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PubMed1997

Insertion site of the locus of enterocyte effacement in enteropathogenic and enterohemorrhagic Escherichia coli differs in relation to the clonal phylogeny of the strains.

The locus of enterocyte effacement pathogenicity island confers the attaching and effacing histopathology on epithelial cells infected with enteropathogenic and enterohemorrhagic Escherichia coli. We investigated the site of insertion of the locus of enterocyte effacement in E. coli strains in relation to their evolution based on conservation of housekeeping proteins in these strains. The results indicate that the insertion site of the locus of enterocyte effacement varies according to the evolutionary lineage, suggesting that it has inserted at multiple times and sites during the evolution of these pathogens.

Bacterial Adhesion↗
PubMed1996

[Polycythemia vera as a multiphasic clonal panmyelopathy: diagnostic profile, chronic pathological progression and effect of therapy on the survival of 74 cases].

PURPOSE: 1. To recognise the clinico-biological profile of a group of patients diagnosed of polycythaemia vera (PV) in our centre in the last 30 years. 2. To identify the evolutive patterns of haematological transformation. 3. To evaluate the effect of therapy on the survival. PATIENTS AND METHODS: The clinical records of 74 patients (median age 62 years, male/female = 0.94, followed-up for 6-357 months, median 64 months) were reviewed. Clinico-biological data at diagnosis, therapy, complications and evolution of the haematological picture were evaluated in each case. The actuarial survival in the series was compared to that of the normal population. RESULTS: The clinico-analytical data and diagnostic features were identical to other series reported. Mild increases of bone marrow reticulin was present in two thirds of the cases, overt myelofibrosis being found in only 10% of the patients. Abnormal karyotype was seen in 9% of the patients (11q-, -Y). Phlebotomy was the only treatment in eight cases, without increased incidence of thrombotic phenomena. The remainders received myelosuppressive therapy (32P, busulphan, pipobroman, hydroxyurea, etc.), thrombotic complications appearing in 8 cases and haemorrhagic complications in 4 others. One of these latter patients developed oesophageal carcinoma. The haematological picture evolved into toxic aplastic anaemia in 2 cases; myelofibrosis with myeloid metaplasia (MF/MM) in 8; myelodysplastic sindromes (MDS) in 5, three of them RAEB; and acute myelogenous leukaemia in 3 cases, two of them as the final stage of previous MF/MM and MDS/ RAEB. The actuarial survival was 71% at ten years and 46% at fifteen years, and the median survival as a whole was 13.5 years. CONCLUSIONS: 1: The treatment, mostly myelosuppressive, given to these patients attained a survival similar to that of the general population. 2: Of the cases with known evolution, 15.6% developed MF/MM, its incidence being higher in patients treated only with phlebotomy (37%). 3: The incidence of malignant evolution, i.e., to RAEB/AML, amongst those patients followed-up was 10.6%.

Adult↗
PubMed2005

A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli: the search for the unit of selection.

Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in Escherichia coli and in Citrobacter rodentium. The locus of enterocyte and effacement in E. coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (i) the complete pathogenic island, (ii) the five operons in which the island is organized, and (iii) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E. coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.

Codon↗
PubMed1990

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.

Base Sequence↗
PubMed2025

SISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection.

SUMMARY: SISTEM is a software package and mathematical framework for simulating tumor evolution and cell migrations at single-cell resolution. Unlike existing frameworks which simulate cancer cell populations under the neutral coalescent or using simple birth-death models, SISTEM simulates tumor populations under somatic clonal selection using an agent-based framework. SISTEM can generate mutation profiles, read counts, and DNA sequencing reads along with ground truth cell lineages and migration graphs under a number of easily customizable mutation and selection models. For improved realism, SISTEM allows for cell fitness to be driven by genomic events of various scales including single nucleotide variants, segmental gains and losses, whole-chromosomal and chromosome-arm aberrations, and whole-genome duplications. SISTEM also includes numerous migration models to simulate metastatic cancers, facilitating the exploration and evaluation of diverse migration patterns. AVAILABILITY AND IMPLEMENTATION: SISTEM is written in Python and is freely available open-source under GNU GPLv3 from: https://github.com/samsonweiner/sistem.

Software↗
PubMed1980

A spontaneous clone of Fanconi anemia fibroblasts with chromosome abnormalities and increased growth potential.

In a diploid fibroblast culture from a patient with Fanconi anemia (FA), we observed the evolution of a chromosomally abnormal clone that had an unusual proliferative advantage and increased growth potential compared with the diploid FA cells. Q-, G-, C-, and Ag-NOR banding analyses revealed that the clonal cells had a chromosomal complement 46,XY, -5, -21, +mar1, +mar2, and were trisomic for a segment of the long arm of chromosome 5 and most of the long arm of No. 21. The retention of chromosome instability in the clonal cells indicates that the alteration in growth characteristics did not result from a mutation to the wild-type allele at the FA locus.

