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In Vivo Protein Fusion Assembly Using Self Excising Ribozyme

ABSTRACT

Introns, self-excising ribozymes, can become a useful tool to create in vivo protein fusions of BioBrick parts. To make this possible, intron sequences are used to flank non-protein parts embedded in coding sequences. An intron sequence with an embedded recombination site is capable of in vivo insertion of a compatible protein fusion part. As an example, a GFP-fusion was created with an intervening lox site that is removed from the final protein using the intron to form a fully functional GFP protein. In vivo protein fusions can be applied to a larger number of modular systems to make complicated expression systems, such as synthetic antibodies or plants capable of Cry-toxin domain shuffling.

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Project

Modeling

Outreach

Human
Practices

Project

The goal of Waterloo's 2011 iGEM project is to implement self-excising ribozymes (introns) as biobricks. But first, what are self-excising ribozymes? Ribozymes are ribonucleic acid (RNA) enzymes and enzymes are reaction catalysts. So ribozymes are just RNA sequences that catalyze a (trans-esterification) reaction to remove itself from the rest of the RNA sequence. Essentially these are considered introns, which are intragenic regions spliced from mRNA to produce mature RNA with a continuous exon (coding region) sequence. Self-excising introns/ribozymes consist of type I and II introns. They are considered self-splicing because they do not require proteins to intitialize the reaction. Therefore, by understanding the sequences and structure of these self-excising introns and making them useable, we can use them as tools to make other experiments easier.

1.0 INTRODUCTION

This design provides a reasonable basis to implement in vivo applications involving RNA level regulatory sequences. The fusion proteins produced surpass strictly what is coded in the DNA. As a result of incorporating ribozyme segments in between two halves of the protein coded in the DNA construct, a regulatory sequence (such as a recombination site) could be included. Since recombination sites can interrupt the functional production of a protein if translated fully (resulting in excess amino acids in the polypeptide), the incorporated ribozyme portions remove them before the translation phase of gene expression so that a functional protein is produced. For example, Cry proteins, which account for the insecticidal activity (toxicity) of Bacillus thuringiensis, could be the fusion protein produced for a particular insecticide. Using our experimental design, the sequence containing the code for the Cry protein (at the DNA stage) is split by ribozyme segments containing a recombination site. In this case, the recombination site is the regulatory sequence that will be removed once transcribed into RNA. At the DNA level, recombination (shuffling) will occur, exchanging DNA strand segments. Therefore, when the shuffled DNA sequence is transcribed into RNA, the recombination site is spliced out of the sequence with the ribozymes, and the resulting RNA code is different than that of the un-shuffled code. Consequently, the translated Cry protein is different. This system would oppose pesticide resistance among the target organism.

1.1 A Little Bit About Group 1 Introns

All group I introns in bacteria have presently been shown to self-splice (with few exceptions) and maintain a conserved secondary structure comprised of a paired element which uses a guanosine (GMP, GDP or GTP) cofactor. Conversely, only a small portion of group II introns have been verified as ribozymes (they are not related to group I introns) and generally have too many regulators to easily work with. It is mainly the structural similarity of these introns that designates them to group II. We will mainly be working with group I introns, such as the Staphylococcus phage twort.ORF143.

 Group I introns contain a conserved core region consisting of two helical domains (P4–P6 and P3–P7). Recent studies have demonstrated that the elements required for catalysis are mostly in the P3 to P7 domain. They are ribozymes that consecutively catalyze two trans-esterification reactions that remove themselves from the precursor RNA and ligate the flanking exons. They consist of a universally conserved core region and subgroup-specific peripheral regions, which are not essential for catalysis but are known to cause a reduction in catalytic efficiency if removed. To compensate for this, a high concentration of magnesium ions, spermidine or other chemicals that stabilize RNA structures can be added. Thus, the peripheral regions likely stabilize the structure of the conserved core region, which is essential for catalysis.

1.2 Trans-Esterification Reactions

The secondary structures, such as P6, formed by group I introns facilitates base pairing between the 5' end of the intron and the 3' end of the exon, as well as generates an internal guide sequence. Additionally, there is a pocket produced to encourage binding of the Guanosine cofactor. The Guanine nucleotide is placed on the first nucleotide of the intron. The 3'OH of Guanosine group nucleophilically attacks and cleaves the bond between the last nucleotide of the first exon and the first nucleotide of the 5' end of the intron; concurrently, trans-esterification occurs between the 3'OH and the 5'phosphorous from the 5' end of the intron. Subsequent conformational rearrangements ensure that the 3'OH of the first exon is placed in proximity of the 3' splice site. In this way, further trans-esterification reactions and splicing occurs.

Retreived June 21, 2011 from Self-Splicing RNAs [1] This diagram shows the trans-esterification reaction and splicing of group I introns from a sequence.

1.3 Fusion Proteins

Fusion proteins are combined forms of smaller protein subunits and are normally constructed at the DNA level by ligating portions of coding regions. A simple construction of traditional fusion protein involves inserting the target gene into a region of the cloned host gene. However, the subsequent project design, in its simple construction, interrupts the cloned protein with ribozyme sequences flanking a stop codon. The method proposed deals with excision and ligation at the RNA level, therefore, the unaltered DNA sequence does not code for a functional protein. The ligation of protein coding sequences can create functional fusion proteins for many applications including antibody or pesticide production; however, this method of production is limited to producing the same fusion protein each time since the sequence is not modified in between the transcription and translation phases of gene expression. One disadvantage of this is the resultant resistance of a pathogen to antibodies or a target organism to pesticides. For example, a specific pesticide (Cry toxin) may eventually not be effective to its target plant if subsequent plant generations inhibit its uptake, overproduce the sensitive antigen protein so that normal cellular function persists, reduce the ability of this protein to bind to the pesticide or metabolically inactivates the herbicide. Similar mechanisms contribute to antibiotic resistance. Any resistant organisms will inevitably prevail in subsequent generations. Recombination sites could potentially be incorporated into the subsequent project design to circumvent some of the difficulties with traditional fusion proteins as a result of host resistance. However, recombination sites may interrupt the functional fusion protein from forming. Ribozyme segments at the RNA regulation level can potentially remove disrupting sequence after such shuffling occurs. Therefore, the intervening sequence maintains its DNA level functionality but is removed when no longer needed at the RNA level. Fusion protein design focused on the DNA level does not have this dynamic regulation.

