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PubMed1977

Chromosomal evolution in a haploid frog cell line: implications for the origin of karyotypic variants.

ICR 2A, a haploid cell line derived from Rana pipiens embryos, has remained haploid in number of chromosones and their relative lengths and centromere positions for 500 cell generations. After this time, two new haryotypes appeared; relative length measurements indicate that the first has a translocation from chromosome 4 to 6, the second translocations from 3 and 4 to 6 and 7. The single exchange karyotype is not a precursor for the double exchange according to a statistical analysis. The double exchange karyotype characterized 90% of some cultures although a selective advantage could not be demonstrated for these cells. The observations suggest that a non-clonal or multicellular origin may account for these karyotypic variants.

Animals↗
PubMed1996

Stromal abnormalities in neoplastic bone marrow diseases.

Bone marrow malignancies are clonal disorders resulting from neoplastic transformation of hematopoietic stem or progenitor cells. Similar to their normal counterparts, transformed blood-forming cells remain dependent on signals from the hematopoiesis-regulating stromal environment for survival and proliferation. There is increasing evidence that the microenvironment may also take a more active part in the disease process. A review of the literature on stromal abnormalities in the leukemias, the myelodysplastic syndromes, and multiple myeloma reveals three principal mechanisms by which stromal derangements can contribute to the evolution of a neoplastic disease. In the simplest case, neoplastic blood-forming cells induce reversible changes in stroma function or composition which result in improved growth conditions for the malignant cells ('malignancy-induced microenvironment'). In the second setting, functionally abnormal end cells derived from the malignant clone become an integral part of the stroma system, selectively stimulating the neoplastic cells and inhibiting normal blood cell formation ('malignant microenvironment'). In the third condition, the emergence of a neoplastic cell population is the consequence of a primary stroma lesion characterized by inability to control regular blood cell formation ('malignancy-inducing microenvironment'). The perception of different stroma-related disease mechanisms may eventually lead to the development of alternative therapeutic approaches.

Acute Disease↗
PubMed1984

Therapy-induced preleukaemia in patients treated for Hodgkin's lymphoma: clinical and therapeutic relevance of sequential chromosome banding studies.

Between January 1978 and December 1982 successful sequential chromosome analyses were carried out on bone marrow cells of five patients previously treated for Hodgkin's lymphoma (HL) presenting unexplained cytopenia or pancytopenia during follow-up. All patients had concurrent morphological examination of bone marrow specimens showing signs of dysplasia and/or hypoplasia, without leukaemic infiltrate. Six other patients treated for HL who had normal haematological parameters served as controls. All the patients with unexplained cytopenias had clonal chromosome abnormalities; monosomy for chromosome No. 5 was the most frequent. No abnormalities were detected in the control group. Two patients have evolved to resistant leukaemia, one died of sepsis before leukaemic conversion while severely neutropenic, and two are in full marrow and cytogenetic recovery after aggressive anti-leukaemic treatment in the pre-leukaemic phase. Our data suggest that cytogenetic studies may be of crucial value in detecting therapy-induced preleukaemia (t-PL) at an early stage of its evolution and in planning appropriate therapy before the establishment of overt leukaemia.

Adult↗
PubMed2001

Substrate sequence selection by retroviral integrase.

Integration of retrovirus DNA is a specific process catalyzed by the integrase protein acting to join the viral substrate DNA (att) sequences of about 10 bases at the ends of the long terminal repeat (LTR) to various sites in the host target cell DNA. Although the interaction is sequence specific, the att sequences of different retroviruses are largely unrelated to one another and usually differ between the two ends of the viral DNA. To define substrate sequence specificity, we designed an "in vitro evolution" scheme to select an optimal substrate sequence by competitive integration in vitro from a large pool of partially randomized substrates. Integrated substrates are enriched by PCR amplification and then regenerated and subjected to subsequent cycles of selection and enrichment. Using this approach, we obtained the optimal substrate sequence of 5'-ACGACAACA-3' for avian sarcoma-leukosis virus (ASLV) and 5'-AACA(A/C)AGCA-3' for human immunodeficiency virus type 1, which differed from those found at both ends of the viral DNA. Clonal analysis of the integration products showed that ASLV integrase can use a wide variety of substrate sequences in vitro, although the consensus sequence was identical to the selected sequence. By a competition assay, the selected nucleotide at position 4 improved the in vitro integration efficiency over that of the wild-type sequence. Viral mutants bearing the optimal sequence replicated at wild-type levels, with the exception of some mutations disrupting the U5 RNA secondary structure important for reverse transcription, which were significantly impaired. Thus, maximizing the efficiency of integration may not be of major importance for efficient retrovirus replication.

