Genome-wide partial correlation analysis of Escherichia coli microarray data.

Transcriptional control is an essential regulatory mechanism employed by bacteria. Much about transcriptional regulation remains to be discovered, even for the most widely studied bacterium, Escherichia coli. In the present study, we made a genome-wide low-order partial correlation analysis of E. coli microarray data with the purpose of recovering regulatory interactions from transcriptome data. As a result, we produced whole genome transcription factor regulation and co-regulation graphs using the predicted interactions, and we demonstrated how they can be used to investigate regulation and biological function. We concluded that partial correlation analysis can be employed as a method to predict putative regulatory interactions from expression data, as a complementary approach to transcription factor binding site tools and other tools designed to detect co-regulated genes.

Genome-wide partial correlation analysis of Escherichia coli microarray data

Transcriptional control is an essential regulatory mechanism employed by bacteria. Much about transcriptional regulation remains to be discovered, even for the most widely studied bacterium, Escherichia coli. In the present study, we made a genome-wide low-order partial correlation analysis of E. coli microarray data with the purpose of recovering regulatory interactions from transcriptome data. As a result, we produced whole genome transcription factor regulation and co-regulation graphs using the predicted interactions, and we demonstrated how they can be used to investigate regulation and biological function. We concluded that partial correlation analysis can be employed as a method to predict putative regulatory interactions from expression data, as a complementary approach to transcription factor binding site tools and other tools designed to detect co-regulated genes.

PCR-assisted contig extension: stepwise strategy for bacterial genome closure.

Finishing is rate limiting for genome projects, and improvements in the efficiency of complete genome-sequence compilation will require improved protocols for gap closure. Here we report a novel approach for extending shotgun contigs and closing gaps that we termed PCR-assisted contig extension (PACE). PACE depends on the capture of rare mismatched interactions that occur between arbitrary primers and template DNA of unknown sequence, even under highly stringent conditions, by means of elevated PCR-cycle repetition and the use of specific anchoring primers corresponding to adjacent regions of known sequence. Using PACE, we have generated extensions with an average of 1 kb from all contigs generated from the shotgun sequencing of a 5-Mb genome, which closed the majority of gaps with a single round of experimentation. This included the generation of multiple extensions for contigs that terminated in one of the eight copies of the rRNA operon. We calculate that the switch from shotgun sequencing to PACE should occur between 5- and 8-fold genome coverage for maximum benefit and minimum overall cost. PACE is a robust and straightforward strategy that should simplify the finishing phase of bacterial genome projects.

Effect of hydrophobicity on in vitro streptococcal adhesion to dental alloys.

Non-specific interactions such as electrostatic interactions, and surface free energy are of importance in bacterial adhesion to dental surfaces as they determine whether or not bacteria are attracted to the surface. The relationship between adherence of Streptococcus mitis, S. mutans, S. oralis and S. sanguinis on precious and non-precious dental alloys, and the bacterial and alloy surface hydrophobicities (a measure of the surface free energy) was studied. The number of adhering bacteria was determined by fluorescence microscopy counts. The hydrophobicity of the bacteria and alloy surfaces were evaluated by adhesion to hexadecane and water contact angles, respectively. Our results showed that (i) the surfaces of the tested alloys were hydrophobic, (ii) S. sanguinis, S. mutans and S. oralis were hydrophobic, and (iii) S. mitis was hydrophilic. S. oralis, the more hydrophobic strain, demonstrated the highest adherence on the tested materials, whereas S. mitis adhered least on the hydrophobic surfaces. For the tested alloys, bacterial adherence was highest for the high gold content alloy, and lowest for the non-precious alloy. Our results showed that for the tested bacterial strains, there was a significant correlation between bacterial adhesion and substratum hydrophobicity: hydrophobic metal surfaces favor adhesion of hydrophobic bacteria.

Automatic enumeration of adherent streptococci or actinomyces on dental alloy by fluorescence image analysis.

The aim of the present study was to develop an automated image analysis method to quantify adherence of Streptococcus sanguinis or Actinomyces viscosus on surfaces of a currently used dental alloy. Counting such bacterial strains was difficult because of their arrangement, thus S. sanguinis being a coccus arranged in chains or pairs, and A. viscosus a long complexly arranged polymorph rod. Direct counting of fluorescently stained adherent bacteria was done visually and with image analysis methods. To differentiate these two morphotypes, two programs were developed: (i) for streptococci, thresholding and selection of the object maxima, and (ii) for actinomyces, two step thresholding and processing of the characteristic points of the object skeletons. The triplicate enumerations for each bacterial strain were not significantly different (p > 0.005) and correlations between visual counting and automated counting were significant (r = 0.91 for S. sanguinis and r = 0.99 for A. viscosus, p <00.0001). These rapid and reproducible methods, allowed us to count either cocci or rods, adherent on an inert substratum, in high density conditions.