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PubMed2005

Techniques for antifungal susceptibility testing of Candida albicans biofilms.

Candida albicans is capable of forming biofilms on a variety of inert and biological surfaces. Cells in biofilms display phenotypic properties that are radically different from their free-floating planktonic counterparts, including their recalcitrance to antimicrobial agents. Consequently, Candida biofilm-associated infections are difficult to treat and to fully eradicate with standard antifungal therapy. Here, we describe a simple, fast, inexpensive and highly reproducible microtiter plate-based assay for the antifungal susceptibility testing of C. albicans biofilms. Because of its simplicity, compatibility with widely available 96-well microplate platform, high throughput, and automation potential, this assay represents an important tool towards the standardization of in vitro antifungal susceptibility testing of fungal biofilms.

Antifungal Agents↗

PubMed2006

Mutation analysis of the FBN1 gene in patients with Marfan syndrome.

Marfan syndrome is an autosomal-dominant connective tissue disorder characterized by pleiotropic manifestations involving the skeletal, ocular, and cardiovascular systems and resulting from mutations in the gene for fibrillin, FBN1. The clinical diagnosis is based on a set of well-defined clinical criteria (Ghent nosology). Nevertheless, the age-related nature of some clinical manifestations and the variable phenotypic expression of the disorder may hamper the diagnosis. In those instances, molecular analysis of the FBN1 gene is helpful to identify at-risk individuals. Mutations are spread over the entire FBNJ gene and there are no particular hot spots. Different standard methodologies are available to identify these mutations, however, one of the most sensitive techniques is denaturing high-performance liquid chromatography. This approach allows the performance of the analysis in a semi-automated manner and has a mutation detection rate of approx 95%.

Cells, Cultured↗

PubMed2003

[Development of a K562 multidrug-resistant cell line and study on proteins with altered expression].

In an attempt to study the whole protein expression alterations of tumer cells after becoming multidrug-resistant, which may provide useful information on new drug target identification, an adriamycin-resistant variant of the human leukemia cell line K562 (K562/ADR) was developed in vitro by continuous exposure to adrimycin. MTT assay was used to determine IC50 of K562/ADR cells to adriamycin (ADR), cisplatin (DDP), 5-fluorouracil (5-FU) and vincristin (VCR). The total proteins of K562 and K562/ADR were separated by two-dimensional gel electrophoresis and visualized by silver staining. Proteins with significant expression alterations were selected and their peptide mass fingerprints (PMFs) were obtained by matrix-assisted laser desorption/ionization time of flying mass spectrometry (MALDI-TOF-MS). The PMFs were used to search NCBInr database by AutoMS-Fit software. The results showed that K562/ADR cell demonstrated cross-resistance to other antineoplastic drugs. The IC50 of K562/ADR cells to ADR, DDP, 5-FU, VDR were much higher than those of K562. The proteins differentially expressed in the two cell lines were identified as cell cycle-related proteins, zinc finger protein 165, etc. These proteins are involved in cell cycling and transcription regulation, whose expression alterations may contribute to the multidrug resistant phenotype of K562/ADR cells.

Antineoplastic Agents↗

PubMedDate not supplied

Epidemiologic markers of Clostridium difficile.

A wide range of epidemiologic markers have been identified for Clostridium difficile. These markers are based on phenotypic characteristics of the organism, such as antibiotic resistance, bacteriocin or bacteriophage susceptibility, electrophoretic protein patterns, and immunologic markers. Methods for determining genetic markers include plasmid and DNA restriction endonuclease analysis and ribosomal RNA restriction patterns. These methods have been applied to various degrees in epidemiologic studies and have contributed to a better understanding of C. difficile-associated disease. The method based on the use of [35S]methionine-labeled proteins and the development of an automated scanner with computer analysis made possible the recognition of 15 distinct types of C. difficile, based on the major radiolabeled protein patterns. These proteins were strain-specific and immunogenic, as demonstrated by immunoblotting and DNA restriction endonuclease analysis. Epidemiologic studies revealed cross-infection among patients, nosocomial acquisition, and a direct relation between symptoms and type of C. difficile. The development of DNA probes based on antibiotic resistance genes, toxin A, and cloned specific common antigens is discussed.

