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PubMed1995

Selection of diversity at putative glycosylation sites in the immunodominant merozoite/piroplasm surface antigen of Theileria parasites.

The immunodominant merozoite/piroplasm surface antigen of Theileria parasites has potential as a diagnostic reagent and as a component of a sub-unit vaccine. This molecule is known to be antigenically diverse, and it is important to determine the nature and extent of this heterogeneity. In the present study nucleotide sequences, representing alleles of the gene (Tams1) encoding this molecule in Theileria annulata were compared to each other and to sequences of homologous genes in Theileria sergenti, Theileria buffeli and Theileria parva. This analysis revealed that a region of the polypeptide which contains putative N-linked glycosylation sites is particularly diverse and, in analogy to retroviral systems, may indicate selection of variable glycosylation sites or amino acid epitopes to evade the bovine immune response. This conclusion was also made from the results of a phylogenetic analysis which compared the variable region of the genes with a second region, which appeared to show no bias for diversity or functional constraint. The results indicated that the variable sequence encoding putative glycosylation sites has diverged, both within and between Theileria species, at a much faster rate than the rest of the molecule. Southern blot analysis of T. annulata populations from within a single geographical region detected six possible variant Tams1 alleles. However, a correlation between restriction-fragment-length polymorphism (RFLP) patterns detected by the Tams1-1 gene probe and geographical location could not be made. In addition, although a high prevalence of one particular RFLP was found, this is unlikely to be the result of a clonal population structure, as we present evidence for significant parasite genotypic variability within a single endemic region.

Amino Acid Sequence↗
PubMed1997

Genetic structure of Trypanosoma cruzi in Central America and its comparison with South American strains.

Genetic characterization by isozyme analysis was performed on 68 isolates of Trypanosoma cruzi; 57 from Guatemala in Central America and 11 from South American countries. Ten zymodemes (isozyme patterns) were identified by examining zymograms of 12 enzymes (13 loci). These zymodemes were classified to 3 major distinctive groups: (1) major Guatemalan, (2) minor Guatemalan and (3) unique South American, by the genetic distances and the phylogenetic dendrogram drawn by UPGMA. Based on the results obtained, genetic structures and phylogenetic relations of T. cruzi in Guatemala and South America are discussed. Clonal reproduction seemed to be consistent with the observation of deviation from Hardy-Weinberg equilibrium in several loci.

Animals↗
PubMed2002

Spatial genetic structure and clonal diversity of island populations of lady's slipper (Cypripedium calceolus) from the Biebrza National Park (northeast Poland).

Three populations of the rare and endangered plant species Cypripedium calceolus were included in a study of genetic diversity and spatial genetic structure in the Biebrza National Park, northeast Poland. Analysis of 11 allozyme loci indicate that the populations of this species contained high genetic variability (P = 45.5%, A= 1.73). On the other hand, the genetic differentiation (FST = 0.014, P < 0.05) among C. calceolus populations was very low when compared to other species with similar life history characteristics. The observed high rate of gene flow (Nm = 18) may suggest that the populations studied derived from each other in the recent past. Five polymorphic allozyme markers identified 109 multilocus genotypes in three populations and the majority of them (67%) were population-specific. One of the populations studied, characterized by particularly extensive vegetative reproduction, showed the lowest clonal diversity (G/N = 0.15) and heterozygosity (HO = 0.111) values and the highest FIS(0.380), when compared to other two populations (G/N = 0.26-0.27, HO= 0.166-178, FIS = 0.024-0.055). This may indicate that clonal reproduction has an important influence on the genetic structure of C. calceolus populations. The longevity of genets, the out-crossing breeding system and the presence of recruitment from seeds are factors maintaining genetic diversity in C. calceolus.

Biological Evolution↗
PubMed2001

Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic.

