Jan Kreft wrote:
> I believe biofilm research in the future should be more
> quantitative. Quantitative analysis of biofilm structure;
> beyond beautiful pictures! Quantitative work on
> pheromones in biofilms.
> That's my $.02.
> Jan Kreft
> Dr. Jan-Ulrich Kreft Phone +44 1222 874000 ext. 6036
> Cardiff School of Biosciences Fax +44 1222 874305
> Cardiff University E-mail Kreft at cardiff.ac.uk> PO Box 915, Cardiff CF1 3TL, UK
I quite agree that some kind of quantification of biofilm
structure is required if we are really going to get a
handle on the relationships between structure and the
numerous variables which may influence structure. However,
this is not a trivial matter. The problem is to find a
parameter or set of parameters that can define a unique
structure. When we consider biofilms we are looking at
patterns made up of the cell clusters and the spaces that
surrounded them (voids or channels). Some parameters such
as percent cover or porosity may be useful for describing
the accumulation process but contain no structural
information. Fractal analysis seems to be the best bet but
even then we can not construct a unique structure from the
fractal dimension alone. To make matters worse when we do
fractal or other pattern analyis we are using images that,
because of imperfections in optical systems contain all
sorts of artifacts. These can be from uneven illumination
due to surfaces not being completely flat, light scatter
from the surface, out of focus haze, differential light
absorption through different thicknesses of biofilm, pH
influences on fluorescence, photo-bleaching, variations in
illumination intensity from 1 day to the next etc. etc..
Confocal microscopy and deconvolution programs can help
reduce, but not eliminate these. Further, image anlysis
requires that images are converted into binary - black and
white. Fuzzy edges do not threshold well. Slight
differences in threshold settings can give very different
patterns and shape perimeter values of which fractal
dimensions are very sensitive. Magnification will also
influence how we see the structure. In my experience
microscopists generally find structures that nicely fit
into the field of view.
So to wrap up I think that the quantification of biofilm
structure is a very difficult, but necessary, problem to
overcome. It will require an interdisciplinary solution
with components of math, image analysis, microscopic
techniques, and microbiology. I am aware that a few groups
have begun to tackle this problem and look foreward to
seeing how thier work progresses. I also think that this is
an area worthy of debate in the newsgroup. I should add
that I am not actively involved in research in
this area but am an interested onloooker.
Paul Stoodley.
----------------------
Paul Stoodley
Environmental Tel: 01392 264348
Microbiology Fax: 01392 263700
Research email: p.stoodley at exeter.ac.uk
Group
Exeter University
Biological Sciences
Hatherly Laboratories
Prince of Wales Road
Exeter EX4 4PS. UK.
-------------------------------------------------------------------
To reply to the group as well as to the originator, make sure that
the address biofilms at net.bio.net is included in the "To:" field.
See the BIOFILMS homepage at http://www.im.dtu.dk/biofilms for info
on how to (un)subscribe and post to the Biofilms newsgroup.
