How doctors actually (do not) involve families in decisions to continue or discontinue life-sustaining treatment in neonatal, pediatric, and adult intensive care: A qualitative study.

BACKGROUND: Intensive care doctors have to find the right balance between sharing crucial decisions with families of patients on the one hand and not overburdening them on the other hand. This requires a tailored approach instead of a model based approach. AIM: To explore how doctors involve families in the decision-making process regarding life-sustaining treatment on the neonatal, pediatric, and adult intensive care. DESIGN: Exploratory inductive thematic analysis of 101 audio-recorded conversations. SETTING/PARTICIPANTS: One hundred four family members (61% female, 39% male) and 71 doctors (60% female, 40% male) of 36 patients (53% female, 47% male) from the neonatal, pediatric, and adult intensive care of a large university medical center participated. RESULTS: We identified eight relevant and distinct communicative behaviors. Doctors' sequential communicative behaviors either reflected consistent approaches-a shared approach or a physician-driven approach-or reflected vacillating between both approaches. Doctors more often displayed a physician-driven or a vacillating approach than a shared approach, especially in the adult intensive care. Doctors did not verify whether their chosen approach matched the families' decision-making preferences. CONCLUSIONS: Even though tailoring doctors' communication to families' preferences is advocated, it does not seem to be integrated into actual practice. To allow for true tailoring, doctors' awareness regarding the impact of their communicative behaviors is key. Educational initiatives should focus especially on improving doctors' skills in tactfully exploring families' decision-making preferences and in mutually sharing knowledge, values, and treatment preferences.

Quantitative analysis of 16S rDNA using competitive PCR and the QPCR System 5000.

A method for precise and accurate quantification of 16S rDNA has been developed that uses competitive PCR and the QPCR System 5000. The method is based on co-amplification of 16S rDNA sequences, along with an internal standard sequence, using only one set of conserved eubacterial primers. Co-amplified PCR products are rapidly identified and quantified by measuring the electrochemiluminescent signals from specific oligonucleotide reporter probes that are directed against a hypervariable 16S rDNA sequence. Because in the exponential phase of amplification the different target sequences and the internal standard sequence are amplified with the same efficiency, unknown amounts of a target sequence in a sample can be inferred by extrapolating against a standard curve that is generated for the internal standard sequence. This method provides a rapid, nonradioactive and reliable way to simultaneously quantify different specific 16S rDNA targets that are present in low numbers, and may thus be suitable for enumeration of specific target microorganisms in environmental samples.

DNA isolation protocols affect the detection limit of PCR approaches of bacteria in samples from the human gastrointestinal tract.

A major concern in molecular ecological studies is the lysis efficiency of different bacteria in a complex ecosystem. We used a PCR-based 16S rDNA approach to determine the effect of two DNA isolation protocols (i.e. the bead beating and Triton-X100 method) on the detection limit of seven feces-associated bacterial species of different genera. Glycogen was used in these protocols to improve the precipitation of small concentrations of DNA in ethanol without affecting the sequential procedures. The PCR detection limit of 16S rDNA amplicons on agarose gel from the seven strains tested varied between 8.0 (+/- 1.3) x 10(4) and 4.3 (+/- 1.6) x 10(6) cells for the bead beating method, and between 8.0 (+/- 1.3) x 10(4) and 5.4 (+/- 0.7) x 10(8) cells for the Triton X-100 method. These large differences are most like due to the difference in cell lysis efficiency, since a competitive PCR experiment did not indicate any preference for gram negative, low G+C gram positive or high G+C gram positive bacteria. Denaturing gradient gel electrophoresis (DGGE) analysis was performed to investigate the effect of both DNA isolation protocols on the lysis efficiency of bacteria in fecal samples. A higher diversity in fecal samples was observed with the bead beating method than with the Triton-X100 method. Bands in the bead beating method-derived DGGE profiles corresponding to bands of cloned sequences of the Clostridium coccoides-Eubacterium rectale group and uncultured Fusobacterium prausnitzii were absent or had low intensity in the Triton X-100 method-derived profiles. The applicability of the bead beating method was further investigated by analyzing biopsy samples from the human colon which contain approximately 10(6) cells.

Bacterial community changes and enrichment of Burkholderia-like bacteria induced by chlorinated benzoates in a peat-forest soil-microcosm.

