Team:Purdue/Notebook

From 2012.igem.org

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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"
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{{Purdue_topbarNotebook}}
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!align="center"|[[Team:Purdue|Home]]
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{{Purdue_CalendarTemplate}}
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!align="center"|[[Team:Purdue/Team|Team]]
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__NOTOC__
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!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Purdue Official Team Profile]
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<html>
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!align="center"|[[Team:Purdue/Project|Project]]
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<h2 id="5/15">
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!align="center"|[[Team:Purdue/Parts|Parts Submitted to the Registry]]
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Monday, May 15
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!align="center"|[[Team:Purdue/Modeling|Modeling]]
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</h2>
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!align="center"|[[Team:Purdue/Notebook|Notebook]]
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!align="center"|[[Team:Purdue/Human Practices|Human Practices]]
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!align="center"|[[Team:Purdue/Safety|Safety]]
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!align="center"|[[Team:Purdue/Attributions|Attributions]]
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|}
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You should make use of the calendar feature on the wiki and start a lab notebook.  This may be looked at by the judges to see how your work progressed throughout the summer.  It is a very useful organizational tool as well.
+
<h5> List of useful contacts on the google doc, including DowAgro </h5>
 +
<h5> Begin to list the different devices/constructs that will be used in our project </h5>
 +
<h5> Attachment (adhesion)<h5>
-
== Monday, May 15 ==
+
<h5> Filtration </h5>
 +
<body>
 +
<ul>
 +
<li>Modularize the sequence so we can test individually (e.g. put a fluorescent protein coding sequence at the end of each segment – construct silica binding protein first with constitutive promoter/repressible promoter to produce fluoresent protein and make sure it does what you think it should)</li>
 +
<li>Investigate multiple silica binding protein (SBP);must choose several top candidates for each element.</li>
 +
</body>
 +
</ul>
 +
<h5> Hierarchy </h5>
 +
<h5> Perfecting the FFL </h5>
 +
<ul>
 +
<li> And (low affinity, not dimer), Or (high affinity)</li>
 +
<li><a href="https://static.igem.org/mediawiki/2012/d/d5/Schematic.jpg">Schematic Diagram</a></li>
 +
</ul>
-
=== List of useful contacts on the google doc, including DowAgro ===
+
<h5> Modeling and Experimental </h5>
-
=== Begin to list the different devices/constructs that will be used in our project===
+
<ul>
-
==== Attachment (adhesion)====
+
<li> Communication in terms of data (e.g. kinetic parameters)</li>
-
===== Filtration =====
+
<li> Review Characterization Data Sheets <li>
-
* Modularize the sequence so we can test individually (e.g. but GFP, RFP, YFP at the end of each segment – construct silica binding protein first with constitutive promoter/repressible promoter to produce promoter and make sure it does what you think it should)
+
<li> Strong integration of modeling translates to a strong performance in the competition. </li>
-
* Investigate multiple silica binding protein (surface protein – silica binding peptide);must choose several top candidates for each element.
+
</ul>
-
==== Hierarchy ====
+
-
==== Perfecting the FFL ====
+
-
* And (low affinity, not dimer), Or (high affinity)
+
-
* [[Media:schematic.jpg| Schematic Diagram]]
+
-
==== Modeling and Experimental ====
+
<h5> List of things we need </h5>
-
* Communication in terms of data (e.g.  kinetic parameters)
+
<ul>
-
* Review Characterization Data Sheets (look in the DropBox for an uploaded link from Sean )
+
<li> Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy)may have the needed cells)</li>
-
* Strong integration of modeling translates to a strong performance in the competition.
+
<li> Antibiotics (AMP, tetracycline)
 +
<li> Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease )
 +
<li> Parts (available in the registry)
 +
<ul>
 +
<li> Constitutive promoter (orthogonal t7 promoter)</li>
 +
<li> Signaling Promoters (investigate the precedent for construction FFL)</li>
 +
<li> RBS –(B0034)</li>
 +
<ul>
 +
<li> Thermodynamic models for designing RBSs, etc (Voights model) </li>
 +
</ul>
 +
<li> Terminators </li>
 +
<li> Proteins Transcription Factors </li>
 +
</ul>
 +
</ul>
-
=== List of things we need ===
+
<h2 id="5/21">
-
* Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy)may have the needed cells)
+
<h2> Monday, May 21 </h2>
-
* Antibiotics (AMP, tetracycline)
+
<ul>
-
* Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease )
+
<h5> We're all looking forward to an exciting iGEM summer! Our SURF students have just arrived and are gradually being introduced to synthetic biology and iGEM. </h5>
-
* Parts (available in the registry)
+
<h5> Sean gave a crash course on synthetic biology to Mrudula, Rachel, Amanda and August. The powerpoint is available <a href="https://static.igem.org/mediawiki/2012/2/24/SynBioIntroduction.ppt">here</a>, compiled by our wonderful graduate mentor, Janie.</h5>
-
** Constitutive promoter (orthogonal t7 promoter)
+
</ul>
-
** Signaling Promoters (investigate the precedent for construction FFL)
+
-
** RBS –(B0034)
+
-
*** Thermodynamic models for designing RBSs, etc (Voights model)
+
-
** Terminators
+
-
** Proteins Transcription Factors
+
-
== Monday, May 21 ==
 
-
* We're all looking forward to an exciting iGEM summer! Our SURF students have just arrived and are gradually being introduced to synthetic biology and iGEM.
 
-
* Sean gave a crash course on synthetic biology to Mrudula, Rachel, Amanda and August. The powerpoint is available [[Media:SynBioIntroduction.ppt|here]], compiled by our wonderful graduate mentor, Janie.
 
-
== Tuesday, May 22 ==
+
<h2 id="5/22">
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* First Journal Club Meeting - Identified the reducible elements of our system
+
<h2> Tuesday, May 22 </h2>
-
* Detailed outline of the project to the SURF students  
+
<h5>
 +
First Journal Club Meeting - we identified the reducible elements of our system, detailed an outline of the project to the SURF students (e.g. What is the advantage of using this entire process? Is not it kind of roundabout?)</li>
-
:* ''What is the advantage of using this entire process? Is not it kind of roundabout?''
+
</h5>
-
:* Diagram of complete device was shown
+
</ul>
 +
<h5> For the NEXT MEETING Tuesday 29th May : </h5>
 +
<ul>
 +
<h5> Identify, in these teams: </h5>
-
For the NEXT MEETING Tuesday 29th May :
+
<li> a. What Adhesion system we want to use (Amanda, Peter, Mrudula) </li>
-
- Identify, in these teams:
+
<li> b. Which silica-binding system we want to use (Rachel, August) </li>
-
a. What Adhesion system we want to use (Amanda, Peter, Mrudula)
+
<li> c. Control Elements (Max, Mrudula, Rachel, Sean) </li>
-
b. Which silica-binding system we want to use (Rachel, August)
+
<li> d. Find strain auxotrophic for RSC (gene which breaks down arabinose) (Jim) </li>
 +
</ul>
-
c. Control Elements (Max, Mrudula, Rachel, Sean)
+
<h5> Announcements: </h5>
 +
<ul>
 +
<li> Be ready to explain your assigned element of the project (starting generally and moving more specifically) </li>
-
d. Find strain auxotrophic for RSC (gene which breaks down arabinose) (Jim)
+
<li> Read the introductory/background elements of the thesis that Dr. Rickus will put in the dropbox </li>
 +
</ul>
 +
<h5> General Announcements </h5>
 +
<ul>
 +
<li> Be ready to work the BioBuilder HighSchool Teacher iGEM workshop during the week of June 4th – June 8th (more details to come) </li>
 +
<li> Everyone is welcome to visit Drs. Rickus and Clase’s lab group meeting on Thursday at 12PM </li>
-
Announcements:
+
</ul>
-
- Be ready to explain your assigned element of the project (starting generally and moving more specifically)
+
<h2 id="5/24">
 +
<h2> Thursday May 24th </h2>
-
- Read the introductory/background elements of the thesis that Dr. Rickus will put in the dropbox
+
<h5>Update on the human practice component available through the <a href="https://static.igem.org/mediawiki/2012/1/1b/CommunitylabsNewTemplate.ppt">Powerpoint</a></h5>
-
General Announcements
+
-
- Be ready to work the BioBuilder HighSchool Teacher iGEM workshop during the week of June 4th – June 8th (more details to come)
 
-
- Everyone is welcome to visit Drs. Rickus and Clase’s lab group meeting on Thursday at 12PM
+
<h2 id="5/29">
 +
<h2> Tuesday, May 29 </h2>
 +
<h5> Overview of small group presentations </h5>
 +
<h5> Adhesion Proteins – Amanda, Mrudula, and Peter </h5>
 +
<ul>
 +
<li> Ag43 : [University of Queensland 2009] PROS: makes chains instead of aggregates, works well in flow, in the registry, abiotic adherence CONS: not concomitant </li>
 +
<li> TibA: PROS: modular, concomitant, auto-transport CONS: not in the registry </li>
 +
<li> AIDA-1: PROS: binds Ag43 and self, in registry, higher shear tolerance CONS: only expressed in certain cells, blocked by Fimbriae (due to length)</li>
 +
<li> FimA-H: [Michigan 2010] PROS: forms chains, compatible w/ E. coli, shear resistant, grows in constant flow, binds well to glycoproteins CONS: inhibits function of other proteins </li>
 +
<li> Curli: [Lyons 2011] PROS: well characterized in registry, amyloid fibers CONS: inhibits Ag43 and AIDA-1 </li>
 +
</ul>
 +
<h5> Decision: </h5>
 +
<ul>
 +
<li> primary: AIDA-1 [order from registry and improve bad sequencing or re-synthesize] </li>
 +
<li> secondary (if AIDA-1 proves unfeasible): TibA [with goal of characterizing part, must synthesize] </li>
 +
</ul>
 +
<h5> Silica Binding Proteins – Rachel and August </h5>
 +
<ul>
 +
<li> INP – Silicatein [MN 2011] – PROS: CONS: very large, no data on viability, not biobrick compatible. </li>
 +
<li> OmpA-Silicatein alpha fusion – PROS: shorter than INP-Silicatein, active in neutral pH, no illegal sites, known to work CONS: must construct fusion peptide vector NOTES: optimum at low temperatures [OmpA - K103006]</li>
 +
<li> R5 peptide: PROS: active at neutral pH, small, has been used in E. coli CONS: part of a larger protein (no silaffin post-translational modifications), contains EcoRI site </li>
 +
</ul>
-
== Thursday May 24th ==
+
<h5> Modeling the Network Motif - Max, Mrudula, Rachel, and Sean </h5>
 +
<ul>
 +
<li> Modeled the simplified system </li>
 +
<li> Matlab and MathCad Model </li>
 +
<li> Need concrete entry parameters for more robust models </li>
 +
</ul>
-
Update on the human practice component available through the [[Media:HPPresentation.pptx| Powerpoint]]
+
<h5> For Next week: </h5>
 +
<ul>
 +
<li> Construct your parts in DNA 2.0 and anything in registry start detailing </li>
 +
</ul>
-
== Tuesday, May 29 ==
 
