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PubMed2006

Identification, phenotypic analysis, and full-length nucleotide sequence of a Dutch Coxsackievirus A20 isolate.

Recombination between (human) enteroviruses is a common event in nature. Recently, it has been recognised that this feature has a major impact on the use of the live-attenuated polio vaccine during the end stage of polio eradication. The constraints for successful recombination between (vaccine-derived) polioviruses and human enteroviruses are, however, largely unknown. Here, we describe the identification and characterisation of a HEV-C field strain, isolated from the stool of a 2-year-old Dutch boy. Serotyping indicated that strain 89490 is a variant of strain CAV20a, which is already a variant of the prototype CAV20 strain. Amino acid sequence identity of 94.1% for the entire P1-region, and 92.4% for the major structural protein (VP1) indicates that this strain is indeed related to CAV20. However, virus neutralisation and Western blot analysis failed to show antigenic homology between the prototype CAV20 strain and our field strain. Furthermore, the 89490 field strain, just like the sub-prototype CAV20a, is able to replicate on RD-cells, while the prototype CAV20 and another sub-prototype CAV20b are not. On the basis of the phylogenetic analysis of the P2 and P3 region we expect that strain 89490 can act as recombination partner for the attenuated poliovirus strains of the Oral Polio Vaccine (OPV).

Blotting, Western↗
PubMedDate not supplied

Phenotypic identification of amplifications of the ADH4 and CUP1 genes of Saccharomyces cerevisiae.

Primary gene amplification, i.e., mutation from one gene copy to multiple gene copies per genome, is important in genomic evolution, as a means of producing anti-cancer drug resistance, and is associated with the progression of tumor malignancy. Primary amplification has not been studied in normal eukaryotic cells because amplifications are extremely rare in these cells. A system has been developed to phenotypically identify co-amplifications of the ADH4 and CUP1 genes of Saccharomyces cerevisiae and 21 independent spontaneous amplifications have been isolated.

Alcohol Dehydrogenase↗
PubMed1997

Isolation and phenotypical identification of spore-forming Bacillus species from Jordanian habitats with larvicidal activity against Drosophila melanogaster.

Spore-forming Bacillus isolates were recovered from different Jordanian habitats. Of 37 samples, 187 colonies were selected. Forty-six (24.6%) of them were pathogenic to the third instar larvae of Drosophila melanogaster. Larvicidal activity of the isolates was from 0% (non-cultivated soil) to 83.3% (decomposed animal residues). The total spore count per gram weight varied from 0.1 x 10(5)-18 x 10(5) among the 37 tested samples. Morphological and microscopical identification of the isolates showed the presence of 16 different Bacillus species. The pathogenic isolates were B. thuringiensis (44) and B. sphaericus (2).

Animals↗
PubMed2000

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis.

Candida dubliniensis is an emerging yeast pathogen generally misclassified as Candida albicans by standard diagnostic procedures. This study examined the efficiency of molecular identification, based on a discriminative PCR test, in a prospective study on the prevalence of C. dubliniensis among 103 oropharyngeal isolates from HIV-infected individuals or transplant recipients, and 30 vaginal isolates. All of the isolates had been classified as C. albicans by standard laboratory procedures. The PCR was evaluated in a blinded fashion against classification achieved by sequencing rDNA. Sequencing results corresponded 100% to the results of the discriminative PCR, indicating the validity of this rapid test. Twenty-one C. dubliniensis isolates were identified, all of them from HIV-infected individuals (prevalence 30%). The internal transcribed spacer regions of the C. dubliniensis isolates were sequenced. Phenotypic features of C. dubliniensis, namely abundant chlamydospore formation, atypical color on CHROMagar, growth defect at 45 degrees C, and colony morphology on Staib agar, were evaluated in a blinded fashion with respect to their discriminative potential, facilitating the design of further epidemiological studies. Carbohydrate assimilation patterns were determined for C. dubliniensis with a novel automated system showing that, in contrast to previous reports, C. dubliniensis is able to utilize D-xylose and trehalose. In evaluating these tests we present a rational approach to identification of the new species and characterization of C. dubliniensis isolates.

