taxa would be due to flanking sequences generally being under some form of selection. Interestingly, the substitution rate at the first nucleotide positions flanking repeats was significantly higher than in sequences further away. Moreover, the substitution rate in repeat units in the very end of microsatellites was significantly higher than that in the middle of repeat regions. Together these observations suggest a relative instability close to the boundary between repetitive and unique sequences. We present three models that potentially could explain such a feature, all involving inefficiency of mismatch repair systems.

Animals↗
PubMed2001

RNA replication kinetics, genetic polymorphism and selection in the case of the hepatitis C virus.

We show in a simple theoretical quasispecies model that the replication dynamics of hepatitis C virus and a related model-system, the bovine viral diarrhoea virus, result in an effective reduction of RNA templates in infected cells. Viral fitness does not translate directly into RNA sequence replication efficiency, and hence the abundance of the viral master sequences diminishes over time. Our results suggest that genes not involved in RNA replication accumulate mutations over time because they do not undergo selection during this phase. The selection of viral RNA occurs not only during replication but also during the ensuing stages of the viral life cycle: (i) envelopment of viral RNA and (ii) successful infection of other cells, which also requires functionality of non-replicative genes. In particular, viral fitness requires the ability of the genome to encode structural proteins which do not encounter selective pressure during RNA replication. We conclude by discussing the potential value of antiviral drugs which inhibit selection on parts of the viral genome.

Hepacivirus↗
PubMed2003

No slave to sex.

Fully asexual lineages cannot purge accumulating mutations from their genome through recombination. In ancient asexuals that have persisted without sex for millions of years, this should lead to high allelic divergences (the 'Meselson effect') as has been shown for bdelloid rotifers. Homogenizing mechanisms can counter this effect, resulting in low genetic diversity within and between individuals. Here, we show that the ancient asexual ostracod species Darwinula stevensoni has very low nucleotide sequence divergence in three nuclear regions. Differences in genetic diversity between embryos and adults furthermore indicate that up to half of the observed genetic changes in adults can be caused by somatic mutations. Likelihood permutation tests confirm the presence of gene conversion in the multi-copy internal transcribed spacer sequence, but reject rare or cryptic forms of sex as a general explanation for the low genetic diversity in D. stevensoni. Other special mechanisms (such as highly efficient DNA repair) might have been selected for in this ancient asexual to overcome the mutational load and Muller's ratchet. In this case, our data support these hypotheses on the prevalence of sex, even if the two extant ancient asexual groups (bdelloids and darwinulids) seem to follow opposite evolutionary strategies.

Animals↗
PubMed2003

Divergent evolution during an experimental adaptive radiation.

How repeatable a process is evolution? Comparative studies of multicellular eukaryotes and experimental studies with unicellular prokaryotes document the repeated evolution of adaptive phenotypes during similar adaptive radiations, suggesting that the outcome of adaptive radiation is broadly reproducible. The goal of this study was to test this hypothesis by using phenotypic traits to infer the genetic basis of adaptation to simple carbon-limited environments in an extensive adaptive radiation. We used a clone of the bacterium Pseudomonas fluorescens to found two sets of experimental lines. The first set of lines was allowed to adapt to one of 23 novel environments for 1100 generations while the second set of lines was allowed to accumulate mutations by drift for 2000 generations. All lines were then assayed in the 95 environments provided by Biolog microplates to determine the phenotypic consequences of selection and drift. Replicate selection lines propagated in a common environment evolved similar adaptive components of their phenotype but showed extensive variation in non-adaptive phenotypic traits. This variation in non-adaptive phenotypic traits primarily resulted from the ascendance of different beneficial mutations in different lines. We argue that these results reconcile experimental and comparative approaches to studying adaptation by demonstrating that the convergent phenotypic evolution that occurs during adaptive radiation may be associated with radically different sets of beneficial mutations.

Adaptation, Biological↗
PubMed1999

Sequence analysis of VP1 and VP7 genes suggests occurrence of a reassortant of G2 rotavirus responsible for an epidemic of gastroenteritis.

