Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “clonal evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources
PubMed2000

Genetic diversity of the tet(M) gene in tetracycline-resistant clonal lineages of Streptococcus pneumoniae.

The aim of the present study was to examine the stability and evolution of tet(M)-mediated resistance to tetracyclines among members of different clonal lineages of Streptococcus pneumoniae. Thirty-two tetracycline-resistant isolates representing three national (Spanish serotype 14, Spanish serotype 15, and Polish serotype 23F) and one international (Spanish serotype 23F) multidrug-resistant epidemic clones were all found to be tet(M) positive and tet(O), tet(K), and tet(L) negative. These isolates all carried the integrase gene, int, which is associated with the Tn1545-Tn916 family of conjugative transposons. High-resolution restriction analysis of tet(M) products identified six alleles, tet(M)1 to tet(M)6: tet(M)1 to tet(M)3 and tet(M)5 in isolates of the Spanish serotype 14 clone, tet(M)4 in both the Spanish serotype 15 and 23F clones, and tet(M)6, the most divergent allele, in the Polish 23F clone. This indicates that tet(M) variation can occur at the inter- and intraclone levels in pneumococci. Two alleles of int were identified, with int1 being found in all isolates apart from members of the international Spanish 23F clone, which carried int2. Susceptibility to tetracycline, doxycycline, and minocycline was evaluated for all isolates with or without preincubation in the presence of subinhibitory concentrations of tetracyclines. Resistance to tetracyclines was found to be inducible in isolates of all clones; however, the strongest induction was observed in the Spanish serotype 15 and 23F clones carrying tet(M)4. Tetracycline was found to be the strongest inducer of resistance, and minocycline was found to be the weakest inducer of resistance.

Bacterial Proteins↗
PubMed1991

[Benign (reactive) lymphoproliferation or malignant lymphoma?].

Pre-stages and early stages of malignant Non-Hodgkin's-lymphomas mark the border area between benign, reactive lymphoproliferation and neoplastic transformation. The advances of immunological classification of lymphoid cells with monoclonal antibodies and molecular genetic analysis have contributed to our present knowledge of pathomorphology, pathophysiology and nosology of malignant lymphomas. The stepwise evolution between polyclonal reactive lymphoproliferation and clonal autonomous growth in malignant lymphomas are presented by discussion of the mucosa-associated lymphomas (MALT-lymphomas) and typical lymphoproliferative diseases.

Cell Transformation, Neoplastic↗
PubMed1987

Analyses of phenotype and genotype in acute lymphoblastic leukemias at first presentation and in relapse.

As a clue to the cellular origin of leukemic populations in relapse we analyzed 11 cases of acute lymphoblastic leukemia (ALL) by immunological and molecular genetic approaches. Blast cells obtained from both initial diagnosis and relapse were immunophenotyped using a variety of monoclonal antibodies; simultaneously we hybridized Southern blots of respective cell samples to immunoglobulin (Ig) heavy and light chain as well as to T-cell receptor beta-chain (T beta) sequences. While similar phenotypes were observed in both states of nine cases, comparison of Ig gene rearrangements revealed clonal variations, ie, appearance of an evoluted or novel leukemic cell clone in relapse beside identical leukemic populations in both states. One pre-T (ALL) patient, presenting with germline configuration of T beta gene sequences at diagnosis, exhibited a rearrangement of T beta gene sequences in recurrent disease. Another patient displayed T-ALL phenotype and T beta gene rearrangement at diagnosis but relapsed with a very immature phenotype and germline configuration for T beta sequences. Our results emphasize the value of molecular analyses in order to unravel the nature of leukemic relapse.

Acute Disease↗
PubMed2003

The extent of homologous recombination in members of the genus Flavivirus.

The family Flaviviridae includes important human pathogens, such as dengue (DEN) virus, yellow fever (YF) virus and hepatitis C virus, many of which have emerged or re-emerged in recent years. Until recently, flavivirus evolution was thought to proceed in a clonal manner, with diversity generated mainly through the accumulation of mutational changes. However, this assumption has now been shown to be invalid, with homologous recombination demonstrated in all three genera of the FLAVIVIRIDAE: Since recombination has important implications for the study of virus evolution, a survey of recombination in the viruses of the genus Flavivirus was carried out. Using envelope gene sequence data and a combination of graphical and phylogenetic analyses, hitherto unreported recombination in Japanese encephalitis virus and St Louis encephalitis virus was detected, as well as further recombinants in DEN virus. However, no evidence for recombination was found in West Nile or YF viruses, or in the tick-borne flavivirus group. It is proposed that the difference between the mosquito- and tick-borne viruses can be accounted for by their differing modes of transmission, whilst the variation among the mosquito-borne flaviviruses reflects both the ecology of the particular host and vector species and also bias in the sampling process.