Anemia, Aplastic↗
PubMedDate not supplied

Evolution to malignancy in a recurrent meningioma: morphological and cytogenetic findings.

The original tumor and 4 relapses of a recurrent meningioma were studied. We analyzed and compared these recurrences by histopathology, PCNA labelling index (PCNA-LI), nuclear count, and cytogenetical findings. The most important changes in the evolution to aggressivity were: recurrences at progressively shorter intervals, increases in the PCNA-LI, and micronecrosis; histological changes such as sheeting and increase of the extracellular matrix and a gradual transformation to a clonally complex karyotype.

Cell Transformation, Neoplastic↗
PubMed1996

Change of genetic architecture in response to sex.

A traditional view is that sexual reproduction increases the potential for phenotypic evolution by expanding the range of genetic variation upon which natural selection can act. However, when nonadditive genetic effects and genetic disequilibria underlie a genetic system, genetic slippage (a change in the mean genotypic value contrary to that promoted by selection) in response to sex may occur. Additionally, depending on whether natural selection is predominantly stabilizing or disruptive, recombination may either enhance or reduce the level of expressed genetic variance. Thus, the role of sexual reproduction in the dynamics of phenotypic evolution depends heavily upon the nature of natural selection and the genetic system of the study population. In the present study, on a permanent lake Daphnia pulicaria population, sexual reproduction results in significant genetic slippage and a significant increase in expressed genetic variance for several traits. These observations provide evidence for substantial genetic disequilibria and nonadditive genetic effects underlying the genetic system of the study population. From these results, the fitness function of the previous clonal selection phase is inferred to be directional and/or stabilizing. The data are also used to infer the effects of natural selection on the mean and the genetic variance of the population.

Analysis of Variance↗
PubMed1995

High-resolution genotyping of Campylobacter coli identifies clones of epidemiologic and evolutionary significance.

Campylobacter coli strains from clinical and other sources were examined in terms of O (heat-stabile; HS) serotype and by several molecular typing techniques. Restriction fragment length polymorphism (RFLP) around the three 16S rRNA genes revealed 10 variants, none found in Campylobacter jejuni. RFLP analysis of a polymerase chain reaction amplicon generated from the flagellin gene (flaA) yielded 11 polymorphism groups, some of them linked to HS serotypes. Enlarged flaA genes, contributing three further polymorphisms, were detected in strains isolated from fresh water. Restriction of the genome with SmaI and pulsed-field gel electrophoresis was the most discriminatory typing method, detecting 33 macrorestriction profiles that subtyped within HS serotypes. The coincidence of HS serotype and the three genotypic markers identified clonal lines of evolutionary and epidemiologic significance.

Animals↗
PubMed1997

When will the biology of aging become useful? Future landmarks in biomedical gerontology.

Where should we look to find the causes of and cure for aging? This essay considers a number of scientific discoveries, not yet made, that might dramatically increase the proportion of biogerontologists doing useful work. I will consider, in turn, problems and prospects in the areas of comparative biology, mammalian and invertebrate genetics, biomarker research, caloric restriction, and clonal senescence and then conclude with a discussion of potential links between aging and late life disease.

Aged↗
PubMed1998

T cell receptor repertoire in rheumatoid arthritis.

CD4+ T cells are a major component of the inflammatory infiltrate in rheumatoid synovitis. Within synovial lesions, clonal CD4+ T cell populations are detectable, supporting the notion of an antigen specific recognition even in the joint. In general, the clonal size of individual T cell clones is small and does not lead to a marked distortion of the synovial T cell receptor (TCR) repertoire. Comparison of TCR sequences derived from different patients has not provided evidence for common sequences. Either multiple antigens are recognized or the TCR repertoire is sufficiently plastic with a multitude of different TCR structures responding to the same antigen(s). However, within one individual, the repertoire of clonal T cell populations is restricted. Identical T cell clones can be identified in different joints and at different timepoints of the disease, emphasizing that the spectrum of antigens recognized is conserved over time and that the T cell response pattern is not subject to evolution. Characterization of antigens involved in the latter stages of the disease may thus provide critical information on disease-initiating events. Recent data have led to the new concept that the role of T cells in rheumatoid arthritis (RA) is not limited to synovial inflammation. Evidence has been provided that the premorbid TCR repertoires of RA patients and normal controls can be distinguished. The T cell repertoire in RA patients is prone to recognize certain microbial products and autoantigens. The selection of this response pattern can only partially be attributed to the disease associated HLA-DRB1 alleles. Additional factors common in RA patients but not in HLA-DR matched control individuals seem to be important in shaping the TCR repertoire. Furthermore, the repertoire of mature T cells in RA patients is characterized by oligoclonality which involves T cells in the peripheral blood compartment. Possibly, these clonal T cell populations react to widespread autoantigens, raising the possibility that RA patients have a defect in controlling peripheral tolerance and an anomaly of lymphoproliferation. In contrast to joint residing CD4+ T cells, expanded clonotypes isolated from the blood of different patients have been described to share TCR beta chain structures. How these characteristic features of the global TCR repertoire in RA patients translate into mechanisms of disease remains to be elucidated.