1.4 The Cre-Lox System

In bacteriophage P1 exists the cre enzyme and recognition sites called lox P sites. This viral recombination system functions to excise a particular DNA sequence by flanking lox P sites and introduce the cre enzyme when the target is to be excised. The cre enzyme both cuts at the lox P site and ligates the remaining sequences together. The excised DNA is then degraded. This is similar to our project design; however, instead of requiring the addition of an enzyme at the desired excision time, the self-excising nature of ribozymes automatically functions during the normal process of gene expression (RNA level).

2.0 PROJECT IN DETAILS

2.1 EXPERIMENTAL DESIGN

Our protocol will involves the insertion of a functional protein, split by the self-removing elements, between CUCUUAGU and AAUAAGAG in the P6 region of twort.ORF143. GFP (green fluorescent protein) is split into two parts, which will be referred to as GFP1 and GFP2. With a constitutive promoter, GFP1 and GFP2 will be separated by a class 1 A2 intron split into two (for now, IN1 and IN2) sequences that flank another sequence inserted into the P6 loop, which was chosen because anything attached to this region will remain outside the protein. Note that this experimental design also contains an in frame stop codon, which is expected to be spliced out of the sequence with IN1 and IN2 and will utilize the RFC53 convention. Following GFP2 is a transcriptional terminator (TT). The method of making this construct is detailed in RFC53. Below is Figure 1 through Figure 3. They illustrate the order of parts in the design and the trans-esterification reaction that results in a function GFP:

Figure 2 shows the experimental design of the sequence immediately following transcription. It contains a constituent promoter, RBS Ribosome Binding Site), GFP1, IN1, in-frame stop codon, IN2, GFP2 and TT. The dotted lines and scissors indicate that the introns will be spliced out of the sequence at these points, however, the introns are self-excising.

Figure 3 is a representative view of the sequence folding in order to catalyze the trans-esterification reaction, however, there are many hairpin loops actually formed. This is the process of post-transcriptional modification. Specifically, Group I intron splicing events utilize a guanosine nucleotide to bind another sequence and dislodge the 5' site, then the cleavage initializes another splicing event with the remaining hydroxyl end to dislodge the rest of the RNA sequence and ligate the remaining exons. The remaining fusion protein code is different than that of the primary transcript.

Figure 4 shows a non-disruptive ligation scar and active GFP after the self-excision of IN1 and IN2. This is the modified RNA transcript prior to translation..

2.2 CONSTRUCTION MAPs AND RFC 53

As per RFC 53 convention, enzyme digestions are followed in the particular order outlined below. The standard procedure makes this technique reproducible, therefore, more easily extrapolated to other applications. Compared to other protein fusion methods, this design facilitates additional regulation within necessary guidelines. However, the embedded post-transcriptional modification in this design is a complication to consider in simpler designs where regulation at this level is not necessary. As such, unnecessary bulk in plasmid vectors is known to add to metabolic load and decrease replication rate compared to non-plasmid carriers.

2.2.1 General Construction Map

Figure 5 graphically shows the laboratory procedure for the experimental design in the form of an enzyme map:

K576005 contains the first component of GFP (GFP1)

K576003 contains the first part of the intron sequence (IN1

J61046 contains the lox site

K576006 contains the second component of GFP (GFP2)

K576004 contains the second part of the intron sequence (IN2)

K576007 contains GFP1 and IN1

K576009 contains GFP1, IN1 and lox1

K576011 contains the promoter (P), ribosomal binding sit (RBS), GFP1, IN1, lox site, IN2, GFP2 and transcriptional terminator (TT). This is the final construct (experimental design)

2.1.2 Controls' Construction Map

Controls are necessary to prove that the design of this experimental investigation is functional and more practically for comparison of fluorescence in the laboratory. In the positive control, GFP1 and GFP2 flank either RFC25 or RFC53, which will not disrupt translation regardless of the linker. Therefore, fluorescence is expected. The experimental run will ideally show fluorescence resulting from the self-excision of IN1 and IN2.

Figure 6 represents the positive control. For consistency, GFP1 and GFP2 are separated by RFC53 (RFC25 could have also be used), which should not disrupt expression of a functional GFP.

In the negative control (using the same constitutive promoter), GFP1 and GFP2, followed by a transcriptional terminator, flank RFC10 (Request For Comments) resulting in a stop-codon-containing scar. No fluorescence is expected for this component (background) because translation is interrupted. This is meant to control for the possibility of a non functional fusion protein. The expectation is that this fusion of GFP1 and GFP2 will not fluoresce, which is a consequence of some fusion protein techniques. Figure 7 shown below details the negative control design:

Figure 7 is an illustration of the negative control containing the interrupted GFP with an in-frame stop codon, ensuring that it is not expressed. Since this sequence contains no excision sites (Group I introns), we do not expect any modification to this area of the RNA.

The figure below shows the construction map for the controls.

K576005 contains the first component of GFP (GFP1)

K576006 contains the second component of GFP (GFP2)

K576013 contains the promoter (P), ribosomal binding site (RBS), GFP and transcriptional terminator (TT). This is the positive control.

K576005 contains the first component of GFP (GFP1))

J61046 contains the lox site

K576006 contains the second component of GFP (GFP2)

contains the promoter (P), ribosomal binding site (RBS), GFP1, lox site, GFP2 and transcriptional terminator (TT). This is the negative control.

2.3 MAKING THE CONSTRUCT WITH RFC 53

Figure 9: Making the Construct: Parts were sequenced into PUC57, digested and ligated into PSB1C3.

Figure 9 is a flow chart of the general work flow involved in the construction of our experimental plasmid, as per RFC53 conventions.

1) The insert is isolated through a series of enzyme digestions. One intron (in blue) is shown here as a representation. The insert is isolated for subsequent ligation.
2) Similarly, the pSB1C3 vector is isolated through enzyme digestion. Note that "N" indicates that this is the vector portion. The vector is also isolated for the ligation step. It must also be noted that pSB1C3 vector contains a cut site of SacI, an enzyme that is used in RFC 53. Relocating the part in BBa_K371053 resolves this issue.
3) The two components (insert and vector) are ligated together to produce the final construct.
4) According to the experimental design, the final construct will contain self-excising ribozymes, which in the last step result in a non-disruptive ligation scar and, therefore, the expression of GFP.

