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PubMed1999

Evaluation of the purity of a purified, inactivated hepatitis A vaccine (VAQTA).

Manufacture of VAQTA, an inactivated hepatitis A virus vaccine, includes extensive purification of the intact virus particle to remove endogenous components from the host cell culture lysate as well as compounds introduced in the upstream purification process. Analysis of the final purified hepatitis A virus product by SDS-PAGE prior to inactivation shows that greater than 95% of the protein in the preparation is found in four protein bands, which have been confirmed to be hepatitis A virus capsid proteins VP0, VP1, VP2 and VP3 based on Western blot and mass spectrometry analyses. Validation of the manufacturing process and direct analysis of the final product were used to demonstrate that no other specific host cell-derived components are detected and that process residuals are all below the limits of detection of the assays used. Establishment of a rigorous standard of high purity for this product was pursued to minimize the impact of impurities during clinical development of this product and will facilitate the incorporation of this product into combination vaccines.

Animals↗
PubMed1998

Application of 23S rDNA-targeted oligonucleotide probes specific for enterococci to water hygiene control.

Identification of enterococci species by hybridization with recently designed species-specific and group-specific 23S rDNA-targeted oligonucleotide probes was superior to results obtained with a common biochemical test panel. Considering these findings, a molecular biological procedure for the detection of enterococci in water samples was developed. A short enrichment is followed by an amplification step and a hybridization reaction in microtiter plate format. The detection limit is about 1 CFU/ml, and results are available within 26 h.

Bacterial Typing Techniques↗
PubMed2001

Screening of an enterovirus specific RT-PCR ELISA method for the quantification of enterovirus genomes in human body fluids by means of a three-level experimental design.

In order to obtain a detection limit as low as possible for a quantitative enterovirus specific RT-PCR ELISA assay, optimal reaction conditions, which give rise to the highest response, need to be determined. This was done by investigating the influence of 13 factors, selected from RT and PCR, in a multivariate approach by means of a well-balanced three-level screening design, derived from a three-level Plackett--Burman design. Optimal reaction conditions could be determined by calculation and evaluation of the effects of the different factors on the response, i.e. the measured absorbance of the ELISA detection. The method will be used to study a possible longitudinal relationship between enteroviruses and the development of multiple sclerosis and juvenile diabetes.

Body Fluids↗
PubMed2002

Molecular quality control machinery contributes to the leukocyte NADPH oxidase deficiency in chronic granulomatous disease.

Chronic granulomatous disease (CGD) is an inherited immunodeficiency disease caused by defects in leukocyte NADPH oxidase. Various inherited defects in one of the membrane-bound components of NADPH oxidase, gp91-phox, cause X-linked (X91) CGD. Analysis of three patients with X91 CGD revealed that different mechanisms of molecular quality control lead to the common phenotype of absence of mature membrane-bound NADPH oxidase complex in leukocytes. In the first patient, aberrant intron splicing created a premature stop codon. However, the mutant mRNA was degraded prematurely, which prevented the production of truncated protein. In the second patient, a frameshift mutation with the potential to generate a gp91-phox polypeptide, with an aberrant and elongated C-terminus, led to barely detectable levels of gp91-phox, even though the reported functional domains of the protein appeared unaffected. In the third patient, a point mutation created a single amino acid change in the predicted FAD-binding site of gp91-phox. Although gp91-phox was detectable with Western blotting, no cytochrome b(558) was expressed on the cell surface. These analyses showed that molecular quality control machinery plays an important role in the pathogenesis of CGD, not only in the X910 but also in the X91- form of this X-linked disease.

Cell Membrane↗
PubMed2001

mRNA quality control: Marking the message for life or death.

A protein complex deposited upstream of exon-exon junctions after pre-mRNA splicing may serve a dual role in mRNA quality control by directing mRNA nuclear export and, possibly, serving as a downstream 'mark' for nonsense-mediated decay.

Animals↗
PubMed2000

The prevalence of anergy in human immunodeficiency virus-infected adolescents and the association of delayed-type hypersensitivity with subject characteristics.

PURPOSE: To examine the prevalence of anergy in HIV-infected adolescents and factors associated with its occurrence. METHODS: Anergy was defined as less than 2mm induration to each of three intradermally applied antigens (Candida albicans, tetanus toxoid, and mumps) between 24 and 96 hours in a population of HIV-infected adolescents aged 12-18 at entry in a national multicenter study of HIV disease progression. CD4(+) T-cell counts and plasma HIV-1 RNA were measured in quality controlled laboratories. Factors associated with the probability of anergy were examined with contingency table comparisons, tree-structured classification, and logistic regression analyses. RESULTS: Overall prevalence of anergy in this clinic-based population of 167 was 11% [7% in males and 12% in females (p = 0.57)]. The sole significant predictor of anergy was decreased CD4(+) T-cell count (p = 0.005). CONCLUSION: The prevalence of anergy is low in this HIV-infected population compared to older infected cohorts. The occurrence of differential rates of anergy in particular age and sex groupings that may be related to intrinsic immunologic differences requires further study.

