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Study of the 16S-23S ribosomal DNA internal spacer of Coxiella burnetii.

The complete 16S-23S ribosomal DNA (rDNA) internal transcribed spacer (ITS) of 22 isolates of the obligate intracellular bacterium Coxiella burnetii, the agent of Q fever, were amplified by the polymerase chain reaction (PCR) and sequenced using an automated laser fluorescent DNA sequencer. The ITS measured 497 base pairs (bp) and encoded isoleucine-tRNA and alanine-tRNA. The comparison of the sequence alignments of the 22 C. burnetii strains revealed very high levels of sequence similitary (> 99%) although they had different geographic origins and phenotypic characteristics. Sequencing of the 16S-23S rDNA ITS of C. burnetii could be utilized for identification of the bacterium but is not applicable to studies of epidemiology, virulence and taxonomy.

Animals↗

Jk(a-b-) red blood cells resist urea lysis.

Falsely high automated platelet counts in a patient with aplastic anemia were found to be due to increased resistance of the red blood cells to urea lysis. The patient's blood group Jk(a-b-). Further investigation revealed that this phenomenon occurred with all of eight bloods of the phenotype Jk(a-b-) but not with red blood cells of other phenotypes tested. We therefore report an association of a rare blood group phenotype with unusual red blood cell behavior in vitro.

Adult↗

High resolution plasma lipoprotein cholesterol profiles by a rapid, high volume semi-automated method.

A new rapid and sensitive method, the single vertical spin autoprofiler (VAP), has been developed for quantitative profiling of the major plasma lipoproteins. The method involves a combination of single vertical spin separation of plasma and continuous on-line analysis of cholesterol. Plasma lipoproteins are first separated by a 45-min spin in a vertical rotor, after which the amount of cholesterol in the effluent of each tube is monitored continuously by a modification of the BMC automated enzymatic cholesterol method; simultaneously, 80% of the sample is diverted by stream-splitting to a fraction collector for further analysis, if desired. VAP not only resolves very low density lipoprotein (VLDL), low density lipoprotein (LDL), and high density lipoprotein (HDL) peaks quantitatively but also detects the presence of intermediate density lipoprotein (IDL) and other lipoprotein variants. VAP was highly reproducible; the inter-run coefficient of variation for cholesterol concentration in VLDL, LDL, and HDL was 4.8%, 2.9%, and 2.4%, respectively. Cholesterol recovery using VAP was 98.5 +/- 3.5%. Lipoprotein-cholesterol profiles of plasma from three major hyperlipoproteinemia phenotypes examined by VAP were qualitatively and quantitatively different from each other and from profiles of normolipidemic individuals. One significant finding was that IDL could be detected in the plasma of all type IV hyperlipoproteinemic subjects examined thus far. Several variant lipoprotein profiles which did not correspond to known phenotypes have also been detected by VAP using plasma from hyperlipidemic as well as from normolipidemic subjects. We submit that VAP is an accurate and rapid method for lipoprotein analysis, either for routine clinical screening or for detailed experimental studies. In addition, VAP provides a visual display of partially to completely resolved lipoprotein classes that is suitable for computer-assisted analysis.-Chung, B. H., J. P. Segrest, J. T. Cone, J. Pfau, J. C. Geer, and L. A. Duncan. High resolution plasma lipoprotein cholesterol profiles by a rapid, high volume semi-automated method.

Animals↗

Knowledge discovery by automated identification and ranking of implicit relationships.

MOTIVATION: New relationships are often implicit from existing information, but the amount and growth of published literature limits the scope of analysis an individual can accomplish. Our goal was to develop and test a computational method to identify relationships within scientific reports, such that large sets of relationships between unrelated items could be sought out and statistically ranked for their potential relevance as a set. RESULTS: We first construct a network of tentative relationships between 'objects' of biomedical research interest (e.g. genes, diseases, phenotypes, chemicals) by identifying their co-occurrences within all electronically available MEDLINE records. Relationships shared by two unrelated objects are then ranked against a random network model to estimate the statistical significance of any given grouping. When compared against known relationships, we find that this ranking correlates with both the probability and frequency of object co-occurrence, demonstrating the method is well suited to discover novel relationships based upon existing shared relationships. To test this, we identified compounds whose shared relationships predicted they might affect the development and/or progression of cardiac hypertrophy. When laboratory tests were performed in a rodent model, chlorpromazine was found to reduce the progression of cardiac hypertrophy.