2.3 Preliminary Testing

Although completion of a preliminary version of the final construct was achieved, lack of GFP fluorescence proved suspicion of questionable band placements during second and third stage electrophoresis. Final diagnostic digestion reaction confirmed abnormalities from designed constructs. Testing via digestion was completed for every intermediate, control and final constructs. Consequently, BBa_K576003, K576004, K576005, and K576006 were the only parts able to be confirmed. All the other intermediates and constructs have questionable band location which disrupted final construct fluorescence.

Figure 10: shows the diagnostic digestion from September 16, 2011: All subclones shown to be correct, however, positive control not correct. Relative placement of GFPs and INTS required further verification and showed incorrect placement. This accounts for lack of fluorescence in final stage.

The above electrophoresis picture describes the resultant bands from the diagnostic digestion. Although bands 5, 6 and 7 (sub clones) have been confirmed, the adjacent positive control (band 8) and all GFP and intron digestions are not consistent with the expected patterns. The GFP-INT and GFP-INT-lox constructions (bands 9, 10 and 11) have been verified as inaccurate. The questionable placements of these bands indicate that the cut sites, thus the fragment length and containing sequence, do not match the planned construction. Therefore, it is not likely that they contain functional GFP, introns or lox, which would result in a lack of fluorescence in the final stage of construction. Further testing to reconstruct the contaminated clones is necessary for the functional final product; however, lab work has stopped due to time constraint. A diagnostic digestion at each step is recommended to circumvent any similar issues upon the continuation of this project.

3.0 PRACTICAL APPLICATION

The biggest advantage of the ribozyme project is the ability to create in vivo protein fusions. These can then be applied to a larger number of modular systems that can be used to make complicated expression systems. One such system is the creation synthetic antibodies. If protein sequences are flanked by intron sequences and then set up along the same stretch of DNA, different combinations of fusion proteins will be created based on how the intron excision occurs. Another system where the ribozyme project can be applied is DNA shuffling experiments. The Cry toxin is used as an effective biopesticide, however for now it has a very small range of insects that it effects. The ways to increase its range would be to change the structure of one of the vital domains so that it is able to recognize a wider spectrum of receptors in the host mid gut cell. To create different variations of this domains an in vivo DNA shuffling experiments using the ribozymes could be carried out.

4.0 REFERENCES

Belfort,M., Cech, T., Celander, D., Chandry, P., Heuer, T. (1991). Folding of group I introns from bacteriophage T4 involves internalization of the catalytic core. Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado. 88(24): 11105–11109.

Belfort, M., Chu, F., Maley, F., Maley, G. and West, D. (1986). Characterization of the lntron in the Phage T4 Thymidylate Synthase Gene and Evidence for Its Self-Excision from the Primary Transcript. Wadsworth Center for Laboratories and Research. Vol. 45, X7-166.

Bernstein, K.E., Bunting, M., Capecchi, M.R., Greer, J.M., Thomas, K.R. (1999). Targeting genes for self-excision in the germ line.

Cassin, P., Gambier, R., Scheppler, J. (2000). Biotechnology Explorations: Applying the Fundamentals. Washington, DC: ASM Press.

Cech, T. (1990). Self-Splicing of Group I Introns. Biochemistry 59:543-8.

Clancy, S. (2008) RNA splicing: introns, exons and spliceosome. Nature Education 1(1). Genetics Primer, Fanconi Anemia Genetics. Last updated 08 February 2004. (http://members.cox.net/amgough/Fanconi-genetics-genetics-primer.htm).

Glick, B., Pasternak, J., Pattern, C. (2010). Molecular Biotechnology Principles and Applications of Recombinant DNA Fourth Edition. Washington, DC: ASM Press.

Goldberg, M., Hartwell, L., Hood, L., Reynolds, A., Silver, L., Veres, R. (2008). Genetics From Genes to Genomes Third Edition. New York: McGraw Hill Companies.

Group 1 Intron Sequence Structure and Database (http://www.rna.whu.edu.cn/gissd/alignment.html). Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado. 88(24): 11105–11109.

Ikawa, Y., Inoue, T., Ohuchi, S., Shiraishi, H. (2002). Modular engineering of Group I introns ribozyme. Graduate School of Biostudies, Kyoto University. 30(15): 3473-3480.

Landthaler, M. and Shub, D. (1999). Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Microbiology Vol. 96, pp.7005–7010.

Minnick, M.F., Raghavan, R. (2009). Group I Introns and Inteins: Disparate Origins but Convergent Parasitic Strategies. Journal of Bacteriology. 191 (20), 6193-6202.

Peters Ph.D., Pamela (N/A). Restriction Enzymes Background Paper An Excellence Classic Collection. (http://www.accessexcellence.org/AE/AEC/CC/restriction.php).

Self-Splicing RNAs (http://mol-biol4masters.masters.grkraj.org/html/RNA_Processing3C-Self_Splicing_RNAs.htm). http://www.bio.davidson.edu/courses/genomics/method/CreLoxP.html

Motivation and Goals

This year’s modelling project focused on extending the work done by the modelling team in 2010.

Waterloo’s 2010 iGEM project, "Staphiscope", utilized amplifier parts developed by Cambridge in 2009 to detect low levels of Staph Aureus. These amplifier parts were characterized by the Cambridge team, but only under control of AraC/pBAD promoter, which differed from the promoter used in our 2010 Staphiscope project.

In order to characterize the amplifiers, a parameter scan was undertaken to find promoter-independent Hill parameters of each amplifier, consistent with data of full system. However, empirical verification of our results was lacking. This year, we sought to obtain this data, which (in conjunction with Cambridge data and model), would allow us to find Hill parameters for each amplifier.

Model

To allow for comparison of data, we used the same model as Cambridge in 2009.

In this model, araC represses the pBAD promoter in the absence of the inducer, arabinose. When arabinose is present, it binds to araC, preventing repression of the promoter and allowing transcription of reporter (GFP). This situation is modelled by a Hill function; we seek the Hill parameters of this function.

Thus, when AraC/pBAD system is induced with arabinose, we expect to see a steady increase of fluorescence from a low level, followed by a plateau of fluorescence at steady state.

Method

To measure fluorescence, we closely followed the assay described in the paper "Measuring the activity of BioBrick promoters using an in vivo reference standard", in the section "Assay of Promoter Collections".