Bacterial community shifts in a peat-forest soil spiked with 3-chlorobenzoate (3CBA) or 2,5-dichlorobenzoate (2,5DCB) were monitored by PCR-amplification of the V6 to V8 regions of the 16S rRNA and rDNA, followed by separation of the amplicons by temperature gradient gel electrophoresis. 3CBA disappeared to non-detectable levels after 15 days by a biologically mediated process, while 2,5DCB remained at the initial concentration values. The experiments were conducted under microcosms systems. Addition of the chlorinated benzoates to the soil resulted in a rapid decrease of the microbial diversity, as judged by a time-dependent reduction in the number of amplicons detected by temperature gradient gel electrophoresis. Few amplicons specifically enriched in the spiked soils were cloned and characterised by sequence analysis. The identity of the cloned DNA and the corresponding soil amplicons was confirmed by hybridisation with a radioactively labelled V6-probe. Analysis of the 16S rDNA sequences indicated that Burkholderia-related bacteria dominated the enriched soil populations under 3CBA stress. In addition, enrichment cultures growing on 3CBA as sole C-source were obtained from the respective spiked soil, which were found to contain bacteria with identical 16S rDNA sequences as those induced by 3CBA stress in soil.

Polymerase chain reaction and denaturing gradient gel electrophoresis monitoring of fecal bifidobacterium populations in a prebiotic and probiotic feeding trial.

A culture-independent approach based on genus-specific PCR and denaturing gradient gel electrophoresis (DGGE) was used to monitor qualitative changes in fecal bifidobacterial communities in a human feeding trial. DNA was extracted directly from feces and bifidobacterial 16S rDNA sequences were amplified using genus-specific PCR. The PCR fragments were subsequently separated in a sequence-specific manner by DGGE in order to obtain a profile of bifidobacterial fragments. The DGGE profiles revealed that in general, administration for two weeks of galactooligosaccharide and/or Bifidobacterium lactis Bb-12 (8 g and 3 x 10(10) cfu per day, respectively) did not affect the qualitative composition of the indigenous Bifidobacterium population, while B. lactis Bb-12 transiently colonised the gut.

Enrichment and immobilization of quinone-respiring bacteria in anaerobic granular sludge.

The capacity of an anaerobic granular sludge for serving as an immobilizing mechanism for quinone-respiring bacteria was evaluated. The inoculum was continuously fed with a basal medium containing the humic model compound, anthraquinone-2,6-disulfonate (AQDS), as a terminal electron acceptor. Complete reduction of AQDS was achieved by the granular sludge for a prolonged period in an anaerobic bioreactor provided with a mixture of volatile fatty acids as a substrate. Phylogenetic analysis revealed the enrichment and immobilization of AQDS-respiring bacteria appearing as dominant organisms in the microbial population of the AQDS-supplemented reactor, compared to a reactor control operated under methanogenic conditions. The consistent quinone-reducing capacity observed in the consortium indicates that it is feasible to apply quinone-reducing microorganisms in continuous bioreactors and this ability can potentially be important in wastewaters rich in humic substances. The quinone reducing activity could also be applied to accelerate the conversion of xenobiotics susceptible to reductive biotransformations such as azo dyes and polychlorinated compounds in continuous bioreactors.

Image analysis, methanogenic activity measurements, and molecular biological techniques to monitor granular sludge from an EGSB reactor fed with oleic acid.

Morphological changes in anaerobic granular sludge fed with increasing loads of oleic acid were quantified by image analysis. The combination of this technique with data on the accumulation of adsorbed long chain fatty acid and with the molecular characterization of microbial community gave insight into the mechanisms of sludge disintegration, flotation and washout. It was found that the bacterial domain was more affected than the archaeal domain during this process. However, no acetoclastic activity and onlya residual hydrogenotrophic activity were detected in the sludge at the end of the operation.

Identification of biomarkers to detect residual pertussis toxin using microarray analysis of dendritic cells.

In this study we aimed to identify genes that are responsive to pertussis toxin (PTx) and might eventually be used as biological markers in a testing strategy to detect residual PTx in vaccines. By microarray analysis we screened six human cell types (bronchial epithelial cell line BEAS-2B, fetal lung fibroblast cell line MRC-5, primary cardiac microvascular endothelial cells, primary pulmonary artery smooth muscle cells, hybrid cell line EA.Hy926 of umbilical vein endothelial cells and epithelial cell line A549 and immature monocyte-derived dendritic cells) for differential gene expression induced by PTx. Immature monocyte-derived dendritic cells (iMoDCs) were the only cells in which PTx induced significant differential expression of genes. Results were confirmed using different donors and further extended by showing specificity for PTx in comparison to Escherichia coli lipopolysaccharide (LPS) and Bordetella pertussis lipo-oligosaccharide (LOS). Statistical analysis indicated 6 genes, namely IFNG, IL2, XCL1, CD69, CSF2 and CXCL10, as significantly upregulated by PTx which was also demonstrated at the protein level for genes encoding secreted proteins. IL-2 and IFN-γ gave the strongest response. The minimal PTx concentrations that induced production of IL-2 and IFN-γ in iMoDCs were 12.5 and 25IU/ml, respectively. High concentrations of LPS slightly induced IFN-γ but not IL-2, while LOS and detoxified pertussis toxin did not induce production of either cytokine. In conclusion, using microarray analysis we evaluated six human cell lines/types for their responsiveness to PTx and found 6 PTx-responsive genes in iMoDCs of which IL2 is the most promising candidate to be used as a biomarker for the detection of residual PTx.