Abstracting and Indexing↗

The homeobox gene GLABRA2 affects seed oil content in Arabidopsis.

Despite a good understanding of genes involved in oil biosynthesis in seed, the mechanism(s) that controls oil accumulation is still not known. To identify genes that control oil accumulation in seed, we have developed a simple screening method to isolate Arabidopsis seed oil mutants. The method includes an initial screen for seed density followed by a seed oil screen using an automated Nuclear Magnetic Resonance (NMR). Using this method, we isolated ten low oil mutants and one high oil mutant. The high oil mutant, p777, accumulated 8% more oil in seed than did wild type, but it showed no differences in seed size, plant growth or development. The high-oil phenotype is caused by the disruption of the GLABRA2 gene, a previously identified gene that encodes a homeobox protein required for normal trichome and root hair development. Knockout of GLABRA2 did not affect LEAFY COTYLEDON 1 and PICKLE expression in developing embryo. The result indicates that in addition to its known function in trichome and root hair development, GLABRA2 is involved in the control of seed oil accumulation.

Adhesives↗

Genotyping microsatellite polymorphisms by agarose gel electrophoresis with ethidium bromide staining: application to quantitative trait loci analysis of seizure susceptibility in mice.

Agarose gel electrophoresis with ethidium bromide staining (AGE/EBS) is an efficient and reliable method for analyzing microsatellite polymorphisms. We report the use of AGE/EBS for analyzing DNA microsatellite polymorphisms in a preliminary quantitative trait loci (QTL) study of seizure susceptibility in which a candidate gene strategy was used to direct initial mapping efforts. F2 intercross progeny, derived from seizure-sensitive DBA/2J (D2) and seizure-resistant C57BL/6J (B6) inbred strains of mice, were tested for their sensitivity to the seizure-inducing effect of pentylenetetrazol (PTZ), a gamma-aminobutyric acid (GABA) receptor antagonist. A semi-automated method is described, in which DNA microsatellites were amplified by polymerase chain reaction (PCR) to yield products of 100-200 base pair (bp) in length. Alleles were separated on 3-6% MetaPhor agarose gels, stained with ethidium bromide, and visualized by ultraviolet (UV) illumination. Univariate analysis of genotype and phenotype data provides evidence for a seizure-related QTL on chromosome 5, near genes coding for the GABAA receptor subunits alpha 5 and gamma 3. Interestingly, this suggestive QTL derives from the more resistant B6 strain, but it nonetheless provides impetus for the characterization of possible strain differences in these two candidate genes. Overall, these results demonstrate that AGE/EBS can be useful for rapid screening of genomic regions of special interest in QTL mapping studies.

Animals↗

Compound heterozygosity for nonsense and missense mutations in the LAMB3 gene in nonlethal junctional epidermolysis bullosa.

Mutations in the genes encoding laminin 5 (LAMA3, LAMB3, and LAMC2) have been delineated in the autosomal recessive blistering skin disorder, junctional epidermolysis bullosa, particularly in the lethal (Herlitz) variant. In this study, we searched for mutations in these genes in two patients with nonlethal forms of junctional epidermolysis bullosa using polymerase chain reaction amplification of genomic DNA, followed by heteroduplex analysis and direct automated nucleotide sequencing. Both patients were found to be compound heterozygotes for the same nonsense mutation on one LAMB3 allele, and different missense mutations on the other LAMB3 allele. The combination of nonsense and a missense mutation in the LAMB3 gene appears to be important in determining the milder clinical phenotype in some cases of the nonlethal forms of junctional epidermolysis bullosa involving abnormalities in laminin 5.

Aged↗

Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase.