Three cultures were grown overnight at 37 degrees Celsius with spinning at 200 rpm: untransformed BW27783, BW27783 containing BBa_I0500, and BW27783 containing BBa_I20260. These were then diluted 1:100 and regrown for roughly 4 hours under the same conditions. They were then diluted to an OD between 0.05 and 0.09, and regrown for 1 hour, again under the same conditions.

After this, the cultures were diluted into a 96-well plate at 8 different concentrations of inducer (arabinose), ranging from 0 to 6.4 uM. The plate was then incubated in a Wallac Victor3 multi-well fluorimeter at 37 degrees Celsius, and repeating measurements of absorbance and fluorescence were taken at 10 minute intervals, with shaking after each measurement. Untransformed BW27783, at each concentration of arabinose, was used to measure background fluorescence, and wells containing only broth were included to measure background absorbance. The machine settings used were identical to those described in the paper referenced above.

With this data, we aimed to calculate the steady-state per-cell GFP concentration during log-phase growth, for both BBa_I0500 and BBa_I20260 (measurement kit for the standard promoter, J23101). The ratio of these values would then characterize the strength of the AraC/pBAD promoter in units of RPU. The justification for this approach can be found in the supplemental material of the paper referenced above.

Results

The results of the experiment were anomalous, and considered too unreliable to be conclusive. There was no clear relationship between cell fluorescence and inducer concentration.

The fluorescence curve did not qualitatively match the predictions of the model; across all concentrations, and for each of the 3 cultures, we observed a high initial fluorescence, with a rapid drop to a lower steady state value. For each culture, this drop in fluorescence aligned well with the growth curve.

In addition, the untransformed BW27783 cells exhibited consistently higher fluorescence than cells containing BBa_I0500, which was highly anomalous. Because of this, we could not reliably use these cells to measure background fluorescence.

Below, a sample graph of Total Fluorescence is shown for each of the 3 cultures. These are curves of the total fluorescence for each culture, averaged over 3 replicates for each culture.

Discussion

It is believed that an error in our strain of BW27783 is most likely responsible for the anomalous qualitative features of our data. This is because for each concentration of inducer, the untransformed BW27783 cells exhibit a fluorescence curve highly similar to that of BW27783 containing BBa_I0500, and yet the untransformed cells should not be expressing GFP.

Prior to the measurement assay, BW27783 cells transformed with BBa_I0500 were plated and examined for fluorescence, both with and without the presence of inducer. The uninduced cells were not found to fluoresce, while the induced cells did fluoresce. The fluorescing cultures were used to make the frozen stock of BBa_I0500 which was used in the measurement assay. This indicates that our untransformed BW27783 should not fluoresce without the presence of inducer. Furthermore, the untransformed BW27783 cells used in the measurement assay were at no point prior to the assay exposed to arabinose.

To explain the fluorescence of the untransformed BW27783 in the measurement assay, it is speculated that our strain of BW27783 exhibits a rapid production of GFP in response to even low concentrations of inducer. Experimental error is also a likely source of inaccuracy in the data, although the qualitative features described were consistent across 3 trials of the experiment. Research into these results is still ongoing.

University of Waterloo: iGEM OUTREACH

The purpose of UW iGEM Outreach has always been and will continue to be the connection between our community and us. To help build a better understanding of synthetic biology, how it has affected the world around us and to create a basic, fundamental knowledge of the subject that can be incorporated into the way we see things. That perspective can be positive or negative, but we aim to provide the baseline knowledge required that will allow our community members to form a fact-based opinion.

This year, UW iGEM: Outreach focused on designing and running workshops targeted at schoolchildren. We hoped to share our love and passion for biology with tomorrow's future scientists and engineers. We plan to continue building on what we currently have and to eventually develop a complete syllabus for all grade levels. These workshops will be available for download for other educators and enthusiasts interested in their own outreach.

Workshop Materials

We have submitted two community bricks! One for our Grade 12 workshop and the other for our Engineering Science Quest activity for Grades 3-4. The downloadable material is the same as what you can find here on our wiki page.
-Synthetic Biology and You: Interactive Workshop for Grades 11-12
-All About Bacteria: How Clean Are Your Hands?

Grades 3-4: All About Bacteria - Outline | Handout (Duration: 2-day workshop, 1.5 hours total)
Grades 5-6: All About DNA - Outline (Duration: 1 hour)
Grade 12: Synthetic Biology and You - Materials | Ppt (part 1) | Ppt (part 2) (Duration: 2-3 hours)

Are you interested in doing any of these activities with kids around this age? Feel free to use any of our materials above and/or contact us at uwigem.outreach.hp@gmail.com. It is an inexpensive, interactive and fun way to have kids involved in genetics, microbiology and synthetic biology at a very early age. And definitely a lot of fun!

Events

We were also fortunate enough this year to have been given the opportunity to run our workshops at two different outreach events, both of which were on a grand scale. Now, we'd like to share our experiences with you.

Grade 12 Outreach Workshop: March 25th, 2011

The first was an organized Grade 12 workshop aimed at biology students to gain a better understanding of synthetic biology, the industries it has been affecting, career prospects as well as two hands-on activities. Over the planning span of 3 months, this event was organized in close accordance with the Kitchener-Waterloo school board and with the Marketing and Recruitment Co-ordinator for Science at the University of Waterloo. Through the creation of a brochure and meeting with individuals from the school board we had sent out an invitation all across the district for students to come in for our event. Eventually we had gotten more than 85 students to attend, which was great as it was the first time we had implemented this idea.

The next step had then been to recruit interested volunteers for the event so we could have our own students give a helping hand and who shared the same passion of sharing knowledge as we did. In order to facilitate this we had sent out emails, gone to various lectures and talked to students all over campus to get them involved. After recruiting 12 volunteers the brainstorming process had begun. We had wanted to have an interactive workshop where students were not just listening to us talk, but were actually involved in a stimulating activity that they could be excited about. The first part of our presentation looked into what was synthetic biology, what were Genetically Modified Organisms (GMOs) and what were the positives and negatives of them. Once that was through we started the first event. The first event we had was to talk about our very own Canadian genetically enhanced Yorkshire pig called the EnviroPig™. It has the capability to digest plant phosphate more efficiently than traditional Yorkshire pigs, which do not contain the enzyme to break it down, phytase. This gene can be found in E.coli which had been inserted into a pig embryo to allow it to produce phytase in its salivary glands. This is a real technology in Canada and is currently a very hot topic of debate among many citizens, so we thought it would be ideal to introduce students to the world of biotechnology right in their very own backyards. Once students had been exposed to the information, we had given them a package which we had compiled giving the positives and negatives of societal, technological, ethical, environmental and economical issues.