-
=== Overview of small group presentations ===
 
-
==== Adhesion Proteins – Amanda, Mrudula, and Peter ====
 
-
* Ag43 : [University of Queensland 2009] PROS: makes chains instead of aggregates, works well in flow, in the registry, abiotic adherence CONS: not concomitant
 
-
* TibA: PROS: modular, concomitant, auto-transport CONS: not in the registry
 
-
* AIDA-1: PROS: binds Ag43 and self, in registry, higher shear tolerance CONS: only expressed in certain cells, blocked by Fimbriae (due to length)
 
-
* FimA-H: [Michigan 2010] PROS: forms chains, compatible w/ E. coli, shear resistant, grows in constant flow, binds well to glycoproteins CONS: inhibits function of other proteins
 
-
* Curli: [Lyons 2011] PROS: well characterized in registry, amyloid fibers CONS: inhibits Ag43 and AIDA-1
 
-
===== Decision: =====
 
-
* primary: AIDA-1 [order from registry and improve bad sequencing or re-synthesize] ====
 
-
* secondary (if AIDA-1 proves unfeasible): TibA [with goal of characterizing part, must synthesize]
 
-
==== Silica Binding Proteins – Rachel and August ====
 
-
* INP – Silicatein [MN 2011] – PROS: CONS: very large, no data on viability, not biobrick compatible.
 
-
* OmpA-Silicatein alpha fusion – PROS: shorter than INP-Silicatein, active in neutral pH, no illegal sites, known to work CONS: must construct fusion peptide vector NOTES: optimum at low temperatures [OmpA - K103006]
 
-
* R5 peptide: PROS: active at neutral pH, small, has been used in E. coli CONS: part of a larger protein (no silaffin post-translational modifications), contains EcoRI site
 
-
==== Modeling the Network Motif - Max, Mrudula, Rachel, and Sean ====
+
<h2 id="5/30">
-
* Modeled the simplified system
+
<h2> Wednesday, May 30 </h2>
-
* Matlab and MathCad Model
+
<h5> In Lab: </h5>
-
* Need concrete entry parameters for more robust models
+
<ul>
 +
<li> Cleaned and organized the laboratory space </li>
 +
<li> Ordered laboratory suppleies </li>
 +
<li> Made <a href="http://www.bd.com/ds/productCenter/244520.asp">LB agar</a> plates and <a href="https://2012.igem.org/Team:Purdue/Protocol#Antibiotics">LB liquid media with ampicillin</a> </li>
 +
<li> Created the adhesions and SBP devices in silico using Gene Designer by DNA 2.0 </li>
 +
</ul>
-
=== For Next week: ===
 
-
* Construct your parts in DNA 2.0 and anything in registry start detailing
 
-
== Wednesday, May 30 ==
+
<h2 id="5/31">
-
* In Lab:
+
<h2> Thursday, May 31 </h2>
-
** Cleaned and organized the laboratory space
+
<h5> Attended Rickus and Porterfield laboratory group meeting </h5>
-
** Ordered laboratory suppleies
+
<ul>
-
** Made LB agar plates and LB liquid media with ampicillin
+
<li> Each person introduced themselves and their research </li>
 +
<li> Decided on the use of future meetings </li>
 +
</ul>
 +
<h5> Researched primer design and began to design primers. These primers will be used for PCR to perform the Gibson assembly method </h5>
-
* Created the adhesions and SBP devices in silico using Gene Designer by DNA 2.0
+
<h2 id="6/1">
 +
<h2> Friday, June 1 </h2>
-
== Thursday, May 31==
+
<h5> Performed Cell Transformations of the following parts: </h5>
-
* Attended Rickus and Porterfielt laboratory group meeting
+
<ul>
-
** Each person introduced themselves and their research
+
<li> Lac promotor and CFP generator (BBa_I13601) </li>
-
** Decided on the use of future meetings
+
<li> PoPs receiver (BBa_F2620)</li>
 +
<li> Tet repressor (BBa_C0040)</li>
 +
<li> Tet promotor with green fluorescent protein (BBa_I13522)</li>
 +
</ul>
 +
<h5> The transformation protocol can be found <a href="http://openwetware.org/wiki/Transforming_chemically_competent_cells">here</a></h5>
 +
<h5> Completed Primer Sequences for surface expression protein </h5>
-
* Researched primer design and began to design primers. These primers will be used for PCR to perform the Gibson assembly method
 
-
== Friday, June 1 ==
+
<h2 id="6/4">
 +
<h2> Monday, June 4 </h2>
 +
<h5> Welcomed Bio Builders workshop participants </h5>
 +
<h5> Janie gave a powerpoint on the basics of synthetic biology to the workshop participants </h5>
 +
<h5> Amanda, August, Max, Mrudula, and Rachel helped the participants with an experiment based on MIT's 2006 iGEM project, a banana scent generator </h5>
 +
<h5> Mrudula and Amanda completed <a href="https://2012.igem.org/Team:Purdue/Protocol#Miniprep">minipreps</a> for the previously transformed parts. The results of the minipreps are shown below. </h5>
 +
<ul>
 +
<li> Tet repressor: 79.8ng/µL </li>
 +
<li> PoPs receiver: 149.6ng/µL </li>
 +
<li> Lac promotor and CFP generator: 46.2ng/µL </li>
 +
<li> Tet promotor wih GFP: 22.9ng/µL </li>
 +
</ul>
-
* Performed Cell Transformations of the following parts:
+
<h5> These concentrations are too low to use in any assembly method; therfore, we will need to attempt transformations and minipreps again before doing any assembly method. </h5>
-
** Lac promotor and CFP generator (BBa_I13601)
+
-
** PoPs receiver (BBa_F2620)
+
-
** Tet repressor (BBa_C0040)
+
-
** Tet promotor with green fluorescent protein (BBa_I13522)
+
-
* The transformation protocol can be found [http://openwetware.org/wiki/Transforming_chemically_competent_cells%7C| here]
+
-
* Completed Primer Sequences for surface expression protein
+
-
== Monday, June 4 ==
 
-
* Welcomed Bio Builders workshop participants
 
-
* Janie gave a powerpoint on the basics of synthetic biology to the workshop participants
 
-
* Amanda, August, Max, Mrudula, and Rachel helped the participants with an experiment based on MIT's 2006 iGEM project, a banana scent generator
 