Drug resistance is a major problem in the treatment of AIDS, due to the very high mutation rate of human immunodeficiency virus (HIV) and subsequent rapid development of resistance to new drugs. Identification of mutations associated with drug resistance is critical for both individualized treatment selection and new drug design. We have performed an automated mutation analysis of HIV Type 1 (HIV-1) protease and reverse transcriptase (RT) from approximately 40,000 AIDS patient plasma samples sequenced by Specialty Laboratories Inc. from 1999 to mid-2002. This data set provides a nearly complete mutagenesis of HIV protease and enables the calculation of statistically significant K(a)/K(s) values for each individual amino acid mutation in protease and RT. Positive selection (i.e., a K(a)/K(s) ratio of >1, indicating increased reproductive fitness) detected 19 of 23 known drug-resistant mutation positions in protease and 20 of 34 such positions in RT. We also discovered 163 new amino acid mutations in HIV protease and RT that are strong candidates for drug resistance or fitness. Our results match available independent data on protease mutations associated with specific drug treatments and mutations with positive reproductive fitness, with high statistical significance (the P values for the observed matches to occur by random chance are 10(-5.2) and 10(-16.6), respectively). Our mutation analysis provides a valuable resource for AIDS research and will be available to academic researchers upon publication at http://www.bioinformatics.ucla.edu/HIV. Our data indicate that positive selection mapping is an analysis that can yield powerful insights from high-throughput sequencing of rapidly mutating pathogens.

Amino Acid Sequence↗

Primary gastric lymphomas (MALTomas): a nuclear image analysis comparison with lymph node monocytoid B-cells and marginal zones of spleen and Peyer's patches.

Centrocyte-like cells of marginal zones of follicles of gastrointestinal lymphoid tissue, which have their analogous in marginal zone of splenic white pulp and in lymph node monocytoid B-lymphocytes, are thought to be the normal counterpart of lymphomas of MALT (MALTomas). However, the cell population of MALTomas is often polymorphic and also contains cells morphologically different from centrocytes. Since conventional morphologic analysis may not be accurate enough and the phenotype may change in different stages of B-cell lineage, the marginal zone of Peyer's patches (PMZ) and splenic white pulp (SMZ), the lymph node monocytoid B-lymphocytes (ML), 3 nodal monocytoid B-cell lymphomas (L) and 16 gastric MALTomas (M) were studied by means of automated nuclear image analysis for area, irregularity, and chromatin texture assessment. Immunophenotyping on paraffin sections and polymerase chain reaction (PCR) for detecting monoclonality and t(14-18) chromosome breakpoints at DNA levels, on paraffin section extractions, were also done. In 14 MALTomas, clonal Ig heavy chain rearrangement was detected and in none of these were found t(14-18) chromosome breakpoints. The nuclei of the control group (PMZ, SMZ and ML) showed the same morphologic characteristics, ie. size, irregularity, chromatin texture. MALTomas and nodal lymphomas were distributed into 3 clusters: (1) with larger nuclei, light chromatin (euchromatin-richer) (5 MALTomas, 2 nodal lymphomas together with the control group); (2) nuclei with the same area size, but darker (eterochromatin-richer) (6 MALTomas and 1 nodal lymphoma); (3) with smaller and darker nuclei (5 MALTomas). Chromatin textural differences were maintained in the same nuclear size class in the 3 clusters. Only a few MALTomas had nuclear features not significantly different from controls, inter-case and intra-case variability being evident.

B-Lymphocytes↗

Identification of glycopeptide-resistant enterococci by VITEK 2 system and conventional and real-time polymerase chain reaction.

Glycopeptide-resistant enterococci (GRE) are important causes of nosocomial infections in the United States and in Europe. Rapid detection of GRE is essential for the implementation of appropriate control measures to prevent the spread of GRE. In this study, we compared the reliability of 3 different methods, VITEK 2 automated system (bioMérieux), a conventional multiplex polymerase chain reaction (m-PCR) protocol, and a real-time PCR protocol performed on the LightCycler system (Roche) for identification of GRE in the routine microbiology laboratory. Species identification and glycopeptide resistance determination was tested with 80 enterococcal isolates with different glycopeptide resistance phenotypes. With the VITEK 2 system, 39% of the strains were correctly identified to species level. Resistance to vancomycin was detected in all isolates; however, discrepancies occurred in the correct detection of teicoplanin resistance. The PCR protocols proved to be suitable for detecting clinically relevant GRE; 90% of the isolates studied were correctly identified with the conventional m-PCR and 100% of vanA and vanB isolates with the real-time PCR protocol, respectively. High specificity and rapidity make the real-time PCR assays superior tools for identification of GRE in clinical samples; however, they do not have the ability to detect vanC.