Arthritis, Rheumatoid↗
PubMed2006

Evolution and global dissemination of macrolide-resistant group A streptococci.

Macrolide-resistant group A streptococci (MRGAS) have been recovered from many countries worldwide. However, the strain typing information that is available has been insufficient for estimating the total number of macrolide-resistant clones, their geographic distributions, and their evolutionary relationships. In this study, sequence-based strain typing was used to characterize 212 MRGAS isolates from 34 countries. Evaluation of clonal complexes, emm type, and resistance gene content [erm(A), erm(B), mef(A), and undefined] indicate that macrolide resistance was acquired by GAS organisms via > or independent genetic events. In contrast to other collections of mostly susceptible GAS, genetic diversification of MRGAS clones has occurred primarily by mutation rather than by recombination. Twenty-two MRGAS clonal complexes were recovered from more than one continent; intercontinental strains represent nearly 80% of the MRGAS isolates under study. The findings suggest that horizontal transfer of macrolide resistance genes to numerous genetic backgrounds and global dissemination of resistant clones and their descendants are both major components of the present-day macrolide resistance problem found within this species.

Biological Evolution↗
PubMed2002

Evolution of total and integrated HIV-1 DNA and change in DNA sequences in patients with sustained plasma virus suppression.

Blood samples from patients with plasma HIV-1 RNA <20 copies/ml for more than 2 years were studied. Significant decreases in total and integrated HIV-1 DNA were observed during the first 15 months of suppressive therapy before the concentrations became stable. Clonal analysis of HIV-1 pol demonstrated that the proportions of resistance mutations in DNA sequences after 2 years were lower than those in baseline DNA and RNA sequences. The changes in the clonal composition of HIV-1 env populations in three patients with evidence of changes in HIV-1 pol populations indicated a shift from predominantly R5-like viruses to predominantly X4-like viruses in two patients and the persistence of predominantly X4-like viruses in the third. Our analyses indicate the reemergence of ancestral sequences from long-lived cells or the residual production of wild-type virus from anatomic sites with limited access to antiretroviral drugs and the preferential infection of cells expressing CXCR4.

Amino Acid Sequence↗
PubMed2003

Fluorescence in situ hybridization analysis of aneuploidization patterns in monoclonal gammopathy of undetermined significance versus multiple myeloma and plasma cell leukemia.

BACKGROUND: Monoclonal gammopathy of undetermined significance (MGUS) is a clonal plasma cell (PC) disorder usually characterized by a benign clinical course. However, in approximately 25% of patients, the disorder has been found to evolve into a multiple myeloma (MM). The mechanism leading to the evolution of MGUS remains unknown. The aim of the current study was, first, to assess by interphase fluorescence in situ hybridization (FISH) the incidence of numerical abnormalities of chromosomes 6, 9, 13, and 17 in MGUS patients and to compare it with that found in MM and PC leukemia (PCL) patients and, second, to explore the potential heterogeneity of the pathologic PC in MGUS as a way to identify unique cytogenetic patterns different from those frequently observed in MM and PCL. METHODS: Numerical abnormalities of chromosomes 6, 9, 13, and 17 were investigated by dual- and triple-color FISH in bone marrow PC from 208 patients corresponding to MGUS (n = 30), MM (n = 158), and PCL (n = 20) cases. In MGUS and MM patients with < 10% PC, both normal and phenotypically aberrant PC were discriminated by multiparameter flow cytometry, the latter subset being specifically sorted for FISH analysis with a purity of 93% +/- 6%. RESULTS: Overall, 57% of the MGUS patients displayed abnormalities for at least 1 of the 4 chromosomes analyzed compared with 75% of both MM and PCL cases. The most common single chromosome abnormalities detected in MGUS were gains of chromosomes 9 (23%) and/or 6 (21%) and loss of chromosomes 13 (21%) and/or 17 (17%). Compared with MM patients, MGUS patients were found to have both a lower incidence of gains of chromosome 9 (23% vs. 54%, P = 0.002) and monosomy 13/13q(-) deletions (21% vs. 38%, P = 0.07); with respect to PCL cases, MGUS patients were found to have a lower incidence of monosomy 13/13q(-) deletions (21% vs. 75%, P < 0.001) together with a slightly higher frequency of gains of both chromosomes 6 (21% vs. 0%, P = 0.05) and 9 (23% vs. 7%, P = 0.1). The simultaneous use of two or three different chromosome probes showed that within the purified compartment of phenotypically aberrant PC from most MGUS patients (67%), more than 1 PC clone could be identified. In contrast, the incidence of 2 or more PC clones was much lower in MM (19%, P < 0.001) and PCL (15%, P = 0.003). Interestingly, although some FISH patterns were shared by both groups of diseases (i.e., monosomy 13/13q(-) deletions alone, gains of chromosome 9 alone or together with trisomy 6), others were found almost exclusively in either MGUS (i.e., a clone with monosomy 6 and/or 17 together with nuclei displaying a normal chromosome number) or in MM (i.e., monosomy 13/13q(-) deletions together with gains of chromosome 6 and/or 9). CONCLUSIONS: In summary, the results of the current study showed that MGUS patients displayed a high incidence of numerical alterations, which are usually associated with the presence of more than one tumor cell clone. It is interesting to note that the cytogenetic patterns observed in the aneuploid PC clones from MGUS patients were frequently different from those observed in both MM and PCL.

