5 min, and 72°C for 1.5 min, followed by a final extension at 72°C for 5.0 min. TA cloning, nucleotide sequencing and sequence analyses Amplified PCR products were separated by 1.0% (w/v) agarose gel electrophoresis in Luminespib nmr 0.5× TBE at 100 V and detected by staining with ethidium bromide. PCR products amplified by the newly constructed two primer pairs were purified using a QIAquick PCR Purification Kit (QIAGEN, Tokyo, Japan) and inserted into the pGEM-T vector

using the pGEM-T Easy Vector System (Promega Corp. Tokyo, Japan). Sequencing of the cloned cadF (-like) gene fragments was performed with a Hitachi DNA autosequencer (SQ5500EL; Hitachi Electronics Engineering Co. Tokyo, Japan), after dideoxy nucleotide sequencing using a Thermo Sequenase Pre-Mixed Cycle Sequencing Kit (Amersham Pharmacia Biotech, Tokyo, Japan). Sequence analysis of the PCR amplicons was carried out using the computer software GENETYX-MAC version 9 (GENETYX Co., Tokyo, Japan). Total cellular RNA purification, reverse transcription-PCR, northern blot hybridization and primer extension analysis Total cellular RNA was extracted and purified from C. lari cells by using RNA protect Bacteria Reagent and RNeasy Mini Kit (QIAGEN). Reverse-transcription (RT)-PCR was carried out with a primer pair of f-cadF2 and r-cadF3 Selleckchem EGFR inhibitor (Figure 1), by using the QIAGEN OneStep RT-PCR Kit (QIAGEN). This primer pair is expected to generate a RT-PCR product of the cadF (-like) structural

gene segment of approximately 780 bp including the Cla_0387 region. Northern blot hybridization analysis was carried out according to the procedure described by Sambrook and Russell (2001) [34],

Parvulin using a PCR amplified cadF (-like) fragment as a probe. The fragment was amplified using a primer pair of f-/r-cadF4 (Figure 1). Random primer extension was performed in order to prepare the fragment probe using a DIG-High Prime (Roche Applied Science, Penzberg, Germany). The transcription initiation site for the cadF (-like) gene was determined by the primer extension analysis with the purified total cellular RNA of C. lari JCM2530T cells. The primer that was selected for this assay was 5′-CTAAATTTCCTTCTGGMGTTGT-3′, which corresponds to the reverse complementary sequence of np 504 through 525. The transcription initiation site was determined by primer extension with the sizes of DNA fragments generated by sequencing reactions. In the present study, the np which the authors used, are for those of C. lari JCM2530T. INK 128 mw Phylogenetic analysis Nucleotide sequences of approximately 980 bp of the full-length cadF (-like) gene, from the isolates of C. lari and the C. lari RM2100 strain, were compared to each other and with the accessible sequence data from some other thermophilic campylobacters using CLUSTAL W software, respectively [35], which was incorporated in the DDBJ. Following this, a phylogenetic tree was constructed by the neighbor-joining (NJ) method [29].