AIDS-Related Opportunistic Infections↗
PubMed2001

Phenotypic identification and development of distinct microvascular compartments in the postnatal mouse spleen.

In this paper we report the development of the sinus network of mouse spleen during the first postnatal month as studied with a set of new rat monoclonal antibodies (mAbs) against mouse splenic endothelial cell subpopulations. One of the new mAbs (IBL-7/1) also stained B-cell lineage cells in the spleen shortly after the birth as confirmed by three-color flow cytometry. This B-cell staining in the primordial follicles vanished by the fourth postnatal week, so that the expression of IBL-7/1 antigen was restricted to the marginal sinus endothelium and some red pulp sinuses and a minor B-cell subset in the spleen, presumably distinct from the follicular B-cell compartment. The other mAb (IBL-9/2) selectively labeled the sinusoids of the deeper part of the red pulp, without any reactivity against hemopoietic cells. The IBL-9/2-reactive cells in newborns appeared as isolated elements throughout spleen, and during the segregation of white and red pulps they formed an extensive network in the red pulp outside the marginal zone. Double-labeling immunofluorescence revealed that most of these sinusoids also stained weakly with IBL-7/1 mAb, whereas the strongly IBL-7/1-positive vessels of this region were IBL-9/2 negative. Neither of these mAbs reacted with the central artery. The comparative phenotypic analysis of the various vascular segments indicates that the splenic sinusoids of the marginal zone and red pulp, respectively, are lined with a heterogeneous array of endothelium. For the precise identification, isolation, and characterization of the possible homing function of these endothelium subsets these region-specific mAbs may be of potential value.

Age Factors↗
PubMed2001

Phenotypic identification of Actinomyces and related species isolated from human sources.

Recent advancements in chemotaxonomic and molecular biology-based identification methods have clarified the taxonomy of the genus Actinomyces and have led to the recognition of several new Actinomyces and related species. Actinomyces-like gram-positive rods have increasingly been isolated from various clinical specimens. Thus, an easily accessible scheme for reliable differentiation at the species level is needed in clinical and oral microbiology laboratories, where bacterial identification is mainly based on conventional biochemical methods. In the present study we designed a two-step protocol that consists of a flowchart that describes rapid, cost-efficient tests for preliminary identification of Actinomyces and closely related species and an updated more comprehensive scheme that also uses fermentation reactions for accurate differentiation of Actinomyces and closely related species.

Actinomyces↗
PubMed2005

Phenotypic identification and technological properties of lactic acid bacteria isolated from traditionally processed fish products of the Eastern Himalayas.

Sukako maacha, gnuchi, sidra and sukuti are traditional smoked and sun-dried fish products of the Eastern Himalayan regions of Nepal and India. A total of 40 samples of sukako maacha (14), gnuchi (6), sidra (10) and sukuti (10) were collected and were analysed for microbial load. Population of lactic acid bacteria (LAB) as well as aerobic mesophilic counts ranged from 4.7-8.3 to 5.1-8.5 log cfu g(-1), respectively. A total of 189 strains of LAB were isolated from sukako maacha, gnuchi, sidra and sukuti samples, out of which 171 strains were cocci and 15 strains, were heterofermentative lactobacilli. LAB were identified on the basis of phenotypic characters including API system as Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. lactis, Lactococcus plantarum, Leuconostoc mesenteroides, Enterococcus faecium, Enterococcus faecalis, Pediococcus pentosaceus and Weissella confusa. LAB strains produced a wide spectrum of enzymes. Some strains of LAB showed antagonistic properties against pathogenic strains. None of the strains produced biogenic amines in the method applied. This paper is the first report on the microbial composition, mostly lactic acid bacteria, of traditionally processed fish products of Eastern Himalayas.

Animals↗
PubMed1999

Phenotypic identification of antigen-dependent and antigen-independent CD8 CTL precursors in the draining lymph node during acute cutaneous herpes simplex virus type 1 infection.

