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PubMed2006

Characterization of some yeasts isolated from foods by traditional and molecular tests.

In this study, 22 yeast strains isolated from foods were characterized by traditional and molecular techniques. With the help of traditional identification tests, yeast strains were grouped in 12 species belonging to 11 genera as follows: Candida parapsilosis, Rhodotorula mucilaginosa, Debaryomyces hansenii, Cryptococcus humicolus, Cryptococcus albidus, Aureobasidium spp., Hanseniaspora valbyensis, Metschnikowia pulcherrima, Lachancea thermotolerans, Pichia anomala, Geotrichum candidum and Yarrowia lipolytica. The patterns obtained by the digestion of ITS-18S rRNA gene with MspI and HaeIII restriction endonucleases were similar among strains belonging to the same species. With the help of randomly amplified polymorphic DNA (RAPD) analysis performed within the same species, discrimination of M. pulcherrima strains could be achieved.

Colony Count, Microbial↗
PubMed2004

Rapid identification of Mycobacterium genavense with a new commercially available molecular test, INNO-LiPA MYCOBACTERIA v2.

We report a rare mesenteric localized Mycobacterium genavense infection in a severely immunocompromised human immunodeficiency virus-infected patient. An INNO-LiPA MYCOBACTERIA v2 test was performed directly on biopsy samples. This new molecular tool could be used for simultaneous identification of mycobacterium species from human specimens, but other studies are needed to validate our first results.

AIDS-Related Opportunistic Infections↗
PubMed1993

Modern diagnosis (with molecular tests) of acute infectious diarrhea.

There have been three significant technical developments in the molecular genetic diagnosis of infectious diarrhea. The first was the replacement of polynucleotide probes with more specific synthetic oligonucleotide probes. The second was the replacement of radiolabeled markers with nonradiolabeled markers, and the third was PCR amplification. In the PCR procedure, it is possible to increase the quantity of target nucleotide sequences to quantities easily detectable with nonradioactive oligonucleotide probes. It is now possible to amplify nucleotide sequences of more than one enteric pathogen with different primers simultaneously and to detect these amplified nucleotide sequences with nonradiolabeled oligonucleotide probes. With a scanning laser system, the results of enteric PCRs will be used to identify enteric pathogens on a routine basis in clinical and public health laboratories. Computers need to be used to analyze these results and transfer this information rapidly to clinicians and public health officials.

Acute Disease↗
PubMed2005

Chronic myeloid leukemia: current application of cytogenetics and molecular testing for diagnosis and treatment.

Chronic myeloid leukemia provides an illustrative disease model for both molecular pathogenesis of cancer and rational drug therapy. Chronic myeloid leukemia is a clonal stem cell disease caused by an acquired somatic mutation that fuses, through chromosomal translocation, the abl and bcr genes on chromosomes 9 and 22, respectively. The bcr/abl gene product is an oncogenic protein that localizes to the cytoskeleton and displays an up-regulated tyrosine kinase activity that leads to the recruitment of downstream effectors of cell proliferation and cell survival and consequently cell transformation. Such molecular information on pathogenesis has facilitated accurate diagnosis, the development of pathogenesis-targeted drug therapy, and most recently the application of molecular techniques for monitoring minimal residual disease after successful therapy. These issues are discussed within the context of clinical practice.

Antimetabolites, Antineoplastic↗
PubMed2005

Evaluation of Brucella abortus S19 vaccine strains by bacteriological tests, molecular analysis of ery loci and virulence in BALB/c mice.

Two Brucella abortus S19 commercial vaccine strains used for vaccination against brucellosis in India and three S19 strains available as international reference were examined by microbiological assays and molecular analysis of the ery loci involved in erythritol metabolism, and tested for residual virulence in BALB/c mice. According to the sensitivity to penicillin and i-erythritol, the five strains tested had the phenotypic characteristics of strain S19. However, on culture medium containing i-erythritol, all strains developed spontaneous i-erythritol resistant colonies at mutation rates ranging from 1.42x10(-2) to 1.33x10(-6). The S19 characteristic 702 bp deletion in the erythrulose 1-phosphate dehydrogenase gene of the ery locus was present only in the three reference strains but not in the two commercial vaccines. Both commercial strains and one of the reference strains showed reduced virulence in BALB/c mice. The presence or absence in S19 strains of the 702 bp deletion in the ery locus had no correlation with either the rates of spontaneous mutation to erythritol resistance or the residual virulence in mice.

Animals↗
PubMed2004

Chloroplast and mitochondrial molecular tests identify European x Japanese larch hybrids.