Antigens, Bacterial↗

PubMed2000

Identification of medically important yeasts using PCR-based detection of DNA sequence polymorphisms in the internal transcribed spacer 2 region of the rRNA genes.

Identification of medically relevant yeasts can be time-consuming and inaccurate with current methods. We evaluated PCR-based detection of sequence polymorphisms in the internal transcribed spacer 2 (ITS2) region of the rRNA genes as a means of fungal identification. Clinical isolates (401), reference strains (6), and type strains (27), representing 34 species of yeasts were examined. The length of PCR-amplified ITS2 region DNA was determined with single-base precision in less than 30 min by using automated capillary electrophoresis. Unique, species-specific PCR products ranging from 237 to 429 bp were obtained from 92% of the clinical isolates. The remaining 8%, divided into groups with ITS2 regions which differed by </=2 bp in mean length, all contained species-specific DNA sequences easily distinguishable by restriction enzyme analysis. These data, and the specificity of length polymorphisms for identifying yeasts, were confirmed by DNA sequence analysis of the ITS2 region from 93 isolates. Phenotypic and ITS2-based identification was concordant for 427 of 434 yeast isolates examined using sequence identity of >/=99%. Seven clinical isolates contained ITS2 sequences that did not agree with their phenotypic identification, and ITS2-based phylogenetic analyses indicate the possibility of new or clinically unusual species in the Rhodotorula and Candida genera. This work establishes an initial database, validated with over 400 clinical isolates, of ITS2 length and sequence polymorphisms for 34 species of yeasts. We conclude that size and restriction analysis of PCR-amplified ITS2 region DNA is a rapid and reliable method to identify clinically significant yeasts, including potentially new or emerging pathogenic species.

DNA, Fungal↗

PubMed2000

Relating genotype and phenotype in breast cancer: an analysis of the prognostic significance of amplification at eight different genes or loci and of p53 mutations.

Breast cancer heterogeneity can be related directly to its variability at the genetic level. Thus, tumor genotyping could be a valuable approach to define breast tumor subtypes. It has been shown that it is possible to delineate subgroups of breast tumors according to specific sets of DNA amplifications. The aim of the present work was to study the prognostic significance of these DNA amplifications. We studied DNA amplification at eight genes or loci (AIB1, CCND1, EMS1, ERBB2, FGFR1, MDM2, MYC, and RMC20C001) as well as p53 mutations in a series of 640 breast cancer patients who had not received presurgical therapy and analyzed the correlations with survival DNA amplification was assessed by Southern blotting and was scored positive when exceeding three to five copies. Mutations in the p53 gene were searched by four-color fluorescent single. strand conformational polymorphism, using an automated sequencer. Of the nine genetic alterations tested, four (CCND1, EMS1, FGFR1, and p53 mutations) showed a significant association with reduced disease-free (DFS) and/or overall survival (OVS) in the unselected set of patients by univariate test. Correlations for p53 were found only when selecting mutations in exons 5 or 7. Analysis of node-negative and -positive subgroups of patients showed that MDM2 amplification and p53 mutations bore prognostic significance in node-negative patients, whereas amplification of CCND1, EMS1, and FGFR1 correlated with poor outcome in node-positive patients. Multivariate analysis on an unselected set of patients retained significance for the amplification of EMS1, FGFR1, and MDM2 with DFS, of CCND1 with OVS, and of RMC20C001 with both DFS and OVS. Interestingly, stratified analysis according to nodal status confirmed results obtained in the univariate tests: significance of MDM2 amplification and p53 mutations in node-negative and that of CCND1, EMS1, and FGFR1 in node-positive patients. We also observed an association between the number of genetic alterations observed in a tumor and poor prognosis. Patients with two or more amplified loci had a worsened outcome. Strongly correlating coamplifications such as CCND1 and FGFR1, as well as ERBB2 and MYC, were associated with a significant reduction of patient survival, thus indicating cooperative effects. Our data support the idea that genetic alterations in breast cancer are not only helpful for phenotyping purposes, but can also represent powerful prognostic indicators in the clinical practice.