Optimal immunological control of cutaneous herpes simplex virus type 1 (HSV-1) infections initiated in the hind footpad of C57BL/6 (B6, H-2b) mice is dependent upon the presence of functional HSV-1-specific T lymphocytes. The class I MHC-restricted, CD8+ T cell subpopulation is involved in the clearance of infectious HSV-1 from the skin and limiting HSV-1 replication and spread within the peripheral nervous system. However, the frequency of HSV-1-specific CTL precursors (CTLp), as a measure of potential anti-viral CD8+ T cell function, is relatively low compared with other acute viral infections. To gain insight into the basis for this low functional frequency, changes in the CD8+ T cell subpopulation phenotype associated with activation and differentiation were investigated. Analysis of the phenotypic changes showed that HSV-1-specific CTLp were found predominantly within a subpopulation of CD8+ T cells expressing high levels of CD44 (CD44high) and high levels of the IL-2 receptor alpha-chain (CD25high). A second activated subpopulation of CD8+ T cells expressing the CD44high CD25low phenotype did not contain detectable HSV-1-specific CTLp, even after the addition of HSV-1-infected stimulator cells as a source of an exogenous Ag. These data suggested that HSV-1-specific CD8+ T cells must increase expression of CD25 before attaining the potential to become CTL effector cells. These findings also indicated that the up-regulation of CD44 alone is not sufficient to identify precisely HSV-1-specific CD8+ T cells.

Acute Disease↗
PubMed1994

Genotypic and phenotypic identification of coli surface antigen 6-positive enterotoxigenic Escherichia coli.

A polynucleotide probe comprising the gene encoding a major structural subunit protein of coli surface antigen 6 (CS6) of enterotoxigenic Escherichia coli (ETEC) was developed. Eighty-nine ETEC isolates were examined in parallel with the probe in a colony hybridization assay and in a recently developed polyclonal-antibody-based inhibition enzyme-linked immunosorbent assay (ELISA). The two assays showed a high level of concordance in the detection of CS6-positive ETEC (kappa = 0.84, P < 0.00001). Thus, 36 of the 89 ETEC isolates were identified as CS6-positive by both assays. Six strains that were negative for other colonization factor antigens were positive with the CS6 probe but negative in the ELISA, suggesting lack of surface CS6 expression in these strains. One strain was probe negative but positive in the ELISA, while the remaining 46 strains were negative in both assays. The phenotypic and genotypic assays will prove useful in vaccine-oriented studies of ETEC disease.

Antigens, Bacterial↗
PubMed1987

Phenotypic identification of suppressor-effector, suppressor-amplifier and suppressor-inducer T cells of B cell differentiation in man.

Using monoclonal anti-Leu8 antibody to isolate subpopulations of human helper/inducer (CD4+) and suppressor/cytotoxic (CD8+) T cells, we have investigated the role of these subpopulations in the regulation of B cell differentiation in the human autologous mixed leukocyte reaction (AMLR). Whereas AMLR-activated CD8+,Leu8- cells were capable of suppressing fresh AMLR cultures in the absence of fresh CD8+ cells, CD8+,Leu8+ cells suppressed only those cultures containing fresh CD8+ cells. On the other hand, CD8+,Leu8- cells became suppressor cells only when cultured in the presence of CD8+,Leu8+ cells. Finally, the development of CD8+ suppressor cells was dependent on the presence of CD4+,Leu8+ cells; CD4+,Leu8- cells were incapable of acting as suppressor-inducer cells, but have been shown previously to mediate T cell help for B cell differentiation. Thus, at least 3 phenotypically distinct subsets of T cells interact sequentially to generate suppression of B cell differentiation induced in the AMLR: CD4+,Leu8+ suppressor/inducer cells, CD8+,Leu8+ suppressor-amplifier cells and CD8+,Leu8- suppressor-effector cells.

Antigens, Differentiation, T-Lymphocyte↗
PubMed1983

Small deletion in src of Rous sarcoma virus modifying transformation phenotypes: identification of 207-nucleotide deletion and its smaller product with protein kinase activity.