Of course, it did not end there! Students were then put into groups of 5 and as mentioned above, one of the key goals of UW iGEM Outreach is to allow members of our community to make informed decisions based on facts. Supplied with markers and paper students were to give a 1-2 minute presentation on why they did/did not believe that the EnviroPig™ should continue receiving funding from the government of Canada. The best and most convincing presentation won- we had great discussions from the negative aspects to positive aspects to even a compiled rap song about the EnviroPig™!

After the first event we continued on with our presentation. Here we discussed current industries that had been affected by synthetic biology. This incorporated the pharmaceutical and biofuels industries specifically. We discussed how pharmaceuticals had incorporated an aspect known as biosynthesis where they could customize and fine-tune certain pathways using standardized parts in order to provide efficient and precise drug delivery systems. In biofuels we talked about first and second generation biofuels and how the use of synthetic biology has the ability to create a ‘superbug’ to look for corresponding metabolic pathways for yielding ideal results. After this we did the second activity.

The second event that had been implemented was to incorporate what we do in our labs, outside of the lab. Essentially, we wanted to introduce the idea of synthetic biology to students and how it was an extension of what we knew as genetic engineering and consisted of students not just from science but from math, engineering and computer science. The activity called, ‘Design Your Own Pathway’ gave a series of scenarios we had given students with a library of BioBricks to create a certain pathway. Progressively each scenario was harder, more complicated and required the use of multiple BioBricks. The BioBricks that we had used were from the library and were real parts. Essentially this was to enable students to have a feel of how we have a ‘mix and match’ concept when it comes to synthetic biology. The activity had been set up as a relay race, where students in the same teams as the previous activity had to race each other to finish all scenarios. The activity and concept had been such a success that after the workshop teachers had asked to use our activity in their own classrooms.

Finally, we completed the presentation with a discussion of career paths that students could pursue that did not necessarily involve working in a lab. We wanted students to understand that the world of synthetic biology and biotechnology encompasses the involvement of individuals from multiple backgrounds and can penetrate into many different industries.

There was such an interest in our workshop that our prospects for the next one are aimed at more than 150 students. One thing’s for sure, mission accomplished and there’s definitely more to come! Would you also like to have your own workshop at your high school or university? Please feel free to view the downloadable materials for the presentation and two activities or contact us at uwigem.outreach.hp@gmail.com.

Engineering Science Quest: July-August 2011

Founded in 1990, the Engineering Science Quest or ESQ is a not-for-profit program that operates with the goal of exposing children in the Kitchener-Waterloo region to the world of engineering, science and technology through engaging them in a variety of hands-on activities. Promotion is primarily done through workshops in-school but also have satellite programs which reach out to rural and Native communities as well.

This is not the first time that UW iGEM has been involved in ESQ and we are proud to say that our continued involvement has allowed us to develop a standard set of activities which we are pleased to present to kids ranging from Grades 3-6 with more than 100 students. Currently we are also developing ideas for older kids that are similar to our activities from the Outreach workshop we had in March for Grades 10-12 and for even younger kids from Grades 1-2. Through involvement with managers specifically for ESQ this year we were able to have continual workshops every week from July 11th- August 12th, 2011. This was done with the recruitment of volunteers who again shared the same passion as we did in connecting with our community to facilitate that baseline knowledge; to get students introduced or even extend their knowledge on the world of synthetic biology and biotechnology.

The first activity for Grades 3-4 was called, “All About Bacteria: Do You Really Need to Wash Your Hands?” In this activity we introduce kids to the idea of biology, bacteria, synthetic biology, and iGEM. We also introduce them to basic ideas of sanitary techniques and tools used in a standard lab such as petri plates, agar, swabs etc. and how to layout an experiment; what is your hypothesis, results and conclusions? Once we discuss these basic concepts we allow the kids to take a swab of their hand and plate it on half of a petri dish. They then clean their hands with sanitizer and swab the other half of the petri dish. They then receive another petri dish where they can swab other places to find other ‘neat’ bacteria that may be lying around on the floor, counters, door knobs or wherever else they want (except up their nose, in their eyes, ears or mouth!). At this point and throughout the activity, interaction with the kids is key, as they always have stories or thoughts and experiences that are enlightening to share- even to us university students.

Once we explain what incubation is, we allow kids to come in the next day and see all the different types of bacteria that may have grown on their petri plates and come up with conclusions from the results they have seen. We provide them with a record sheet where they are able to write down what they saw such as; morphology, colour, its surface and even elevation. To be able to interact with kids at such a young age and to introduce them to concepts which students are normally exposed to in higher grades, allows them to explore a part of their world that they never knew existed. Building curiosity at a basal level helps us connect with our community and bridge the gap towards making more informed decisions.

The second activity for Grades 5-6 was called, “DNA Extraction from Your Cheeks”. This activity centers around the idea of DNA, where it is found, what it looks like and how every living organism contains very similar genomes, proteins and enzymes. There were four steps to this process, first to collect cheek cells, second to burst cells open to release DNA, third to separate DNA from proteins and debris and finally isolate the concentrated DNA. Kids obtain a cup of Gatorade containing a saline solution and swish the drink in their mouth for about a minute while gently chewing on their cheek cells. Then detergent is added to the test tube and meat tenderizer is added and the tube is inverted gently a couple of times. Cold rubbing alcohol is then added with a pipette which should allow the DNA to be visible. Then kids transfer the DNA into a PCR tube where they can hang it on a string to make a really neat necklace.

Kids were keen and interested in these activities, especially learning about various different concepts that they had not yet been exposed to. “Who knew that DNA could come out of your own cheeks?” was the idea we wanted to pass along- that every living organism contains DNA. From bacteria to animals.

Are you interested in doing these activities with kids around this age? Feel free to contact us at uwigem.outreach.hp@gmail.com. It is an inexpensive, interactive and fun way to have kids involved in genetics, microbiology and synthetic biology at a very early age.

