0), and the DNA was precipitated with 2.5 M ammonium acetate in ethanol. After two washes with 80% (v/v) ethanol, the DNA pellet was dried and resuspended in 10 μl, 0.2 μl filtrated, double-distilled water. Following the manufacturer’s descriptions the cloning was done by using a Zero blunt TOPO cloning kit (Invitrogen Corporation). Fifty to hundred colonies from each cloning were
picked and sequenced Selleckchem NSC23766 by pyrosequencing. A PYROMark Q96 ID was used to short DNA sequencing of the approximately 40-60 bp clone insert using the recommended protocol (Biotage AB, Uppsala, Sweden) as described previously using the primer PyroBact64f . The sequences (tags) were imported into the software BioNumerics 4.61 and manually checked, aligned and filtered for high quality sequences. Sanger sequencing with an Applied Biosystem PND-1186 chemical structure 3130 Genetic Analyzer (Foster City, CA, USA) was used to check consensus tags for the pyrosequencing accuracy. The Sequence match analysis tool in the Ribosomal database project 10 http://rdp.cme.msu.edu/ was used to assign the Phylogenetic position of each consensus tag. The search criteria were for both type and non-type strains, both environmental (uncultured) sequences and isolates, near-full-length
sequences (>1200 bases) of good quality. If there was a consensus at the genus level the tag was assigned this taxonomic classification. If no such consensus was found, the classification proceeded up one level to family and again if no taxonomic affiliation could be assigned the tag continued to be proceeded up the tree as described by Huse et al., . In some cases it was not possible to assign a domain and these sequences might represent new novel organisms or the sequences might be biased, Ribonucleotide reductase in these cases the tags were excluded from the dataset. In total 364 sequences were finally included in the alignment. The
phylogenetic analysis was done by downloading 16S rRNA gene sequences longer than 1,200 base pair from the RDP database of the Ralstonia type strains http://rdp.cme.msu.edu. The RDP alignment was used and a phylogenetic tree was constructed by using the Ward algorithm in the software Bionumerics. Burkholderia cepacia (GenBank accession no. AF097530) was used as an out-group. Statistics The statistical analysis was done in two steps: First, the association between one predictor at a time and the NEC score was analysed by robust least squares methodology Napabucasin manufacturer adjusting for gestational age. This is equivalent to a normal linear GEE modal with working independence correlation structure on child level. For each predictor the estimated change in expected NEC score is reported with Wald 95% confidence limits in parentheses. The overall association between the predictor and the NEC score is evaluated by a robust score-test. Second, we formulate a normal linear GEE model including gestational age and all predictors with a robust score-test p-value below 0.1 in the above analyse.