-
== Tuesday, June 5 ==
+
<h2 id="6/5">
-
* Amanda, August, Mrudula, Rachel, and Soo spent the morning watching presentations on abstraction and devices with the Bio Builder workshop participants
+
<h2> Tuesday, June 5 </h2>
-
* Soo gave a presentation to the participants on how to use TinkerCell
+
<h5> Amanda, August, Mrudula, Rachel, and Soo spent the morning watching presentations on abstraction and devices with the Bio Builder workshop participants
-
* The iGEM team helped  the Bio Builder participants to transform green and purple fluorescent protein into E. coli
+
Soo gave a presentation to the participants on how to use TinkerCell
 +
The iGEM team helped  the Bio Builder participants to transform green and purple fluorescent protein into E. coli
 +
</h5>
 +
<ul>
 +
<h5> Created a timeline for the rest of the summer as seen below </h5>
 +
<li> Week 3: </li>
 +
<ul>
 +
<li>Design and order primers for Gibson assembly </li>
 +
<li> Order reagents </li>
 +
<li> Complete a miniprep for the previously transformed parts </li>
 +
<li> Select plasmid backbones </li>
 +
</ul>
 +
<li> Week 4: </li> 
 +
<ul>
 +
<li> PCR parts for Gibson assembly </li>
 +
<li> Complete Gibson assembly </li>
 +
<li> Decide on which parts will be synthetic </li>
 +
<li> What devices can be synthesized or should we synthesize individual parts? </li>
 +
<li> Create competent cells </li>
 +
</ul>
 +
<li>Week 5:</li>
 +
<ul>
 +
<li>Complete plasmid midi and mega preps </li>
 +
<li> Transform parts into expression vectors </li>
 +
</ul>
 +
<li> Week 6: </li>
 +
<ul>
 +
<li> Complete functional analysis of protein expression </li>
 +
<li> Construct the full system </li>
 +
</ul>
 +
<li> Week 7: </li>
 +
<ul>
 +
<li> Build the flow system for biofilm establishment </li>
 +
<li> Complete functional analysis of biofilm thickness </li>
 +
</ul>
 +
<li> Week 8-10: </li>
 +
<ul>
 +
<li> Iterate and improve on flow setup </li>
 +
</ul>
 +
</ul>
-
* Created a timeline for the rest of the summer as seen below
+
<h2 id="6/6">
-
** Week 3:
+
<h2> Wednesday, June 6 </h2>
-
*** Design and order primers for Gibson assembly
+
<h5>
-
*** Order reagents
+
Sean gave a presentation to the Bio Builder participants on 3A and Gibson assembly
-
*** Complete a miniprep for the previously transformed parts
+
Sean lead a 3A assembly lab with the participants
-
*** Select plasmid backbones
+
Worked on designing primers </h5>
-
** Week 4:
+
-
*** PCR parts for Gibson assembly
+
-
*** Complete Gibson assembly
+
-
*** Decide on which parts will be synthetic
+
-
**** What devices can be synthesized or should we synthesize individual parts?
+
-
*** Create competent cells
+
-
** Week 5:
+
-
*** Complete plasmid midi and mega preps
+
-
*** Transform parts into expression vectors
+
-
** Week 6:
+
-
*** Complete functional analysis of protein expression
+
-
*** Construct the full system
+
-
** Week 7:
+
-
*** Build the flow system for biofilm establishment
+
-
*** Complet functional analysis of biofilm thickness
+
-
** Week 8-10:
+
-
*** Iterate and improve on flow setup
+
-
== Wednesday, June 6 ==
+
<h2 id="6/7">
-
* Sean gave a presentation to the Bio Builder participants on 3A and Gibson assembly
+
<h2> Thursday, June 7 </h2>
-
* Sean lead a 3A assembly lab with the participants
+
<h5> Continued to design primers <h5>
-
* Worked on designing primers
+
<h2 id="6/11">
 +
<h2> Monday, June 11 </h2>
 +
<h5> We attempted to optimize our primers using online guidlines and software. </h5>
 +
<ul>
 +
<li><a href="http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm">Here</a> is a website that details primer design. </li>
 +
<li>We used a <a href="http://www.neb.com/nebecomm/tech_reference/TmCalc/Default.asp">calculator</a> and an <a href="http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/">Oligo Analyzer</a> which can calculate the liklihood of occurances such as hairpins and dimers. </li>
 +
</ul>
 +
<h5>
 +
Upon analysis, we found that the primers that would be required to use Gibson assembly were not ideal. In some cases, the forward and the reverse primers did not have Tm values that were close enough to each other. We also had difficulty with making our primers a reasonable length. Furthermore, many of the primers had a high probability (Gibson free energy value lower than zero) of froming dimers or hairpins. Finally, we deicided that it would most likely be more successful to use 3A assembly instead of Gibson.
 +
In order to save time and ensure the accuracy of the sequence, we decided to synthesize instead of assemble the whole silica making device in a high copy plasmid.
 +
Welcomed Rubeena to the iGEM team. We are looking forward to working with her! </h5>
-
== Thursday, June 7 ==
+
<h2 id="6/13">
-
* Continued to design primers
+
<h2> Wednesday, June 13 </h2>
 +
<h5> August, Mrudula, and Rachel were trained on how to use the flow cytometer
 +
Made competent cells (DH5a). The protocol for making competent cells is found <a href="http://partsregistry.org/Help:Protocols/Competent_Cells">here</a></h5>
-
== Monday, June 11 ==
+
<h2 id="6/14">
-
* We attempted to optimize our primers using online guidlines and software.
+
<h2> Thursday, June 14 </h2>
-
**[http://bioweb.uwlax.edu/genweb/molecular/seq_anal/primer_design/primer_design.htm| Here] is a website that details primer design.
+
<h5>Rachel had a demonstration on how to make silica. The procedure is shown <a href="https://2012.igem.org/Team:Purdue/Protocol#Silica">here</a>.
-
**We used a [http://www.neb.com/nebecomm/tech_reference/TmCalc/Default.asp| Tm calclator] and an [http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/| Oligo Analyzer] which can calculate the liklihood of occurances such as hairpins and dimers.  
+
We welcomed Chris to the iGEM team. We know he will be a great asset to the team!
-
* Upon analysis, we found that the primers that would be required to use Gibson assembly were not ideal. In some cases, the forward and the reverse primers did not have Tm values that were close enough to each other. We also had difficulty with making our primers a reasonable length. Furthermore, many of the primers had a high probability (Gibson free energy value lower than zero) of froming dimers or hairpins. Finally, we deicided that it would most likely be more successful to use 3A assembly instead of Gibson.
+
We had an overview meeting for Rubeena and Chris to help them catch up on the project. </h5>
-
* Welcomed Rubeena to the iGEM team. We are looking forward to working with her!
+
-
== Tuesday, June 12 ==
+
<h2 id="6/15">
-
* insert meeting minutes
+
<h2> Friday, June 15 </h2>
 +
<h5> We transformed all of the parts needed for the adhesion device. These included the following </h5>
 +
<ul>
 +
<li> AIDA-1 (BBa_K257018) </li>
 +
<li> Plasmid (pSB1AK3) </li>
 +
<li> pTet (BBa_R0040) </li>
 +
<li> RBS (BBa_B0034) </li>
 +
<li> Terminator (BBa_B0015) </li>
 +
<li> Plasmid (pSB1AC3) </li>
 +
<li> CFP (BBa_E0020) </li>
 +
</ul>
-
== Wednesday, June 13 ==
+
<h5> <a href="https://static.igem.org/mediawiki/2012/0/0d/June_15.ppt">Here</a> is a powerpoint summarizing our team meeting. </h5>
-
* August, Mrudula, and Rachel were trained on how to use the flow cytometer
+
-
* Made competent cells (DH5α). The protocol for making competent cells is found [http://partsregistry.org/Help:Protocols/Competent_Cells| here]
+
-
== Thursday, June 14 ==
+
<h2 id="6/16">
-
* Rachel had a demonstration on how to make silica. The procedure is shown [[#Silica Creation| here]].
+
<h2> Saturday, June 16 </h2>
-
* We welcomed Chris to the iGEM team. We know he will be a great asset to the team!
+
<h5> Removed the following parts from the incubator and placed in the refrigerator with parafilm wax </h5>
-
* We had an overview meeting for Rubeena and Chris to help them catch up on the project.
+
<ul>
 +
<li> BBa_E00032 (GFP device from plates) </li>
 +
<li> Bba_ </li>
 +
</ul>
-
== Friday, June 15 ==
+
<h2 id="6/17">
-
* We transformed all of the parts needed for the adhesion device. These included the following
+
<h2> Sunday, June 17 </h2>
-
** AIDA-1 (BBa_K257018)
+
<h5> We reevaluated our previous decision to synthesize the silica making device. We have now decided to use Gibson assembly to create the OmpA-silicatein fusion sequence and 3A assembly for the rest of the device. We believe that this will save money and, considering the time taken to order and deliver the sequence, will not take any more time than synthesizing. </h5>
-
** Plasmid (pSB1AK3)
+
-
** pTet (BBa_R0040)
+
-
** RBS (BBa_B0034)
+
-
** Terminator (BBa_B0015)
+
-
** Plasmid (pSB1AC3)
+
-
** CFP (BBa_E0020)
+
-
* insert meeting minutes
+
<h2 id="6/18">
 +
<h2> Monday, June 18 </h2>
 +
<h5> Completed <a href="https://2012.igem.org/Team:Purdue/Protocol#Miniprep">minipreps</a> on recently transformed parts. The results are shown below. </h5>
 +
<ul>
 +
<li> GFP: 17.5ng/µL and 7.6 ng/µL </li>
 +
<li> AIDA-1: 8.7ng/µL and 6ng/µL </li>
 +
<li> pSB1AC3: 5.2ng/µL snd 4.2ng/µL </li>
 +
<li> CFP: 13.6ng/µL and 12.7ng/µL </li>
 +
<li> RBS (BBa_B0032): 24.9ng/µL and 24.2ng/µL </li>
 +
<li> PoPs: 107.8ng/µL and 131.4ng/µL </li>
 +
<li> pSB1AK3: 7.0ng/µL </li>
 +
<li> Terminator: 11.5ng/µL </li>
 +
<li> RBS (BBa_B0034): 21.0ng/µL and 21.5ng/µL </li>
 +
<li> pTet: 5.2ng/µL </li>
 +
</ul>
-
== Saturday, June 16 ==
+
<h5> These concentrations are too low to proceed with 3A assembly. Therefore, we are going to grow more of the transformed bacteria, and we are going to perform more minipreps. </h5>
-
* Removed the following parts from the incubator and placed in the refrigerator with parafilm wax
+
-
** BBa_E00032 (GFP device from plates)
+
-
** Bba_
+
-
== '''Protocols''' ==
+
<h2 id="6/19">
-
=== LB Agar ===
+
<h2> Tuesday, June 19 </h2>
-
* We used a premade [http://www.bd.com/| Becton, Dickinson and Comapny] mix to make our [http://www.bd.com/ds/productCenter/244520.asp| LB agar].
+
<h5> August completed a second round of <a href="https://2012.igem.org/Team:Purdue/Protocol#Miniprep">minipreps</a>. The results are listed below. </h5>
 +
<ul>
 +
<li> RBS (BBa_B0034): 14.8ng/µL </li>
 +
<li> RBS (BBa_C0040): 5.0ng/µL </li>
 +
<li> CFP: 9.0ng/µL </li>
 +
<li> PoPs: 14.9ng/µL </li>
 +
<li> AIDA-1: 7.0ng/µL </li>
 +
</ul>
-
=== Adding Antibiotics to LB ===
+
<h5> <a href="https://static.igem.org/mediawiki/2012/6/6d/June_19.ppt">Here</a> is a powerpoint summarizing our team meeting. </h5>
-
*How to make LB liquid plus antibiotics:
+
-
**Ampicillin – The frozen stock solutions of ampicillin are at 50mg/ml and 100mg/ml in H2O, and are marked with a red sticker.  The final concentration for LB liquid culture is 50ul/ml. To obtain this in 100ml (the amount in each LB bottle), add 100ul stock solution.  
+
-
**Kanamycin – The frozen stock solutions of kanamycin are at 50mg/ml in H2O, and are marked with green.  The final concentration for LB liquid culture for growing plasmids is 50ug/ml, and for cosmids is 20ug/ml.  To obtain 50ng/ml in 100ml of LB, add 100ul stock solution, and to obtain 20ug/ml, add 40ul stock solution.  
+
-
**Tetracycline – The frozen stock solutions of tetracycline are at 15mg/ml in methanol and are marked with black.  The final concentration for LB liquid culture is 15ug/ml. To obtain this in 100ml of LB, add 100ul stock solution.
+
-
**Chloramphenicol – The frozen stock solutions of chloramphenicol are at 25mg/ml in 100% ethanol and are marked with purple.  The final concentration for LB liquid culture is 25mg/ml.  To obtain this in 100ml of LB, add 100ul stock solution.
+
-
*How to make LB plates plus antibiotics:
+
<h2 id="6/20">
-
**Follow the recipe card in box for making LB plates, being sure to add the agar.  After autoclaving, and when the agar has cooled enough that it’s not too hot to touch (about 1 to 1.5hrs), add antibiotics as follows:
+
<h2> Wednesday, June 20 </h2>
-
**Ampicillin – add 1ml ampicillin (at 100mg/ml) per liter of agar to obtain a final concentration of 100ug/ml.  Mark the plate with a single red line on the side.
+
<h5> Due to the low yields from our previous tranformations and minipreps, we have decided to attempt our transformations with a new protocol. The new protocol can be found <a href="https://2012.igem.org/Team:Purdue/Protocol#UpdatedTransformation">here</a> </h5>
-
**Kanamycin – add 1ml kanamycin stock (at 50mg/ml) per liter of agar to obtain a final concentration of 50ug/ml. Mark the plates with a single green line on the side.
+
-
**Tetracycline – add 1ml tetracycline stock (at 15mg/ml) per liter of agar to obtain a final concentration of 15ug/ml.  Mark the plates with a single black line on the side.
+
-
**Chloramphenicol – add 1ml chloramphenicol stock (at 25mg/ml) per liter of agar to obtain a final concentration of 100ug/ml.  Mark the plates with a single purple line on the side.
+
-
=== SOB Media Recipe ===
+
<h5> Today, we transformed pLac, TetR, terminator (BBa_B0015), RBS (BBa_B0034), pSB1A3, and pSB1C3. </h5>
-
* 2% w/v bacto-tryptone (20 g)
+
-
* 0.5% w/v Yeast extract (5 g)
+
-
* 8.56mM NaCl (0.5 g) or 10mM NaCl (0.584 g)
+
-
* 2.5mM KCl (0.186 g)
+
-
* ddH2O to 1000 mL[4]
+
-
* For maximum effectiveness, SOB media should have its pH adjusted to 7.0 by adding concentrated sodium hydroxide.
+
<h5> The minipreps gave the following results </h5>
-
* Autoclave media to ensure sterility
+
<ol>
 +
<li> RBS: 14.8ng/µL </li>
 +
<li> TetR: 5.0ng/µL </li>
 +
<li> CFP: 9.0ng/µL </li>
 +
<li> PoPs: 14.5ng/µL </li>
 +
<li> AIDA-1: 7.0ng/µL </li>
 +
</ol>
-
=== SOC Recipe ===
 
-
In addition to the contents of [[#SOB Media Contents| SOB media]]
 
-
* 10mM MgCl2 (0.952 g) or 20mM MgSO4 (2.408 g)[2]
 
-
* 20mM glucose (3.603 g)
 
-
* Alternatively, SOC can be made by adding small amounts of concentrated magnesium chloride and glucose solutions to pre-prepared SOB.
 