Breast Neoplasms↗

PubMed2005

Exiguobacterium mexicanum sp. nov. and Exiguobacterium artemiae sp. nov., isolated from the brine shrimp Artemia franciscana.

Two Gram-positive strains isolated from cysts of the brine shrimp Artemia franciscana were subjected to a polyphasic taxonomic analysis. Based on 16S rRNA gene sequence comparison and composition of isoprenoid quinones, peptidoglycan and fatty acids, these organisms are members of the genus Exiguobacterium. Both strains showed 95.9% 16S rRNA gene sequence similarity to one another. The 16S rRNA gene sequences of strain 8N(T) and 9AN(T) were 97.5% and 98.9% similar to those of Exiguobacterium aurantiacum DSM 6208(T) and Exiguobacterium undae DSM 14481(T), respectively. Based on differences in chemotaxonomic and physiological characteristics, results of DNA-DNA hybridization and automated riboprinting, two novel species of the genus Exiguobacterium are proposed, Exiguobacterium mexicanum sp. nov. (type strain 8N(T)=DSM 16483(T)=CIP 108859(T)) and Exiguobacterium artemiae sp. nov. (type strain 9AN(T)=DSM 16484(T)=CIP 108858(T)).

Animals↗

PubMed1999

The role of paraoxonase (PON1) in the detoxication of organophosphates and its human polymorphism.

In human populations, serum paraoxonase (PON1) exhibits a substrate dependent polymorphism. The Arg192 isoform hydrolyzes paraoxon rapidly but diazoxon, soman and especially sarin slowly. On the other hand, the Gln192 isoform hydrolyzes paraoxon slowly, but diazoxon, soman and sarin more rapidly than the Arg192 isoform. Our experiments with a mouse model system have convincingly shown that PON1 plays a major role in the detoxication of organophosphate (OP) compounds processed through the P450/PON1 pathway. Recent studies have also shown that PON1 plays an important role in the metabolism of oxidized lipid compounds. Currently, there is an effort underway to identify genes and polymorphisms that play an important role in 'environmental susceptibility'. The PON1 polymorphism has been cited as a prime example of such a genetic polymorphism. The advent of the polymerase chain reaction (PCR) for DNA amplification with improvements, modifications and automation has provided a very convenient way to do individual genotyping. It is tempting to set up large scale PCR analyses of populations to determine individuals at risk for environmental exposures affected by the PON1 polymorphism. In fact, a number of such studies have already been carried out in examining the relationship of the PON1 polymorphism to vascular disease. We advocate the use of a high throughput two-dimensional enzyme assay that provides both PON1 genotype and phenotype (PON1 status). The high level of variation of gene expression within each genetic class in humans, together with our animal model studies indicate that it is very important to determine PON status as opposed to PON1 genotype alone. Experiments in rats and mice have shown that injection of PON1 purified from rabbit serum by the i.v., i.p. or i.m. route, significantly increases PON1 activities in rodents' plasma. Under these conditions, the acute toxicity (assessed by the degree of acetylcholinesterase inhibition) of paraoxon and chlorpyrifos oxon is significantly decreased, compared to control animals. Protection is maximal when PON1 is administered before the OPs, but still occurs when PON1 is utilized as a post-exposure treatment. Furthermore, protection by PON1 is also provided toward the parent compound chlorpyrifos. Pon1-knockout mice display a much greater sensitivity to chlorpyrifos oxon toxicity than wild mice. However, the acute toxicity of guthion, which is not a substrate for PON1, does not differ between knockout and wild mice. These observations underline the importance of considering both genetic variability of enzyme isoform as well as enzyme level (PON1 status) and the developmental time course of appearance of PON1 in developing risk assessment models.