G2 rotavirus was prevalent in a 1993 epidemic of acute gastroenteritis in Taiwan. In this study, the genetic relationship among G2 rotavirus strains was analysed. The VP7 genes were amplified and sequenced. Except for one strain isolated in 1981, the nucleotide sequences of the VP7 genes of most of the G2 rotaviruses were very similar (identity > 97%) and were closely related to that of a Japanese G2 reference strain, S2. The genetic relatedness of G2 rotaviruses was analysed further by RNA-RNA hybridization. The genomes of the major G2 strains of 1993 did not hybridize well with those of the G2 strains of previous seasons in RNA segments 1, 6 and 7. Partial nucleotide sequences of the VP1 gene were analysed and appeared to be similar among the major G2 strains from the same epidemic (identity > 98%), whereas the identity of the VP1 genes of the major G2 strains of the 1993 epidemic to those of previous seasons was only about 84%. Since the numbers of mutations accumulated in the VP1 and VP7 genes over a period of 10 years were comparable, the significant change in the VP1 genes of the major strains of the 1993 epidemic suggests that these G2 rotaviruses had evolved by genetic reassortment.

Amino Acid Sequence↗
PubMed1982

Secretion of tyrosinase in Streptomyces glaucescens.

In Streptomyces glaucescens, the intracellular and the extracellular enzyme forms of tyrosinase were found to be indentical in molecular weight (29 000), in copper content (0.21%), in the 19 amino acids at the amino-terminal end and in the ratio of cresolase to catecholase activity (0,005). The tyrosinase secretion process exhibited a constant rate of 0.15 units h-1 (mg protein)-1. Under highly induced conditions intracellular tyrosinase was accumulated. Mutations responsible for the non-melanogenic, tyrosinase-positive non-secretor mutant type are located chromosomally on the upper right arc of the S. glaucescens map near the ade-1 marker.

Catechol Oxidase↗
PubMed2001

Siderophore uptake and use by the yeast Saccharomyces cerevisiae.

The non-reductive uptake of several siderophores (ferrioxamine B, ferrichrome, triacetylfusarinine C and ferricrocin) by various strains of Saccharomyces cerevisiae was studied. Several aspects of siderophore transport were examined, including specificity of transport, regulation of transport and intracellular localization of the ferri-siderophores. Ferrioxamine B was taken up preferentially via the products of the SIT1 gene and triacetylfusarinine C by the TAF1 gene product, but the specificity was not absolute. Ferrichrome and ferricrocin uptake was not dependent on a single major facilitator superfamily (MFS) gene product. The apparent specificity of transport was strongly dependent on the genetic background of the cells. Non-reductive uptake of siderophores was induced under more stringent conditions (of iron deprivation) than was the reductive uptake of ferric citrate. Regulation of transport depended on the transcriptional factors Aft1 and Tup1/Ssn6. Cells disrupted for the TUP1 or SSN6 genes were constitutively derepressed for the uptake of ferrichrome, ferricrocin or ferrioxamine B, but not for the uptake of triacetylfusarinine C. Cells bearing the AFT1(up) mutation accumulated large amounts of ferric siderophores. Intracellular decomplexation of the siderophores occurred when transcription of the AFT1(up) gene was repressed. Ferrioxamine B and ferrichrome seemed to accumulate in an endosomal compartment, as shown by biochemical studies and by confocal microscopy study of cells loaded with a fluorescent derivative of ferrichrome. Endocytosis was, however, not involved in the non-reductive uptake of siderophores.

Carrier Proteins↗
PubMed2025

The DREAM complex links somatic mutation, lifespan, and disease.

The DREAM complex has emerged as a central repressor of DNA repair, raising questions as to whether such repression exerts long-term effects on human health. Here we establish that DREAM activity significantly impacts lifetime somatic mutation burden, and that such effects are linked to altered lifespan and age-related disease pathology. First, joint profiling of DREAM activity and somatic mutations across a single-cell atlas of 21 mouse tissues shows that cellular niches with lower DREAM activity have decreased mutation rates. Second, DREAM activity predicts the varied lifespans observed across 92 mammals, with low activity marking longer-lived species. Third, reduced DREAM activity in Alzheimer's patients predicts late disease onset and decreased risk for severe neuropathology. Finally, we show DREAM knockout protects against mutation accumulation in vivo, reducing single-base substitutions by 4.2% and insertion/deletions by 19.6% in brains of mice. These findings position DREAM as a key regulator of aging.

Journal Article↗
PubMed1996

Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair.

Saccharomyces cerevisiae encodes six genes, MSH1-6, which encode proteins related to the bacterial MutS protein. In this study the role of MSH2, MSH3, and MSH6 in mismatch repair has been examined by measuring the rate of accumulating mutations and mutation spectrum in strains containing different combinations of msh2, msh3, and msh6 mutations and by studying the physical interaction between the MSH2 protein and the MSH3 and MSH6 proteins. The results indicate that S. cerevisiae has two pathways of MSH2-dependent mismatch repair: one that recognized single-base mispairs and requires MSH2 and MSH6, and a second that recognizes insertion/deletion mispairs and requires a combination of either MSH2 and MSH6 or MSH2 and MSH3. The redundancy of MSH3 and MSH6 explains the greater prevalence of hmsh2 mutations in HNPCC families and suggests how the role of hmsh3 and hmsh6 mutations in cancer susceptibility could be analyzed.