-
* For maximum effectiveness, SOC media should have its pH adjusted to 7.0 by adding concentrated sodium hydroxide.
+
<h2 id="6/21">
-
* Autoclave media to ensure sterility
+
<h2> Thursday, June 21 </h2>
 +
<h5> Due to the low yield of our transformations and minipreps, we have now decided to troubleshoot our transformation procedures. To do this, we will be doing a transformation with Tarun, a graduate mentor to the team. We will be using Tarun's procedures and supplies. We will also have a control plate that will contain cells that had no DNA inserted. If these transformations succeed, then we will have narrowed the possibilities of what went wrong with our procedures. Tarun's transformation procedure can be found on the <a href="https://2012.igem.org/Team:Purdue/Protocol#Tarun">here</a>. We performed these test transformations with BBa_I13602 (CFP). </h5>
-
=== Creating Chemically Competent Cells ===
+
Upon closer inspection of the AIDA-1 biobrick (BBa_K257018), we have found the following problems
-
* The protocol for creating chemically competent cells is provided by the parts registry and can be found [http://partsregistry.org/Help:Protocols/Competent_Cells| here].
+
<ul>
 +
<li> the sequencing is bad </li>
 +
<ul>
 +
<li> there are large gaps from the sequencing as compared to what was documented. Specifically, the sequenced biobrick was missing approximately 500bp </li>
 +
<li> the sequence was supposed to be 1326bp long. We have decided that it would cost too much to have the biobrick sequenced ourselves </li>
 +
</ul>
 +
<li> the gel is bad </li>
 +
</ul>
 +
For the above reasons, we have decided to not use AIDA-1. After reevaluating the other adhesion options, we have decided to use Curli (BBa_342003). Due to its inconsistant sequencing, we have decided to have the part found in the kit sequenced ourselves.  
-
=== Transforming Chemically Competent Cells ===
+
<h2 id="6/22">
-
* The protocol for transforming chemically competent cells is provided by Open Wet Ware and can be found [http://openwetware.org/wiki/Transforming_chemically_competent_cells| here].
+
<h2> Friday, June 22 </h2>
 +
<h5> Due to our increasing size, we have decided to divide into committees. These committees will help us divide the workload fairly and ensure that all tasks are being completed in a timely manner. The committees and their members are listed below. An asteric indicates the committee head. </h5>
 +
<ul>
 +
<li><b> Wetlab </b></li>
 +
<ul>
 +
<li> OmpA-silicatein </li>
 +
<ul>
 +
*August<br />Haefa
 +
</ul>
 +
<li> Curli </li>
 +
<ul>
 +
*Rubeena
 +
</ul>
 +
</ul>
 +
<li><b> Purchasing </b></li>
 +
<ul>
 +
*Peter
 +
</ul>
 +
<li><b> Human Practices </b></li>
 +
<ul>
 +
*Peter<br />*Max
 +
</ul>
 +
<li><b> Experimental Design/Characterization </b></li>
 +
<ul>
 +
*Amanda<br />*Mrudula<br />Chris<br />Arthi<br />Rachel<br />Jim
 +
</ul>
 +
<li><b> Project Planning </b></li>
 +
<ul>
 +
*Namita
 +
</ul>
 +
<li><b> Wiki </b></li>
 +
<ul>
 +
*Rachel<br />Sean (background)
 +
</ul>
 +
</ul>
-
=== Mini Prep Procedures ===
+
<h5> We checked our test transformations from yesterday. None of the plates showed growth.</h5>
-
* For this procedure, we used the [http://www.qiagen.com/products/plasmid/qiaprepminiprepsystem/qiaprepspinminiprepkit.aspx#Tabs=t0| QIAprep Spin Miniprep Kit] by [http://www.qiagen.com/default.aspx| Qiagen].
+
-
1) Add 1.5mL of overnight culture to a micorcentrifuge tube
+
-
2) Spin for 3 minutes at 800rpm
+
<h5> <a href="https://static.igem.org/mediawiki/2012/1/1d/June_22.ppt">Here</a> is a powerpoint summarizing our team meeting. </h5>
-
3) Decant the supernatant so that the DNA pellet is all that remains
+
<h2 id="6/25">
 +
<h2> Monday, June 25 </h2>
 +
<h5> The foci of this week are to troubleshoot our transformations and research ways to characterize our constructs once they are assembled. August and Mrudula will be in lab troubleshooting. Amanda and Mrudula will be resarching ways to characterize a biofilm. Rachel will be researching ways to characterize a silica coat. </h5>
-
4) Repeat steps 1-3 three times
+
<h2 id="6/26">
 +
<h2> Tuesday, June 26 </h2>
 +
<h5> <a href="https://static.igem.org/mediawiki/2012/8/85/June_26.ppt">Here</a> is a powerpoint summarizing our team meeting. </h5>
-
5) Add 250μL of buffer P2 and invert several times to mix (do not allow the solution to sit for more than 5 minutes)
+
<h2 id="6/29">
 +
<h2> Friday, June 29 </h2>
 +
<h5> We went to Dow Agro, one of our sponsors, to give them an overview of our project. The powerpoint presentation we gave can be found  <a href="https://2012.igem.org/wiki/index.php?title=Special:Upload&wpDestFile=DowPresentation.pptx">Powerpoint</a>. After we gave our presentation, we asked the Dow representative, Ryan, if he had any guidance with concern to Gibson assembly. </h5>
-
6) Add 300μL of buffer N3 and immediately invert to mix
+
<h2 id="6/30">
 +
<h2> Saturday, June 30 </h2>
 +
<h5> Part of the team volunteered at the high school Jamboree. We saw many amazing teams with remarkable ideas! Congratulations to all the teams for their hard work over the past semester, and good luck as future iGEMers! </h5>
-
7) Centrifuge at 13,000rpm for 10 minutes
+
<h2 id="7/1">
 +
<h2> Sunday, July 1 </h2>
 +
<h5> We attempted another test <a href="https://2012.igem.org/Team:Purdue/Protocol#Tarun">transformation</a>, this time using bought Excel 10ß competent cells. We had both a negative and positive control. We also plated different concentrations of the final solution to see if we were over or under plating. We also used agar plates with ampicillin that Tarun made. We used store bought SOC. The part used was BBa_J04450. </h5>
-
8) Apply the supernatant to the QIAprep spin column by decanting or pipetting
+
<h2 id="7/2">
 +
<h2> Monday, July 2 </h2>
 +
<h5> The tranformations performed yesterday were successful. Both the positive control and the plaes with our part showed growth. The transformation efficiency was extremely high. We got single colonies on the plates with 50µL and overgrowth on the plates that had 150µL. We will only plate at 50µL from now on. </h5>
-
9) Centrifuge at 13,000rpm for 1 minute and discard flow through
+
<h5> Due to time constraints, we have decided to synthesize both of our constructs. In parallel to characterization of the synthesized constructs, we are going to assemble both constructs using Gibson assembly. The assembles constructs will differ from the synthesized constructs in that the promoter will be a PoPs device and there will be a fluorescent protein on each. In this way, we can find if the addition of these two characterization parts will affect the functionality of our constructs. </h5>
 +
<br>
 +
<h5>The synthesized constructs were ordered from <a href="https://www.dna20.com/">DNA 2.0</a>. Pictures of the Gene Designer (DNA 2.0 software) renditions of the three constructs are given below.</h5>
 +
<ul>
 +
<li> <a href="https://2012.igem.org/File:OmpA-Silicatein.jpeg">Silicatein construct</a> </li>
 +
<li> <a href="https://2012.igem.org/File:Curli_without_GFP.jpg">Curli</a> </li>
 +
</ul>
-
10) Wash the QIAprep spin column by adding 500μL buffer PB
+
<h5> We transformed Curli so that we can have it sequenced soon </h5>
-
11) Centrifuge at 13,000rpm for 1 minute and discard flow through
+
List of What Needs to get Done this Week:
 +
<ul>
 +
<li> Research protocols on setting up and running experiments using biofilms </li>
 +
<li> Research flow and static protocols for biofilms </li>
 +
<li> Research ways to characterize silica matrix and acquire quantifiable data </li>
 +
<li> Create timelines for each assay researched </li>
 +
<li> Order reagents and get training on any equipment needed for assays </li>
 +
</ul>
-
12) Wash the QIAprep spin column by adding 750μL Buffer PE
+
<h2 id="7/3">
 +
<h2> Tuesday, July 3 </h2>
 +
<h5> We are now awaiting the delivery of our synthesized constructs. In preparation, we are researching the varying types of assays that we may be able to use. You can find information about the different assays we researched can be found <a href="https://2012.igem.org/Team:Purdue/Characterization">here</a>. </h5>
-
13) Centrifuge at 13,000rpm for 1 minute and discard flow through
+
<h5> Silicatein-Alpha Characterization </h5>
 +
We have decided to use scanning electron 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> from Invitrogen).
-
14) Centrifuge at 13,000rpm for 1 minute
+
Further assays will be done once the two constructs are used within the same bacteria.
-
15) Place the QIAprep column in a clean 1.5mL microcentrifuge tube
+
Researched stages of biofilm formation:
-
16) Elute the DNA by adding 50μL of Buffer EB to the center of the QIAprep spin column
+
<p>  1. Initial Attachment  -  attachment occurs via van der waals forces</p>
 +
<p>  2. Irreversible Attachment  -  this is where the EPS forms</p>
 +
<p>  3. Maturation I  -  matrix formed with adhesion proteins</p>
 +
<p>  4. Maturation II  -  the full biofilm forms</p>
 +
<p>  5. Dispersion  -  bacteria released</p>
-
17) Let stand for 1 minute
+
Also researched shear stress modeling, chassis development, microsensors, and confocal microscopy assays.
-
18) Qunatify DNA concentration with nanodrop
+
<br><br>
 +
Furthermore, research was done on different ways to characterize the silica coat. Three extremely helpful articles are listed below.
 +
<ul>
 +
<li> <a href="http://onlinelibrary.wiley.com/doi/10.1002/bit.23195/full">Cell-Mediated Deposition of Porous Silica on Bacterial Biofilms</a> </li>
 +
<li> <a href="http://www.springerlink.com/content/9352q2105531m466/fulltext.pdf">Sol-gel synthsis and structure of silica hybrid materials</a> </li>
 +
<li> <a href="http://www.sciencedirect.com/science/article/pii/S0165027009001071">Thin-film silica sol-gel coatings for neural microelectrodes</a> </li>
 +
</ul>
 +
<br>
 +
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>
 +
<br></br>
 +
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>).
-
=== PCR protocol ===
 