Anti-Bacterial Agents↗

Compound heterozygosity for nonsense ans missense mutations in the LAMB3 gene in nonlethal junctional epidermolysis bullosa.

Mutations in the genes encoding laminin 5 (LAMA3, LAMB3, and LAMC2) have been delineated in the autosomal recessive blistering skin disorder, junctional epidermolysis bullosa, particularly in the lethal (Herlitz) variant. In this study, we searched for mutations in these genes in two patients with nonlethal forms of junctional epidermolysis bullosa using polymerase chain reaction amplification of genomic DA, followed by heteroduplex analysis and direct automated nucleotide sequencing. Both patients were found to be compound heterozygotes for the same nonsense mutation on one LAMB3 allele, and different missense mutations on the other LAMB3 allele. The combination of a nonsense and a missense mutation in the LAMB3 gene appears to be important in determining the milder clinical phenotype in some cases of the nonlethal forms of junctional epidermolysis bullosa involving abnormalities in laminin 5.

Aged↗

Molecular characterization of new polymorphisms at the beta2, alpha1, gamma2 GABA(A) receptor subunit genes associated to a rat nonpreferring ethanol phenotype.

Recent preclinical and clinical studies have indicated a possible involvement of the genes encoding for the GABA(A) receptor subunits alpha6, beta2, alpha1 and gamma2 in the genetic susceptibility to alcohol abuse. We have recently found an (R) to (Q) mutation in codon 100 of the alpha6 GABA(A) subunit, that segregated in a rat line selectively bred for its voluntary ethanol aversion, Sardinian alcohol nonpreferring (sNP), but not in their Sardinian alcohol preferring (sP) counterpart, selected for its ethanol preference. In the present study the molecular composition of other GABA(A) subunits (beta2, alpha1 and gamma2) were analyzed in order to further investigate the involvement of the GABA(A) receptors in the genetic predisposition to voluntary alcohol intake. Automated sequencing analysis indicated the presence of six new silent substitutions (289 T-->C in the beta2 gene; 115 G-->A in the alpha1 gene; 157 G-->A, 174 C-->T, 347 A-->G and 385 A-->T in the gamma2 gene), in sNP but not in sP rats. These polymorphisms were linked to the alpha6 R100Q mutation previously described in sNP rats. The strict association between the alpha6 point mutation and the new polymorphisms found in the beta2, alpha1 and gamma2 genes, demonstrate that such genes belong to the same cluster and are inherited together in the rat. These results sustain the synteny for these clusters between the rodent and human genomes, and suggest that mutated GABA(A) beta2, alpha6, alpha1 and gamma2 subunit genes might contribute to the expression of an ethanol nonpreferring phenotype in a rat line that voluntarily avoids alcoholic solutions.

Alcohol-Induced Disorders, Nervous System↗

Evaluation of a flow cytometric method for simultaneous leukocyte phenotyping and quantification by fluorescent microspheres.

We describe a flow cytometric method using a newly designed product, fluorochrome-containing microspheres (Flow Count fluorospheres), which facilitates the precise quantification of cells in whole blood samples or heterogeneous cell suspensions on a single-cell level. These microparticles are easily distinguishable from other events of interest and can be detected by their light-scattering and fluorescence properties. In contrast to the traditional manual or automated cell-counting techniques, this method offers the opportunity to quantify cells simultaneously with flow cytometric immunophenotyping without additional cell loss or other cell preparation steps. We evaluated the accuracy and reproducibility of this flow cytometric method on the determination of CD45+ leukocyte counts and compared the results with those obtained by conventional techniques. Particular interest was focused on the behavior of cells and fluorospheres regarding their sedimentation rate over the period of analysis. The data from 48 blood samples with low, normal, and high leukocyte counts confirmed the reliability and comparability of the flow cytometric method, permitting the determination of white blood cell concentration at least to a limit of 100 cells/microL. A broad field of applications will benefit from this flow cytometric supplement because it is easy to perform and highly accurate. The results appear to be transferable to clinical decision-making monitoring of CD4+ lymphocytes in patients infected with human immunodeficiency virus or of CD34+ hematopoietic cells, optimizing the harvest for peripheral blood stem cell transplantation.

