Rapid and reliable genotyping of polymorphic loci modifying correct splicing of CFTR pre-mRNA using mass spectrometry

We describe a fast and unambiguous method for haplotyping the (TG)mTn repeat in IVS8 and determining three other single nucleotide polymorphisms (SNPs) in exons 10, 14a and 24 in the cystic fibrosis transmembrane conductance regulator (CFTR) gene affecting correct splicing of the CFTR pre-mRNA using primer extension and mass spectrometry. The diagnostic products are generated by primer extension (PEX) reactions, which require a single detection primer complementary to a region downstream of a target strand's variable site. On addition of a polymerase and an appropriate mixture of dNTP's and 2', 3'-dideoxynucleotide triphosphates (ddNTP's), the primer is extended through the mutation region until the first ddNTP is incorporated and the mass of the extension products determines the composition of the variable site. Analysis of patient DNA assigned the correct and unambiguous haplotype for the (TG)mTn repeat in intron 8 of the CFTR gene. Additional crucial SNPs influencing correct splicing in exon 10, 14 and 24 can easily be detected by biplexing the assay to genotype allelic variants important for correct splicing of the CFTR pre-mRNA. Different PEX reactions with subsequent mass spectrometry generate sufficient data, to enable unambiguous and easy haplotyping of the (TG)mTn repeat in the CFTR gene. The method can be easily extended to the inclusion of additional SNPs of interest by biplexing some of the PEX reactions. All experimental steps required for PEX are amenable to the high degree of automation desirable for a high-throughput diagnostic setting, facilitating the work of clinicians involved in the diagnosis of non-classic cystic fibrosis.

Are mutans streptococci detected in preschool children a reliable predictive factor for dental caries risk? A systematic review

Research suggests that mutans streptococci play an important role in cariogenesis in children but the usefulness of bacterial testing in risk assessment is unknown. Our objective was to summarize the literature assessing the association of mutans streptococci and dental caries in preschool children, (Pre)Medline (1966-2003), Embase (1980-2003), the Cochrane Register of Controlled Trials (2003, issue 3), and reference lists of included studies were searched. All abstracts found by the electronic searches (n = 981) were independently scrutinized by 2 reviewers. Minimal requirements for inclusion were assessment of preschool children without caries at baseline, reporting of mutans streptococci present in saliva or plaque at baseline and assessment of caries presence after a minimum of 6 months of follow-up. Participants' details, test methods, methodological characteristics and findings were extracted by one reviewer and cross-checked by another. Homogeneity was tested using chi2 tests. Results of plaque and saliva testing were pooled separately using a fixed effects model. Methodological quality of reports was low. Out of 9 studies included, data from 3 reports on plaque test assessment alone (n = 300) and from 4 reports on saliva test assessment alone (n = 451) were available for pooled analysis. The pooled risk ratio (95% CI) was 3.85 (2.48-5.96) in studies using plaque tests and 2.11 (1.47-3.02) in those using saliva testing. Presence of mutans streptococci, both in plaque or saliva of young caries-free children, appears to be associated with a considerable increase in caries risk. Lack of adjustment for potential confounders in the original studies, however, limits the extent to which interpretations for practice can be made.

How reliable and robust are current biomarkers for copper status?

Cu is an essential nutrient for man, but can be toxic if intakes are too high. In sensitive populations, marginal over- or under-exposure can have detrimental effects. Malnourished children, the elderly, and pregnant or lactating females may be susceptible for Cu deficiency. Cu status and exposure in the population can currently not be easily measured, as neither plasma Cu nor plasma cuproenzymes reflect Cu status precisely. Some blood markers (such as ceruloplasmin) indicate severe Cu depletion, but do not inversely respond to Cu excess, and are not suitable to indicate marginal states. A biomarker of Cu is needed that is sensitive to small changes in Cu status, and that responds to Cu excess as well as deficiency. Such a marker will aid in monitoring Cu status in large populations, and will help to avoid chronic health effects (for example, liver damage in chronic toxicity, osteoporosis, loss of collagen stability, or increased susceptibility to infections in deficiency). The advent of high-throughput technologies has enabled us to screen for potential biomarkers in the whole proteome of a cell, not excluding markers that have no direct link to Cu. Further, this screening allows us to search for a whole group of proteins that, in combination, reflect Cu status. The present review emphasises the need to find sensitive biomarkers for Cu, examines potential markers of Cu status already available, and discusses methods to identify a novel suite of biomarkers.