Hybrids between European and Japanese larches combine the properties of both parental species (drought resistance, canker resistance, stem straightness) and exhibit a fast growth rate. They are produced in seed orchards, generally by natural pollination. Seeds are collected and used for afforestation as interspecific hybrids. However, there are no convenient tests to assess the interspecific hybrid proportion. In the present study, we developed diagnostic molecular markers suitable for the individual identification of hybrids, whatever their developmental stage. Our strategy involved testing a combination of maternally inherited markers from the mitochondrial genome (mtDNA) and paternally inherited markers from the chloroplast genome (cpDNA). Hybrids were then identified by the presence of a mitochondrial sequence inherited from one parental species and a chloroplast sequence inherited from the other parental species. To achieve this aim, markers discriminating both parental species were first sought. Amplifications of mitochondrial and chloroplast sequences were performed using specific PCR primers. After testing 33 primer pairs in combination with nine restriction enzymes, we detected one mitochondrial marker, f13 which was amplified in Japanese larch and absent in European larch, and one chloroplast marker, ll- TaqI which showed different restriction patterns depending on the species. A restriction fragment of 601 bp was obtained in Japanese larch while two fragments of 120 bp and 481 bp were observed in European larch. These patterns were found in all 197 individuals tested from the two pure species. These markers were then used for the evaluation of the hybrid proportion in a seed lot produced from seed orchards; this was assessed as between 43% and 53% depending on the parental species. The male and female parental species could be determined for each progeny.

DNA, Chloroplast↗
PubMed2006

Genomics basics: DNA structure, gene expression, cloning, genetic mapping, and molecular tests.

Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25,000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.

Chromosome Mapping↗
PubMed1997

[Incorporating molecular tests into the practice of public health].

Public Health has evolved in accordance with basic scientific and technologic advances. Molecular biology has provided sophisticated laboratory techniques and fine diagnostic tools that are being exploited in the area of Public Health in order to deepen our knowledge of the natural history of diseases, identify populations at risk, diagnose infectious process and different pathologies in the early stages of the illness and limit the damage produced by a late diagnosis. The modern molecular techniques provide a promising insight into the identification and measurement of molecular structures linked to the pathological process, the genotypic identification of infectious agents, the level of exposure and the susceptibility at individual as well as population levels. This paper describes its applications in the area of Public Health and highlights its limits and potential risks.

Blood Banks↗
PubMed1998

Clinical, cytogenetic, and molecular testing of Argentine patients with retinoblastoma.

PURPOSE: The purpose of this study is to determine the clinical, chromosomal, and molecular characteristics of Argentine patients with unilateral and bilateral retinoblastoma. STUDY DESIGN: Eighty-six patients belonging to 82 families were studied; 59% of them were examined during the first year of life. Leukocoria was the most common reason for consultation. Other presenting signs were strabismus and glaucoma. Enucleation of the affected eye was performed in 85% of the cases and the complication rate was 13%. RESULTS: An appropriate therapy allowed the survival of 84 of the 86 patients. Two children with malformations and growth retardation had an abnormal karyotype with a deletion in 13q14. Segregation analysis of polymorphic sites within the retinoblastoma gene and the parental origin of the allele lost in the tumor were analyzed in 30 of the 82 families. Five mutant alleles transmitted through the germline and six de novo germline mutant alleles were identified in 12 patients with hereditary retinoblastoma. Most de novo germline mutant alleles were paternally derived. Molecular analysis of nonhereditary retinoblastoma showed loss of heterozygosity in three of eight cases. From these, two maternal alleles and one paternal allele were lost, thus not indicating a significant difference in the parental origin for the lost allele. CONCLUSIONS: These data are useful for deoxyribonucleic acid diagnosis of susceptibility to retinoblastoma in relatives of hereditary patients, even if mutations have not been identified.

Alleles↗
PubMed1998

Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae.

A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.

Animals↗
PubMed2002

Effective management of hepatitis C molecular testing improves test use without compromising patient management.

CONTEXT: The availability of effective antiviral therapy for hepatitis C has increased the need for molecular detection and quantification of circulating hepatitis C viral particles. The limits of detection differ for the quantitative and qualitative reverse transcriptase polymerase chain reaction (RT-PCR) assays; furthermore, adequate patient assessment requires both detection of hepatitis C virus when it is present and quantitation of the viral load when possible. The combination of these factors promotes the simultaneous ordering of both tests with the possibility of generating redundant test information. OBJECTIVE: To reduce the number of unnecessary hepatitis C tests performed. METHODS: We established a reflexive testing protocol for quantitative and qualitative RT-PCR testing for hepatitis C. RESULTS: During a 3(1/2)-month interval, 170 qualitative RT-PCR hepatitis C tests were eliminated (a 59.4% reduction in the number of these tests). This reduction was achieved without a clinically significant change in turnaround time or a compromise of patient care. CONCLUSIONS: Establishing the quantitative and qualitative RT-PCR tests in-house and adopting the reflexive testing protocol was cost-effective and did not compromise patient management or care.

Hepacivirus↗
PubMedDate not supplied

Molecular testing of Helicobacter pylori-associated chronic gastritis and premalignant gastric lesions: clinical implications.