Dengue Virus↗
PubMed2005

The evolutionary origin of genetic instability in cancer development.

The standard model of carcinogenesis is currently being questioned. The main controversy concerns genetic instability and has links to fundamental questions in evolutionary biology. This paper aims to clarify the underlying conflict between the linear configuration of the standard model and the non-linear dynamics of Darwinian evolution. It addresses the problem of applying the concept of clonal selection to genetically unstable cells and presents an alternative perspective based on the principles of molecular evolution. This model explains genetic instability in terms of competition between genetic strategies and draws lines to basic aspects of evolutionary biology.

Animals↗
PubMed1986

Myelodysplastic syndromes: their history, evolution and relation to acute myeloid leukaemia.

The myelodysplastic syndromes (MDS) constitute a heterogeneous group of clonal disorders arising from a multipotent haemopoietic progenitor which share a leukaemic propensity, 30% of cases culminating in acute myeloid leukaemia (AML). Their pathogenesis probably entails multiple steps, phenotypic progression being determined by either expansion or evolution of the abnormal clone. The clonal origin of certain cases of de novo AML is analogous to that of MDS and evidence that they share a common pathogenesis and distinct biological characteristics is beginning to emerge.

Chromosome Aberrations↗
PubMed2005

Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.

Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such "ubiquitous dispersal" has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological "species" will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.

Journal Article↗
PubMed1990

Functional studies of bone marrow haemopoietic and stromal cells in the myelodysplastic syndrome (MDS).

Long-term bone marrow culture (LTBMC) was used to investigate the proliferative behaviour of marrow cells from a spectrum of cases of the myelodysplastic syndrome (MDS), and the results compared with those obtained in the conventional short-term clonal assay. Two broad patterns of growth were revealed in LTBMC. In one group the incidence of haemopoietic progenitor cells steadily declined to abnormally low levels at 4 weeks, while in a second group they were maintained near normal levels for periods of up to 7 weeks. These growth patterns, which were not predictable from clonogenic assays on the marrow cells prior to LTBMC, or from the morphology of the bone marrow, may reflect the stage of evolution of the disease. Further studies of clonality are required to establish whether or not patients exhibiting the second pattern have a potentiality to harbour residual normal haemopoiesis. LTBMC was also used to study the function of MDS marrow stroma in terms of its ability to sustain the growth of normal haemopoietic progenitor cells. Although the phenotype of the cultured adherent cell layer, obtained from some patients, was atypical, no consistent functional defect of MDS stroma could be identified by studying the level of haemopoiesis reached by normal cells seeded into MDS stroma.

Adolescent↗
PubMed2001

Breaking up and getting together: evolution of symbiosis and cloning by fission in sea anemones (Genus Anthopleura).

Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura, a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.

Animals↗
PubMed2003

The non-clonal and transitory nature of HIV in vivo.

From a posteriori analyses of genetic variation, recombination can only be identified when the parental genomes are distinct. For viruses like HIV-1, this requires the producer cell to be infected by more than one virus. Using fluorescence in situ hybridisation, the provirus copy numbers in splenocytes from two HIV-1 patients were determined. More than 75% of infected splenocytes harboured two or more proviruses, range 1-8, with a mean of approximately 3-4 per cell. Sequencing of amplified DNA from single laser micro-dissected cells showed an extraordinary degree of diversity while numerous recombinants were evident. Given the dynamics of HIV-1 turnover in vivo and a recombination rate of approximately 3 cross-overs per cycle, some genomes from a fifteen year old infection may have undergone as many cross-overs as bases in the genome. Thus, recombination profoundly influences HIV evolution and gives it a non-clonal and transitory nature in vivo.

HIV Infections↗
PubMed2003

The in vitro evolution of BCG vaccines.