Animals↗

PubMed2000

Resistance to antiretroviral drugs in patients with primary HIV-1 infection. Investigators of the Quebec Primary Infection Study.

The widespread use of antiretroviral agents (ARVs) and the growing occurrence of HIV strains resistant to these drugs have given rise to serious concerns regarding the transmission of resistant viruses to newly infected persons. Plasma viral RNA from 80 individuals newly infected between 1997 and 1999 was genotyped by automated sequencing to analyze the profile of viruses resistant to nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs) and to protease inhibitors (PIs). The prevalence of mutations that conferred primary resistance to PIs (L10I, D30Y, V82A, L90M) was 15% of the cohort. RT genotypic variants, associated with high-level resistance to ARVs, were observed in 21% of individuals, including NRTI, NNRTI and multidrug (MDR) resistance in 6, 5, and 10% of cases, respectively. The phenotypic susceptibility of viral isolates to ARVs was also assayed and showed transmission of high-level resistance to ZDV, 3TC, and PIs in those individuals with MDR. The transmission of drug-resistant HIV genotypic variants is a serious problem that merits further attention by public health officials, virologists, and clinicians.

Anti-HIV Agents↗

PubMed2000

Elevated levels of FMR1 mRNA in carrier males: a new mechanism of involvement in the fragile-X syndrome.

Fragile-X syndrome is a trinucleotide-repeat-expansion disorder in which the clinical phenotype is believed to result from transcriptional silencing of the fragile-X mental retardation 1 (FMR1) gene as the number of CGG repeats exceeds approximately 200. For premutation alleles ( approximately 55-200 repeats), no abnormalities in FMR1-gene expression have been described, despite growing evidence of clinical involvement in premutation carriers. To address this (apparent) paradox, we have determined, for 16 carrier males (55-192 repeats), the relative levels of leukocyte FMR1 mRNA, by use of automated fluorescence-detection reverse transcriptase-PCR, and the percent of lymphocytes that are immunoreactive for FMR1 protein (FMRP). For some alleles with>100 repeats, there was a reduction in the number of FMRP-positive cells. Unexpectedly, FMR1 mRNA levels were elevated at least fivefold within this same range. No significant increase in FMR1 mRNA stability was observed in a lymphoblastoid cell line (160 repeats) derived from one of the carrier males, suggesting that the increased message levels are due to an increased rate of transcription. Current results support a mechanism of involvement in premutation carriers, in which reduced translational efficiency is at least partially compensated through increased transcriptional activity. Thus, diminished translational efficiency may be important throughout much of the premutation range, with a mechanistic switch occurring in the full-mutation range as the FMR1 gene is silenced.

Fragile X Messenger Ribonucleoprotein 1↗

PubMed1994

Molecular genetic methods for mapping disease genes.

Recent technological enhancements in molecular genetics have significantly improved our ability to locate disease genes by linkage analysis. Despite the introduction of molecular methods such as PCR and the discovery of highly polymorphic SSRs, genotyping is still rate-limiting for localizing disease genes by linkage. These methods have been, until recently, highly technical, time-consuming, and expensive. The challenge of mapping the major genes that render one susceptible to environmentally initiated lung disorders such as asthma will require efficient and highly accurate methods of genotyping. We have shown that genotyping by semi-automated fluorescence-based techniques is both highly accurate and efficient. These methods may improve productivity by more than an order of magnitude and can be easily adapted to most linkage studies.

Asthma↗

PubMed2004

Highly specific and accurate selection of siRNAs for high-throughput functional assays.

MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es.

Algorithms↗

PubMed2001

Extensive allelic variation among Francisella tularensis strains in a short-sequence tandem repeat region.