An emerging theme in medical microbiology is that extensive variation exists in gene content among strains of many pathogenic bacterial species. However, this topic has not been investigated on a genome scale with strains recovered from patients with well-defined clinical conditions. Staphylococcus aureus is a major human pathogen and also causes economically important infections in cows and sheep. A DNA microarray representing >90% of the S. aureus genome was used to characterize genomic diversity, evolutionary relationships, and virulence gene distribution among 36 strains of divergent clonal lineages, including methicillin-resistant strains and organisms causing toxic shock syndrome. Genetic variation in S. aureus is very extensive, with approximately 22% of the genome comprised of dispensable genetic material. Eighteen large regions of difference were identified, and 10 of these regions have genes that encode putative virulence factors or proteins mediating antibiotic resistance. We find that lateral gene transfer has played a fundamental role in the evolution of S. aureus. The mec gene has been horizontally transferred into distinct S. aureus chromosomal backgrounds at least five times, demonstrating that methicillin-resistant strains have evolved multiple independent times, rather than from a single ancestral strain. This finding resolves a long-standing controversy in S. aureus research. The epidemic of toxic shock syndrome that occurred in the 1970s was caused by a change in the host environment, rather than rapid geographic dissemination of a new hypervirulent strain. DNA microarray analysis of large samples of clinically characterized strains provides broad insights into evolution, pathogenesis, and disease emergence.

Animals↗
PubMed1999

P15INK4b gene methylation and myelodysplastic syndromes.

Myelodysplastic syndromes (MDS) are clonal disorders, which frequently undergo leukemic transformation. It was recently shown that the promoter of the p15INK4b but not the p16INK4a gene is frequently and selectively hypermethylated in MDS. The p15INK4b gene is a cyclin dependent kinase inhibitor gene, which is actively transcribed after TGFbeta exposure. Methylation of the p15INK4b gene is significantly correlated with blastic bone marrow involvement, and sequential analyses have shown that methylation increases with disease evolution toward AML. These data strongly suggest that p15INK4b gene methylation is a mechanism allowing leukemic cells to escape to inhibitory signals from the bone marrow environment, however the exact role of p15INK4b gene methylation in disruption of the signal mediated by TGFbeta remains to be investigated.

Acute Disease↗
PubMed2004

Developmental success, stability, and plasticity in closely related parthenogenetic and sexual lizards (Heteronotia, Gekkonidae).

The developmental trajectory of an organism is influenced by the interaction between its genes and the environment in which it develops. For example, the phenotypic traits of a hatchling reptile can be influenced by the organism's genotype, by incubation temperature, and by genetically coded norms of reaction for thermally labile traits. The evolution of parthenogenesis provides a unique opportunity to explore such effects: a hybrid origin of this trait in vertebrates modifies important aspects of the genotype (e.g., heterozygosity, polyploidy) and may thus impact not only on the phenotype generally, but also on the ways in which incubation temperature affects expression of the phenotype. The scarcity of vertebrate parthenogenesis has been attributed to developmental disruptions, but previous work has rarely considered reaction norms of embryogenesis in this respect. We used closely related sexual and asexual races of the Australian gecko Heteronotia binoei, which include those with multiple origins of parthenogenesis, to explore the ways in which reproductive modes (sexual, asexual), incubation temperatures (24, 27, and 30 degrees C), and the interaction between these factors affected hatchling phenotypes. The hatchling traits we considered included incubation period, incidence of deformities, hatchling survivorship, body size and shape, scalation (including fluctuating asymmetry), locomotor performance, and growth rate. Developmental success was slightly reduced (higher proportion of abnormal offspring) in parthenogenetic lineages although there was no major difference in hatching success. Incubation temperature affected a suite of traits including incubation period, tail length, body mass relative to egg mass, labial scale counts, running speed, growth rate, and hatchling survival. Our data also reveal an interaction between reproductive modes and thermal regimes, with the phenotypic traits of parthenogenetic lizards less sensitive to incubation temperature than was the case for their sexual relatives. Thus, the evolution of asexual reproduction in this species complex has modified both mean hatchling viability and the norms of reaction linking hatchling phenotypes to incubation temperature. Discussions on the reasons why parthenogenetic organisms are scarce in nature should take into account interactive effects such as these; future work could usefully try to tease apart the roles of parthenogenesis, its hybrid origin (and thus effects on ploidy and heterozygosity, etc.), and clonal selection in generating these divergent embryonic responses.

Analysis of Variance↗
PubMed1994

Development of an immune system.

