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PubMed2003

Analysis of the clonal relationship among clinical isolates of Salmonella enterica serovar Infantis by different typing methods.

Salmonella Infantis has been the second most common serovar in Argentina in the last two years, being isolated mostly from paediatric hospitalised patients. In order to determine the clonal relationship among Salmonella Infantis strains, we examined 15 isolates from paediatric patient faeces in Argentina (12 geographically related and 3 geographically non-related) by using antimicrobial susceptibility, plasmid profiling, repetitive extragenic palindromic (REP) PCR, enterobacterial repetitive intergenic consensus (ERIC) PCR, and low-frequency restriction analysis of chromosomal DNA by pulsed field gel electrophoresis (PFGE). Four Spanish strains were included as controls of clonal diversity in molecular techniques. Antibiotype and plasmid profile was not useful as epidemiological tools. PFGE and REP-PCR were able to discriminate between Argentinean and Spanish isolates of Salmonella Infantis allowing to detect genetically related strains in three different cities. This finding indicates that a possible spread of a clone of this serovar in the North-eastern Region of Argentina has taken place in 1998.

Argentina↗
PubMed1988

Gene probe analysis demonstrates independent clonal evolution of co-existent chronic myeloid and chronic lymphocytic leukaemia.

We describe a case of Philadelphia-positive chronic myeloid leukaemia occurring simultaneously with B-cell chronic lymphocytic leukaemia in a 69-yr-old male. Gene probe analysis of DNA from both peripheral blood and bone marrow provided evidence for the independent evolution of 2 clones in this case, with a predominant population showing immunoglobulin heavy chain gene rearrangement and a smaller population showing a rearrangement within the breakpoint cluster region of chromosome 22.

Aged↗
PubMed1984

Alloantigen-induced cytotoxicity against syngeneic tumor cells: analysis at the clonal level.

It has been shown that peritoneal exudate cells (PEC) from BALB/c mice immunized with minor histocompatibility antigens presented by DBA/2 or B10.D2 spleen cells are capable of lysing syngeneic YC8 tumor cells in a 4-hr 51Cr-release assay. In this study, we employed limiting dilution analysis to determine the frequency of CTL precursors (CTL-P) reactive against both the specific DBA/2 (or P815) target and the syngeneic tumor YC8. The mean frequency of anti-DBA/2 CTL-P in PEC from BALB/c mice immunized with DBA/2 was 1/302. Between one-third and one-fifth of limiting dilution microcultures that exhibited lytic activity against DBA/2 lymphoblasts (or P815) were also able to lyse YC8. No lysis of YC8 was observed in the absence of a parallel lysis on DBA/2 lymphoblasts or P815 target cells. T cell clones, derived by micromanipulation from microcultures selected for cytotoxic activity against YC8 and/or P815, maintained either the specific anti-allogeneic or the doubly reactive ( antiallogeneic plus anti-syngeneic tumor) phenotype. Fourteen clones (six specific and eight doubly reactive) were tested for cytotoxic activity on a panel of target cells with different haplotypes. All showed H-2-restricted specificity for minor histocompatibility antigens shared by DBA/2 and B10.D2. The restriction element for some of the clones mapped in the K region of the H-2 complex, whereas for other clones the restriction element mapped in the D region; both K- and D-restricted clones were able to lyse YC8. When the clones that exhibited lysis on YC8 were tested on two other BALB/c tumor targets, LSTRA, a Moloney virus induced lymphoma, and RL male-1, a radiation induced lymphoma, two of seven were found to lyse all three syngeneic tumor targets equally well, but not syngeneic BALB/c blasts. These clones were functionally categorized as conventional CTL because they were unable to proliferate when cultured with antigen in the absence of exogenous lymphokines, and were unable to produce lymphokine with IL 2 activity when stimulated by the appropriate splenocytes. When tested in vivo in a Winn assay, a strong anti-tumor activity against YC8 was exerted by the anti-DBA/2 clones DY4 -3 and DY16 -3. These clones lysed both YC8 and the immunizing target cells in vitro. No in vivo effect in neutralizing YC8 tumor growth was observed with clone D2-1, a clone that lysed DBA/2 targets but not YC8 in vitro.