Introduction

Synthetic Biology has been perceived as a field of science that has introduced tools, concepts and technologies which are sometimes sociologically and ethically insupportable. The non-scientific community has developed a stigma against the application of various synthetic biology technologies. The problem does not lie within the technology, but by an institution’s poorly executed strategy in educating the prospective end user about the relative benefit of its product. At times, the rate of technological advancements in the bioengineering industry surpasses the end-user’s ability to understand the necessity of the technology.

The science behind these synthetic biology tools has been the current driver in instilling a sense of appeal and intrigue within the scientific community. However, it is critical that the institutions that develop these technologies educate the non-scientific community of the importance and benefit of these tools to help relieve these evolving stigmas.

This year, the University of Waterloo’s Human Practices team’s focus was to develop a marketing strategy for their 2010 design project, the Staphiscope. The Staphiscope is an enhancement to the existing conventional plating methods that are used to detect Methicillin Resistant Staphylococus Aureus.

The scope of the analysis includes:

.

What is the selling point of the product? What differentiates the Staphiscope from what already exists and is accepted by the non-scientific community?

Does the concept of competition exist within synthetic biology? If so, how does an institution market the Staphiscope to optimize their opportunities for growth?

How can the marketing strategy approach be differentiated to ensure that both the scientific and non-scientific community are exposed to the relative benefits of the Staphiscope?

How do we channels the knowledge and learnings acquired within the synthetic biology industry and channel it to other stakeholders that will prospectively be impacted by the technology?

The purpose of the analysis is to ensure that the scientific industry understands the importance of bridging the scientific theory of a product to its economic feasibility. Moreover, it encourages institutions who participate in developing synthetic biology technologies to align their perception of a revolutionary design to what will be socially acknowledged by a non-scientific community.

What is the Staphiscope?

Methicilin resistant Staphylococcus aureus (MRSA) are bacteria whose presence has been quite problematic in terms of human pathogenic infections. Since its discovery in the 1880s, Staphylococcus aureus has been the known cause for several kinds of minor skin, and major post-surgical infections. Prior to 1940, mortality rates in relation to this pathogenic organism reached 80% (Deurenberg and Stobberingh, 2008.) The first wave of resistant S. aureus came two years after the introduction of penicillin for medicinal practice in 1940. In less than twenty years, most of the S. aureus strains known to man were unaffected by the antibiotic. In the late 1950s, a penicillinase-resistant penicillin was brought forth to the medicinal market; this was methicilin (Deurenberg and Stobberingh, 2008.) The bacterium's subsequent resistance to methicilin came two years after its introduction in 1959. The mecA gene responsible for methicillin resistance is also to blame for the organisms’ desensitization to several classes of antibiotics (Deurenberg and Stobberingh, 2008). This has led to the creation of the term: MRSA, now commonly used worldwide.

While an MRSA infection is much like a S. aureus infection, the difference comes in the lack of sensitivity of the MRSA to several classes of antibiotics. This makes MRSA infections a serious threat in both health and economical aspects.

The infection could be easily transferred directly (through regular skin-to-skin contact), as well as indirectly (through contamination of surfaces). The ease with which infection could occur, as well as the high mortality rate involved with the infection, make MRSA a serious threat to the health of patients worldwide (Durai et al., 2010.) There are only a few methods, which currently exit for MRSA screening. These are plating, liquid-broth inoculation, and PCR (polymerase chain reaction) assays. While these will be discussed in further detail later on in the report, it is important to note that these methods could be costly and time consuming, and could sometimes present incorrect results (Durai et al., 2010.)

In 2010, the International Genetically Engineered team at the university of Waterloo had been working on a method which can be used in supplement to the already-existing ones for the detection of MRSA infections. It is a proof of concept for diagnosing the presence of Staphylococcus aureus in an infection site before it has had the chance to create an infection. This synthetic biology–based diagnostic method will take advantage of the quorum sensing mechanism of Staphylococcus aureus, and utilize Escherichia coli as the sensor and reporter. For more information with regards to the Design of the Staphiscope please see the University of Waterloo’s 2010 iGEM Page: https://2010.igem.org/Team:Waterloo

Who are the “Competitors”?

Treatment of an S. aureus infection is of extreme importance, as outcomes can range from simple pustules to death. Early detection and treatment of S. aureus carriers can reduce healthcare costs and greatly improve the health of the patient. There are only a few methods currently available to hospitals for the diagnosis of S. aureus infection. These methods are time consuming, expensive and, in some cases, not very reliable. The purpose of the Staphiscope is to provide the option of accelerating the method of detecting S. aureus, without compromising reliability. It will be a particularly useful tool in speeding up the conventional methods of serial plating.

The following section analyzes the current products on the market and compares them to the Staphiscope.

BD GeneOhm StaphSR

Traditional culture methods for the detection of S. aureus are usually 2-3 days. The new BD GeneOhm™ StaphSR delivers a diagnosis in less than 2 hours, using rapid real-time PCR. Also, it can simultaneously detect and differentiate Methicillin-Resistant S. aureus and S. aureus from a positive result (blood culture). Currently under development are additional specimen claims – nasal and wound samples. Nasal claim will be able to determine colonization status and the wound claim will add to the rapid identification of positively infected patients. Obtaining positive results in a timely fashion aids clinicians in the prevention and control of infections.

Method

Specimen is prepared by transferring an aliquot of positive blood culture into a buffer team and then vortexed at high speed.

Cell suspension is lysed (via vortex and centrifuge) and heated. Then the lysis is cooled. Molecular reagents are reconstituted and the sample undergoes PCR. Results are obtained in about 1 hour.

References

"BD - GeneOhm - Products." BD: Medical Supplies, Devices and Technology; Laboratory Products; Antibodies. BD, 2011. Web. 23 July 2011. .

GenoType MRSA

Genotype MRSA uses DNA Strip Technology to identify both S. aureus and S. epidermidis cultures. Therefore, coagulase-positive and coagulase-negative staphylococci are differentiated. Simultaenously, the product can also detect Methicillin-Resistant S. aureus and S. aureus , which is incredibly important for therapeutic purposes. The test is performed from an overnight culture and guarantees results in only 4 hours.