The bacillus Calmette-Géurin (BCG) family of vaccines currently implemented to prevent tuberculosis (TB) consist of clonal bacterial strains independently shaped by nearly a half-century of evolution. Derived from virulent Mycobacterium bovis, daughter strains of BCG were additionally passaged under the same laboratory conditions that resulted in its original attenuation. Genomic loss of the RD1 region has been demonstrated to coincide with attenuation from virulence, while deletions occurring after the loss of RD1 are speculated to be responsible for BCG's over-attenuation. To provide a more complete description of their total genomic variation, the genomic content of BCG strains are investigated by Affymetrix GeneChip. Because clinical isolates of M. tuberculosis have previously been characterized via GeneChip interrogation, analysis permits the comparison of in vivo versus in vitro evolution of M. tuberculosis complex subspecies. The contrast between the two modes of evolution are discussed in its relevance towards TB pathogenicity.

BCG Vaccine↗
PubMed2005

Instability of clonality in gastric lymphoid infiltrates: a study with emphasis on serial biopsies.

The evolution of low-grade B-cell mucosa-associated lymphoid-tissue (MALT) lymphoma of the stomach is a multistage process, reflected in the histologic continuum from Helicobacter pylori-chronic gastritis, to low-grade and high-grade lymphoma. Interestingly, in daily gastric biopsy sign-out, the authors observed that some biopsies showed monoclonality on polymerase chain reaction (PCR) even though there were no definite histologic features of malignancy and vice versa. To address the question, the authors studied the endoscopic gastric biopsies at first presentation of 46 patients to examine any clonality differences among various histologic patterns within the spectrum of MALT lymphoma evolution. The gastric biopsies were reviewed histologically and graded according to the Wotherspoon-Isaacson histologic scoring system from grade 0 (normal) to grade 5 (MALT lymphoma). The clonality of cases in each grade was determined by performing nested PCR for immunoglobulin heavy chain (IgH) gene rearrangement using FR2/JH and FR3/JH primer sets. The monoclonality rates among different grades were as follows: grade 2, 6.3% (1 of 16); grade 3, 27.3% (3 of 11); grade 4, 83.3% (5 of 6); grade 5, 69.2% (9 of 13). Statistically significant difference of monoclonality rate is demonstrated in histologic grade 4 versus grades 2 and 3, and grade 5 versus grade 2 (P < 0.05, Fisher exact test). The authors went on to examine the progress of disease by following up the clinical status, histologic changes, and clonality fluctuation of these cases. Four of the 8 patients with monoclonality on PCR, but no definite lymphoma at first presentation later progressed to frank MALT lymphoma. Our study shows that, during the progression to MALT lymphoma, there is an instability of clonality. Clonality can fluctuate between polyclonality, oligoclonality, and monoclonality, none of which defines an irreversible stage for progression to MALT lymphoma. Monoclonality is a risk factor for development of MALT lymphoma. Those cases with dense gastric mucosal lymphoid infiltrate (without definite MALT lymphoma) and monoclonality on PCR need to be closely monitored and Helicobacter infection promptly treated if present. In combination with clinicohistologic examination, PCR can serve as a complementary tool in arriving at a definite diagnosis of MALT lymphoma in cases with borderline histologic features.

Adult↗
PubMed2006

Selective acquisition of novel mating type and vegetative incompatibility genes via interspecies gene transfer in the globally invading eukaryote Ophiostoma novo-ulmi.

The Dutch elm disease fungus Ophiostoma novo-ulmi, which has destroyed billions of elm trees worldwide, originally invaded Europe as a series of clonal populations with a single mating type (MAT-2) and a single vegetative incompatibility (vic) type. The populations then rapidly became diverse with the appearance of the MAT-1 type and many vegetative incompatibility types. Here, we have investigated the mechanism using isolates from sites in Portugal at which the rapid evolution of O. novo-ulmi populations from clonality to heterogeneity was well established. We show by genetic mapping of vic and MAT loci with AFLP markers and by sequence analysis of MAT loci that this diversification was due to selective acquisition by O. novo-ulmi of the MAT-1 and vic loci from another species, Ophiostoma ulmi. A global survey showed that interspecies transfer of the MAT-1 locus occurred on many occasions as O. novo-ulmi spread across the world. We discuss the possibility that fixation of the MAT-1 and vic loci occurred in response to spread of deleterious viruses in the originally clonal populations. The process demonstrates the potential of interspecies gene transfer for facilitating rapid adaptation of invasive organisms to a new environment.

Ascomycota↗
PubMed2004

Cutaneous mastocytosis in children: a clinical analysis of 71 cases.