Minimally, an immune response is an induced cellular and/or humoral defense mechanism specific for the challenging agent. The system is a cognitive one inasmuch as a second stimulus with the same antigen can specifically induce either an enhanced response (memory) or diminished response (tolerance). The cells responsible for the initial antigen-specific recognition in higher vertebrates are clonally restricted T and B lymphocytes. Accessory cells are necessary for the processing and presentation of antigen, and physiologic mediators (cytokines) are essential for proliferation, interaction, and regulation of the system. Although it now appears that the recombination mechanisms essential for the anticipatory immune response occurred late in the deuterostome stream leading to vertebrates, molecules required for cell adhesion and regulation are widely spread in phylogeny. Their emergence must have preceded the divergence between ancestral protostomes and deuterostomes. Genetic mechanisms underlying the generation of diversity in the light and heavy chains of antibodies of mammals may be quite distinct in primitive vertebrates, particularly elasmobranchs, the ancestors of which diverged from those of mammals more than 400 million years ago. Despite this, clonal selection of antigen receptors of lymphocytes is most probably universal within the vertebrates. There is no need to force induced recognition in protostomes (e.g. insects) or lower deuterostomes (e.g. echinoderms) into mammalian models of immunity.

Animals↗
PubMed2002

Distinct contributions of CD4(+) and CD8(+) naive and memory T-cell subsets to overall T-cell-receptor repertoire complexity following transplantation of T-cell-depleted CD34-selected hematopoietic progenitor cells from unrelated donors.

Normalization of restricted T-cell-receptor (TCR) repertoire is critical following T-cell-depleted (TCD) stem cell transplantation. We present a prospective study analyzing respective contributions of naive and memory T-cell subsets within the CD4(+) and CD8(+) compartments to the evolution of overall TCR-repertoire complexity following transplantation of CD34-selected peripheral blood progenitor cells from unrelated donors. During the first year after transplantation, sorted CD4/45RA, CD4/45R0, CD8/45RA, and CD8/45R0 subsets were analyzed at 3-month intervals for TCR-repertoire complexity by CDR3 size spectratyping. Skew in TCR-repertoire was observed only in early memory-type T cells. CD4(+) and CD8(+) subsets differed in clonal distribution of CDR3 sizes, with rapid Gaussian normalization of bands in CD4/45R0(+) T cells. Naive T cells displayed normal repertoire complexity and contributed significantly to skew correction. Our data provide direct evidence for an important role of de novo maturation of naive T cells in normalization of an initially restricted TCR-repertoire following transplantation of CD34-selected, TCD-depleted peripheral blood progenitors from unrelated donors.

Antigens, CD34↗
PubMed2004

Estimating the number of hematopoietic or lymphoid stem cells giving rise to clonal chromosome aberrations in blood T lymphocytes.

Quantifying the proliferative capacity of long-term hematopoietic stem cells in humans is important for bone marrow transplantation and gene therapy. Obtaining appropriate data is difficult, however, because the experimental tools are limited. We hypothesized that tracking clonal descendants originating from hematopoietic stem cells would be possible if we used clonal chromosome aberrations as unique tags of individual hematopoietic stem cells in vivo. Using FISH, we screened 500 blood T lymphocytes from each of 513 atomic bomb survivors and detected 96 clones composed of at least three cells with identical aberrations. The number of clones was inversely related to their population size, which we interpreted to mean that the progenitor cells were heterogeneous in the number of progeny that they could produce. The absolute number of progenitor cells contributing to the formation of the observed clones was estimated as about two in an unexposed individual. Further, scrutiny of ten clones revealed that lymphocyte clones could originate roughly equally from hematopoietic stem cells or from mature T lymphocytes, thereby suggesting that the estimated two progenitor cells are shared as one hematopoietic stem cell and one mature T cell. Our model predicts that one out of ten people bears a non- aberrant clone comprising >10% of the total lymphocytes, which indicates that clonal expansions are common and probably are not health-threatening.

Adolescent↗
PubMed1980

Dysmyelopoietic syndrome: sequential clinical and cytogenetic studies.