Adenosine Triphosphatases↗
PubMed2002

Solvable senescence model showing a mortality plateau.

We present some analytic results for the steady states of the Penna model of senescence, generalized to allow genetically identical individuals to die at different ages via an arbitrary survival function. Modeling this with a Fermi function (of modest width) we obtain a clear mortality plateau late in life: something that has so far eluded explanation within such mutation accumulation models. This suggests that factors causing variable mortality within genetically identical subpopulations, which include environmental effects, may be essential to understanding the mortality plateau seen in many real species.

Journal Article↗
PubMed2001

Rapid loss of stress resistance in Drosophila melanogaster under adaptation to laboratory culture.

We investigate changes in resistance to desiccation and starvation during adaptation of Drosophila melanogaster to laboratory culture. We test the hypothesis that resistance to environmental stresses is lost under laboratory adaptation. For both traits, there was a rapid loss of resistance over a three-year period. The rapidity of the response suggested that mutation accumulation could not account for it. Rather, resistance to environmental stresses appeared to be lost as a correlated response to selection on another trait, such as early fertility, with which stress resistance is negatively genetically correlated. These results suggest that caution is needed when extrapolating from evolution of stress resistance in long-established laboratory stocks to patterns of responses and correlated responses in natural populations.

Adaptation, Physiological↗
PubMed2005

Normal and leukaemic stem cells.

The blood-related cancer leukaemias were the first diseases where human cancer stem cells, or leukaemic stem cells (LSC), were isolated. The haematopoietic system is one of the best tissues for investigating cancer stem cells, because the developmental hierarchy of normal blood formation is well defined. Leukaemias can now be viewed as aberrant haematopoietic processes initiated by rare LSC that have maintained or reacquired the capacity for indefinite proliferation through accumulated mutations and/or epigenetic changes. Yet, despite their critical importance, much remains to be learned about the developmental origin of LSC and the mechanisms responsible for their emergence in the course of the disease. This report will review our current knowledge on normal and LSC development and examine the impact of these discoveries may have clinically and in our understanding of the leukaemogenic process.

Acute Disease↗
PubMed2005

Cancer stem cells: lessons from leukaemia.

Increasing evidence suggests that leukaemias are sustained by leukaemic stem cells. Leukaemia can indeed be viewed as aberrant haematopoietic processes initiated by rare leukaemic stem cells that have maintained or re-acquired the capacity for indefinite proliferation through accumulated mutations and/or epigenetic changes. Yet, despite their critical importance, much remains to be learned about the developmental origin of leukaemic stem cells and the molecular pathways underlying the transformation of normal cells into leukaemic stem cells. This report will review our current knowledge on leukaemic stem cells development and finally demonstrate how these discoveries provide a paradigm for identification of cancer stem cells from solid tumours.

Animals↗
PubMed2005

Isolation and characterization of human mammary stem cells.

Since stem cells are present throughout the lifetime of an organism, it is thought that they may accumulate mutations, eventually leading to cancer. In the breast, tumours are predominantly oestrogen and progesterone receptor-positive (ERalpha/PR+). We therefore studied the biology of ERalpha/PR-positive cells and their relationship to stem cells in normal human mammary epithelium. We demonstrated that ERalpha/PR-positive cells co-express the putative stem cell markers p21(CIP1/WAF1), cytokeratin (CK) 19 and Musashi-1 when examined using dual label immunofluorescence on tissue sections. Next, we isolated a Hoechst dye-effluxing 'side population' (SP) from the epithelium using flow cytometry and demonstrated them to be undifferentiated cells by lack of expression of myoepithelial and luminal cell-specific antigens such as CALLA and MUC1. Epithelial SP cells were shown to be enriched for the putative stem cell markers p21(CIP1/WAF1), Musashi-1 and ERalpha/PR-positive cells. Lastly, SP cells, compared to non-SP, were highly enriched for the capacity to produce colonies containing multiple lineages in 3D basement membrane (Matrigel) culture. We conclude that breast stem cells include two populations: a primitive ERalpha/PR-negative stem cell necessary for development and a shorter term ERalpha/PR-positive stem cell necessary for adult tissue homeostasis during menstrual cycling. We speculate these two basic stem cell types may therefore be the cells of origin for ERalpha-positive and -negative breast tumours.

Breast↗