Both increased and decreased protein level lists were analyzed using the overall list of detected proteins as the background. Potentially interesting clusters identified by DAVID were then examined manually. Confocal microscopy S. gordonii stained with hexidium iodide 15 μg ml-1, (Molecular Probes, Carlsbad, CA), F. nucleatum stained 5- (and 6-) carboxyfluorescein (4 μg ml-1, Molecular Probes) and P. gingivalis (2 x 108 cells of each species) were added together, centrifuged
and incubated under anaerobic conditions for 18 h before removal of the supernatant and gentle re-suspension of the cells. The cell suspension (0.5 ml) was added to a glass I-BET-762 purchase coverslip before fixing with 4% paraformaldehyde. Detection of P. gingivalis was achieved using a specific anti-whole cell P. gingivalis antibody and anti-rabbit alexa 547 (Molecular Probes) conjugated CFTRinh-172 cost secondary. Coverslips were imaged using an Olympus FV500 laser scanning confocal microscope. A series of XYZ image stacks were digitally reconstructed using Volocity image analysis program (Improvision, Waltham, MA). Acknowledgements This work was supported by the NIH NIDCR under grants DE014372, DE12505 and DE11111. Additional funding was provided by the UW Office
of Research, College of Engineering and the Department of Chemical Engineering. We thank Qiangwei Xia and Fred Taub for the FileMaker database, David A. C. Beck for help with the computations. Electronic supplementary material Additional file 1: Summary. This file contains a short summary of all the relative abundance ratios mentioned in this report. Prior to DMXAA manufacturer permanent archiving at JGI (http://www.jgi.doe.gov/) and LANL (http://semiglobe.lanl.gov/) with the mass spectral data in XML compatible format, summaries of the protein identifications in the form of tab-delimited text files will be available on a University next of Washington server (http://depts.washington.edu/mhlab/), rather than on the BMC Microbiology web site due to their large size. Request a password from the corresponding
author. These files include details such as SEQUEST scores, peptide sequence, percentage of peptide coverage by observed ions in the CID spectrum, spectral counts, and other information at the individual peptide and protein level as calculated using DTASelect [41]. Spectral counts and coverage information for each protein can also be found in the files listed below. Ratios for protein comparisons with statistically increased levels are shown in red highlight, ratios for statistically decreased levels are shown in green highlight. The pale red and green highlights indicate the q-values for statistically increased or decreased levels respectively. (PDF 3 MB) Additional file 2: SgFn_vs_Sg. A more detailed presentation of the relative abundance ratios for the comparison of SgFn and the Sg controls, including both raw and normalized spectral counts.