Clinical and cytogenetic studies were done on 8 patients with dysmyelopoietic syndrome: 6 of these patients had refractory anemia with an excess of blasts (RAEB), and 2 patients had chronic myelomonocytic leukemia (CMML) according to the French-American-British classification. The ages of these 8 patients (3 female and 5 male) ranged from 45 to 70 yr (median, 61.5 yr). Seven of the 8 patients died 3-86 mo (median, 11 mo) after the onset of symptoms of hemorrhage or infections. Cytogenetic studies of bone marrow cells with the Q-banding technique showed clonal karyotypic abnormalities in 7 of the 8 patients (87.5%). Five of the 7 chromosomally abnormal patients had very complex karyotypes; all 7 patients, however, had at least 1 of 4 specific changes: -5 (or 5Q-), -7, +8, and +21. Three of the 7 patients with abnormal karyotypes had had some exposure to potential mutagenic/carcinogenic agents. Five of the 7 patients had serial cytogenetic analyses, 4 of which showed evolution of the karyotype to further complexity; in 2 cases, this coincided with the evolution of the disease into acute leukemia. The median survival time of patients whose initial cytogenetic samples showed both normal and abnormal metaphases was more than twice that of patients who had only abnormal metaphases initially (12 mo versus 4.5 mo).

Aged↗
PubMed2004

Contrasting genetic structure of adults and progeny in a Louisiana iris hybrid population.

Studies of natural hybridization have suggested that it may be a creative stimulus for adaptive evolution and speciation. An important step in this process is the establishment of fit recombinant genotypes that are buffered from subsequent recombination with unlike genotypes. We used molecular markers and a two-generation sampling strategy to infer the extent of recombination in a Louisiana iris hybrid zone consisting predominantly of Iris fulva-type floral phenotypes. Genotypic diversity was fairly high, indicating that sexual reproduction is frequent relative to clonal reproduction. However, we observed strong spatial genetic structure even after controlling for clonality, which implies a low level of pollen and seed dispersal. We therefore used cluster analysis to explore the hypothesis that the fulva-type hybrids are an admixture of groups between which there has been limited recombination. Our results indicate that several such groups are present in the population and are strongly localized spatially. This spatial pattern is not attributable strictly to a lack of mating opportunities between dissimilar genotypes for two reasons: (1) relatedness of flowering pairs was uncorrelated with the degree of overlap in flowering, and (2) paternity analysis shows that pollen movement among the outcross fraction occurred over large distances, with roughly half of all paternity attributed to pollen flow from outside the population. We also found evidence of strong inbreeding depression, indicated by contrasting estimates of the rate of self-fertilization and the average inbreeding coefficient of fulva-type hybrids. We conclude that groups of similar hybrid genotypes can be buffered from recombination at small spatial scales relative to pollen flow, and selection against certain recombinant genotypes may be as important as or more important than clonal reproduction and inbreeding.

Cluster Analysis↗
PubMed2004

Vancomycin susceptibility within methicillin-resistant Staphylococcus aureus lineages.

Methicillin-resistant Staphylococcus aureus (MRSA) with reduced vancomycin susceptibility vancomycin-intermediate S. aureus (VISA) has been reported from many countries. Whether resistance is evolving regularly in different genetic backgrounds or in a single clone with a genetic predisposition, as early results suggest, is unclear. We have studied 101 MRSA with reduced vancomycin susceptibility from nine countries by multilocus sequence typing (MLST), characterization of SCCmec (staphylococcal chromosomal cassette mec), and agr (accessory gene regulator). We found nine genotypes by MLST, with isolates within all five major hospital MRSA lineages. Most isolates (88/101) belonged to two of the earliest MRSA clones that have global prevalence. Our results show that reduced susceptibility to vancomycin has emerged in many successful epidemic lineages with no clear clonal disposition. Increasing antimicrobial resistance in genetically distinct pandemic clones may lead to MRSA infections that will become increasingly difficult to treat.

Anti-Bacterial Agents↗
PubMed1993

Cytogenetic evolution in primary tumors, local recurrences, and pulmonary metastases of two soft tissue sarcomas.