Helicobacter pylori-associated gastritis may progress or be complicated by peptic ulcer and gastric malignancy, including gastric carcinoma and mucosa-associated lymphoid tissue lymphoma. Predicting who develops malignancy remains a clinical challenge. The molecular understanding of pathways that are associated with progression of the normal gastric epithelium to malignancy together with classic histologic parameters are promising ways of tackling this problem. Ideally, molecular tools used for screening should be available as noninvasive tests, such as examination of markers detectable in blood samples, but these are not currently available. In contrast, molecular markers that correlate with cancer risk can be examined in the epithelium after endoscopic biopsy and can be of importance in identifying individuals at risk, especially if combined with other parameters of gastric cancer risk.

Biomarkers, Tumor↗
PubMed2005

Facioscapulohumeral muscular dystrophy molecular testing using a non radioactive protocol.

Although the facioscapulohumeral muscular dystrophy (FSHD) locus was mapped to 4q35 chromosomal region in 1990, no gene transcript has been as yet identified. Molecular diagnosis is based mainly on the detection of deletions of a 3.3 kb-tandem repeat array in the locus. This procedure offers almost 95% accuracy but is quite complicated and therefore a simpler test would be preferable. We describe a convenient non-radioactive protocol which requires a simple PCR probe synthesis and labelling procedure, thus facilitating and accelerating the standard Southern blot based DNA test. 134 individuals (113 affected and 21 unaffected relatives) were studied and a causal deletion was detected in 72.

Blotting, Southern↗
PubMed2001

Serological and molecular testing in viral hepatitis: an update.

The routine serological diagnoses of the three major forms of viral hepatitis - A, B and C - as well as delta hepatitis, are important in the evaluation of acute and chronic viral hepatitis. Increasingly, molecular virology is also being used to evaluate patients with chronic hepatitis C, with genotype and viral load testing to plan therapy.

Cytogenetic Analysis↗
PubMed2005

Experience and strategy for the molecular testing of Duchenne muscular dystrophy.

Mutations in the dystrophin gene result in both Duchenne and Becker muscular dystrophies (DMD and BMD). Approximately two-thirds of the affected patients have large deletions or duplications. Using the multiplex polymerase chain reaction and Southern blotting techniques, the detection of these larger mutations is relatively straightforward. Detection of the point mutations in the remaining one-third of the patients has been challenging, mainly due to the large gene size and lack of hotspots or prevalent mutations. However, with the addition of some of the newer molecular screening methods, it is becoming more feasible for clinical laboratories to test for point mutations in the larger genes like dystrophin. Here we review the clinical features, describe the mutation distributions, evaluate current molecular strategies, and illustrate how the genetic findings have impacted the current clinical diagnostics of Duchenne and Becker muscular dystrophies.

Dystrophin↗
PubMed1997

Cytogenetic and fragile X molecular testing of individuals with mental retardation of unknown etiology.

The aim of this program was to investigate the patients with Mental Retardation Of Unknown Etiology (MROUE), on the island of Cyprus. The MROUE patients were examined cytogenetically for gross chromosomal abnormalities, and by molecular methods for the Fragile X syndrome pathology. Specialized physicians examined all institutionalized or non institutionalized patients throughout Cyprus. Cytogenetic analysis was carried out on 105 individuals, six of which showed various chromosomal aberrations. PCR and Southern blot analysis were carried out on 170 patients referred for exclusion of the Fragile X syndrome. Three patients had positive findings. Although the number of cases elucidated with this general approach was not spectacular, it allowed the resolution of a few clinically equivocal cases, to the satisfaction of the clinicians and, most importantly, the relatives involved. We believe that such screening programs should continue until all cases are thoroughly examined, thus providing definite genetic counseling and psychological support, at least in those cases that are clearly resolved. Equally important is the prospect for prevention through prenatal diagnostic programs, that are already available for such conditions.

Adolescent↗
PubMed2005

High-throughput molecular testing of ticks using a liquid-handling robot.

To meet the need for high-throughput sample testing, DNA extraction kits based on the 96-well plate format have been developed for use with blood and tissue samples. These methods have not been applied to DNA extractions from ticks. To meet this need, we developed a high-throughput method for DNA extraction and polymerase chain reaction (PCR) testing of tick samples. A liquid-handling robot was used to extract DNA in a 96-well binding column plate with vacuum manifold. The quantity, purity, and quality of DNA recovered from Ixodes scapularis Say, 1821 nymphs with this method were reproducible and comparable with existing manual DNA extraction techniques. The DNA yield from pools of five nymphal ticks averaged 0.432 +/- 0.04 microg (95% CI). The robot also prepared real-time PCR reactions in 96-well plates, directly from the extracted DNA. A modification of the existing P20 tool resulted in accurate pipetting of 1- to 2-microl volumes with a reproducibility of +/- 0.038 microl when dispensing 1.0 microl. By using this process, 96 samples can be extracted and tested while reducing human labor to approximately 30 min.

Animals↗