Computational protocol: L-Arginine Destabilizes Oral Multi-Species Biofilm Communities Developed in Human Saliva

Similar protocols

Protocol publication

[…] Biofilms were examined using a Leica (Leica, Exon, PA) SPE confocal laser scanning microscope (CLSM) equipped with a 10X 0.4 NA HC PL APO infinity corrected objective lens (for static saliva biofilm microplate assays) or a 40X 1.25 NA HCX PL APO infinity corrected objective lens (for flowing saliva biofilm Bioflux assays). A 488 nm laser (15% power) was used to excite the LIVE/DEAD stained biofilms. For unbiased image acquisition and analyses, gain and offset settings were kept constant and the emission capture gates (Syto 9: EM: 510–540 nm and propidium iodide: EM: 620–650 nm) were set to be the same for every experiment. Imaris software (Bitplane, Zurich, Switzerland) was used to render and visualize biofilms. COMSTAT [] and IMAGEJ [] were used to assess parameters such as biofilm biovolume (the total volume occupied by fluorescent cells per unit of substratum area), average biofilm thickness (the mean biofilm thickness in a field of view), (dimensionless) biofilm roughness (a measure of how much the thickness of the biofilm varies), and viability (percentage of fluorescent green staining of biofilm by Syto 9). For image analysis using COMSTAT, all image stacks underwent manual thresholding checks that were based upon visual inspection of 3D biofilm renderings in IMARIS and histograms calculated in IMAGEJ. […]

Pipeline specifications

Software tools Imaris, Comstat, ImageJ
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Homo sapiens
Diseases Bacterial Infections, Carcinoma, Renal Cell
Chemicals Amino Acids, Arginine, Cetylpyridinium