Adolescent↗
PubMed2001

[Statistical Process Control applied to viral genome screening: experimental approach].

During the National Multicentric Study concerning the introduction of NAT for HCV and HIV-1 viruses in blood donation screening which was supervised by the Medical and Scientific departments of the French Blood Establishment (Etablissement français du sang--EFS), Transcription-Mediated transcription Amplification (TMA) technology (Chiron/Gen Probe) was experimented in the Molecular Biology Laboratory of Montpellier, EFS Pyrénées-Méditerranée. After a preliminary phase of qualification of the material and training of the technicians, routine screening of homologous blood and apheresis donations using this technology was applied for two months. In order to evaluate the different NAT systems, exhaustive daily operations and data were registered. Among these, the luminescence results expressed as RLU of the positive and negative calibrators and the associated internal controls were analysed using Control Charts, Statistical Process Control methods, which allow us to display rapidly process drift and to anticipate the appearance of incidents. This study demonstrated the interest of these quality control methods, mainly used for industrial purposes, to follow and to increase the quality of any transfusion process. it also showed the difficulties of the post-investigations of uncontrolled sources of variations of a process which was experimental. Such tools are in total accordance with the new version of the ISO 9000 norms which are particularly focused on the use of adapted indicators for processes control, and could be extended to other transfusion activities, such as blood collection and component preparation.

Blood Component Removal↗
PubMed1998

Simultaneous quantitation of substance P-encoding preprotachykinin alternatively spliced mRNAs and substance P receptor NK-1 mRNA by an RNase protection assay.

Tachykinins form a family of peptides with neurotransmitter/neuromodulator function. Four tachykinins, substance P, neurokinin A, neuropeptide gamma and neuropeptide K, are encoded by the same PreProTachykinin (PPT) gene. Alternatively spliced mRNAs encode different combinations of these peptides (Brown, E.R., Harlan, R.E., Krause, J.E., Gonadal steroid regulation of substance P (SP) and SP-encoding mRNA in the rat anterior pituitary and hypothalamus, Endocrinology, 126 (1990) 330-340; Krause, J.E., Chirgwin, J.M., Carter, M.S., Xu, Z.S., Hershey, A.D., Three rat preprotachykinin mRNAs encode the neuropeptides substance P and neurokinin A, Proc. Natl. Acad. Sci. USA, 84 (1987) 881-885). The proportion of PPT mRNAs varies from tissue to tissue (Carter, M.S., Krause, J.E., Structure, expression, and some regulatory mechanisms of the rat preprotachykinin gene encoding substance P, neurokinin A, neuropeptide K, and neuropeptide gamma, J. Neurosci., 10 (1990) 2203-2214), and within the rat hypothalamus according to the estrous cycle-related hormonal status (Gautreau, A., Duval, P., Kerdelhué, B., Variations in substance P-encoding preprotachykinin and substance P receptor NK-1 mRNA transcripts in the rat hypothalamus throughout the estrous cycle: a correlation between amounts of beta-preprotachykinin and NK-1 mRNA, Mol. Brain Res., (1997) in press). Tachykinin receptors as well as tachykinins are regulated at the mRNA level. A fully quantitative method is needed to deal with the complex physiological regulation of the tachykinin system. Here, we describe an RNase protection assay that allows the simultaneous quantitation of alternatively spliced PPT mRNAs, Substance P receptor NK-1 mRNA, and glyceraldehyde-3-phosphodehydrogenase (GAPDH) mRNA as an internal control, in the rat hypothalamus. The advantages of this method are its high sensitivity (0.1 pg) and a wide range of linearity (more than 3 orders of magnitude). Moreover, this protocol provides guidelines to set up a quantitative multiprobe RNase protection assay for other genes.

Alternative Splicing↗
PubMed2001

Quality control for nucleic acid tests: common ground and special issues.

Traditional clinical laboratory quality control practices are being applied to new technologies for the detection and quantitation of nucleic acids in clinical samples, often with limited knowledge of the probability for clinically significant error detection or for false run rejection of such practices. This article reviews traditional quality control practices, discusses the possibilities for a more rational approach to quality control for nucleic acid tests and suggests some steps that can lead to quality improvement for these tests.

Clinical Laboratory Techniques↗
PubMed2003

Molecular analysis of cerebrospinal fluid in viral diseases of the central nervous system.