Real-time multiplex PCR assays for reliable detection of Clostridium perfringens toxin genes in animal isolates

Typing of Clostridium perfringens strains by PCR-based determination of toxin genes proved to be a reliable method for diagnosis of enterotoxaemia in various animal species. We report the establishment and validation of three real-time fluorogenic (TaqMan) multiplex PCRs for the detection of C. perfringens alpha-, beta-, beta2-, epsilon-, entero- and iota-toxin genes. The composition of the PCRs was chosen with regard to robustness of the assays and in order to increase sensitivity compared to the conventional simplex PCRs. The combination of probe dyes selected for the real-time assays (FAM/TAMRA, Cy-5/BHQ-2 and VIC/TAMRA) as well as the designation of the chromosome-borne alpha-toxin as internal positive control allowed the creation of highly specific and sensitive, as well as time and cost effective PCRs. One hundred and three strains of C. perfringens isolated in Switzerland derived from clinical or suspected cases of enterotoxaemia in 10 different animal species were tested. The toxin genotypes were in agreement in both the conventional PCRs and the newly designed multiplex PCRs. Furthermore, the real-time PCR carried out as simplex allows to quantitate the copy numbers of plasmid-borne toxin genes in relation to the chromosomally located alpha-toxin gene.

Radiographic analysis of femoroacetabular impingement with Hip2Norm-reliable and validated

The purpose of this study was to validate the accuracy, consistency, and reproducibility/reliability of a new method for correction of pelvic tilt and rotation of radiographic hip parameters for pincer type of femoroacetabular impingement on an anteroposterior pelvic radiograph. Thirty cadaver hips and 100 randomized, blinded AP pelvic radiographs were used for investigation. To detect the software accuracy, the calculated femoral head coverage and classic hip parameters determined with our software were compared to reference measurements based on CT scans or conventional radiographs in a neutral orientation as gold standard. To investigate software consistency, differences among the different parameters for each cadaver pelvis were calculated when reckoned back from a random to the neutral orientation. Intra- and interobserver comparisons were used to analyze the reliability and reproducibility of all parameters. All but two parameters showed a good-to-very good accuracy with the reference measurements. No relevant systematic errors were detected in the Bland-Altman analysis. Software consistency was good-to-very good for all parameters. A good-to-very good reliability and reproducibility was found for a substantial number of the evaluated radiographic acetabular parameters. The software appears to be an accurate, consistent, reliable, and reproducible method for analysis of acetabular pathomorphologies.

Distance doubling visual acuity test: a reliable test for nonorganic visual loss

BACKGROUND: To determine the value of the distance doubling visual acuity test in the diagnosis of nonorganic visual loss in a comparative observational case series. METHODS: Twenty-one consecutive patients with nonorganic visual acuity loss and 21 subjects with organic visual loss as controls were included. Best corrected visual acuity was tested at the normal distance of 5 meters using Landolt Cs. The patient was then repositioned and best corrected visual acuity was tested with the previous optotypes at double the distance via a mirror. RESULTS: Nonorganic visual acuity loss was identified in 21 of 21 patients. Sensitivity and specificity of distance-doubling visual acuity test in functional visual loss were found to be 100% (CI; 83%-100%) and 100% (CI; 82%-100%), respectively. CONCLUSION: Distance doubling visual acuity test is widely used to detect nonorganic visual loss. Our results show that this test has a high specificity and sensitivity to detect nonorganic visual impairment.

Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicons and a proper normalization

Quantitative reverse transcriptase real-time PCR (QRT-PCR) is a robust method to quantitate RNA abundance. The procedure is highly sensitive and reproducible as long as the initial RNA is intact. However, breaks in the RNA due to chemical or enzymatic cleavage may reduce the number of RNA molecules that contain intact amplicons. As a consequence, the number of molecules available for amplification decreases. We determined the relation between RNA fragmentation and threshold values (Ct values) in subsequent QRT-PCR for four genes in an experimental model of intact and partially hydrolyzed RNA derived from a cell line and we describe the relation between RNA integrity, amplicon size and Ct values in this biologically homogenous system. We demonstrate that degradation-related shifts of Ct values can be compensated by calculating delta Ct values between test genes and the mean values of several control genes. These delta Ct values are less sensitive to fragmentation of the RNA and are unaffected by varying amounts of input RNA. The feasibility of the procedure was demonstrated by comparing Ct values from a larger panel of genes in intact and in partially degraded RNA. We compared Ct values from intact RNA derived from well-preserved tumor material and from fragmented RNA derived from formalin-fixed, paraffin-embedded (FFPE) samples of the same tumors. We demonstrate that the relative abundance of gene expression can be based on FFPE material even when the amount of RNA in the sample and the extent of fragmentation are not known.