Adult↗
PubMed1986

Karyotypic evolution in human malignant melanoma.

Chromosome studies were performed on direct preparations, early passage cultures, and cell lines derived from melanocytic lesions of 37 patients. There were six congenital or common acquired nevi, six dysplastic nevi, one early primary melanoma (radial growth phase), three complex melanomas (RGP with foci of vertical growth phase), six advanced primary melanomas (VGP), and 26 metastases. The karyotype was normal in the six common nevi. A chromosomally abnormal clone with a single karyotypic alteration was found in two dysplastic nevi. All melanomas had clones with multiple cytogenetic changes. Nonrandom abnormalities involving translocations or deletions in the short arm of chromosome #1, either arm of chromosome #6, and/or extra copies of the short arm of chromosome #7 were present in all melanomas. These were not obviously associated with a particular stage of disease, except that the only nonrandom alteration in the early (RGP) melanoma involved chromosome #6. In four cases, cytogenetic data were available on both a primary melanoma and its metastases. In each instance there were common alterations (demonstrating the clonality of the disease), as well as additional changes in the metastases. Our findings indicate that demonstrable somatic genetic abnormalities increase in severity with clinical progression of melanocytic disease, but additional data are required to establish the significance of specific karyotypic changes (and the involved genes) in the clinical evolution of these disorders.

Chromosome Aberrations↗
PubMed2004

Statistical analyses of karyotypic complexity in head and neck squamous cell carcinoma.

More than 250 head and neck squamous cell carcinomas (HNSCCs) with clonal chromosomal abnormalities have been reported. Even though the pattern of aberrations is nonrandom, no specific primary or secondary karyotypic abnormalities have been identified. One explanation for the still-rudimentary understanding of the cytogenetic evolution in HNSCC could be the pronounced karyotypic complexity seen in these tumors. In an attempt to overcome this difficulty, we have applied several statistical methods such as hierarchical cluster analysis, multidimensional scaling, and k-means clustering, which allow the identification and interpretation of karyotypic pathways, as well as establishing a temporal order of chromosomal imbalances on 241 published and 70 previously unpublished HNSCC karyotypes. From the analysis of the distribution of the number of imbalances per tumor we suggest that the carcinomas evolve through three phases representing different stages of chromosomal instability. Two major cytogenetic pathways, one dominated by gains and another by losses, were identified by means of principal component analysis. These were initiated by +7 and by any of the aberrations 1p-, 3p-, or 7q-, respectively.

Allelic Imbalance↗
PubMed1999

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification.

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

Journal Article↗
PubMed2005

Recombination hotspots and population structure in Plasmodium falciparum.

Understanding the influences of population structure, selection, and recombination on polymorphism and linkage disequilibrium (LD) is integral to mapping genes contributing to drug resistance or virulence in Plasmodium falciparum. The parasite's short generation time, coupled with a high cross-over rate, can cause rapid LD break-down. However, observations of low genetic variation have led to suggestions of effective clonality: selfing, population admixture, and selection may preserve LD in populations. Indeed, extensive LD surrounding drug-resistant genes has been observed, indicating that recombination and selection play important roles in shaping recent parasite genome evolution. These studies, however, provide only limited information about haplotype variation at local scales. Here we describe the first (to our knowledge) chromosome-wide SNP haplotype and population recombination maps for a global collection of malaria parasites, including the 3D7 isolate, whose genome has been sequenced previously. The parasites are clustered according to continental origin, but alternative groupings were obtained using SNPs at 37 putative transporter genes that are potentially under selection. Geographic isolation and highly variable multiple infection rates are the major factors affecting haplotype structure. Variation in effective recombination rates is high, both among populations and along the chromosome, with recombination hotspots conserved among populations at chromosome ends. This study supports the feasibility of genome-wide association studies in some parasite populations.

Africa↗