Alpharetrovirus↗
PubMed2004

Mutation of all Runx (AML1/core) sites in the enhancer of T-lymphomagenic SL3-3 murine leukemia virus unmasks a significant potential for myeloid leukemia induction and favors enhancer evolution toward induction of other disease patterns.

SL3-3 murine leukemia virus is a potent inducer of T-lymphomas in mice. Using inbred NMRI mice, it was previously reported that a mutant of SL3-3 with all enhancer Runx (AML1/core) sites disrupted by 3-bp mutations (SL3-3dm) induces predominantly non-T-cell tumors with severely extended latency (S. Ethelberg, J. Lovmand, J. Schmidt, A. Luz, and F. S. Pedersen, J. Virol. 71:7273-7280, 1997). By use of three-color flow cytometry and molecular and histopathological analyses, we have now performed a detailed phenotypic characterization of SL3-3- and SL3-3dm-induced tumors in this mouse strain. All wild-type induced tumors had clonal T-cell receptor beta rearrangements, and the vast majority were CD3(+) CD4(+) CD8(-) T-lymphomas. Such a consistent phenotypic pattern is unusual for murine leukemia virus-induced T-lymphomas. The mutant virus induced malignancies of four distinct hematopoietic lineages: myeloid, T lymphoid, B lymphoid, and erythroid. The most common disease was myeloid leukemia with maturation. Thus, mutation of all Runx motifs in the enhancer of SL3-3 severely impedes viral T-lymphomagenicity and thereby discloses a considerable and formerly unappreciated potential of this virus for myeloid leukemia induction. Proviral enhancers with complex structural alterations (deletions, insertions, and/or duplications) were found in most SL3-3dm-induced T-lymphoid tumors and immature myeloid leukemias but not in any cases of myeloid leukemia with maturation, mature B-lymphoma, or erythroleukemia. Altogether, our results indicate that the SL3-3dm enhancer in itself promotes induction of myeloid leukemia with maturation but that structural changes may arise in vivo and redirect viral disease specificity to induction of T-lymphoid or immature myeloid leukemias, which typically develop with moderately shorter latencies.

Animals↗
PubMed2006

Multilocus sequence typing scheme for Enterococcus faecalis reveals hospital-adapted genetic complexes in a background of high rates of recombination.

A multilocus sequence typing (MLST) scheme based on seven housekeeping genes was used to investigate the epidemiology and population structure of Enterococcus faecalis. MLST of 110 isolates from different sources and geographic locations revealed 55 different sequence types that grouped into four major clonal complexes (CC2, CC9, CC10, and CC21) by use of eBURST. Two of these clonal complexes, CC2 and CC9, are particularly fit in the hospital environment, as CC2 includes the previously described BVE clonal complex identified by an alternative MLST scheme and CC9 includes exclusively isolates from hospitalized patients. Identical alleles were found in genetically diverse isolates with no linkage disequilibrium, while the different MLST loci gave incongruent phylogenetic trees. This demonstrates that recombination is an important mechanism driving genetic variation in E. faecalis and suggests an epidemic population structure for E. faecalis. Our novel MLST scheme provides an excellent tool for investigating local and short-term epidemiology as well as global epidemiology, population structure, and genetic evolution of E. faecalis.

Alleles↗
PubMed2002

DNA target motifs of somatic mutagenesis in antibody genes.

During humoral immunity to T-cell-dependent antigens, responding B lymphocytes selectively mutate their antibody variable region genes at a high rate. This, together with the process of clonal selection, ultimately enhances the affinity and specificity of the antibody molecule and memory B cells that express it as a receptor. Despite several decades of investigation, the mutation mechanism has remained unresolved, largely due to the convoluted nature of experimental systems used to approach it. Somatic mutations preferentially occur within specific oligonudeotide motifs, and this targeting is consistent in all immunoglobulin genes of humans and mice that we have examined, suggesting that a conserved mechanism operates in both species. Our mutation targeting analyses implicate evolution of germline variable gene sequences to direct somatic mutations to specific codon positions in a manner that regulates the frequency of amino acid replacements to the benefit of the antibody product. Finally, our recent strand bias analyses support the idea that somatic mutation occurs preferentially, perhaps exclusively, at two bases on both strands of DNA. These and related observations from other laboratories support a mutation model that invokes at least two error-prone polymerases that have distinct template biases and requirements for elements of postreplicative mismatch repair.