Establishment of the Ph. Eur. BRP for varicella vaccine batch 1.

The European Pharmacopoeia (Ph. Eur.) monograph for varicella vaccine (live) (0648) requires a vial of an appropriate reference material to be titred in triplicate to validate each assay and the virus concentration of the reference preparation is monitored using a control chart to determine the assay consistency. An international collaborative study involving 9 participants from 7 countries and including both OMCLs and manufacturers was carried out to establish a common reference material for this purpose and establish a Ph. Eur. Biological Reference Preparation. Two candidate reference preparations (X and Y), obtained from 2 different EU manufacturers, were assayed by the participants using their in-house PFU assay methods. Both candidates were found to be suitable for this purpose. Based on logistical considerations, candidate X (4.37 log(10)0 PFU/vial) has been established as BRP batch 1 of varicella vaccine (live) and was adopted at the June 2009 session of the European Pharmacopoeia Commission for immediate use. Candidate Y (3.82 log(10) PFU/vial) will be established as BRP batch 2 upon depletion of BRP batch 1 provided that the stability data supports this.

Prominent occurrence of ribosomes from an uncultured bacterium of the Verrucomicrobiales cluster in grassland soils.

An uncultured bacterium of the Verrucomicrobiales cluster was identified by its 16S rDNA sequence as a major bacterium in Dutch Drentse A grassland soils. Potential metabolic activity of the according organism was estimated by applying direct ribosome isolation from soil and partial amplification of the 16S rRNA via RT-PCR using bacteria-specific primers. Temperature gradient gel electrophoresis separated the amplicons sequence specifically into reproducible fingerprints. One of the fingerprint bands matched with the signal of clone DA101. Southern blot hybridization with a DA101-specific V6 probe confirmed sequence identity. It is the first time that an organism of the Verrucomicrobiales cluster has been indicated as a potential major metabolizer in environmental microbial communities.

Statistical evaluation of numbers of animals to be used in vaccine potency testing: a practical approach.

Some of the guidelines for potency testing of vaccines issued by regulatory bodies such as the European Pharmacopoeia (EP) and WHO are detailed and stringent (e.g. EP monograph for Newcastle Disease (ND) Vaccine (inactivated)), whereas others only stipulate that the number of animals used should be sufficient to meet the required accuracy (e.g. EP monograph for Hepatitis A vaccine (inactivated)). Simulation studies in our laboratory using historical ND potency test data indicated that the number of animals specified in the monograph is too high; a considerable reduction from 10 to seven animals per group does not substantially influence the precision of the results. Multipoint models (e.g. EP monograph for Tetanus Vaccine (adsorbed)) require at least three dilutions per vaccine for testing for response linearity. However, when historical data clearly show that in the range used the response curves are linear, it is superfluous to verify this in every test. Furthermore, linearity has little priority for a valid parallel line assay calculation. A simulation study using historical Diphtheria potency test data showed that calculations using two dilutions per vaccine in relatively small groups of animals produced results comparable to those obtained from the full assay. This procedure still enables calculation of the relative potency, in contrast to the 1 + 1 method, which gives only a pass or fail result, while the number of animals required is only slightly higher. This method could be applied in cases where the 1 + 1 method fails. In conclusion, by providing guidelines on methods in which proven consistency in production and testing may be taken into account, manufacturers are more stimulated to look for other (cheaper) ways to test the potency of a vaccine using less animals.

Oligonucleotide Probes That Hybridize with rRNA as a Tool To Study Frankia Strains in Root Nodules.

Oligonucleotide probes that hybridize with specific sequences in variable regions of the 16S rRNA of the nitrogen-fixing actinomycete Frankia were used for the identification of Frankia strains in nodules. Frankia cells were released from plant tissue by grinding glutaraldehyde-fixed root nodules in guanidine hydrochloride solution. rRNA was obtained after sonication, precipitation with ethanol, and purification by phenolchloroform extraction. Degradation of rRNA, evident in Northern blots, did not affect hybridization with the oligonucleotides. Nodules of about 1 mg (fresh weight) provided sufficient rRNA for reliable detection of the Frankia strain. The utility of this rRNA extraction method was tested in a competition experiment between two effective Frankia strains on cloned Alnus glutinosa plants.

In situ detection of an uncultured predominant bacillus in Dutch grassland soils.