-
1) For a 25ul rxn:
 
-
* Use 1ul of 60ng/ul or 100ng/ul DNA
 
-
* Use 1ul of each primer at 3.2pmole/ul concentration or 1.25ul of each primer at 100ng/ul concentration
 
-
* 2.5ul 10x PCR Buffer w/ Mg (1.5mM)
 
-
* 0.5ul 25mM MgCl2
 
-
* 0.5ul dNTP
 
-
* 0.125ul Taq
 
-
* 18.375ul sterile water to equal a 25ul rxn
 
-
*if not making master mix, dilute Taq so that you can add 1ul of Taq and 17.5ul sterile water to equal a 25ul rxn
+
<h2 id="7/5">
-
           
+
<h2> Thursday, July 5 </h2>
-
2) For a 50ul rxn:
+
Researched possible competitors in the field of bioreactor filtration.
-
* Use 2ul of 60ng/ul or 100ng/ul DNA
+
-
* Use 2ul of each primer at 3.2pmole/ul concentration or 2.5ul of each primer at 100ng/ul concentration
+
-
* 5ul 10x PCR Buffer w/ Mg
+
-
* 1ul 25mM MgCl2
+
-
* 1ul dNTP
+
-
* 0.25ul Taq
+
-
* 36.75ul sterile water to equal a 50ul rxn
+
-
*if not making a master mix, dilute Taq so that you can add 1ul of Taq and 36ul sterile water to equal a 50ul rxn
+
<ul>
 +
<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>
 +
<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>
 +
<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>
 +
<li> ABEC - produces bioreactors, but could not find more detail into what kind </li>
 +
</ul>
-
3) Keep the reagents on ice.
+
<h2 id="7/6">
 +
<h2> Friday, July 6 </h2>
 +
<h5> <a href="https://static.igem.org/mediawiki/2012/7/72/July_6.ppt">Here</a> is a powerpoint summarizing our team meeting. </h5>
-
4) Add the Taq last, and keep it in the freezer until you are ready to add it.
+
<h2 id="7/8">
 +
<h2> Sunday, July 8 </h2>
 +
<h5> Research was done on growing a static biofilm.
 +
<a href="http://media.wiley.com/CurrentProtocols/0471729256/0471729256-sampleUnit.pdf">"Growing and Analyzing Static Biofilms"</a> was a very helpful article. </h5>
-
5) Vortex briefly and quick spin.
+
<br>Created a cell culture to have competent cells for a biofilm culture.</br>
-
6) Cycle:
+
<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="http://media.wiley.com/CurrentProtocols/0471729256/0471729256-sampleUnit.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>
-
* 95°C for 1-5minutes (usually 4min)
+
-
* 95°C for 1min
 
-
* 55°C for 1min. Cycle 30 times
+
<h2 id="7/9">
 +
<h2> Monday, July 9 </h2>
-
* 72°C for 1.5 to 2min (usually 2min)
+
<br>Performed the <a href="https://2012.igem.org/Team:Purdue/Protocol#Stationary Phase"> Growth 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.A typical bacterial growth curve is shown below. This is what we expect our curves to look like. </br>
 +
<br>
 +
<img border="1" align="left" src="https://static.igem.org/mediawiki/2012/e/e6/Bacterial_growth_curve.jpg" width="400" height="296"/>
 +
<br><br><br><br><br><br><br><br><br><br><br><br><br><br>
-
* 72°C for 10min
+
Below 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.
 +
<br>
-
* 4°C hold
+
<img border="1" align="left" src="https://static.igem.org/mediawiki/2012/f/f0/Growth_Rate_NEB_and_DH5.jpg" width="481" height="292"/>
 +
<br><br><br><br><br><br><br><br><br><br><br><br><br>
-
* A video showing the theory behind PCR can he found [http://www.youtube.com/watch?v=HMC7c2T8fVk&feature=fvwrel| here]
 
-
=== 3A Assembly ===
+
<br>Also worked out the lab plan for the rest of the week.</br>
-
* The protocol for 3A assembly is provided by Open Wet Ware and can be found [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly| here]
+
-
=== Gibson Assembly ===
 
-
Prepare a master mix, as detailed below. Store them in 15 ul aliquots at -20 °C. Then:
 
-
1) Thaw a 15 μl assembly mixture aliquot and keep on ice until ready to be used.
+
<h2 id="7/10">
 +
<h2> Tuesday, July 10 </h2>
-
2) Add 5 μl of DNA to be assembled to the master mixture. The DNA should be in equimolar amounts. Use 10-100 ng of each ~6 kb DNA fragment. For larger DNA segments, increasingly proportionate amounts of DNA should be added (e.g. 250 ng of each 150 kb DNA segment).
+
We did the same <a href="https://2012.igem.org/Team:Purdue/Protocol#Stationary Phase"> Growth 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>
-
3) Incubate at 50 °C for 15 to 60 min (60 min is optimal).  
+
<br>
 +
Below is the results of the growth rate assay for XL-10 Gold. The plots show the expected shape with a lag, log, and stationary phase.
 +
<img border="1" src="https://static.igem.org/mediawiki/2012/8/8d/Growth_Curve_XL10.jpg" width="482" height="292"/>
 +
<br><br>
-
4) [[#Transforming Chemically Competent Cells| Transform]] as usual
+
<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.
-
* The protocol for Gibson assembly is provided by Open Wet Ware
+
<br>
-
* The original paper for the Gibson assembly protocol can be found [http://www.nature.com/nmeth/journal/v6/n5/full/nmeth.1318.html| here]
+
Also researched and developed the static biofilm assay that we can do to determine the biofilm rates of our non-transformed E.coli.</br>
-
=== Silica Creation ===
 
-
1) Obtain 14.4g of nanopure water
 
-
2) Obtain 50µL of .04M HCL and combine it with the water. Put this solution in an ice bath
+
<h2 id="7/11">
 +
<h2> Wednesday, July 11 </h2>
 +
<h5> Chris T created primers for a test Gibson reaction. The test construct will be a the plasmid pGA3K3, PoPs device (BBa_F2620), an RFP with RBS(BBa_K093005), and a double terminator (BBa_B0014). The primers can be viewed in this <a href="https://static.igem.org/mediawiki/2012/d/d7/PoPS_Characterization_Circuit_Primers_Color.pdf">document </a>. We ordered the primers from <a href="http://www.idtdna.com/site">Integrated DNA Technologies</a>. </h5>
-
3) Obtain 7.6g of tetramethyl orthosilicate (TMOS) in a separate container
+
<h2 id="7/13">
 +
<h2> Friday, July 13 </h2>
-
4) Combine the TMOS and HCL/water
+
<br>Performed the <a href="https://2012.igem.org/Team:Purdue/Protocol#Static Biofilm"> Static Biofilm Assay</a>.</br>
-
5) Immediately begin the vortex the solution. The solution will be cloudy while the reaction is taking place. Once
+
<br>Had a team meeting, discussed goals for the following week:</br>
-
the solution is clear again, the reaction is finished. This will take approximately 5 minutes
+
<ul>
 +
<li> Write out protocols and email them to the entire team for revisions </li>
 +
<li> Plan a meeting to go through and troubleshoot the protocols together </li>
 +
<li> Find a way to determine the optimized concentration of curli</li>
 +
<li> Purchase all materials needed for future protocols </li>
 +
</ul>
-
6) When the reaction is finished, let the solution set for 1-2 minutes
+
<h2 id="7/16">
 +
<h2> Monday, July 16 </h2>
-
7) Use a rotary evaporator at 47ºC to remove the methane from the solution. This should take 2-3 minutes. The final solution volume should be approximately 13mL
+
<br>Researched how Membrane Aerated Bioreactor work and how we will use one for testing.</br>
 +
There are multiple types of Membrane Aerated Biofilms: MABR (the type we will be using in our experiments), Membrane biofilter, and extractive membrane bioreactor (EMB).  These reactors can be in shell and tube or plate and frame configurations.  We will be using the shell and tube configuration. The two limiting substrates are introduced at opposite ends of the bioreactor. The limiting substrates are C-substrate (carbon substrate) and/or oxygen. The biofilm thickness must be less than the oxygen penetration (50-200 micrometers) but stay less than 150 micrometers for best performance.
 +
<br>
-
8) If the silica is to be used immediately, put it on ice. It can be stored for up to a week if it is refrigerated.  
+
<h2 id="7/19">
 +
<h2> Thursday, July 19 </h2>
 +
<h5> We attempted to do <a href="https://2012.igem.org/Team:Purdue/Protocol#PCR">PCR</a> for the parts for which Chris made <a href="https://static.igem.org/mediawiki/2012/d/d7/PoPS_Characterization_Circuit_Primers_Color.pdf">primers</a>. To prove that the PCR was successful, we ran aliquotes of the reaction products through a gel. An image of the gel can be seen <a href="https://static.igem.org/mediawiki/2012/a/ac/Rachel_PCR.jpg">here</a>. No bands can be seen for the aliquotes; therfore, we concluded that the PCR did not work. We believe that there was a problem with the cycler; therefore, we will be trying the procedure again with a different machine.  
-
9) Filter the silica before use
+
<h2 id="7/23">
 +
<h2> Monday, July 23 </h2>
 +
<h5> We attempted <a href="https://2012.igem.org/Team:Purdue/Protocol#PCR">PCR</a> again with a different machine. Unfortunately, we used too high of a concentration of primers. Therefore, when we ran a gel, two bands appeared for each sample. The excess primer would greatly lower the efficiency of a Gibson reaction. Furthermore, the bands on the gel all had similar size even though the parts are not of similar size. Therefore, we believe that nonspecific amplification took place. An image of the gel can be seen <a href="https://static.igem.org/mediawiki/2012/5/5e/Max_and_Mrudula_PCR.jpg">here</a>. </h5>
-
* The procedures are provided by Rickus lab group.
+
There were some modifications to the <a href="https://2012.igem.org/Team:Purdue/Protocol#Static Biofilm">Static Biofilm Assay</a> Protocol.  Once the plates had grown for a long enough time period (every hour for 1-8 hours and then 24 hours and 48 hours) they were transferred to the 4 degree freezer.  The plates were then removed, the excess liquid was dumped out, and the plates were then sprayed off with water and dumped out again.  The plates were than stained with crystal violet with the following steps:
 +
<ul>
 +
<li> add 125 microliters of crystal violet to each well plate </li>
 +
<li> let sit for 15 minutes </li>
 +
<li> wash off (Note: at this point the plates are stable for several weeks) </li>
 +
</ul>
 +
Analyzing Plates:
 +
<ul>
 +
<li> 500 microliters of 80% ethanol | 20% acetone were added to each well </li>
 +
<li> 300 microliters (or enough until the well were full) were taken from the 24 well plate to the 96 well plates </li>
 +
<li> this was then analyzed using the spectrophotometer to determine the OD of each sample </li>
 +
</ul>
 +
 