The karyotypic pattern at different stages of tumor development may provide information on tumor progression but few data are available regarding human solid tumors. Cytogenetic analysis was performed on the primary tumor and four lung metastases of a synovial sarcoma, and the primary tumor, two consecutive local recurrences, and six pulmonary metastases, obtained at two different occasions, of a malignant fibrous histiocytoma (MFH). Simultaneous existence of more than one cytogenetically aberrant clone was also assessed through analysis of more than one sample from the same surgical specimen. Clonal chromosome aberrations were detected in all samples from the synovial sarcoma, and in both local recurrences and five of the metastases from the MFH. All clones in both tumors were cytogenetically related. The primary synovial sarcoma tumor contained two clones, one of which was also found in the lung metastases, together with a third clone that had acquired additional aberrations. Four clones with a near-tetraploid chromosome number and complex aberrations were identified in the MFH. Likely evolutionary pathways could be deduced in both cases. In the patient with synovial sarcoma one of the pulmonary metastases, rather than the primary tumor, might well have been the source of another of the pulmonary metastases. In the MFH the cytogenetic findings indicated the presence of two co-existing lineages in the primary tumor, one giving rise to the local recurrences and one to the pulmonary metastases. Our findings show that cytogenetic analysis can be used to establish the chronologic relationships between different clones in primary tumors, local recurrences and distant metastases, to determine what genetic changes are of importance for the metastatic capability of tumor cells, and to help establish the origin of the metastatic lesions.

Chromosome Aberrations↗
PubMed2002

Secrets of success of a human pathogen: molecular evolution of pandemic clones of meticillin-resistant Staphylococcus aureus.

The first European isolate of meticillin-resistant Staphylococcus aureus (MRSA) was detected in 1960. Since then MRSA has become a leading cause of nosocomial infections worldwide. Using molecular typing techniques--primarily pulsed-field gel electrophoresis (PFGE)--we identified five major MRSA clones that accounted for almost 70% of the over 3000 MRSA isolates recovered in hospitals mainly in southern and eastern Europe, South America, and the USA. Most of our surveillance studies were done in these areas. Multilocus sequencing typing (MLST) of representative isolates of this collection showed that these five pandemic MRSA clones have evolved from only two distinct ancestral genetic backgrounds, one of which can be traced back to the very first European MRSA isolates and also to meticillin susceptible S aureus strains circulating in Danish hospitals during the mid to late 1950s--i.e., shortly before the introduction of meticillin into therapy. The second lineage with a completely different MLST profile included MRSA frequently recovered in the USA, Japan, and among paediatric isolates from several parts of the world. A few isolates with a third distinct MLST type corresponding to that of EMRSA-16 were also detected in the early Danish isolates. The four structural types of mec element, the heterologous DNA segment containing the meticillin resistance determinant mecA, were present in unique combinations with the MRSA clonal types. Our findings establish evolutionary associations in the most widely spread pandemic clones of MRSA. The epidemiological factors that contributed to the massive dissemination of a few MRSA clones are not well understood. We suggest, however, that the secrets of effectiveness of MRSA could be hidden in the unique genetic background of a surprisingly few lineages of S aureus particularly well able to cope with the contemporary clinical environment.

DNA, Bacterial↗
PubMed1989

Rearranged Epstein-Barr virus genomes and clonal origin in nasopharyngeal carcinoma.

Epstein-Barr virus (EBV) is known to be associated with two malignant diseases, nasopharyngeal carcinoma (NPC) and endemic Burkitt's lymphoma. In this study, the genomes of EBV in biopsy specimens from 4 NPC patients in Japan were analyzed using Southern blot hybridization. The NPC tissues of all examined cases contained rearranged EBV genomes whose BamHI H fragments were larger than those of prototype EBV genomes. One of them had a BamHI fragment containing contiguous sequences of BamHI Y and H. A single-sized EBV DNA terminus was observed in these NPC tissues, implying the evolution of the carcinoma from a single EBV-infected cell.

Antibodies, Viral↗
PubMed2005

Evolution of erythromycin resistance in Streptococcus pneumoniae in Italy.