Partial deletion in the src gene and the gene product were characterized in a deletion mutant, dl5, isolated from the Prague strain of Rous sarcoma virus. The mutant induced fusiform-like transformed cells, unlike the parental Prague strain, which induced round transformed cells. Determination of the total nucleotide sequences of src in dl5 and the Prague strain of Rous sarcoma virus demonstrated that in the former two deletions of 196 and 11 nucleotides had occurred at positions 403 and 696, respectively, from the 5' end of src. A protein with a molecular weight of 52,000 (p52src) was detected in cells infected with dl5, as predicted from the deletion size in src. From the nucleotide sequence, it was predicted that p52src had two deletions of 65 and 4 amino acids at positions 135 and 232, respectively, from the N-terminal methionine of p60src and also had 33 amino acid changes between these two deletion sites due to alteration of the reading frame. p52src, which contained deletions and alterations of amino acids near the N-terminus, showed protein kinase activity similar to that of p60src and functioned in the infected cells. These results strongly suggest that changes in the N-terminal region of p60src modified its transforming ability, causing induction of the fusiform-like transformation phenotype.

Avian Sarcoma Viruses↗
PubMed1990

Phenotypic identification of T lymphocytes subset in recurrent aphthous stomatitis.

Recurrent aphthous stomatitis (RAS) is characterized by recurring ulcers in the oral mucosa as abnormality of the immune response, autoimmune or abnormal immunological reaction to antigens of oral bacteria. This study was conducted on 25 patients 15 suffering RAS of the minor form and 10 of the major form and 15 student as control. The T lymphocytes were determined by the monoclonal antibodies (OKT) using the indirect immunofluorescent technique of Hoffman percentage of cells having surface fluorescence was calculated and the monoclonal antibody coated cells visualized and enumerated. It was concluded from this study that the two clinical entities of RAS may be of the same immunopathologic etiology but the difference lies in the T cell subpopulation and the ratio of T helper to T suppressor T4/T8.

Adolescent↗
PubMed1995

Phenotypic identification of specific and nonspecific suppressor T-cell populations involved in the in vivo response to alloantigen.

The monoclonal antibody 984.D4.6 (ma984) has been previously shown to recognize antigen-specific suppressor T-cells in an in vitro alloantigenic mixed-lymphocyte response system. In addition, an antiserum generated in rabbits to the N-terminal sequence of the nonspecific suppressor factor SIRS (soluble immune response suppressor) has been shown to block the suppressive activity of nonspecific, concanavalin A-activated suppressor cells. In the present studies we have used these antibodies to investigate the development of T-suppressor activity in mice immunized with alloantigen. These studies demonstrate the development of two populations of suppressor cells, one of which is antigen nonspecific and inhibitable with anti-SIRS and a second that is antigen-specific and sensitive to removal by lysis with ma984 plus complement. These populations of suppressor cells arise well after the peak of cytolytic T-cell activity in response to alloantigen indicating asynchrony in the development of the immune response to alloantigen.

Animals↗
PubMed1987

Phenotypic identification of memory cytolytic T lymphocytes in a subset of Lyt-2+ cells.

Murine peripheral Lyt-2+ T cells could be subdivided according to surface expression of the Pgp-1 glycoprotein into major (71%) Pgp-1- and minor (29%) Pgp-1+ subsets. A striking correlation was observed between Pgp-1 expression and enrichment for antigen-specific memory cytolytic T lymphocyte precursors (CTLp). After immunization with the male minor transplantation antigen H-Y, virtually all the H-Y-specific CTLp were found in the minor Pgp-1+ subset of Lyt-2+ cells. In addition, after alloimmunization the frequency of allospecific CTLp resistant to inhibition by anti-Lyt-2 antibody was markedly enriched within the Pgp-1+ cells, suggesting an enrichment for CTLp bearing high avidity antigen receptors. Taken together, these data suggest that surface Pgp-1 expression is stably acquired at the time of primary antigenic stimulation by virgin T cells. As such, Pgp-1 represents an important marker for identifying a subset of Lyt-2+ T cells with the quantitative and qualitative properties of memory CTLp.

Animals↗
PubMed2000

Mapping of c-fos gene expression in the brain during morphine dependence and precipitated withdrawal, and phenotypic identification of the striatal neurons involved.

