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<h1>Background</h1>
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<p>Biofilm is a multi-cellular bacteria community, which is
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<h1>Project Abstract</h1>
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prevalent in diverse natural and artificial settings. It is best known
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                <p>This model is used for simulating biofilm formation and the stratification of concentration of oxygen
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for its robust adaptability and strong resistance to environmental
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stress. We intended to utilize and modify this natural multicellular
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structure to develop a new kind of extracellular scaffold, constructing
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a stratified protein expression system using the naturally formed graded
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oxygen concentration within the bacteria biofilm.<br />
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<p>Biofilm formation process can be roughly divided into four
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stages: bacteria attachment, micro colony formation, biofilm maturation
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                    <h1>Introduction</h1>
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and biofilm dispersion. The best sample for the observation is the
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                    <p ><strong>Compartment:</strong>The biofilm itself is distinguished from the overlying water and the substratum to which it is attached. A mass-transport boundary layer separates the biofilm from the overlying water.</p>
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matured biofilm, which, according to previous studies, was formed after
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<p>Within each compartment are<strong> components</strong>: include different types of biomass ,substrates , products. biomass is often divided into active microbial species, inert cells, and extracellular polymeric substances(EPS).</p>
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48 hours after inoculation with only exception in bubbling method
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<p >The components can undergo transformation, transport, and transfer <strong>processes</strong>. For
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(Bandara HM et al. 2009; Klausen M. et al. 2003.). <br />
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example, substrate is consumed, and this leads to the synthesis of new active biomass.</p>
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<p>All process affecting each component in each compartment are mathematically linked together into a<strong> mass balance equation</strong> that contains rate terms and parameters for each process.
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<p><strong>Model Selection:</strong>Many kinds of Mathematics models have been founded to describe a system of biofilm. Models
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<p></p>
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of different dimensions (1d, 2d, 3d) focus on different properties of a biofilm. Since we care most
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<p>Based on the references (Almeida C. et al. 2011; Rani SA et al.
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about the oxygen concentration gradients perpendicular to the substratum, <strong>numerical
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2007), we’ve developed three different biofilm formation methods:
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1-dimensional dynamic model(N1)</strong> would be a proper choice for us.</p>
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Bubbling method, Rubber tube method and cell culture plate method. The
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biofilm formed in the two former ways were observed through
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cryo-sectioning coupled with normal fluorescence microscopy while
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confocal laser scanning microscope was employed to obtain the biofilm
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images of the third method. In addition to the above, we’ve tested
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different material’s applicability in biofilm formation experiments and
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<hr/>
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introduced autoinducer AI-2 as an accelerator molecule.</p>
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<p><strong>The biofilm:</strong>A biofilm is a gel-like aggregation of microorganisms and other particles embedded in
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<img src="https://static.igem.org/mediawiki/2011/9/9d/ZjuYU1.gif"
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extracellular polymeric substancs. A biofilm contains water inside it, but its main physical
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characteristic is that it is a solid phase. A biofilm normally is anchored to a solid surface called the
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substratum on one side and in contact with liquid on its other side. Frequently, a mass-transfer
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boundary layer is included between the bulk liquid and the biofilm itself. Thus, following figure
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illustrates a biofilm having four compartments: the substratum, the biofilm itself, the boundary
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layer, and the bulk liquid outside of the biofilm. While it is complex even for a homogeneous biofilm morphology, we assume the biofilm surface is flat and all material below the maximum biofilm thickness as part of the biofilm components, and they have a constant density.</p>
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<p><strong>the mass-transport boundary layer</strong>Experimental observations clearly indicate strong concentration gradients for solutes just
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outside the biofilm when these solutes are utilized or produced by the microorganisms in the
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biofilm. Consequently, the solute concentrations at the biofilm surface and in a completely
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mixed bulk liquid often are significantly different.So we introduce the mass-transport boundary layer,which is a hypothetical layer of liquid above the biofilm and
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in which all the resistance to mass transport of dissolved components outside the biofilm
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<p><strong>The bulk liquid:</strong> In our experiments, the bulk liquid is large compared to the biofilm. So the simplest way seems to consider it as a boundary condition of the biofilm compartment and specify the concentrations of dissolved. However, dissolved components can exchange between the biofilm and the bulk liquid, and it has a profound impact on the concentrations in the bulk liquid. Thus we include the bulk liquid not only as a boundary condition, but also as a separate, completely mixed compartment, varying according to the inflow, outflow, and the exchanges with the biofilm.</p>
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<p><strong>The substratum:</strong> In our basic model, the substratum is a separate compartment and impermeable. So it does not have much effect on the biofilm system. However in some bioreactor, the substratum may be permeable, or include organic solids that are biodegraded by attached microorganisms.
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Latest revision as of 18:22, 28 October 2011

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> Biofilm Background

Biofilm

Rainbofilm

Xfilm

Parts

Achievements

Tools

Background

Biofilm is a multi-cellular bacteria community, which is prevalent in diverse natural and artificial settings. It is best known for its robust adaptability and strong resistance to environmental stress. We intended to utilize and modify this natural multicellular structure to develop a new kind of extracellular scaffold, constructing a stratified protein expression system using the naturally formed graded oxygen concentration within the bacteria biofilm.

Biofilm formation process can be roughly divided into four stages: bacteria attachment, micro colony formation, biofilm maturation and biofilm dispersion. The best sample for the observation is the matured biofilm, which, according to previous studies, was formed after 48 hours after inoculation with only exception in bubbling method (Bandara HM et al. 2009; Klausen M. et al. 2003.).

Based on the references (Almeida C. et al. 2011; Rani SA et al. 2007), we’ve developed three different biofilm formation methods: Bubbling method, Rubber tube method and cell culture plate method. The biofilm formed in the two former ways were observed through cryo-sectioning coupled with normal fluorescence microscopy while confocal laser scanning microscope was employed to obtain the biofilm images of the third method. In addition to the above, we’ve tested different material’s applicability in biofilm formation experiments and introduced autoinducer AI-2 as an accelerator molecule.