The use of nucleic acid (NA) amplification techniques has transformed the diagnosis of viral infections of the central nervous system (CNS). Because of their enhanced sensitivity, these methods enable detection of even low amounts of viral genomes in cerebrospinal fluid. Following more than 10 years of experience, the polymerase chain reaction or other NA-based amplification techniques are nowadays performed in most diagnostic laboratories and have become the test of choice for the diagnosis of several viral CNS infections, such as herpes encephalitis, enterovirus meningitis and other viral infections occurring in human immunodeficiency virus-infected persons. Furthermore, they have been useful to establish a viral etiology in neurological syndromes of dubious origin and to recognise unusual or poorly characterised CNS diseases. Quantitative methods have provided a valuable additional tool for clinical management of these diseases, whereas post-amplification techniques have enabled precise genome characterisation. Current efforts are aiming at further improvement of the diagnostic efficiency of molecular techniques, their speed and standardisation, and to reduce the costs. The most relevant NA amplification strategies and clinical applications of to date will be the object of this review.

AIDS-Related Opportunistic Infections↗
PubMed2003

An international external quality assessment of nucleic acid amplification of herpes simplex virus.

BACKGROUND: There is an increasing awareness of the need for external quality control of diagnostic virology. OBJECTIVES: To assess the quality of nucleic acid amplification tests (NAT) of herpes simplex within Europe. STUDY DESIGN: Herpes simplex virus (HSV) proficiency panels were produced at the Swedish Institute for Infectious Disease Control on behalf of the European Union Concerted Action for Quality Control of Nucleic Acid Amplification in 1999 and 2000. Nine reference laboratories evaluated the production process. Each panel consisted of 12 coded samples with various concentrations of inactivated, freeze-dried HSV type 1 (HSV-1), and HSV type 2 (HSV-2), or negative controls. Positive samples included HSV-1 and HSV-2 in a range of concentrations (2 x 10(2) to 2 x 10(7) genome copies per ml) similar to those found in cerebrospinal fluids from patients with HSV encephalitis. RESULTS: Sixty-six participants reported a total of 76 data sets for panel 1, and 71 reported 78 data sets for panel 2. The majority of the participants employed qualitative 'in-house' polymerase chain reaction (PCR) methods, either in a single, nested or semi-nested format. For panel 2, 9 laboratories reported use of 'real-time' PCR in contrast to 3 for panel 1. Three laboratories submitted quantitative results on both panels. Thirty percent of the data sets had correct results for the entire panel 1. In 6 data sets (8%) a total of 11 false positive results were reported. For panel 2, 28% of the data sets had correct result. Nineteen false positive results were reported in 14 data sets (18%), but most of the incorrect results reflected a lack of test sensitivity. CONCLUSIONS: The relatively high frequency of false positive results and the large number of false-negative results, albeit at low copy number, stress the need for improvement in the quality of HSV NAT and for external quality control programmes.

False Negative Reactions↗
PubMed2005

Precision profiling and components of variability analysis for Affymetrix microarray assays run in a clinical context.

Although gene expression profiling using microarray technology is widely used in research environments, adoption of microarray testing in clinical laboratories is currently limited. In an attempt to determine how such assays would perform in a clinical laboratory, we evaluated the analytical variability of Affymetrix microarray probesets using two generations of human Affymetrix chips (U95Av2 and U133A). The study was designed to mimic potential clinical applications by using multiple operators, machines, and reagent lots, and by performing analyses throughout a period of several months. A mixed model analysis was used to evaluate the relative contributions of multiple factors to overall variability, including operator, instrument, run, cRNA/cDNA synthesis, and changes in reagent lots. Under these conditions, the average probeset coefficient of variation (CV) was relatively low for present probesets on both generations of chips (mean coefficient of variation, 21.9% and 27.2% for U95Av2 and U133A chips, respectively). The largest contribution to overall variation was chip-to-chip (residual) variability, which was responsible for between 40 to 60% of the total variability observed. Changes in individual reagent lots and instrumentation contributed very little to the overall variability. We conclude that the approach demonstrated here could be applied to clinical validation of Affymetrix-based assays and that the analytical precision of this technique is sufficient to answer many biological questions.

DNA, Complementary↗
PubMed2003

A model of molecular interactions on short oligonucleotide microarrays.

High-density short oligonucleotide microarrays have become a widely used tool for measuring gene expression on a large scale. However, details of the mechanism of binding on microarrays remain unclear. Short oligonucleotide probes currently synthesized on microarrays are often ineffective as a result of limited sequence specificity or low sensitivity. Here, we describe a model of binding interactions on microarrays that reveals how probe signals depend on probe sequences and why certain probes are ineffective. The model indicates that the amount of nonspecific binding can be estimated from a simple rule. Using this model, we have developed an improved measure of gene expression for use in data analysis.

Binding Sites↗
PubMed2003

Whither RNAi?

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Animals↗
PubMed2002

Post-analysis follow-up and validation of microarray experiments.

Measurement of gene-expression profiles using microarray technology is becoming increasingly popular among the biomedical research community. Although there has been great progress in this field, investigators are still confronted with a difficult question after completing their experiments: how to validate the large data sets that are generated? This review summarizes current approaches to verifying global expression results, discusses the caveats that must be considered, and describes some methods that are being developed to address outstanding problems.

Animals↗