Members of the genus Francisella and the species F. tularensis appear to be genetically very similar despite pronounced differences in virulence and geographic localization, and currently used typing methods do not allow discrimination of individual strains. Here we show that a number of short-sequence tandem repeat (SSTR) loci are present in F. tularensis genomes and that two of these loci, SSTR9 and SSTR16, are together highly discriminatory. Labeled PCR amplification products from the loci were identified by an automated DNA sequencer for size determination, and each allelic variant was sequenced. Simpson's index of diversity was 0.97 based on an analysis of 39 nonrelated F. tularensis isolates. The locus showing the highest discrimination, SSTR9, gave an index of diversity of 0.95. Thirty-two strains isolated from humans during five outbreaks of tularemia showed much less variation. For example, 11 of 12 strains isolated in the Ljusdal area, Sweden in 1995 and 1998 had identical allelic variants. Phenotypic variants of strains and extensively cultured replicates within strains did not differ, and, for example, the same allelic combination was present in 55 isolates of the live-vaccine strain of F. tularensis and another one was present in all 13 isolates of a strain passaged in animals. The analysis of short-sequence repeats of F. tularensis strains appears to be a powerful tool for discrimination of individual strains and may be useful for a detailed analysis of the epidemiology of this potent pathogen.

Alleles↗

PubMed2002

CYBB mutation analysis in X-linked chronic granulomatous disease.

Chronic granulomatous disease (CGD) results from mutations of phagocyte NADPH oxidase. Seventy percent are X-linked (X-)CGD with absent or defective gp91(phox) protein encoded by the CYBB gene. A subset of X-CGD patients demonstrates partial oxidase activity and/or varied levels of the gp91(phox) protein. Definitive genotypic diagnosis in these unusual patients requires mutation analysis. Typically, CYBB mutation analysis has relied on initial screening of cDNA by single-stranded conformation polymorphism analysis, followed by selective sequencing. We report a fluorescent, automated method for CYBB mutation analysis using genomic DNA that provides more rapid and reliable results. Moreover, the use of genomic DNA in this approach allows mutation detection in the mRNA coding region, promoter/enhancer region, and intronic sequences flanking splice junctions and does not require mRNA preparation. The PCR conditions were optimized for each exon, including those with A+T-rich regions. We analyzed DNA from two unusual X-CGD patients and established the genetic basis for their phenotype. We also sequenced 100 normal X chromosomes to establish wild-type consensus sequences and identify polymorphisms.

Base Sequence↗

PubMed2001

Automated 5' nuclease assay for detection of virulence factors in porcine Escherichia coli.

This paper describes the development of a 5' nuclease assay for detection of virulence factor genes responsible for colonization factors and toxins in Escherichia coli isolated from pigs. Colonization factors were F4, F5, F6, F18, F41 and the outer membrane protein intimin. Toxins were heat stable (STa, STb, EAST1) and heat labile (LT) enterotoxins and the verocytotoxin variant 2e (VT2e). To correctly identify false negative results, an endogenous internal control targeting the E. coli 16 S rRNA gene was incorporated in each test tube. The assay was evaluated using a collection of E. coli reference strains which have previously been examined with phenotypical assays or DNA hybridization. Furthermore, the assay was evaluated by testing porcine E. coli field strains, previously characterized. The 5' nuclease assay correctly detected the presence of virulence genes in all reference strains. When testing field strains there was generally excellent agreement with results obtained by laboratories in Belgium and Germany. In conclusion, the 5' nuclease assay developed is a fast and specific tool for detection of E. coli virulence genes in the veterinary diagnostic laboratory.

5'-Nucleotidase↗

PubMed2005

Are the arginine vasopressin V1a receptor microsatellites related to hypersexuality in children with a prepubertal and early adolescent bipolar disorder phenotype?