Animals↗
PubMed2000

Analysis of a clonal selection event during transposon-mediated nested-deletion formation in rare BAC and PAC clones.

Nested deletions from one end of the genomic DNA in bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs) are readily generated by inserting a loxP site-containing Tn10 minitransposon into the recombinant clone and transducing with P1 phage. Although the size of clones in the deletion series is largely random, in about 5% of BACs and PACs the distribution appears skewed to a certain length, and in rare cases (<1%) is definitely skewed to a particular size. Here we investigate this relatively rare phenomenon and validate that sequence-specific transposon insertions are not the cause of such skewed nested-deletion libraries. Instead, a detailed analysis of our experiments with a BAC clone demonstrating this unusual feature indicates that deletions of a certain size arise from clonal expansion of a transposon insertion as a result of transient derepression of the transposase gene prior to IPTG induction. Transposition itself shows no bias to any particular region of insert DNA in the clone. We suggest a simple modification to the procedure for generating nested-deletions that allows all BACs and PACs to produce nested-deletions of random size. These findings should provide additional insight into the causes of site selectivity in genomic clones with other inducible transposon systems.

Chromosomes, Artificial↗
PubMed1992

Success of DNA fingerprinting after failure of biotyping, antimicrobial susceptibility testing, and plasmid analysis to reveal clonality of multiple blood and urine isolates from a patient with Escherichia coli urosepsis.

Multiple isolates of Escherichia coli from the blood and urine of a 60-year-old woman with acute pyelonephritis exhibited different biotypes, antimicrobial susceptibility patterns, and plasmid profiles, suggesting the presence of polymicrobial bacteriuria and leaving in question the origin of the bacteremia. Only after bacterial restriction endonuclease analysis of total bacterial DNA was it discovered that all isolates represented the same strain, with plasmid instability possibly accounting for the varied antimicrobial susceptibility patterns observed. We conclude that the biotype, antimicrobial susceptibility profile, and plasmid profile are sometimes inadequate to clarify the relationships between different clinical isolates of E. coli from a single patient and can lead to erroneous epidemiologic conclusions. DNA fingerprinting can resolve dilemmas these less precise techniques leave unresolved.

Anti-Bacterial Agents↗
PubMed1982

Human cytotoxic T cell structures associated with expression of cytolysis. I. Analysis at the clonal cell level of the cytolysis-inhibiting effect of 7 monoclonal antibodies.

Monoclonal antibodies (mAb) derived from BALB/c mice immunized with human anti-HLA-A2 cloned cytotoxic T lymphocytes (CTL) were screened for their ability to block, in the absence of complement, the cytolytic activity of the immunizing CTL clone. Eight cytolysis-inhibiting mAb have been derived. One of these was directed against a monomorphic determinant expressed on HLA-class I molecules and thus probably inhibited cytolysis via a target cell antigen-masking effect. The 7 other mAb recognized "CTL function-associated structures" and did not have to interfere with target cell antigens in order to inhibit cytolysis. F(ab')2 and Fab fragments of these 7 mAb were also inhibitory. Competitive inhibition of binding and preliminary biochemical analysis suggested that these 7 mAb defined on cloned CTL various epitopes of a structure of 30 kDa disulfide-bonded into several multimeric forms when analyzed without reduction. The inhibitory effect of these 7 mAb has been investigated on a series of short-term (1 month) and long-term (greater than 10 months) expanded cloned CTL lines derived in vitro from an in vivo allosensitized individual exhibiting various specificities. Unexpectedly, only 10% of these CTL clones were inhibited. Flow cytofluorimetric analysis further revealed that noninhibited and inhibited CTL clones expressed similar amounts of the 30-kDa structure. Consequently, the inhibition of CTL was heterogeneous when analyzed at the clonal level and not simply related to the presence or absence of this structure. Furthermore, the ability of CTL clones to be inhibited appeared to be unrelated to their HLA-A, B or C specificity or to their lytic activity. The connections between this mAb-defined structure and CTL function are discussed.