Method

Culture is isolated from a sample or a primary culture is used.
DNA is extracted via methods producing amplifiable DNA from bacteria (for example QIAamp DNA Mini Kit from Qiagen).
Nucleic acids are selectively replicated in an amplification reaction. In the next step, the amplicons are chemically denatured, since detection on the DNA•STRIP® is done using single-stranded DNA. During the conjugate reaction, the specifically bound amplicon is marked with the enzyme alkaline phosphatase and is then made visible in a colorimetric detection reaction. In this way, a specific banding pattern develops on the DNA•STRIP®. Using a test-specific evaluation template, the test result can be read out quickly and clearly.

References

"GenoType® MRSA | Identification of MRSA from Cultured Material." Hain Lifescience | Ihr Partner in Der Modernen Labordiagnostik. Hain Lifescience, 2011. Web. 23 July 2011. .

"DNA•STRIP® Technology." Hain Lifescience | Ihr Partner in Der Modernen Labordiagnostik. Hain Lifescience, 2011. Web. 23 July 2011. .

Brilliance Agar

Brilliance Agar is a chromogenic screening plate used for the diagnosis of Methicillin-Resistant S. aureus. It uses a novel chromogen to show a blue colour when Methicillin-Resistant S. aureus phosphatase activity. For sensitivity, it contains antibacterial compounds which inhibit growth of various competitor bacteria. This product has high sensitivity and specificity, which minimizes healthcare costs. However, results are presumptive and would need to be confirmed. Organisms with atypical resistance can give false negative results.

Method

Patient is inoculated using a screening swab or an isolated colony or liquid suspension is used. Sample is plated on Brilliance Agar. Plates are incubated at 37 ºC. Results are obtained in 18 hours. Methicillin-Resistant S. aureus grows as denim blue colonies.

References

"Brilliance MRSA AGAR." Oxoid - Worldclass Manufacturer of Dehydrated Culture Media and Diagnostics Products. Oxoid, 2010. Web. 23 July 2011. .

Competitive Analysis Matrix

Rating Scale

Methodology for Rating Scale

The Competitive Analysis Matrix uses a format that divides the product’s market profile into several categories, providing a framework that ensures all issues are considered. Each category is scored in the course of the ratings process (using a numerical scoring system). Products are scored 1 through 27; those facing greater competitive threats would wind up with an overall low market profile score. Please note that ratings represent, in the end, an opinion. Please note, thorough assessment of each product’s market profile requires a broader framework, involving a comprehensive review of the product’s competitive position.

Conclusions

Based on a comparison and competitive analysis of the Staphiscope and the three major detection products on the market, the Staphiscope was found to have the highest market profile score. It uniquely scored highest in reliability and ease of use. Although all products on the market signify great innovation in the field, Staphiscope has great potential to gain market share.

Porter’s Five Forces analysis

Marketing Strategy

Pitching the Staphiscope to a Research and Development Company When pitching the Staphiscope to the R&D industry, it is of paramount importance to establish its competitive advantage over traditional methods for S. aureus detection. To have a competitive advantage, a product or company must excel in at least one of the three following categories while remaining equal to its competitors in the others (Szarka, 2010):

Market access

Infrastructure

Technology

Market access refers to how easily the target demographic can get the product. Even a revolutionary technology can be hampered by a lack of market access. Infrastructure is related to whether or not a supply chain exists, as well as facilities for production and distribution. The third point, technology, is where the Staphiscope excels; its superior technology is what will separate it from competitors. Other selling points of the Staphiscope include its speed, efficiency, and room for expansion (could this technique be applied to other cases?). Conversely, there are also barriers that must be overcome when pitching to the R&D industry; namely, one must avoid falling prey to “not invented here” syndrome (Szarka, 2010). This term applies to the mindset some companies have of only trusting in-house innovation, and can be difficult to alter. Other barriers include the lacking of Staphiscope use on a commercial scale, and public perception regarding E. coli. While the latter issue can be combated via a public awareness campaign, the former is simply a fact of any innovative technology.
Companies such as Amyris Biotechnologies and Codon Devices have attempted to commercialize in the field of synthetic biology. Their experiences provide valuable lessons that can applied to the Staphiscope (Wilan, 2005). The most relevant of these is that patent protection should be a serious concern when developing a novel technology, especially in such a burgeoning and competitive field. Consolidating IP ownership and control early is equally important, as doing so will prevent a lack of unified vision from stalling the Staphiscope’s progress. Of course, there are a plethora of patent and IP issues surrounding the field of synthetic biology that must be dealt with before or during the commercialization process. Chief amongst these is the scope of protection that can be provided to new technologies (Chugh Sakushyma, 2009). Additionally, looking for a pharmaceutical partner can help ease the transition into commercialization.
It is important to realize that commercialization is a multi-year effort. As such, it can be beneficial to develop a commercialization plan (Office of Technology Transfer). This plan gives a general outline of what information the R&D industry will be looking for when it comes time to make a pitch. Details about market size and growth rates, predicted sales figures for the first five years, licensing agreements and more can all prove invaluable when attempting to bring a product to market. Preparedness in regards to this information can make the difference between a successful pitch and an unsuccessful one.
In summary, pitching the Staphiscope to the R&D industry is a complex process that must be handled correctly to ensure its successful commercialization.

References

Office of Technology Transfer. Argonne National Laboratory. “Commercialization Plan Worksheet”. http://www.anl.gov/techtransfer/pdf/LicensingQuestionaire1-0.pdf

Wilan, K.H. Nature Publishing Group. 2005. “Commercializing synthetic biology”. http://www.nature.com/bioent/startup/072005/full/bioent870.html

Chugh, A., Saukshyma, T. 2009. “Commercializing synthetic biology: Socio-ethical concerns and challenges under intellectual property regime”. http://stopogm.net/webfm_send/315

Szarka, M. “Adventures in Commercialization”. 2010. http://webcast.utm.utoronto.ca/1/watch/515.aspx

How Do We Achieve Public Acceptance?

For years, it has been believed that the prevalence of MRSA infections has resided within the walls of either a hospital or health care facility. Due to understated hygienic practices, a modified and relatively more virulent strain of Staphylococcus Aureus has also threatened several community based settings. In addition to Hospital Acquired MRSA, general health practitioners must also take into account the occurrence of community acquired MRSA. It is important to educate the public about the applications and relative benefit of the Staphiscope. Thus, there needs to be a channel of communication that allows for a transfer of knowledge between the scientific and non-scientific community.