Antigens, CD34↗

Yeast identification in the clinical microbiology laboratory: phenotypical methods.

Emerging yeast pathogens are favoured by increasing numbers of immunocompromised patients and by certain current medical practices. These yeasts differ in their antifungal drug susceptibilities, and rapid species identification is imperative. A large variety of methods have been developed with the aim of facilitating rapid, accurate yeast identification. Significant recent commercial introductions have included species-specific direct enzymatic colour tests, differential chromogenic isolation plates, direct immunological tests, and enhanced manual and automated biochemical and enzymatic panels. Chromogenic isolation media demonstrate better detection rates of yeasts in mixed cultures than traditional media, and allow the direct identification of Candida albicans by means of colony colour. Comparative evaluation of rapid methods for C. albicans identification, including the germ tube test, shows that chromogenic media may be economically advantageous. Accurate tests for single species include the Bichrolatex Albicans and Krusei Color tests, both immunologically based, as well as the Remel Rapid Trehalose Assimilation Broth for C. glabrata. Among broad-spectrum tests, the RapID Yeast Plus system gives same-day identification of clinical yeasts, but performance depends on inoculum density and geographic isolate source. The API 20 C AUX system is considered a reference method, but newer systems such as Auxacolor and Fungichrom are as accurate and are more convenient. Among automated systems, the ID 32 C strip, the Vitek Yeast Biochemical Card and the Vitek 2 ID-YST system correctly identify >93% of common yeasts, but the ID-YST is the most accurate with uncommon yeasts, including C. dubliniensis. Spectroscopic methods such as Fourier transformed-infrared spectroscopy offer potential advantages for the future. Overall, the advantages of rapid yeast identification methods include relative simplicity and low cost. For all rapid methods, meticulous, standardized multicenter comparisons are needed before tests are fully accepted.

Candida↗

Techniques used to define human MHC antigens: serology.

The classical, routine test employed for definition of HLA antigens expressed in humans (tissue typing) is the complement-mediated cytotoxicity assay developed by Terasaki and McClelland in the early 1960s. In both healthy persons and patients, the assay target cells are usually lymphocytes obtained from peripheral blood, but when typing cadaver donors, splenic or lymph node lymphocytes can be used. HLA-A, B, Cw (class I) antigens are expressed on all nucleated cells while HLA-DR, DQ (class II) are restricted to B lymphocytes and immune activated cells. Tissue typing has been achieved using culture cells from amniocentesis and typing of cell lines is possible with small modifications to the standardised cytotoxicity assay. Usually, target cells are incubated under oil with typing antisera at 22 degrees C in a 60- or 72-well Terasaki tray. After 30 min rabbit serum is added as a source of complement. After a further 60 min incubation the test is stained. A positive reaction results in target cell death. There are local variations to this test. Automation of the assay is now commonplace, from reagent dispensing to automated reading of finished assay. The use of antibody-coated magnetisable microspheres has enabled separation of pure B lymphocyte samples for class II typing and has reduced incubation times through antigen modulation. It is possible to define antibodies to HLA antigens in the same assay using target cells with known HLA phenotypes.

Complement System Proteins↗

Inducible amp C beta-lactamase producing gram-negative bacilli from blood stream infections: frequency, antimicrobial susceptibility, and molecular epidemiology in a national surveillance program (SCOPE).