Animals↗
PubMed2002

Polymerase chain reaction analysis of the clonality of Porphyromonas gingivalis and collagenase gene.

OBJECTIVE: To investigate the genotypic characterization of Porphyromonas gingivalis (Pg) and the heterogeneity of a potential virulence factor-PrtC. METHODS: Arbitrarily primed polymerase chain reaction (AP-PCR) was applied to 80 Pg strains isolated from 24 unrelated Chinese periodontitis patients. PCR reaction was used to detect a fragment of the collagenase gene (PrtC gene). To evaluate the sequence heterogeneity of the Pg PrtC genes, sequence analysis of four PrtC gene of clinical isolates was performed. RESULTS: Random primer OPA-05 and OPA-17 distinguished 7 AP-PCR profiles (I through VII). The majority of the strains belonged to type VII which accounted for 25.8%. A 548bp fragment of PrtC gene was detected from 24 clinical strains. The PCR products were verified by the restriction endonucleases PstI and PvuI. Sequence analysis showed 4 PrtC genes were heterogeneous in their nucleotide composition and differed from reference strain Pg 53977. CONCLUSIONS: The results demonstrated genetic diversity existed among these clinical strains isolated from Chinese periodontitis patients and the PrtC genes are heterogeneous in their nucleotide sequence.

Adult↗
PubMed1992

Heterogeneity in the anti-HLA-DR immune response elicited by the antiidiotypic monoclonal antibody F5-444. Analysis at the clonal level.

A total of 630 hybridomas were generated from a BALB/c mouse immunized with the anti-id mAb F5-444, which binds an idiotope within the antigen-combining site of mAb AC1.59. The latter recognizes a determinant shared by HLA-DR1, DRw8, DR9 antigens and subtypes of HLA-DR4 and DR6 that is poorly expressed by HLA-DRw16 and DRw17 antigens. Eight anti-anti-id mAb were shown with serological and immunochemical assays to react with HLA-DR antigens. Detailed analysis of these anti-HLA-DR anti-anti-id mAb showed that they differ from the original anti-HLA-DR mAb AC1.59 and among themselves in either isotype, fine specificity, extent of reactivity with the nominal antigen, differential reactivity with soluble or cell-bound antigen, and/or idiotype profile. These observations emphasize the need to characterize a panel of antigen-binding anti-anti-id mAb in order to evaluate the degree of similarity existing between antigen-binding antibodies induced by an anti-id mAb and the original antigen-binding mAb.

Animals↗
PubMedDate not supplied

[Somatic hypermutagenesis in immunoglobulin genes. II. Properties of somatic mutations and clonal selection].

Analysis of the collection of 203 somatic mutations in immunoglobulin genes was carried out. It was shown, that the high frequency of these mutations in CDRs of V-genes may be connected with the high concentration of repeats in these regions. In addition, the observed clusterization of mutations may emerge from simultaneous correction of several pertubations of complementarity in the heteroduplex, formed by the repeat regions. It was revealed, that somatic mutations in FRs are characterized by reliably smaller changes of some important amino acid physical-chemical properties than in CDRs. These data obviously indicate the occurrence of B-lymphocytes clonal selection. Analysis of synonymous substitutions has shown, that stabilizing selection seems to provide the conservatism of FRs (it leads to the conservation of the protein three-dimensional structure) and movement selection may provide the proliferation of B-lymphocytes with considerable changes in CDRs, if these mutations improve antigens binding. Preferential fixation of transitions in comparison with transversions, particularly expressed in FRs, may also be connected with the fact, that transitions lead to smaller changes of amino acid physical-chemical properties and they are rejected by selection to a smaller extent.

Amino Acids↗
PubMed1996

Clonal and functional analysis for the augmentation of tumour-infiltrating lymphocytes by interleukin 4.