OBJECTIVES: To evaluate erythromycin resistance in recent invasive isolates of Streptococcus pneumoniae in Italy, to study the phenotypic and genotypic characteristics of the isolates, and to compare data with those obtained in a previous survey. METHODS: Invasive pneumococcal isolates were obtained from 56 laboratories throughout the country, in 2001-2003. Isolates were serotyped and antimicrobial susceptibilities determined by Sensititre panels and Etest. A new PCR was performed to detect erythromycin resistance genes. Typing methods for selected erythromycin-resistant isolates included PFGE and multilocus sequence typing (MLST). RESULTS: One hundred and fifty-five isolates out of 444 (34.9%) were resistant to erythromycin: 95 isolates (21.4%) carried erm(B), 56 (12.6%) carried mef(A) and three carried both genes. One isolate, carrying neither erm(B) nor mef(A), showed a point mutation in domain V of the 23S rRNA genes. The mef(A)-positive isolates carried subtype mef(A) (47 isolates), subtype mef(E) (nine isolates), and both subtype mef(E) and erm(B) (three isolates). All subtype mef(A) strains, except two, belonged to serotype 14, appeared to be clonally related by PFGE and related to the England14-9 clone by MLST. The two isolates belonging to other serotypes showed different genetic backgrounds. CONCLUSIONS: Erythromycin resistance in S. pneumoniae has increased in the last few years in Italy. erm(B) is still the predominant resistance determinant; however, the increase in erythromycin resistance (34.9% versus 28.8% of the previous years) is mainly due to an increase in the proportion of isolates carrying the efflux pump mef(A), whereas the proportion of isolates carrying erm(B) has not changed.

Drug Resistance, Bacterial↗
PubMed1999

Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution.

To address the evolution of human immunodeficiency virus type 1 (HIV-1) within a single host, we analyzed the HIV-1 C2-V5 env regions of both cell-free genomic-RNA- and proviral-DNA-derived clones. Sequential samples were collected over a period of 3 years from six untreated subjects (three typical progressors [TPs] and three slow progressors [SPs], all with a comparable length of infection except one. The evolutionary analysis of the C2-V5 env sequences performed on 506 molecular clones (253 RNA- and 253 DNA-derived sequences) highlighted a series of differences between TPs and SPs. In particular, (i) clonal sequences from SPs (DNA and RNA) showed lower nucleotide similarity than those from TPs (P = 0. 0001), (ii) DNA clones from SPs showed higher intra- and intersample nucleotide divergence than those from TPs (P < 0.05), (iii) higher host-selective pressure was generally detectable in SPs (DNA and RNA sequences), and (iv) the increase in the genetic distance of DNA and RNA sequences over time was paralleled by an increase in both synonymous (Ks) and nonsynonymous (Ka) substitutions in TPs but only in nonsynonymous substitutions in SPs. Several individual peculiarities of the HIV-1 evolutionary dynamics emerged when the V3, V4, and V5 env regions of both TPs and SPs were evaluated separately. These peculiarities, probably reflecting host-specific features of selective constraints and their continuous modulation, are documented by the dynamics of Ka/Ks ratios of hypervariable env domains.

Base Sequence↗
PubMed1998

Molecular evolution of a pathogenicity island from enterohemorrhagic Escherichia coli O157:H7.

We report the complete 43,359-bp sequence of the locus of enterocyte effacement (LEE) from EDL933, an enterohemorrhagic Escherichia coli O157:H7 serovar originally isolated from contaminated hamburger implicated in an outbreak of hemorrhagic colitis. The locus was isolated from the EDL933 chromosome with a homologous-recombination-driven targeting vector. Recent completion of the LEE sequence from enteropathogenic E. coli (EPEC) E2348/69 afforded the opportunity for a comparative analysis of the entire pathogenicity island. We have identified a total of 54 open reading frames in the EDL933 LEE. Of these, 13 fall within a putative P4 family prophage designated 933L. The prophage is not present in E2348/69 but is found in a closely related EPEC O55:H7 serovar and other O157:H7 isolates. The remaining 41 genes are shared by the two complete LEEs, and we describe the nature and extent of variation among the two strains for each gene. The rate of divergence is heterogeneous along the locus. Most genes show greater than 95% identity between the two strains, but other genes vary more than expected for clonal divergence among E. coli strains. Several of these highly divergent genes encode proteins that are known to be involved in interactions with the host cell. This pattern suggests recombinational divergence coupled with natural selection and has implications for our understanding of the interaction of both pathogens with their host, for the emergence of O157:H7, and for the evolutionary history of pathogens in general.

Amino Acid Sequence↗