Animals↗
PubMed1990

Epidemiology and immunovirology of human T-cell leukemia/lymphoma virus type I-associated adult T-cell leukemia and chronic myelopathies as seen in France.

Seventeen patients with adult T-cell leukemia (ATL) and 21 with tropical spastic paraparesis/human T-cell leukemia/lymphoma virus type I (HTLV-I)-associated myelopathy (TSP/HAM) were observed during a 3-yr survey (1986-1988) in some hospitals in Paris, France. Most of them were black, originating from high-HTLV-I-endemic areas (West Indies or Africa), but two cases of TSP/HAM occurred in French Caucasians. In one case, the patient acquired the virus from a transfusion during a cardiac transplantation. Most of the ATL cases were diagnosed as acute leukemia or lymphoma, with a proliferation of CD2+, CD3+, CD4+, CD8-, DR+, and CD25+ lymphoid cells. Only three cases were diagnosed as a smoldering ATL. All of the TSP/HAM cases exhibited a spastic paraparesis with a chronic and slow evolution and high HTLV-I antibody titers in serum and cerebrospinal fluid, with a high HTLV-I antibody index and specific HTLV-I immunoglobulin = oligoclonal bands. In TSP/HAM, a high percentage of DR-expressing cells (15 to 40%) was found, with a slightly elevated CD4/CD8 ratio. This was associated with the presence of 1 to 10% abnormally shaped nuclei in lymphoid cells and a polyclonal integration of HTLV-I proviruses in these peripheral blood mononuclear cells. On the contrary, a clonal integration was always found in the ATL malignant cells (leukemic, lymph node, and cutaneous infiltrate). Long-term interleukin 2-dependent T-cell lines (CD2+, CD3+, CD4+, and WT31+) with activated T-cell markers (CD25+ and DR+) producing HTLV-I were established from ATL and TSP/HAM peripheral blood mononuclear cells.

Antigens, CD↗
PubMed2003

Immunity and the animation of the genome.

Expression of genes in the right place at the right time is fundamental to all of life. The ontogeny of effector and memory T cells is a robust example of this important principle. Although lymphocytes represent a late addition in animal evolution, they are serving as an exceptional model system to unlock the mysteries surrounding the way in which the genome is animated. It will be speculated here that further insight into fundamental principles of genome function may arise from study of immunity. Likewise, such information may be key to understanding and altering immunobiology.

Animals↗
PubMed1990

A clonal theory of parasitic protozoa: the population structures of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas, and Trypanosoma and their medical and taxonomical consequences.

We propose a general theory of clonal reproduction for parasitic protozoa, which has important medical and biological consequences. Many parasitic protozoa have been assumed to reproduce sexually, because of diploidy and occasional sexuality in the laboratory. However, a population genetic analysis of extensive data on biochemical polymorphisms indicates that the two fundamental consequences of sexual reproduction (i.e., segregation and recombination) are apparently rare or absent in natural populations of the parasitic protozoa. Moreover, the clones recorded appear to be stable over large geographical areas and long periods of time. A clonal population structure demands that the medical attributes of clones be separately characterized; ubiquitous clones call for priority characterization. Uniparental reproduction renders unsatisfactory Linnean taxonomy; this needs to be supplemented by the "natural clone" as an additional taxonomic unit, which is best defined by means of genetic markers.

Animals↗
PubMed2000

CD8(+) T-cell selection, function, and death in the primary immune response in vivo.

The primary immune response to Epstein Barr virus (EBV) is characterized by striking proliferation of EBV-specific CD8(+) T cells. In this study we have investigated the clonal composition and functional properties of the cells mediating this primary response and have analyzed the mechanisms that control the downregulation of the primary response and the selection of memory cells. We show that massively expanded T-cell clones often dominate the primary antigen-specific T-cell response. Despite the enormous extent of expansion, the virus-specific T cells express high levels of intracellular perforin and are potently cytotoxic. They are, however, functionally heterogeneous in their ability to secrete proinflammatory cytokines, with subpopulations of the antigen-specific T cells being hyporesponsive. The primary response is closely regulated, and the majority of cells are programmed to die via a cytokine-rescuable pathway, leaving only small populations of memory T cells surviving. Comparison of the clonal composition of primary and memory responses in vivo shows that the clones that dominate the primary response are relatively heavily culled during the downregulation of the primary response and the establishment of T-cell memory.