In the adoptive immunotherapy for cancer, the amounts of induced effector cells play a major role in improving therapeutic efficacy. We have already demonstrated that interleukin 4 (IL-4) augments proliferation of tumour-infiltrating lymphocytes (TILs) without altering the cytotoxic activity against autologous tumour cells. The present study is designed to investigate how IL-4 augments TILs by using established TIL clones in terms of IL-2/IL-2 receptor system. CD4+, CD8+ and CD4+ CD8+ (double positive) TIL clones were established from cancer patients. At clonal level, IL-4 augmented the proliferation of IL-2-activated TIL clones irrespective of phenotypes. In order to clarify the mechanism of IL-4 at clonal level, the blocking assay by anti-IL-2 receptor alpha and beta chain and binding assay of IL-2 on the cell surface and the measurement of the internalisation of IL-2 in the cell were performed. It was clarified that IL-4 up-regulated the IL-2 receptor and then augmented the action of IL-2 molecule on the cell surface stimulated by IL-4. Furthermore, binding IL-2 internalised rapidly into the cells. Thus, it is suggested that signal transduction is augmented and proliferation of TILs is enhanced by IL-4 via the action of IL-2/IL-2 receptor system.

DNA↗
PubMed2001

Clonal and pathotypic analysis of archetypal Escherichia coli cystitis isolate NU14.

Escherichia coli NU14, a cystitis isolate used to study the pathogenesis of cystitis and to develop a FimH (type 1 fimbrial adhesin) vaccine, was assessed for extended virulence genotype, phylogenetic background, and FimH sequence and binding phenotype(s). NU14 exhibited the same virulence genotype and was derived from the same (meningitis- and cystitis-associated) subclone of E. coli O18:K1:H7 as the archetypal neonatal bacterial meningitis (NBM) isolate RS218. NU14 also displayed the same Ser62Ala FimH polymorphism as did NBM isolates RS218 and IHE3034-conferring both collagen binding and a distinct monomannose binding capability (which characterizes uropathogenic but not commensal E. coli and dramatically increases adherence to uroepithelial cells). These findings establish that strain NU14 exhibits numerous urovirulence-associated traits and derives from the single most prevalent clonal group in acute cystitis. They provide further evidence of clonal and pathotypic similarities between cystitis and NBM isolates of E. coli O18:K1:H7.

Adhesins, Bacterial↗
PubMed1990

Clonal and systemic analysis of long-term hematopoiesis in the mouse.

We have analyzed the temporal in vivo fate of 142 individual stem cell clones in 63 reconstituted mice. Long-term sequential analyses of the four major peripheral blood lineages, obtained from animals engrafted with genetically marked stem cells, indicate that developmental behavior is primarily a function of time. As such, the first 4-6 months post-engraftment is characterized by frequent fluctuations in stem cell proliferation and differentiation behavior. Gradually, a stable hematopoietic system emerges, dominated by a small number of totipotent clones. We demonstrate that single stem cell clones are sufficient to maintain hematopoiesis over the lifetime of an animal and suggest that mono- or oligoclonality may be a hallmark of long-term reconstituted systems. A model is proposed, wherein lineage-restricted differentiation and dramatic clonal flux are consequences of mechanisms acting on an expanding pool of totipotent cells and are not indicative of intrinsically distinct stem cell classes.

Animals↗
PubMed2001

Simple sequence repeat analysis of a clonally propagated species: a tool for managing a grape germplasm collection.

The USDA germplasm repositories help to preserve the genetic variability of important crop species by collecting and maintaining representative cultivars and related germplasm. Simple sequence repeat markers with high allelic diversity were used to type 41 grapevines from 40 accessions. All vines were either seedless table grape cultivars or cultivars with names similar to table grape cultivars. The proportion of shared alleles was selected as the most appropriate statistical measure of genetic distance for this population. In conjunction with morphological traits, known synonyms were confirmed and a previously unknown synonym was discovered. An alleged synonym in the literature was disproved by the DNA data. The data were consistent with known parentage, where such data were available. Two mislabeled vines in the USDA collection were identified. UPGMA grouped the cultivars loosely into three groups: a group of nine mostly Middle Eastern cultivars, a group of 22 accessions mostly from Russia and Afghanistan that were morphologically similar to 'Thompson Seedless', and a third very loose group of 11 accessions consisting mostly of eastern European wine grape cultivars. The limitations and usefulness of this type of analysis are discussed.