The c-fos gene is expressed in the central nervous system in response to various neuronal stimuli. Using in situ hybridization, we examined the effects of chronic morphine treatment and withdrawal on c-fos mRNA in the rat brain, and particularly within identified striatal neurons. Morphine dependence was induced by subcutaneous implantation of two pellets of morphine for 6 days and withdrawal was precipitated by administration of naltrexone. Placebo animals and morphine-dependent rats showed a very weak c-fos mRNA expression in all the structures studied. Our study emphasized the spatial variations in c-fos mRNA expression, and also revealed a peak expression of c-fos mRNA at 1 h after naltrexone-precipitated withdrawal in the projection areas of dopaminergic neurons, noradrenergic neurons and in several regions expressing opiate receptors. Interestingly, morphine withdrawal induces c-fos mRNA expression in the two efferent populations of the striatum (i.e. striatonigral and striatopallidal neurons) both in the caudate putamen and nucleus accumbens. Moreover, the proportions of activated neurons during morphine withdrawal are different in the caudate putamen (mostly in striatopallidal neurons) and in the shell and core parts of the nucleus accumbens (mostly in striatonigral neurons). The activation of striatopallidal neurons suggests a predominant dopaminergic regulation on c-fos gene expression in the striatum during withdrawal. On the contrary, c-fos induction in striatonigral neurons during withdrawal seems to involve a more complex regulation like opioid-dopamine interactions via the mu opioid receptor and the D1 dopamine receptor coexpressed on this neuronal population or the implication of other neurotransmitter systems.

Animals↗
PubMed2005

Phenotypic identification of Candida albicans by growth on chocolate agar.

In this study, we describe a simple method for the identification of Candida albicans in clinical samples. A total of 383 clinical isolates of Candida species were streaked onto chocolate agar and incubated for 48 h at 37 degrees C in the presence of an atmosphere of 6% CO2. All 208 of the C. albicans isolates tested, developed an easy to identify filamentous colony morphology. Of 175 other Candida species tested, 172 (98.3%) were distinguishable from C. albicans by their smooth colony morphology. Three isolates (1.7%) exhibited weak filamentation after prolonged incubation. Although not a routine medium in medical mycology a significant advantage of using chocolate agar lies in its use in clinical bacteriology laboratories for the isolation of fastidious bacteria. Implementation of the proposed method is applicable across a range of specimen types, thus allowing the direct identification of C. albicans in clinical samples. This simple method may allow a quicker entry into directed treatment.

Candida albicans↗
PubMed2003

16S ribosomal RNA sequence-based identification of veterinary clinical bacteria.

This study evaluated 16S rRNA gene sequence analysis methods as tools for identification of 22 phenotypically difficult to identify veterinary clinical bacterial isolates in a veterinary diagnostic laboratory. The study compared 16S rRNA gene sequencing and conventional phenotypic identification methods. Using 16S rRNA full-gene sequencing, 95% (21/22) of the isolates were identified to the genus level and 86% (19/22) to the species level. The conventional or commercially available manual identification phenotypic characterization methods presumptively identified 91% (20/22) of the isolates to the genus level and 1 isolate to the species level. However, only 55% (12/22) or 4.5% (1/22) of the phenotypic identifications were correct at the genus or species level when they were compared with the 16S rRNA full-gene sequencing. This study also compared 16S rRNA full-gene and partial-gene sequencing. The results demonstrated that the best 16S rRNA gene-sequencing approach is full-gene sequencing because it gives the most precise species identification. Sequencing of the variable regions 1, 2, and 3 of the 16S rRNA gene could be used for tentative identification because the ability of this sequencing to identify bacteria to the genus level is similar to that of the 16S rRNA full-gene sequencing. This method identified only 14% (3/22) isolates differently to the species level compared with the 16S rRNA full gene sequence. Sequencing of the variable regions 7, 8, and 9 is not recommended because it gives more ambiguous identifications. The cost of a 16S RNA full-gene-sequencing analysis was Can 160 dollars and Can 60 dollars for a partial 16S rRNA gene sequence, i.e., sequencing of variable regions 1, 2, and 3 or variable regions 7, 8 and 9.

Bacteria↗