Antigens, Viral↗
PubMed2025

Effects of recombination on multi-drug resistance evolution in Plasmodium falciparum malaria.

When multiple beneficial alleles at multiple loci are present in a population but not linked together in any one individual, there is no general evolutionary result that determines whether recombination will speed up or slow down the emergence and evolution of genotypes carrying multiple beneficial alleles. Translated to infectious disease control, this evolutionary uncertainty means that when multiple types of drug resistance are present we do not know whether recombination will act more strongly to (1) bring together single-resistant genotypes into multi-drug resistant (MDR) genotypes, or (2) break apart MDR genotypes into single-resistant genotypes. In this paper, we introduce a new version of an established and validated individual-based malaria transmission model where we have added 25 drug-resistance related loci, individual mosquito bites, and mosquitoes feeding on multiple hosts in a single meal (interrupted feeds) allowing for recombination events of different Plasmodium falciparum genotypes from different hosts. Recombination among P. falciparum genotypes in this model occurs from two sources of variation, multi-clonal infections in single hosts and interrupted feeds on multiple hosts, and we show that 80% to 97% of MDR recombinant falciparum genotypes are projected to occur from single uninterrupted bites on hosts with multi-clonal infections (for malaria prevalence > 5%). Increases in the model's interrupted feeding rate slowly increase the number of recombination events occurring from interrupted feeds. A comparison of drug-resistance management strategies with this new model shows that, over a 15-year timeframe, triple artemisinin-combination therapies (ACT) strategies show the largest reductions in treatment failures and the longest delays until artemisinin resistance reaches a critical 1% threshold. Multiple first-line therapies (MFT) are second best under these criteria, and ACT cycling approaches are third best. When compared to cycling strategies, MFT strategies generate a greater diversity of recombinant genotypes but fewer recombination events generating MDR and slower emergence of these recombinant MDR genotypes.

Plasmodium falciparum↗
PubMed2007

Uncovering the biodiversity of genetic and reproductive systems: time for a more open approach. American Society of Naturalists E. O. Wilson Award winner address.

Important scientific findings frequently arise from serendipitous findings. Unfortunately, many scientists are not prepared to take advantage of unexpected results and to question established paradigms, and this prevents them from capitalizing on their good fortune. In this essay, I first explain how pure serendipity led us to discover unusual modes of reproduction such as clonal reproduction by males and a green-beard gene. Next, I argue that the reproductive systems of ants and other organisms are probably much more diverse than is generally appreciated. This leads me to advocate for a new "molecular naturalist" approach to reproductive systems and a more "naturalistic" approach in population and evolutionary genetics. Finally, I make two further points. The first is that our current funding and education systems tend to hinder originality and curiosity. The other is that the field of ecology and evolution, and more generally all of science, would benefit from a shift in values from scientific productivity to scientific creativity. A few suggestions are made to this effect.

Animals↗
PubMed1997

Giant cell granulomatous pulmonary and myocardial lesions in necrobiotic xanthogranuloma with paraproteinemia.

OBJECTIVE: To report three cases of pulmonary or myocardial disease (or both) and necrobiotic xanthogranuloma. MATERIAL AND METHODS: Giant cell granulomas of the lung and myocardium were demonstrated in three patients who had pulmonary and myocardial lesions of necrobiotic xanthogranuloma in conjunction with skin lesions, leukopenia, paraproteinemia, and complement deficiencies. The patients were two men who were 47 and 64 years of age and a 39-year-old woman. RESULTS: Biopsies of skin and visceral lesions showed asteroid and cytoplasmic inclusions. B-cell lymphoid nodules were found. In one of the male patients, a major clonal T-cell receptor gene rearrangement was detected in the peripheral blood. Prednisone was ineffective in two of the patients. The other patient experienced regression of skin lesions and diminishment of a chest nodule after receiving alkylating agent therapy. CONCLUSION: Establishing the correct diagnosis is important, and apparently it is possible to establish the nature of the myocardial and pulmonary lesions with use of appropriate scans and by biopsy. Successful treatment of necrobiotic xanthogranuloma skin lesions with corticosteroids or alkylating agents (or both) implies that evolution of serious disease that compromises the heart and lungs could be controlled.