 +
<h2 id="7/24">
 +
<h2> Tuesday, July 24 </h2>
 +
<h5> We attempted <a href="https://2012.igem.org/Team:Purdue/Protocol#PCR">PCR</a> for a third time. This time, the gel shows single bands of varying size. An image of the gel can be seen <a href="https://static.igem.org/mediawiki/2012/9/93/PCR_3.jpg">here</a>. We are now going to proceed to the Gibson reaction. </h5>
 +
<br>
 +
<a href="https://2012.igem.org/wiki/index.php?title=Special:Upload&wpDestFile=">Upload</a>
 +
 
 +
<h2 id="7/26">
 +
<h2> Thursday, July 26 </h2>
 +
 
 +
Purpose: To make a solution to grow XL-10 gold strain of <i>E.coli</i> so that it can be integrated into a membrane aerated biofilm reactor (MABR)
 +
 
 +
Materials:
 +
<ul>
 +
<li> SOB - 250 mL </li>
 +
<li> 10 mM MgCl2 (.238 g) </li>
 +
<li> 20 mM glucose (.900 g) </li>
 +
<li> 250 microliters of cultured XL-10 gold culture </li>
 +
</ul>
 +
Procedure: Add all the ingredients together in a flask and swirl.  Place in 37 degree room and shake at 220 rpm. Check OD.
 +
<br>
 +
 
 +
Feeding Solution for current biofilm:
 +
<ul>
 +
<li> 200 mL nutrient (glucose and nitrogen)</li>
 +
<li> 1mL solution 2 and 3 </li>
 +
<li> 100 microliters solution 1 </li>
 +
</ul>
 +
 
 +
<h2 id="7/27">
 +
<h2> Friday, July 27 </h2>
 +
 
 +
Purpose: Ruoxi Wu i helping set up the membrane aerated biofilm reactor (MABR)
 +
 
 +
<br>
 +
Now that we have the culture growing, we have to determine what media will be the best that can be used to sustain the cells once they are in the reactor.
 +
The nutrient solutions that Wen, Jane, and Ruoxi are using are specific to <i>Pseudomanas aeruginosa</i>. This research is to determine the protocol for the bioreactor specifically the media.
 +
 
 +
Research for media:
 +
Design and performance study of a novel immobolized hollow fiber membrane bioreactor by Ping Wang (1st author)
 +
<ul>
 +
<li> nutrients are supplied to the forming biofilm through diffusion (very poor efficiency) </li>
 +
<li> only the cells in a thin layer close to the surface of oxygen and media are active </li>
 +
<li> The bacterial strain used in this paper is <i>E.coli</i> DM5d </li>
 +
<li> The growth limiting substate is M9 medium </li>
 +
<li> Glucose concentration in medium is equal to 5 g/L </li>
 +
<li> Protocol from Paper to culture bacterial cells: </li>
 +
<ul>
 +
<li> Agar plates with single columns Fl streaking DH5d </li>
 +
<li> new agar plates made every 14 days </li>
 +
<li> pick single colony into 100 mL media </li
 +
<li> culture overnight at 37 degrees Celsius and 120 rpm </li>
 +
<li> check OD 600 </li>
 +
</ul>
 +
</ul>
 +
Researched preparation of <a href="https://2012.igem.org/Team:Purdue/Protocol#M9">M9 minimal media recipe</a>.
 +
 
 +
<br>
 +
 
 +
<h2 id="8/6">
 +
<h2> Monday, August 6 </h2>
 +
Purpose: PBS is used to clean out the waste from the bioreactor
 +
 
 +
Materials:
 +
<ul>
 +
<li> NaCl </li>
 +
<li> KCl </li>
 +
<li> Na2HPO4 </li>
 +
<li> KH2PO4 </li>
 +
<li> Distilled H20 </li>
 +
<li> HCl </li>
 +
</ul>
 +
Procedure:
 +
<ul>
 +
<li> Combine 80 g NaCl, 2 g KCl, 14.4 g Na2HPO4 (dibasic anhydrous), 18.1 g Na2HPO4 * 2H2O (dibasic dihydrate), 27.2 g Na2HPO4 * 7H20 (dibasic heptahydrate), 2.4 g KH2PO4 (monobasic anhydrous) and 800 mL H20 </li>
 +
<li> Adjust pH to 2.4 with HCl </li>
 +
<li> Add H20 to 1 L </li>
 +
<li> Autoclave </li>
 +
 
 +
<h2 id="8/17">
 +
<h2> Friday, August 17 </h2>
 +
Purpose: To measure the biofilm's detachment and viability after growing for 15 days
 +
 
 +
Materials:
 +
<ul>
 +
<li> ISOTON </li>
 +
<li> PBS </li>
 +
<li> Small Biocontainer </li>
 +
<li> Tweezers and scissors </li>
 +
<li> Beaker </li>
 +
</ul>
 +
 
 +
Procedure:
 +
<ul>
 +
<li> Turn off the pump and take out the feed loop fl the beaker </li>
 +
<li> Lay the bioreactor on its side and let enough of the media solution drain out so that one biofilm is revealed (collect media in a beaker) </li>
 +
<li> Remove the biofilm using tweezers </li>
 +
<li> Cut into small 1.5" - 2" pieces </li>
 +
<li> Place in containers and pour some of the media into the dishes to keep the biofilms submerged </li>
 +
</ul>
 +
This biofilm is now ready to be tested
 +
 
 +
Purpose: The purpose of this experiement is to determine how much of the biofilm comes off (detaches) from the tube when placed under different water flows
 +
 
 +
Materials:
 +
<ul>
 +
<li> Biofilm holders </li>
 +
<li> ISOTON </li>
 +
</ul>
 +
 
 +
Procedure:
 +
<ul>
 +
<li> Once the biofilm has been extracted from the bioreactor and it is in small pieces, this procedure can be started </li>
 +
<li> Places the small pieces in the holder that Wen zang constructed </li>
 +
<li> Set up a pump to pump water into the tube and back out into a waste container </li>
 +
<li> Make sure the biofilm is completely submerged the entire time </li>
 +
<li> Collect the PBS that flows over the biofilm in a beaker </li>
 +
<li> Measure the amount of run off and the time to determine the flow rate </li>
 +
<li> Save the sample </li>
 +
<li> To determine the amount of cells in the sample a Multisizer 4 Coulter Counter was used - this tells the concentration of particles of different sizes found in the sample </li>
 +
<li> Different flow rates were used to analyze the biofilm </li>
 +
</body>
 +
</html>

Latest revision as of 23:52, 25 October 2012


May 2012
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June 2012
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July 2012
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September 2012
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Monday, May 15

List of useful contacts on the google doc, including DowAgro
Begin to list the different devices/constructs that will be used in our project
Attachment (adhesion)
Filtration
  • Modularize the sequence so we can test individually (e.g. put a fluorescent protein coding sequence at the end of each segment – construct silica binding protein first with constitutive promoter/repressible promoter to produce fluoresent protein and make sure it does what you think it should)
  • Investigate multiple silica binding protein (SBP);must choose several top candidates for each element.
Hierarchy
Perfecting the FFL
Modeling and Experimental
  • Communication in terms of data (e.g. kinetic parameters)
  • Review Characterization Data Sheets
  • Strong integration of modeling translates to a strong performance in the competition.
List of things we need
  • Competent Cells (Laris Avramova (core molecular biologist, 222), Tarun (electron microscopy)may have the needed cells)
  • Antibiotics (AMP, tetracycline)
  • Enzymes (Pst1, Xba1, EcoR1, Spe1, Ligase, polymerase/PCR reagents, T5exonuclease )
  • Parts (available in the registry)
    • Constitutive promoter (orthogonal t7 promoter)
    • Signaling Promoters (investigate the precedent for construction FFL)
    • RBS –(B0034)
      • Thermodynamic models for designing RBSs, etc (Voights model)
    • Terminators
    • Proteins Transcription Factors

Monday, May 21

    We're all looking forward to an exciting iGEM summer! Our SURF students have just arrived and are gradually being introduced to synthetic biology and iGEM.
    Sean gave a crash course on synthetic biology to Mrudula, Rachel, Amanda and August. The powerpoint is available here, compiled by our wonderful graduate mentor, Janie.