Structural characterization and reliable biomechanical assessment of integrative cartilage repair

Structural and functional characterization of integrative cartilage repair in controlled model systems can play a key role in the development of innovative strategies to improve the long-term outcome of many cartilage repair procedures. In this work, we first developed a method to reproducibly generate geometrically defined disk/ring cartilage composites and to remove outgrown fibrous layers which can encapsulate cartilaginous tissues during culture. We then used the model system to test the hypothesis that such fibrous layers lead to an overestimation of biomechanical parameters of integration at the disk/ring interface. Transmission electron microscopy images of the composites after 6 weeks of culture indicated that collagen fibrils in the fibrous tissue layer were well integrated into the collagen network of the cartilage disk and ring, whereas molecular bridging between opposing disk/ring cartilage surfaces was less pronounced and restricted to regions with narrow interfacial regions (< 2 microm). Stress-strain profiles generated from mechanical push-out tests for composites with the layers removed displayed a single and distinct peak, whereas profiles for composites with the layers left intact consisted of multiple superimposed peaks. As compared to composites with removed layers, composites with intact layers had significantly higher adhesive strengths (161+/-9 vs. 71+/-11 kPa) and adhesion energies (15.0+/-0.7 vs. 2.7+/-0.4 mJ/mm2). By combining structural and functional analyses, we demonstrated that the outgrowing tissue formed during in vitro culture of cartilaginous specimens should be eliminated in order to reliably quantify biomechanical parameters related to integrative cartilage repair.

How reliable is an undetectable viral load?

OBJECTIVES: An article by the Swiss AIDS Commission states that patients with stably suppressed viraemia [i.e. several successive HIV-1 RNA plasma concentrations (viral loads, VL) below the limits of detection during 6 months or more of highly active antiretroviral therapy (HAART)] are unlikely to be infectious. Questions then arise: how reliable is the undetectability of the VL, given the history of measures? What factors determine reliability? METHODS: We assessed the probability (henceforth termed reliability) that the n+1 VL would exceed 50 or 1000 HIV-1 RNA copies/mL when the nth one had been <50 copies/mL in 6168 patients of the Swiss HIV Cohort Study who were continuing to take HAART between 2003 and 2007. General estimating equations were used to analyse potential factors of reliability. RESULTS: With a cut-off at 50 copies/mL, reliability was 84.5% (n=1), increasing to 94.5% (n=5). Compliance, the current type of HAART and the first antiretroviral therapy (ART) received (HAART or not) were predictive factors of reliability. With a cut-off at 1000 copies/mL, reliability was 97.5% (n=1), increasing to 99.1% (n=4). Chart review revealed that patients had stopped their treatment, admitted to major problems with compliance or were taking non-HAART ART in 72.2% of these cases. Viral escape caused by resistance was found in 5.6%. No explanation was found in the charts of 22.2% of cases. CONCLUSIONS: After several successive VLs at <50 copies/mL, reliability reaches approximately 94% with a cut-off of 50 copies/mL and approximately 99% with a cut-off at 1000 copies/mL. Compliance is the most important factor predicting reliability.

Are implants more reliable than severely compromised endodontically treated teeth as abutments for zirconia-based FPDs? : In vitro results of long-term preclinical load simulation

OBJECTIVES The aim was to study the impact of the defect size of endodontically treated incisors compared to dental implants as abutments on the survival of zirconia two-unit anterior cantilever-fixed partial dentures (2U-FPDs) during 10-year simulation. MATERIALS AND METHODS Human maxillary central incisors were endodontically treated and divided into three groups (n = 24): I, access cavities rebuilt with composite core; II, teeth decoronated and restored with composite; and III as II supported by fiber posts. In group IV, implants with individual zirconia abutments were used. Specimens were restored with zirconia 2U-FPDs and exposed to two sequences of thermal cycling and mechanical loading. Statistics: Kaplan-Meier; log-rank tests. RESULTS During TCML in group I two tooth fractures and two debondings with chipping were found. Solely chippings occurred in groups II (2×), IV (2×), and III (1×). No significant different survival was found for the different abutments (p = 0.085) or FPDs (p = 0.526). Load capability differed significantly between groups I (176 N) and III (670 N), and III and IV (324 N) (p < 0.024). CONCLUSION Within the limitations of an in vitro study, it can be concluded that zirconia-framework 2U-FPDs on decoronated teeth with/without post showed comparable in vitro reliability as restorations on implants. The results indicated that restorations on teeth with only access cavity perform worse in survival and linear loading. CLINICAL RELEVANCE Even severe defects do not justify per se a replacement of this particular tooth by a dental implant from load capability point of view.