Alleles↗
PubMed1991

Molecular characterization of single memory B cells.

Primary antigenic exposure results in an initial antibody response and the T cell-dependent induction of B-cell memory. Memory B-cell differentiation is characterized by somatic hypermutation in antibody variable region genes (V) and selection of B cells expressing high-affinity variants of this antigen receptor. Despite our current understanding of B-cell memory, the origin of memory B cells and the regulation of their differentiation remain elusive. This is largely due to the difficulties in observing and purifying this minor component of the immunized spleen. Further, molecular characterization of memory B cells requires hybridoma formation which restricts analyses to only those clones capable of fusion and does not allow isolation of cells in a normal physiological state. We have therefore developed a unique system which allows isolation and unambiguous enumeration of IgG1+ memory B cells, based on six-parameter flow cytometry, secretion of antibody in clonal cultures and analysis of clonally expressed V genes using the polymerase chain reaction. Here we report that single IgG1+ antigen-binding B cells from an early secondary immune response proliferate in lipopolysaccharide-driven microcultures and produce antigen-specific IgG1 antibodies. Individual B-cell clones in these cultures express somatically mutated heavy chain V genes, confirming their designation as memory B cells. Although isolated memory B cells undergo extensive proliferation in vitro, V gene sequence analysis of their individual progeny shows that further hypermutation does not occur.

Amino Acid Sequence↗
PubMed1995

Interleukin 5 expressing allergen-specific T-lymphocytes in patients with house dust mite sensitization: analysis at a clonal level.

Interleukin 5 (IL-5) is a T-cell lymphokine known to stimulate development, functional activity, and in vitro survival of eosinophils. Tissue and blood eosinophilia occurring during allergic responses of the immune system are potentially mediated by IL-5 secreting T-cells. To test this hypothesis a series of allergen-specific T-cell clones were established from peripheral blood and skin lymphocytes of patients with atopic dermatitis and house dust mite sensitization. In addition, alloreactive T-cell clones were also prepared from peripheral blood lymphocytes of healthy donors. Cloned T-cells were analyzed for IL-5 mRNA expression and IL-5 secretion by means of in vitro gene amplification using the reverse transcriptase polymerase chain reaction and IL-5 specific oligonucleotide hybridization, as well as IL-5-specific ELISA. A majority of allergen-specific long-term cultured T-cell clones (84%) of different donors and of either phenotype (CD8+ or CD4+) disclosed IL-5 transcripts on stimulation with lectins. Almost all clones exhibiting IL-5 transcripts also released immunoreactive IL-5 protein into their culture supernatants. In contrast, only 2% of alloreactive T-cell clones obtained from healthy donors and none of alloreactive T-cell clones of one atopic patient investigated expressed detectable amounts of IL-5 mRNA in response to lectin stimulation, all of whom were CD4+. These results suggest that eosinophilia observed in allergic responses in the peripheral blood and in tissues at the site of induced late-phase cutaneous reaction may be associated with IL-5 release by allergen-specific T-cells.

Animals↗
PubMed1983

Microsurgical analysis of the clonal age and the cell-cycle stage required for the onset of autogamy in Paramecium tetraurelia.

When autogamy was induced in competent cells of Paramecium tetraurelia by depriving them of food, the onset of autogamy was preceded by a critical fission which occurred in the starvation medium. When the cells were fed again immediately after the fission, they did not undergo autogamy. However, they did undergo autogamy when they were fed later than 1 hr after the critical fission. The irreversible differentiation for autogamy seems to be at about 1 hr after the critical fission. This procedure thus provides the opportunity to induce autogamy synchronously. The result of macronuclear transplantation demonstrated that autogamy was under the control of macronucleus. Moreover, the clonal age required for autogamy was found to be shortened by repetitive elimination of a part of the macronucleus. The result can be explained by the hypothesis that clonal age is measured in rounds of chromosome replication or DNA synthesis rather than cell divisions.

Animals↗