A surveillance study of nosocomial blood stream infections [Surveillance and Control of Pathogens of Epidemiologic Importance (SCOPE)] was conducted during a 14-month period in 1995 to 1996 in approximately 50 American medical centers. Among the 4725 blood stream infections, the etiologic agent was Enterobacter spp. in 230, Citrobacter freundii in 24, and Serratia marcescens in 65. The vast majority of these isolates (89%) had been sent to the University of Iowa including 198 Enterobacter spp. (46 Enterobacter aerogenes, 141 Enterobacter cloacae, 11 other Enterobacter spp.), 23 C. freundii, and 62 S. marcescens. Because these species are capable of producing Amp C beta-lactamase, we examined their susceptibility to 12 broad-spectrum antimicrobial agents. The frequency of resistance to ceftazidime and the molecular epidemiology of ceftazidime-resistant strains was also examined. Among the Enterobacter spp. and C. freundii isolates, resistance to third generation cephalosporins (ceftazidime, ceftriaxone) and broad-spectrum semisynthetic penicillins (piperacillin), with or without an enzyme inhibitor (piperacillin/tazobactam), was high, e.g., 35 to 50%. The S. marcescens isolates were quite susceptible to all agents tested. Both imipenem and cefepime were active against virtually all isolates tested including 84 stably derepressed Amp C-producing ceftazidime-resistant strains of Enterobacter spp. and C. freundii. The overall rank order of activity for the six best agents against these Amp C-producing strains was: imipenem (100% susceptible) > amikacin = cefepime (98.6%) > ciprofloxacin = gentamicin = ofloxacin (93.6 to 94.0%). Molecular typing studies of ceftazidime-resistant E. cloacae using an automated ribotyping system, as well as pulsed-field gel electrophoresis, indicated that although clonal spread of a single strain occurred in some of the medical centers, most of the episodes of bacteremia were caused by patient-unique strains. Control of these resistant organisms will require attention to microbiologic recognition of phenotypes, to infection control practices, and to limiting the overuse of certain extended spectrum beta-lactams.

Anti-Bacterial Agents↗

IL-1beta and LPS induce anorexia by distinct mechanisms differentially dependent on microsomal prostaglandin E synthase-1.

Recent work demonstrated that the febrile response to peripheral immune stimulation with proinflammatory cytokine IL-1beta or bacterial wall lipopolysaccharide (LPS) is mediated by induced synthesis of prostaglandin E(2) by the terminal enzyme microsomal prostaglandin E synthase-1 (mPGES-1). The present study examined whether a similar mechanism might also mediate the anorexia induced by these inflammatory agents. Transgenic mice with a deletion of the Ptges gene, which encodes mPGES-1, and wild-type controls were injected intraperitoneally with IL-1beta, LPS, or saline. Mice were free fed, and food intake was continuously monitored with an automated system for 12 h. Body weight was recorded every 24 h for 4 days. The IL-1beta induced anorexia in wild-type but not knock-out mice, and so it was almost completely dependent on mPGES-1. In contrast, LPS induced anorexia of the same magnitude in both phenotypes, and hence it was independent of mPGES-1. However, when the mice were prestarved for 22 h, LPS induced anorexia and concomitant body weight loss in the knock-out animals that was attenuated compared with the wild-type controls. These data suggest that IL-1beta and LPS induce anorexia by distinct immune-to-brain signaling pathways and that the anorexia induced by LPS is mediated by a mechanism different from the fever induced by LPS. However, nutritional state and/or motivational factors also seem to influence the pathways for immune signaling to the brain. Furthermore, both IL-1beta and LPS caused reduced meal size but not meal frequency, suggesting that both agents exerted an anhedonic effect during these experimental conditions.

Animals↗

Familial keratoconus with cataract: linkage to the long arm of chromosome 15 and exclusion of candidate genes.

PURPOSE: Keratoconus and cataract are common causes of visual morbidity. Both conditions show genetic predisposition. The purpose of this study was to map the disease locus in a large three-generation family affected by combined early-onset autosomal dominant anterior polar cataract and clinically severe keratoconus. Uniquely, in this family both disorders were present and fully penetrant in those affected. METHODS: Thirty members of the family were examined clinically on two occasions, at an interval of 5 years, to establish their phenotypes and determine the progression of the disease. Genomic DNA was extracted from blood samples of 16 affected and 14 unaffected individuals, and typed with more than 350 highly polymorphic microsatellite loci in a genome-wide linkage screen. Markers were amplified by PCR with fluorescently labeled primers and sized with an automated DNA analyser before calculation of lod scores. After linkage was established, several positional candidate genes were assessed by PCR-based DNA sequencing. RESULTS: The locus for keratoconus with cataract was mapped to a 6.5-Mb region of the long arm of chromosome 15, at 22.33-24.2 between CYP11A and D15S211. The positional and functional candidate genes CTSH, CRABP1, IREB2, and RASGRF1 were excluded as the cause of keratoconus with cataract in this family. CONCLUSIONS: This is the first report of a family with autosomal dominant inheritance of keratoconus in association with cataract. The causative gene maps to the long arm of chromosome 15 but has not yet been identified.

Adolescent↗