OBJECTIVE: To characterize the clinical features, response to therapy, evolution and prognosis of cutaneous mastocytosis in children. BACKGROUND: Mastocytosis in children, instead of being induced by a potentially oncogenic c-kit mutation, is probably a clonal disease with benign prognosis. METHODS: The clinicopathological features, evolution and response to treatment were analysed in 71 children with mastocytosis. RESULTS: There were 53 (75%) cases of urticaria pigmentosa, 12 (17%) cases of mastocytoma, and six (8%) cases of diffuse cutaneous mastocytosis. In 92% of cases disease onset was in the first year of life. There was a male predominance 1.8 : 1. Treatment did not modify the disease evolution. Eighty per cent of patients improved or had spontaneous resolution of the disease. CONCLUSION: The most frequent clinical form of mastocytosis was urticaria pigmentosa followed by mastocytoma and diffuse cutaneous mastocytosis. Darier's sign was present in 94% of cases. A negative Darier's sign does not rule out mastocytosis. In contrast to adults, mastocytosis in children usually has a benign course making sophisticated or invasive diagnostic tests unnecessary. A classification of paediatric cutaneous mastocytosis is proposed.

Adolescent↗
PubMed2002

A prospective study on the evolution of the T-cell repertoire in patients with Sézary syndrome treated by extracorporeal photopheresis.

Sézary syndrome is a leukemic form of epidermotropic cutaneous T-cell lymphoma related to the malignant proliferation of clonal CD4(+) T cells. Extracorporeal photochemotherapy may induce a transient improvement of the clinical signs, but its efficiency is discussed. To investigate the frequency of the T-cell clone in the peripheral blood of patients with Sézary syndrome and to monitor its evolution in patients treated using extracorporeal photopheresis or chemotherapy, we used the immunoscope technique. In one patient, we observed a decrease of the relative frequency of the clone from 15.6% to 0%, paralleling a complete remission of the clinical disease and a disappearance of the circulating Sézary cells. In the other cases, the evolution of the relative frequency paralleled the initial improvement of the clinical status and the absence of long-term efficiency in patients treated with extracorporeal photopheresis or chemotherapy. We observed a quick-acting direct cytotoxicity of the association 8MOP + UVA on the T-cell clone. The immunoscope technique appears to be an efficient tool to appreciate the amount of tumoral cells and to monitor the evolution of the clonal component in the Sézary syndrome.

Aged↗
PubMed2006

Predominance of clonal reproduction, but recombinant origins of new genotypes in the free-floating aquatic bladderwort Utricularia australis f. tenuicaulis (Lentibulariaceae).

Aquatic plants are a biological group sharing several adaptations to aquatic conditions. The most striking evolutionary convergence in this group is the extensive reliance on clonal reproduction, which largely determines the patterns and process of evolution in aquatic plants. Utricularia australis f. tenuicaulis is a free-floating aquatic bladderwort that reproduces both sexually via seeds and clonally via turions and shoot fragments. Amplified fragment length polymorphism analysis was conducted on 267 ramets collected from 30 populations in Japan. The genotypic diversity within populations was extremely low, regardless of the geographical distribution range: the mean number of genotypes per population (G) was 1.4 and the mean genotypic diversity (D), including monoclonal populations, was 0.17. In contrast to the predominance of a few clones within populations, many of the populations investigated had different genotypes; a large portion of the genetic variation was explained by variation among populations. Character compatibility analysis clearly revealed that somatic mutations did not contribute to the origin of genotypic diversity in this aquatic bladderwort; instead, rare-to-sporadic sexual reproduction probably generated new genotypes. Thus, future studies should examine the role of sexual reproduction in this species from the viewpoint of long-term evolutionary benefits.

Ecosystem↗
PubMed2002

Prokaryotic evolution in light of gene transfer.

Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.

Evolution, Molecular↗
PubMed1999

Red queen dynamics, competition and critical points in a model of RNA virus quasispecies.

RNA viruses offer a unique opportunity for the study of evolution at the molecular level. Recent experiments involving clonal populations of RNA viruses have shown that competition among virus strains of approximately equal relative fitness can result in the eventual competitive exclusion of one of the species. As competition proceeds in time, both the winners and the losers exhibited absolute gains in fitness, consistent with the "Red Queen" hypothesis of evolution. Further experiments involving closely related evolving quasispecies revealed a highly predictable nonlinear behavior suggesting a deterministic component in the underlying quasispecies dynamics. This is apparently in contradiction with the standard view of RNA virus evolution as a highly unpredictable process. In this paper we present a simple model which allows previous hypothesis to be tested and provides an interpretation for the observed experimental results.

Cloning, Molecular↗