Tuesday, May 22

First Journal Club Meeting - we identified the reducible elements of our system, detailed an outline of the project to the SURF students (e.g. What is the advantage of using this entire process? Is not it kind of roundabout?)
For the NEXT MEETING Tuesday 29th May :
    Identify, in these teams:
  • a. What Adhesion system we want to use (Amanda, Peter, Mrudula)
  • b. Which silica-binding system we want to use (Rachel, August)
  • c. Control Elements (Max, Mrudula, Rachel, Sean)
  • d. Find strain auxotrophic for RSC (gene which breaks down arabinose) (Jim)
Announcements:
  • Be ready to explain your assigned element of the project (starting generally and moving more specifically)
  • Read the introductory/background elements of the thesis that Dr. Rickus will put in the dropbox
General Announcements
  • Be ready to work the BioBuilder HighSchool Teacher iGEM workshop during the week of June 4th – June 8th (more details to come)
  • Everyone is welcome to visit Drs. Rickus and Clase’s lab group meeting on Thursday at 12PM

Thursday May 24th

Update on the human practice component available through the Powerpoint

Tuesday, May 29

Overview of small group presentations
Adhesion Proteins – Amanda, Mrudula, and Peter
  • Ag43 : [University of Queensland 2009] PROS: makes chains instead of aggregates, works well in flow, in the registry, abiotic adherence CONS: not concomitant
  • TibA: PROS: modular, concomitant, auto-transport CONS: not in the registry
  • AIDA-1: PROS: binds Ag43 and self, in registry, higher shear tolerance CONS: only expressed in certain cells, blocked by Fimbriae (due to length)
  • FimA-H: [Michigan 2010] PROS: forms chains, compatible w/ E. coli, shear resistant, grows in constant flow, binds well to glycoproteins CONS: inhibits function of other proteins
  • Curli: [Lyons 2011] PROS: well characterized in registry, amyloid fibers CONS: inhibits Ag43 and AIDA-1
Decision:
  • primary: AIDA-1 [order from registry and improve bad sequencing or re-synthesize]
  • secondary (if AIDA-1 proves unfeasible): TibA [with goal of characterizing part, must synthesize]
Silica Binding Proteins – Rachel and August
  • INP – Silicatein [MN 2011] – PROS: CONS: very large, no data on viability, not biobrick compatible.
  • OmpA-Silicatein alpha fusion – PROS: shorter than INP-Silicatein, active in neutral pH, no illegal sites, known to work CONS: must construct fusion peptide vector NOTES: optimum at low temperatures [OmpA - K103006]
  • R5 peptide: PROS: active at neutral pH, small, has been used in E. coli CONS: part of a larger protein (no silaffin post-translational modifications), contains EcoRI site
Modeling the Network Motif - Max, Mrudula, Rachel, and Sean
  • Modeled the simplified system
  • Matlab and MathCad Model
  • Need concrete entry parameters for more robust models
For Next week:
  • Construct your parts in DNA 2.0 and anything in registry start detailing

Wednesday, May 30

In Lab:
  • Cleaned and organized the laboratory space
  • Ordered laboratory suppleies
  • Made LB agar plates and LB liquid media with ampicillin
  • Created the adhesions and SBP devices in silico using Gene Designer by DNA 2.0

Thursday, May 31

Attended Rickus and Porterfield laboratory group meeting
  • Each person introduced themselves and their research
  • Decided on the use of future meetings
Researched primer design and began to design primers. These primers will be used for PCR to perform the Gibson assembly method

Friday, June 1

Performed Cell Transformations of the following parts:
  • Lac promotor and CFP generator (BBa_I13601)
  • PoPs receiver (BBa_F2620)
  • Tet repressor (BBa_C0040)
  • Tet promotor with green fluorescent protein (BBa_I13522)
The transformation protocol can be found here
Completed Primer Sequences for surface expression protein

Monday, June 4

Welcomed Bio Builders workshop participants
Janie gave a powerpoint on the basics of synthetic biology to the workshop participants
Amanda, August, Max, Mrudula, and Rachel helped the participants with an experiment based on MIT's 2006 iGEM project, a banana scent generator
Mrudula and Amanda completed minipreps for the previously transformed parts. The results of the minipreps are shown below.
  • Tet repressor: 79.8ng/µL
  • PoPs receiver: 149.6ng/µL
  • Lac promotor and CFP generator: 46.2ng/µL
  • Tet promotor wih GFP: 22.9ng/µL
These concentrations are too low to use in any assembly method; therfore, we will need to attempt transformations and minipreps again before doing any assembly method.

Tuesday, June 5

Amanda, August, Mrudula, Rachel, and Soo spent the morning watching presentations on abstraction and devices with the Bio Builder workshop participants Soo gave a presentation to the participants on how to use TinkerCell The iGEM team helped the Bio Builder participants to transform green and purple fluorescent protein into E. coli
    Created a timeline for the rest of the summer as seen below
  • Week 3:
    • Design and order primers for Gibson assembly
    • Order reagents
    • Complete a miniprep for the previously transformed parts
    • Select plasmid backbones
  • Week 4:
    • PCR parts for Gibson assembly
    • Complete Gibson assembly
    • Decide on which parts will be synthetic
    • What devices can be synthesized or should we synthesize individual parts?
    • Create competent cells
  • Week 5:
    • Complete plasmid midi and mega preps
    • Transform parts into expression vectors
  • Week 6:
    • Complete functional analysis of protein expression
    • Construct the full system
  • Week 7:
    • Build the flow system for biofilm establishment
    • Complete functional analysis of biofilm thickness
  • Week 8-10:
    • Iterate and improve on flow setup

Wednesday, June 6

Sean gave a presentation to the Bio Builder participants on 3A and Gibson assembly Sean lead a 3A assembly lab with the participants Worked on designing primers

Thursday, June 7

Continued to design primers

Monday, June 11

We attempted to optimize our primers using online guidlines and software.
  • Here is a website that details primer design.
  • We used a calculator and an Oligo Analyzer which can calculate the liklihood of occurances such as hairpins and dimers.
Upon analysis, we found that the primers that would be required to use Gibson assembly were not ideal. In some cases, the forward and the reverse primers did not have Tm values that were close enough to each other. We also had difficulty with making our primers a reasonable length. Furthermore, many of the primers had a high probability (Gibson free energy value lower than zero) of froming dimers or hairpins. Finally, we deicided that it would most likely be more successful to use 3A assembly instead of Gibson. In order to save time and ensure the accuracy of the sequence, we decided to synthesize instead of assemble the whole silica making device in a high copy plasmid. Welcomed Rubeena to the iGEM team. We are looking forward to working with her!

Wednesday, June 13

August, Mrudula, and Rachel were trained on how to use the flow cytometer Made competent cells (DH5a). The protocol for making competent cells is found here

Thursday, June 14

Rachel had a demonstration on how to make silica. The procedure is shown here. We welcomed Chris to the iGEM team. We know he will be a great asset to the team! We had an overview meeting for Rubeena and Chris to help them catch up on the project.

Friday, June 15

We transformed all of the parts needed for the adhesion device. These included the following
  • AIDA-1 (BBa_K257018)
  • Plasmid (pSB1AK3)
  • pTet (BBa_R0040)
  • RBS (BBa_B0034)
  • Terminator (BBa_B0015)
  • Plasmid (pSB1AC3)
  • CFP (BBa_E0020)
Here is a powerpoint summarizing our team meeting.

Saturday, June 16

Removed the following parts from the incubator and placed in the refrigerator with parafilm wax
  • BBa_E00032 (GFP device from plates)
  • Bba_

Sunday, June 17

We reevaluated our previous decision to synthesize the silica making device. We have now decided to use Gibson assembly to create the OmpA-silicatein fusion sequence and 3A assembly for the rest of the device. We believe that this will save money and, considering the time taken to order and deliver the sequence, will not take any more time than synthesizing.

Monday, June 18

Completed minipreps on recently transformed parts. The results are shown below.
  • GFP: 17.5ng/µL and 7.6 ng/µL
  • AIDA-1: 8.7ng/µL and 6ng/µL
  • pSB1AC3: 5.2ng/µL snd 4.2ng/µL
  • CFP: 13.6ng/µL and 12.7ng/µL
  • RBS (BBa_B0032): 24.9ng/µL and 24.2ng/µL
  • PoPs: 107.8ng/µL and 131.4ng/µL
  • pSB1AK3: 7.0ng/µL
  • Terminator: 11.5ng/µL
  • RBS (BBa_B0034): 21.0ng/µL and 21.5ng/µL
  • pTet: 5.2ng/µL
These concentrations are too low to proceed with 3A assembly. Therefore, we are going to grow more of the transformed bacteria, and we are going to perform more minipreps.

Tuesday, June 19

August completed a second round of minipreps. The results are listed below.
  • RBS (BBa_B0034): 14.8ng/µL
  • RBS (BBa_C0040): 5.0ng/µL
  • CFP: 9.0ng/µL
  • PoPs: 14.9ng/µL
  • AIDA-1: 7.0ng/µL
Here is a powerpoint summarizing our team meeting.

Wednesday, June 20

Due to the low yields from our previous tranformations and minipreps, we have decided to attempt our transformations with a new protocol. The new protocol can be found here
Today, we transformed pLac, TetR, terminator (BBa_B0015), RBS (BBa_B0034), pSB1A3, and pSB1C3.
The minipreps gave the following results
  1. RBS: 14.8ng/µL
  2. TetR: 5.0ng/µL
  3. CFP: 9.0ng/µL
  4. PoPs: 14.5ng/µL
  5. AIDA-1: 7.0ng/µL

Thursday, June 21

Due to the low yield of our transformations and minipreps, we have now decided to troubleshoot our transformation procedures. To do this, we will be doing a transformation with Tarun, a graduate mentor to the team. We will be using Tarun's procedures and supplies. We will also have a control plate that will contain cells that had no DNA inserted. If these transformations succeed, then we will have narrowed the possibilities of what went wrong with our procedures. Tarun's transformation procedure can be found on the here. We performed these test transformations with BBa_I13602 (CFP).
Upon closer inspection of the AIDA-1 biobrick (BBa_K257018), we have found the following problems
  • the sequencing is bad
    • there are large gaps from the sequencing as compared to what was documented. Specifically, the sequenced biobrick was missing approximately 500bp
    • the sequence was supposed to be 1326bp long. We have decided that it would cost too much to have the biobrick sequenced ourselves
  • the gel is bad
For the above reasons, we have decided to not use AIDA-1. After reevaluating the other adhesion options, we have decided to use Curli (BBa_342003). Due to its inconsistant sequencing, we have decided to have the part found in the kit sequenced ourselves.

Friday, June 22

Due to our increasing size, we have decided to divide into committees. These committees will help us divide the workload fairly and ensure that all tasks are being completed in a timely manner. The committees and their members are listed below. An asteric indicates the committee head.
  • Wetlab
    • OmpA-silicatein
        • *August
        Haefa
    • Curli
        • *Rubeena
  • Purchasing
      • *Peter
  • Human Practices
      • *Peter
      *Max
  • Experimental Design/Characterization
      • *Amanda
      *Mrudula
      Chris
      Arthi
      Rachel
      Jim
  • Project Planning
      • *Namita
  • Wiki
      • *Rachel
      Sean (background)
We checked our test transformations from yesterday. None of the plates showed growth.
Here is a powerpoint summarizing our team meeting.

Monday, June 25

The foci of this week are to troubleshoot our transformations and research ways to characterize our constructs once they are assembled. August and Mrudula will be in lab troubleshooting. Amanda and Mrudula will be resarching ways to characterize a biofilm. Rachel will be researching ways to characterize a silica coat.

Tuesday, June 26

Here is a powerpoint summarizing our team meeting.

Friday, June 29

We went to Dow Agro, one of our sponsors, to give them an overview of our project. The powerpoint presentation we gave can be found Powerpoint. After we gave our presentation, we asked the Dow representative, Ryan, if he had any guidance with concern to Gibson assembly.

Saturday, June 30

Part of the team volunteered at the high school Jamboree. We saw many amazing teams with remarkable ideas! Congratulations to all the teams for their hard work over the past semester, and good luck as future iGEMers!

