We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments on DNA microarrays. Such analyses have applications in the study of microbial communities. Unlike in the classical SBH (sequencing by hybridization) procedure, where multiple probes are on a DNA chip, in our app...

We evaluated the performance of matrix-assisted laser desorption ionization-time flight mass spectrometry (MALDI-TOF MS) associated with Bruker BioTyper TM V7.0.0 database for identification 713 bacterial strains isolated from seafood products and sea water samples (ANSES B3PA collection) under culture conditions that may have been significantly different those used to create reference spectrum...

30 milled rice samples were collected from retailers in four states of Malaysia. These samples were evaluated for Eurotium spp. contaminations by direct plating on malt extract salt agar (MESA). All Eurotium were isolated and identified based on morphology and nucleotide sequences of internal transcribed spacer 1 (ITS1) and ITS2 of the rDNA.  Four Eurotium species (E. rubrum, E. amstelodami, E....

There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR specific AMF, amplified part (c. 2.5 kb) rDNA spanning majority small subunit rRNA (SSU)...