Uncultured predominant Bacillus ribotype DA001 in Dutch Drentse A grassland soils, as revealed by its 16S rRNA sequence, was detected in soil by fluorescent whole-cell in situ hybridization. A prominent rod-shaped cell type was identified in bacterial suspensions prepared from soil by a multiple 16S rRNA probing approach.

Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints.

A novel approach was developed to quantify rRNA sequences in complex bacterial communities. The main bacterial 16S rRNAs in Drentse A grassland soils (The Netherlands) were amplified by reverse transcription (RT)-PCR with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (TGGE). The primer pair used (primers U968-GC and L1401) was found to amplify with the same efficiency 16S rRNAs from bacterial cultures containing different taxa and cloned 16S ribosomal DNA amplicons from uncultured soil bacteria. The sequence-specific efficiency of amplification was determined by monitoring the amplification kinetics by kinetic PCR. The primer-specific amplification efficiency was assessed by competitive PCR and RT-PCR, and identical input amounts of different 16S rRNAs resulted in identical amplicon yields. The sequence-specific detection system used for competitive amplifications was TGGE, which also has been found to be suitable for simultaneous quantification of more than one sequence. We demonstrate that this approach can be applied to TGGE fingerprints of soil bacteria to estimate the ratios of the bacterial 16S rRNAs.

Spatial distribution of 16S rRNA levels from uncultured acidobacteria in soil.

The activity of uncultured acidobacteria was monitored in Dutch grassland soils by quantifying their ribosomes. These bacteria were detectable by five different 16S rRNA RT-PCR products in temperature gradient gel electrophoresis fingerprints. The ribosomes in surface soil samples were quantified with multiple competitive RT-PCR along a 1.5-km transect through the grassland. In total, the five members of the acidobacteria were estimated to contribute 4 x 1010 to 1 x 1011 ribosomes g soil-1, representing 7-14% of all bacterial ribosomes. These results indicate that ribosomes from acidobacteria are continuously present and abundant in soil and might contribute significantly to microbial activity in soil.

Genetic diversity of Datisca cannabina-compatible Frankia strains as determined by sequence analysis of the PCR-amplified 16S rRNA gene.

The presence of Frankia strains in soil samples collected from northern areas of Pakistan was detected by inoculating Coriaria nepalensis and Datisca cannabina plants. The abundance of compatible Frankia strains in some areas was indicated by profuse nodulation of the host plants, whereas soil samples from other localities failed to result in nodulation. An oligonucleotide probe (COR/DAT) directed against the 16S rRNA gene of the endophytes of Coriaria and Datisca spp. that did not cross-react with the RNA gene of Frankia strains isolated from other hosts was developed. Genetic diversity among Frankia strains nodulating D. cannabina was determined by sequence analysis of the partial 16S rRNA gene amplified from nodules induced by soil samples from different localities by PCR. Four types of Frankia sequences and one non-Frankia sequence were detected by hybridization with a Frankia genus probe and the COR/DAT probe as well as by sequence analysis of the cloned PCR products.

Factors affecting the error in the Loo-Riegelman method for estimating the rate of drug absorption. Some suggestions for a practical sampling schedule.

During the development of a new computer program for the Loo-Riegelman method for the estimation of the rate drug absorption, it was found that many factors can affect the accuracy of the estimated absorption rate constant (ka). In this paper a survey of the factors affecting the errors in the estimation of ka by the Loo-Riegelman method is made. By simulating data and computer techniques, the effects of factors related to each step in the calculation procedure as well as the influence of certain pharmacokinetic parameters were studied in detail. If these factors are not well controlled, the estimated error in ka will become very large, in some cases even surpassing 30%. In addition, it was derived that careful attention has to be paid to both sampling time and the number of plasma samples. A "trial and error" method for obtaining an optimal sampling schedule that minimizes the error of ka is presented.

Application of temperature-gradient gel electrophoresis in taxonomy of coryneform bacteria.

Strains belonging to the Gram-positive coryneform soil bacteria were screened genotypically by temperature-gradient gel electrophoresis (TGGE). This method allows the sequence-specific separation of amplified fragments of 16S rRNA genes. A total of 115 reference strains representing the majority of the species of the genera Aeromicrobium, Agromyces, Arthrobacter, Aureobacterium, Cellulomonas, Curtobacterium, Nocardioides and Terrabacter were characterized. Depending on the genus investigated, the resolution limit of the technique appeared to be at the species or genus level or intermediate between the two. Aberrant TGGE profiles of strains within particular taxa revealed genomic heterogeneity and generic misclassification of nine strains studied. Beyond that, indications of 16S rRNA gene heterogeneity were found within the genomes of three Curtobacterium strains. The misclassifications revealed by TGGE were confirmed using whole-cell fatty acid methyl ester analysis and subsequent comparison with a database. TGGE has been demonstrated to be a useful tool in bacterial taxonomy.