PP875 Biofilms

PP875 - Bacterial Adhesion and Biofilm Formation

Week One	Biofilm Development and Dispersal
	22March06 - NOTES
Discussion Paper	Dow et al. 2003
Background Papers	Aoki et al. 2005 Gjermansen et al. 2005 Klausen et al. 2003 Moorthy and Watnick 2004 Rice et al. 2005 Webb et al. 2003

Week Two	Bacterial Ecology and Biofilms - NOTES
	29March06
Discussion Paper	Monier and Lindow, 2003
Background Papers	Axtell and Beattie, 2002 Jacques et al., 2005 Monier and Lindow, 2005a Monier and Lindow, 2005b Monier and Lindow, 2004 Morris et al. 1998

Week Three	Proteomics and Genomics
	5April06
Discussion Paper	Ram et al., 2005
Mass Spec Methods	Norbeck et al., 2005 Conrads et al., 2000
Background Papers	Beloin and Ghigo, 2005 de Souza et al., 2003 Lazazzera 2005 Stanely et al., 2003 Moorthy and Watnick 2005

Week Four	Host Factors
	12April06
Discussion Paper	Darby et al., 2005
Background Papers	Cipollo et al., 2004 Erickson et al., 2006 Jarrett et al., 2004 Marcell and Beattie, 2002 Tan and Darby, 2004

Week Five	Biocontrol
	19April06 - FIRST
Discussion Paper	Bais et al. 2004
Background Papers	Branda et al., 2006 Chu et al., 2006 Kearns et al. 2005 Stanley et al. 2005

Week Five	Cyclic Diguanylate and GGDEF Proteins
	19April06 - SECOND
Discussion Paper	Garcia et al., 2004
Background Papers	Hickman et al., 2005 Mendez-Ortiz et al., 2006 Romling and Amikam, 2006 Romling et al., 2005 Sim et al., 2006 Sim et al., 2004 Tischler et al., 2005 Tischler and Camilli, 2004

Week Six	Small Molecules
	26April06 - FIRST
Discussion Paper	Banin et al., 2006
Background Papers	Banin et al. 2005 Koutsoudis et al., 2006 Prithiviraj et al, 2005 Ren et al, 2005 Wolfe et al., 2003

Week Six	Extracellular DNA
	26April06 - SECOND
Discussion Paper	Allesen-Holm et al., 2006
Background Papers	Petersen et al., 2005 Steinberger and Holden, 2005 van Schaik et al., 2005 Whitchurch et al., 2005

Week Seven	Flagella
	3May06 - FIRST
Discussion Paper	Kirov et al., 2004
Background Papers	Klausen et al., 2003

Week Seven	Extracellular DNA
	3May06 - SECOND
Discussion Paper
Background Papers	Cohen-Krausz, et al., 2002 Henneberger et al., 2006 Moissl et al., 2005 Moissl et al., 2003

Proposed Go Terms

Monolayer formation

Microcoloby formation

Macrocolony formation

Dispersal: genes required for dispersion from a biofilm

Cell-to-cell communications within a species

Cell-to-cell communication between species

Metabolism modulation during biofilm formation

Flocculation

Protection from UV, phage, predators, antimicrobials while in biofilms

Hydrophobicity

Matrix synthesis

Biofilm Definition
from Donlan, R. M. and J. W. Costerton. 2002. Biofilms: survival mechanisms of clinically relevant microorganisms. Clin. Microbiol. Rev. 15:167-193.

"A microbially derived sessile community characterized by cells that are irreversibly attached to a substratum or interface or to each other, are embedded in a matrix of extracellular polymeric substances that they have produced, and exhibit an altered phenotype with respect to growth rate and gene transcription. This definition will be useful, because some bacterial populations that fulfilled the earlier criteria of a biofilm, which involved matrix formation and growth at a surface, did not actually assume the biofilm phenotype. These "nonbiofilm" populations, which include colonies of bacteria growing on the surface of agar, behave like planktonic cells "stranded" on a surface and exhibit none of the inherent resistance characteristics of true biofilms."

To consider during our discussions:

1. Must cells be irreversibly attached?

2. Must the cells produce the matrix? How are cells associated with a biofilm, but not producing matrix defined?

3. An altered phenotype compared to what?

Microbiology Lingo
Genes are designated by lowercase italics: motA
Proteins are designated by capitalizing the first letter: MotA
Insertion mutatations are denoted by a :: followed by the insertion: motA::cat (This means that the motA gene has a cat gene inserted into it.)
Deletions are described with a triangle (the Greek letter delta): delta motA (I haven't figured out how to add the Greek symbol font to this webpage yet!)

A link to describe what an operon is: Maricopa textbook

A short description of how epifluorescence microscopy works: Epifluorescence

Some descriptions of how confocal microscopy works: confocal

Other Links

BioCyc

Center for Biofilm Engineering

Gene Ontology

Return to Charkowski Lab Page