Development of LNA oligonucleotide–PCR clamping technique in investigating the community structures of plant-associated bacteria

<div><p>Simultaneous extraction of plant organelle (mitochondria and plastid) genes during the DNA extraction step is major limitation in investigating the community structures of plant-associated bacteria. Although locked nucleic acid (LNA) oligonucleotides was designed to selectively amplify the bacterial small subunit rRNA genes by applying the PCR clamping technique, those for plastids were applicable only for particular plants, while those for mitochondria were available throughout most plants. To widen the applicable range, new LNA oligonucleotides specific for plastids were designed, and the efficacy was investigated. PCR without LNA oligonucleotides predominantly amplified the organelle genes, while bacterial genes were predominantly observed in having applied the LNA oligonucleotides. Denaturing gradient gel electrophoresis (DGGE) analysis displayed additional bacterial DGGE bands, the amplicons of which were prepared using the LNA oligonucleotides. Thus, new designed LNA oligonucleotides specific for plastids were effective and have widened the scope in investigating the community structures of plant-associated bacteria.</p></div

Contact investigation protocol for tuberculosis.

<p>The subjects were stratified into 3 groups according to the results of QFT-3G, chest X-ray, and chest CT.</p

CT findings of active TB.

<p>A chest CT image of the left upper lobe of the lung in a 19-year-old subject demonstrated clustered non-calcified nodules associated with dilated peripheral airways (thin arrows) and a cavitation (arrow head) with dilated and thickened subsegmental bronchus (white arrow).</p

Comparison of QFT-3G values at screening between the active TB group and latent (LTBI) group.

<p>Comparison showed a statistically significantly higher value in the active TB group than in the LTBI group.</p

Comparison of QFT-3G values between the positive and negative culture groups at diagnosis of active TB.

<p>Comparison showed no significant difference between the 2 groups.</p

Bacteriologically positive cases of active tuberculosis diagnosed by the investigation protocol.

<p>Ten of 24 subjects diagnosed with active TB in the protocol showed positive culture for <i>M. tuberculosis</i>. Of these 10 subjects, 3 were missed by chest X-ray.</p

Comparison of QFT-3G values at diagnosis and after treatment of active TB.

<p>Comparison showed a statistically significant reduction of QFT-3G values after treatment.</p