Adult↗
PubMedDate not supplied

[Comparative characteristics of immunological, clinical and morphological features of human lymphoid tumors in respect with tumor genesis and progression].

We describe three lymphoid tumors with the same immunophenotype characteristic for chronic lymphoid leukemia (CD19+/CD5+, clonality of the light immunoglobulin chains, CD23+ and CD10-). However, clinical picture and morphology of neoplastic cells dictate different clinical forms of these cases: chronic lymphoid leukemia, large cell transformation of chronic lymphoid leukemia and diffuse large B-cell lymphoma. Taking into account that immunophenotype reflects the origin of tumor, while clinical outcome and morphological features of cells reflect the stage of tumor progression and/or pathway of tumor formation, we discuss the approach to natural classification of lymphoid tumors based on the process of their evolution.

Antigens, CD19↗
PubMed2005

Evolution of the intrahepatic T cell repertoire during chronic hepatitis C virus infection.

Chronic hepatitis C virus (HCV) infection is characterized by extensive infiltration of inflammatory cells in the liver, where there is a compartmentalization of HCV-reactive T lymphocytes. Previous studies have demonstrated a broad intrahepatic TCR repertoire; however, there is little information regarding the stability of this intrahepatic T cell population. We studied the T cell repertoires in sequential liver biopsy samples from five individuals with chronic HCV infection using TCR spectratype analysis; four subjects had been treated with IFN-alpha during the interval between biopsies. Transcripts from most TCRBV families were detectable in the liver tissues, and 25-85% of these had skewed spectratype profiles indicative of T cell clonal expansions. Most of the intrahepatic T cell expansions were not evident in an analysis of peripheral blood T cells collected at the same time as the liver biopsy. Detailed analysis using TCRBJ-primed run-off reactions revealed that the intrahepatic TCR repertoires were not stable within an individual, although some TCR clonotypes were maintained for at least 45 months.

Biopsy↗
PubMed2002

Geographic patterns of clonal diversity in the earth mite species Penthaleus major with particular emphasis on species margins.

Patterns of clonal diversity in parthenogenetic species can be influenced by occasional sexual reproduction, selection due to environmental heterogeneity, and genetic drift. Here we investigate geographic patterns of clonal diversity in the obligate parthenogenetic earth mite species, Penthaleus major, in southeastern Australia. Spatial autocorrelation analysis indicated a relationship between geographic distance and clonal diversity at the sites. However, there was no evidence for an association between distance and clonal composition or the frequency of the two most common clones. Regression analyses indicated that clonal diversity and the frequency of one of the common clonal groups were associated with latitude and/or climatic variables, whereas the other common group was not associated with any of those variables. In four transects (each 250-400 km in length) extending from the center of the distribution of P. major to its margins, there was a consistent and continuous decline in clonal diversity as the margin was approached but no evidence that one clonal group predominated at the margin. This argues against the importance of a general-purpose genotype being favored at margins and suggests that either selection acts to decrease local diversity at sites near the margin or that diversity declines due to drift at these sites.

Animals↗
PubMed2006

Does selection by resistant hosts trigger local adaptation in plant-pathogen systems?

Understanding the consequences of selection by host resistance on pathogen population structure provides useful insights into the dynamics of host-parasite co-evolution processes and is crucial for effective disease management through resistant cultivars. We tested general vs. local population adaptation to host cultivars, by characterizing a French collection of Phytophthora infestans (the causal organism of potato late blight) sampled during two consecutive years on cultivars exhibiting various levels of resistance. Local populations were structured by the host for virulence (qualitative pathogenicity) but also for aggressiveness (quantitative pathogenicity). All populations had a low genotypic diversity for amplified fragment length polymorphisms (AFLPs), and presumably consisted of a few closely related clonal lineages. No correlation was detected between pathogenicity traits and AFLP genotypes. The data support the hypothesis of general adaptation for aggressiveness, to which directional selection for virulence is superimposed when race-specific resistance is introduced.

DNA Fingerprinting↗