OBJECTIVE: To examine family-based transmission of the number of 5' flanking arginine vasopressin V1a receptor (AVPR1A) microsatellites, which include [(GATA)(14)] and complex [(CT)(4)-TT-(CT)(8)-(GT)(24)] repeats, in probands with a prepubertal and early adolescent bipolar disorder phenotype (PEA-BP). Preferential transmission of the number of AVPR1A microsatellite repeats to hypersexual and uninhibited people-seeking probands was hypothesized, based on reports from preclinical work in the literature. METHODS: Probands were 83 participants in an ongoing controlled study of PEA-BP. The PEA-BP phenotype was defined by DSM-IV mania with at least one of the cardinal symptoms of mania (elation and/or grandiosity) to avoid diagnosing mania only by symptoms that overlapped with those for attention-deficit hyperactivity disorder (ADHD). Comprehensive assessment of the probands included separate Washington University in St. Louis Kiddie Schedule for Affective Disorders and Schizophrenia (WASH-U-KSADS) interviews of parents about their children and of children about themselves. Hypersexuality and uninhibited people-seeking were assessed from the corresponding WASH-U-KSADS items. Microsatellite genotyping of the AVPR1A repeats was conducted using fluorescently labeled primers and detected by laser-induced fluorescence. Alleles were determined with the assistance of semi-automated allele-calling software. There were 32 complete, biological trios (28 informative families) for the GATA repeat and 34 complete, biological trios (30 informative families) for the complex repeat. Data were analyzed using case-control and family-based association methods. RESULTS: Preferential transmission of AVPR1A GATA or complex repeats was not significant for hypersexuality or uninhibited people-seeking, using the transmission disequilibrium test. Similarly, case-control analyses found no significant associations between hypersexuality or uninhibited people-seeking and the number of AVPR1A GATA or complex repeats. For p < 0.05, there was about 80% power to detect odds ratios of 5.0 and 4.0 (in the family-based analyses) and 3.5 and 2.6 (in the case-control analyses), for allele frequencies of 0.1 and 0.5, respectively. CONCLUSION: Preferential transmission of AVPR1A to hypersexual or uninhibited people-seeking probands was not supported.

Adolescent↗

PubMed1991

The use of the PhP-KE biochemical fingerprinting system in epidemiological studies of faecal Enterobacter cloacae strains from infants in Swedish neonatal wards.

The PhenePlate (PhP) biochemical fingerprinting system is an automated method for typing of bacteria, based on the evaluation of the kinetics of biochemical reactions, performed in microtitre plates. In the present study the PhP-Klebsiella/Enterobacter (KE) system was evaluated for typing of Enterobacter cloacae and employed to study the epidemiology of faecal E. cloacae strains isolated from infants in 22 Swedish neonatal wards. The PhP-KE system showed a high reproducibility and discrimination for E. cloacae isolates. Among 64 epidemiologically unrelated E. cloacae strains, 49 distinct phenotypes were found, and the diversity index was 0.985. E. cloacae was found as a part of the dominating Gram-negative aerobic bacterial flora in 83 out of 953 infants studied. The incidences of E. cloacae colonization varied between 0 and 35% in different wards, but in contrast to previous data for Klebsiella spp. and Escherichia coli, there was little evidence of spread of particular strains in the wards. We also discuss two different measures of nosocomial transmission of bacterial strains: transmissible strains and epidemic index.

Bacterial Typing Techniques↗

PubMed2003

Motor coordination, exploration, and spatial learning in a natural mouse mutation (nervous) with Purkinje cell degeneration.

The nervous mouse mutation causes a relatively selective degeneration of Purkinje cells in the cerebellar cortex. The mutants were compared to age-matched controls of the same background strain in tests of motor activity and coordination, spontaneous alternation, and spatial learning in the Morris water maze. As expected from their ataxia, the nervous mutants were impaired in stationary beam, coat-hanger, and rotorod tests of motor coordination. The nervous mutants were also impaired in the submerged but not in the visible platform condition of the Morris water maze, attributable to a spatial deficit, and displayed a higher level of motor activity in an automated chamber. The deficit in spontaneous alternation rates seen in nervous mutants is accountable by reduced motivation, disinhibition, or spatial disorientation.

Analysis of Variance↗