Team:Purdue/References2

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<h1>References and Citations </h1>
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<h1> Characterization & Experimental Design</h1>
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<h5> Meeting 7/2/12 </h5>
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List of What Needs to get Done this Week:
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<ul>
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<li> Research protocols on setting up and running experiments using biofilms </li>
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<li> Research flow and static protocols for biofilms </li>
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<li> Research ways to characterize silica matrix and acquire quantifiable data </li>
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<li> Create timelines for each assay researched </li>
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<li> Order reagents and get training on any equipment needed for assays </li>
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</ul>
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<h5> 7/3/12 </h5>
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Researched stages of biofilm formation:
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<p>  1. Initial Attachment  -  attachment occurs via van der waals forces</p>
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<p>  2. Irreversible Attachment  -  this is where the EPS forms</p>
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<p>  3. Maturation I  -  matrix formed with adhesion proteins</p>
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<p>  4. Maturation II  -  the full biofilm forms</p>
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<p>  5. Dispersion  -  bacteria released</p>
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Also researched shear stress modeling, chassis development, microsensors, and confocal microscopy assays.
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<h5>7/5/12</h5>
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Researched possible competitors in the field of bioreactor filtration.
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<ul>
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<li> Hydro Engineering - produces "Hydrokleen", which is a bioreactor filtration system that would generally be used in industrial plants and acts as a water recycler. </li>
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<li> Seven Trent Services - produces Tetra Amphidrone fixed sequencing Batch Biological Filter, a waste water treatment process that uses a biological filter to remove various pollutants </li>
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<li> Kinetics -  this company makes a range of water treatment processes and machines that can be used in industry as well as consumer markets </li>
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<li> ABEC - produces bioreactors, but could not find more detail into what kind </li>
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<h5>7/8/12</h5>
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<br>Performed a cell culture to have competent cells for a biofilm culture.</br>
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<br>Also did research into developing a static biofilm assay to test how well our bacteria makes biofilm before and after our transformation. <a href="https://static.igem.org/mediawiki/2012/e/e9/Growing_and_Analyzing_Static_Biofilms.pdf">"Growing and Analyzing Static Biofilms"</a> by Judisth H. Mernitt, Daniel E. Kadouri, and George A. O'Toole was helpful in determining how we would do this assay.</br>
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<h5>7/9/12</h5>
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<br>Performed the <a href="https://2012.igem.org/Team:Purdue/Protocol#Stationary Phase"> Gorwth Rate Assay</a> on NEB Beta and DH5 Alpha E.coli strains to determine the time frame we will use to grow our static biofilms.</br>
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<img border="1" align="left" src="https://static.igem.org/mediawiki/2012/f/f0/Growth_Rate_NEB_and_DH5.jpg" width="481" height="292"/>
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To the left is the results of the growth rate assay for NEB Beta and DH5 alpha. Overall, the plots show the expected shape with a lag, log, and stationary phase.
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<br>Also worked out the lab plan for the rest of the week.</br>
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<h5>7/10/12</h5>
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<br>We did the same <a href="https://2012.igem.org/Team:Purdue/Protocol#Stationary Phase"> Gorwth Rate Assay</a> as yesterday, but with the XL-10 Gold E.coli strain because we think it will work better for the biofilm purposes.</br>
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<img border="1" src="https://static.igem.org/mediawiki/2012/8/8d/Growth_Curve_XL10.jpg" width="482" height="292"/>
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<br> <a href="https://static.igem.org/mediawiki/2012/4/41/Bacteria_Growth_Rate.xls">Here </a> is the excel file containing all of the data from the three growth rate assays.
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<br>Also researched and developed the static biofilm assay that we can do to determine the biofilm rates of our non-transformed E.coli.</br>
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<h5>7/13/12</h5>
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<br>Performed the <a href="https://2012.igem.org/Team:Purdue/Protocol#Static Biofilm"> Static Biofilm Assay</a>.</br>
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<br>Had a team meeting, discussed goals for the following week:</br>
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<ul>
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<li> Write out protocols and email them to the entire team for revisions </li>
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<li> Plan a meeting to go through and troubleshoot the protocols together </li>
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<li> Find a way to determine the optimized concentration of curli</li>
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<li> Purchase all materials needed for future protocols </li>
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</ul>
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<h5>7/16/12</h5>
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<br>Researched how Membrane Aerated Bioreactor work and how we will use one for testing.</br>
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<h2> Silica Characterization </h2>
 
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Research was done on different ways to characterize the silica coat. Three extremely helpful articles are listed below.
 
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<li> <a href="https://static.igem.org/mediawiki/2012/2/2e/Cell-Mediated_Deposition_of_Porous_Silica_on_Bacterial_Biofilms.pdf">Cell-Mediated Deposition of Porous Silica on Bacterial Biofilms</a> </li>
 
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<li> <a href="https://static.igem.org/mediawiki/2012/9/93/Sol-gel_synthsis_and_structure_of_silica_hybrid_materials.pdf">Sol-gel synthsis and structure of silica hybrid materials</a> </li>
 
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<li> <a href="https://static.igem.org/mediawiki/2012/d/d7/Thin-film_silica_sol-gel_coatings_for_neural_microelectrodes.pdf">Thin-film silica sol-gel coatings for neural microelectrodes</a> </li>
 
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A powerpoint highlighting possible characterization methods is given <a href="https://static.igem.org/mediawiki/2012/8/8e/Experiments_for_Silica_Characterization.ppt">here</a>
 
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After discussion with the team and our faculty advisor, Dr. Rickus, we have decided to use the scanning eletron microscopy (SEM), x-ray diffraction (XRD), and a live/dead assay (specifically, the <a href="http://products.invitrogen.com/ivgn/product/L7012?ICID=search-product">Baclight Bacterial Viability Kit</a>).
 
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Latest revision as of 21:12, 18 July 2012

References and Citations

Retrieved from "http://2012.igem.org/Team:Purdue/References2"