Sunday, July 1

We attempted another test transformation, this time using bought Excel 10ß competent cells. We had both a negative and positive control. We also plated different concentrations of the final solution to see if we were over or under plating. We also used agar plates with ampicillin that Tarun made. We used store bought SOC. The part used was BBa_J04450.

Monday, July 2

The tranformations performed yesterday were successful. Both the positive control and the plaes with our part showed growth. The transformation efficiency was extremely high. We got single colonies on the plates with 50µL and overgrowth on the plates that had 150µL. We will only plate at 50µL from now on.
Due to time constraints, we have decided to synthesize both of our constructs. In parallel to characterization of the synthesized constructs, we are going to assemble both constructs using Gibson assembly. The assembles constructs will differ from the synthesized constructs in that the promoter will be a PoPs device and there will be a fluorescent protein on each. In this way, we can find if the addition of these two characterization parts will affect the functionality of our constructs.

The synthesized constructs were ordered from DNA 2.0. Pictures of the Gene Designer (DNA 2.0 software) renditions of the three constructs are given below.
We transformed Curli so that we can have it sequenced soon
List of What Needs to get Done this Week:
  • Research protocols on setting up and running experiments using biofilms
  • Research flow and static protocols for biofilms
  • Research ways to characterize silica matrix and acquire quantifiable data
  • Create timelines for each assay researched
  • Order reagents and get training on any equipment needed for assays

Tuesday, July 3

We are now awaiting the delivery of our synthesized constructs. In preparation, we are researching the varying types of assays that we may be able to use. You can find information about the different assays we researched can be found here.
Silicatein-Alpha Characterization
We have decided to use scanning electron microscopy (SEM), x-ray diffraction (XRD), and a live dead assay (specifically, the Baclight Bacterial Viability Kit from Invitrogen). Further assays will be done once the two constructs are used within the same bacteria. Researched stages of biofilm formation:

1. Initial Attachment - attachment occurs via van der waals forces

2. Irreversible Attachment - this is where the EPS forms

3. Maturation I - matrix formed with adhesion proteins

4. Maturation II - the full biofilm forms

5. Dispersion - bacteria released

Also researched shear stress modeling, chassis development, microsensors, and confocal microscopy assays.

Furthermore, research was done on different ways to characterize the silica coat. Three extremely helpful articles are listed below.
A powerpoint highlighting possible characterization methods is given here

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 Baclight Bacterial Viability Kit).

Thursday, July 5

Researched possible competitors in the field of bioreactor filtration.
  • Hydro Engineering - produces "Hydrokleen", which is a bioreactor filtration system that would generally be used in industrial plants and acts as a water recycler.
  • 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
  • Kinetics - this company makes a range of water treatment processes and machines that can be used in industry as well as consumer markets
  • ABEC - produces bioreactors, but could not find more detail into what kind

Friday, July 6

Here is a powerpoint summarizing our team meeting.

Sunday, July 8

Research was done on growing a static biofilm. "Growing and Analyzing Static Biofilms" was a very helpful article.

Created a cell culture to have competent cells for a biofilm culture.

Also did research into developing a static biofilm assay to test how well our bacteria makes biofilm before and after our transformation. "Growing and Analyzing Static Biofilms" by Judisth H. Mernitt, Daniel E. Kadouri, and George A. O'Toole was helpful in determining how we would do this assay.

Monday, July 9


Performed the Growth Rate Assay on NEB Beta and DH5 Alpha E.coli strains to determine the time frame we will use to grow our static biofilms.A typical bacterial growth curve is shown below. This is what we expect our curves to look like.















Below 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.














Also worked out the lab plan for the rest of the week.

Tuesday, July 10

We did the same Growth Rate Assay as yesterday, but with the XL-10 Gold E.coli strain because we think it will work better for the biofilm purposes.

Below is the results of the growth rate assay for XL-10 Gold. The plots show the expected shape with a lag, log, and stationary phase.

Here is the excel file containing all of the data from the three growth rate assays.
Also researched and developed the static biofilm assay that we can do to determine the biofilm rates of our non-transformed E.coli.

Wednesday, July 11

Chris T created primers for a test Gibson reaction. The test construct will be a the plasmid pGA3K3, PoPs device (BBa_F2620), an RFP with RBS(BBa_K093005), and a double terminator (BBa_B0014). The primers can be viewed in this document . We ordered the primers from Integrated DNA Technologies.

Friday, July 13


Performed the Static Biofilm Assay.

Had a team meeting, discussed goals for the following week:
  • Write out protocols and email them to the entire team for revisions
  • Plan a meeting to go through and troubleshoot the protocols together
  • Find a way to determine the optimized concentration of curli
  • Purchase all materials needed for future protocols

Monday, July 16


Researched how Membrane Aerated Bioreactor work and how we will use one for testing.
There are multiple types of Membrane Aerated Biofilms: MABR (the type we will be using in our experiments), Membrane biofilter, and extractive membrane bioreactor (EMB). These reactors can be in shell and tube or plate and frame configurations. We will be using the shell and tube configuration. The two limiting substrates are introduced at opposite ends of the bioreactor. The limiting substrates are C-substrate (carbon substrate) and/or oxygen. The biofilm thickness must be less than the oxygen penetration (50-200 micrometers) but stay less than 150 micrometers for best performance.

Thursday, July 19

We attempted to do PCR for the parts for which Chris made primers. To prove that the PCR was successful, we ran aliquotes of the reaction products through a gel. An image of the gel can be seen here. No bands can be seen for the aliquotes; therfore, we concluded that the PCR did not work. We believe that there was a problem with the cycler; therefore, we will be trying the procedure again with a different machine.

Monday, July 23

We attempted PCR again with a different machine. Unfortunately, we used too high of a concentration of primers. Therefore, when we ran a gel, two bands appeared for each sample. The excess primer would greatly lower the efficiency of a Gibson reaction. Furthermore, the bands on the gel all had similar size even though the parts are not of similar size. Therefore, we believe that nonspecific amplification took place. An image of the gel can be seen here.
There were some modifications to the Static Biofilm Assay Protocol. Once the plates had grown for a long enough time period (every hour for 1-8 hours and then 24 hours and 48 hours) they were transferred to the 4 degree freezer. The plates were then removed, the excess liquid was dumped out, and the plates were then sprayed off with water and dumped out again. The plates were than stained with crystal violet with the following steps:
  • add 125 microliters of crystal violet to each well plate
  • let sit for 15 minutes
  • wash off (Note: at this point the plates are stable for several weeks)
Analyzing Plates:
  • 500 microliters of 80% ethanol | 20% acetone were added to each well
  • 300 microliters (or enough until the well were full) were taken from the 24 well plate to the 96 well plates
  • this was then analyzed using the spectrophotometer to determine the OD of each sample

Tuesday, July 24

We attempted PCR for a third time. This time, the gel shows single bands of varying size. An image of the gel can be seen here. We are now going to proceed to the Gibson reaction.

Upload

Thursday, July 26

Purpose: To make a solution to grow XL-10 gold strain of E.coli so that it can be integrated into a membrane aerated biofilm reactor (MABR) Materials:
  • SOB - 250 mL
  • 10 mM MgCl2 (.238 g)
  • 20 mM glucose (.900 g)
  • 250 microliters of cultured XL-10 gold culture
Procedure: Add all the ingredients together in a flask and swirl. Place in 37 degree room and shake at 220 rpm. Check OD.
Feeding Solution for current biofilm:
  • 200 mL nutrient (glucose and nitrogen)
  • 1mL solution 2 and 3
  • 100 microliters solution 1

Friday, July 27

Purpose: Ruoxi Wu i helping set up the membrane aerated biofilm reactor (MABR)
Now that we have the culture growing, we have to determine what media will be the best that can be used to sustain the cells once they are in the reactor. The nutrient solutions that Wen, Jane, and Ruoxi are using are specific to Pseudomanas aeruginosa. This research is to determine the protocol for the bioreactor specifically the media. Research for media: Design and performance study of a novel immobolized hollow fiber membrane bioreactor by Ping Wang (1st author)
  • nutrients are supplied to the forming biofilm through diffusion (very poor efficiency)
  • only the cells in a thin layer close to the surface of oxygen and media are active
  • The bacterial strain used in this paper is E.coli DM5d
  • The growth limiting substate is M9 medium
  • Glucose concentration in medium is equal to 5 g/L
  • Protocol from Paper to culture bacterial cells:
    • Agar plates with single columns Fl streaking DH5d
    • new agar plates made every 14 days
    • pick single colony into 100 mL media
      • culture overnight at 37 degrees Celsius and 120 rpm
    • check OD 600
Researched preparation of M9 minimal media recipe.

Monday, August 6

Purpose: PBS is used to clean out the waste from the bioreactor Materials:
  • NaCl
  • KCl
  • Na2HPO4
  • KH2PO4
  • Distilled H20
  • HCl
Procedure:
  • Combine 80 g NaCl, 2 g KCl, 14.4 g Na2HPO4 (dibasic anhydrous), 18.1 g Na2HPO4 * 2H2O (dibasic dihydrate), 27.2 g Na2HPO4 * 7H20 (dibasic heptahydrate), 2.4 g KH2PO4 (monobasic anhydrous) and 800 mL H20
  • Adjust pH to 2.4 with HCl
  • Add H20 to 1 L
  • Autoclave

    • Friday, August 17

    Purpose: To measure the biofilm's detachment and viability after growing for 15 days Materials:
    • ISOTON
    • PBS
    • Small Biocontainer
    • Tweezers and scissors
    • Beaker
    Procedure:
    • Turn off the pump and take out the feed loop fl the beaker
    • Lay the bioreactor on its side and let enough of the media solution drain out so that one biofilm is revealed (collect media in a beaker)
    • Remove the biofilm using tweezers
    • Cut into small 1.5" - 2" pieces
    • Place in containers and pour some of the media into the dishes to keep the biofilms submerged
    This biofilm is now ready to be tested Purpose: The purpose of this experiement is to determine how much of the biofilm comes off (detaches) from the tube when placed under different water flows Materials:
    • Biofilm holders
    • ISOTON
    Procedure:
    • Once the biofilm has been extracted from the bioreactor and it is in small pieces, this procedure can be started
    • Places the small pieces in the holder that Wen zang constructed
    • Set up a pump to pump water into the tube and back out into a waste container
    • Make sure the biofilm is completely submerged the entire time
    • Collect the PBS that flows over the biofilm in a beaker
    • Measure the amount of run off and the time to determine the flow rate
    • Save the sample
    • To determine the amount of cells in the sample a Multisizer 4 Coulter Counter was used - this tells the concentration of particles of different sizes found in the sample
    • Different flow rates were used to analyze the biofilm

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