Who Do We Want To Educate?

Given that MRSA may not only be spread within a hospital but also within the community, there are quite a few demographics that would gain value in understanding the benefit of the Staphiscope.

Hospital Setting

At least 2% of patients in hospitals or health-care facilities are likely to carry a strain of Staphylococcus Aureus that is resistant to antibiotics such as Methicillin. The following individuals are susceptible in contracting an MRSA infection:

Individuals who have weak immune systems

People receiving kidney dialysis or cancer treatments

Individuals who have been hospitalized or have had surgery over the past year

MRSA within the Community

Patients who are discharged may have an inactive form of MRSA that remains colonized in their system. Thus, those who live within the community are still at risk of acquiring and suffering from antibiotic resistant Staph infections that are relatively more virulent. MRSA has been detected and acquired by healthy people in both institutionalized and individual based settings. The following individuals are susceptible in contracting MRSA in the community:

Day-care facilities or facilities in which equipment of personal items are shared

Military bases

Individuals who get tattoos

The Strategy

In the field of synthetic biology, there is an unrecognized paradox that hinders the level of interdisciplinary communication between the scientific and non-scientific community. The stigmas built outside the realms of a scientific community grow at a greater rate than a scientist’s ability to answer the plethora of questions surrounding the regulation, safety and potentiality of these synthetic biology technologies. Another problem lies in a scientific institution’s inclination to address the ethical concerns surrounding their synthetic biology technology or process. Generally an individual who has not be previously exposed to the field, will construct an ethical judgement proceeding the phase where a company is about to commercialize their product. At this critical stage of a company’s product plan, stakeholders are reluctant in addressing these ethical concerns as it may discourage their ability to advance and innovate their existing technology. Regardless of the threats that these ethical judgments have previously imposed, there is a necessity in developing an approach in which the end result is an internationally renowned sense of public acceptance and support. “Without public support and understanding of research into synthetic biology, both funding and regulation are unlikely to support significant scientific advances” (Gaisser, et. al, 2009). To address this issue, an expert committee in Europe supported by the New and Emerging Science and Technology programme set out a roadmap that outlines the four interconnected attributes that will instil a sense of public acceptance within the non-scientific community. These four attributes are:

Scientific Milestones

Knowledge Transfer

Funding

Regulation

This roadmap outlines that without the implementation of a knowledge transfer strategy, there is limited confidence attaining in achievements under the other three key areas of the model. Scientific milestones would not be achievable without a sustained level of funding provided through other groups impacted by the prospective commercialization of these synthetic biology tools. Moreover, regulation of synthetic biology tools is influenced by the ethically themed perceptions created by both the scientific and non-scientific community.
The knowledge transfer strategy would be an interdisciplinary model that would impact the following stakeholders:

Natural and Social Scientists

Engineers

Industry Representatives

Non-governmental organizations

Non-scientific community (ie. hospital staff, hospital patients and members within institutionalized settings)

Decision makers (ie. potential investors)

Funding Agencies

Knowledge Transfer Strategy

In this context, knowledge transfer is the exchange of research knowledge between the institution producing the synthetic biology technology and their target end-user. The purpose of the knowledge transfer strategy is to develop a communication platform between all stakeholders to mitigate the unsourced perceptions, bias’ and stigmas against the field of synthetic biology. Moreover, it is better to develop an interdisciplinary team at the early stages of the technology development phases versus segregating the two communities until the technology is prospectively in its commercialization phase.

Method

The following are examples of methods that can be used by the synthetic biology industry in promoting tools such as the Staphiscope to its potential end-users (ie. individuals within hospitals and community facilities)

Development of an interdisciplinary network that consists of synthetic biologists, engineers, potential investors, and the general public

Sustainable dialogue between all stakeholders within the interdisciplinary network. This can be achieved through: Workshops that aim in exchanging information to individuals that will benefit from the application of the Staphiscope in either a hospital or community based setting

Educational materials that are specifically tailored to the different parties that could be impacted by the commercialization of the StaphiScope (ie. Hospital Microbiologists, Patients, and the General Public)

Incorporating the General Public and other stakeholders at the research phase of the technology development process. This results in a mutual benefit to both the institution as well as the end-user in that they are able to collaboratively discuss the ethical feasibility of the technology.

Use of knowledge broker- A knowledge broker is essentially an intermediary resource that assists in translating research knowledge to information that is comprehensible to a member that is not from the field of synthetic biology. An individual that has attained perceptions, knowledge and experiences from the scientific, business and social field is best suited to convey the importance of the Staphiscope to the stakeholders that have been listed above.

Partnerships between Synthetic Biology institutions and hospitals or other community based facilities.

Synthetic biologists must consider the importance of implementing an approach to help relieve the prospective stigmas that could potentially impact the relative success of their technology. The general public plays an influential role in the innovation capabilities of these synthetic biology technologies. Thus it is critical that these synthetic biology institutions involve the public and create awareness of their technologies at all stages of the research and development stage. Integrating a strategy that incorporates the exchange of knowledge is a fundamental leverage that would help create an aura of public acceptance and support all dimensions of the synthetic biology roadmap.

Human Practices Commercialization Toolkit

Following the Regional Jamboree, the Human Practices team began to develop the tools, templates and models that would assist a synthetic biology community and its associate stakeholders to understand the commercialization process. More importantly, our aim is to develop informational material that would achieve the integration of a knowledge transfer strategy in the field of synthetic biology. By streamlining the knowledge transfer strategy throughout each stage of the commercialization process, we are able to achieve a paralleled level of communication between the scientific and non-scientific community. Below is a sample of the toolkit our team has developed.

The Commercialization Road Map

The University of Waterloo Human Practices Team has devised a commercialization road map specific to the field of synthetic biology. The purpose of this road map is to outline the different stages of the technology development process. More importantly, it indicates what initiatives must be completed at each stage, who needs to be involved, and the strategies that can be utilized to attain the intended end-goal; A Scientific Milestone. To view the road map please click the link below.
Synthetic Biology Commercialization Roadmap

The Knowledge Transfer Strategy Action Plan

The University of Waterloo Human Practices Team has devised a knowledge transfer strategy to help parallel the level of communication between the scientific and non-scientific community. This document outlines the strategies that are currently being used or proposed at the University of Waterloo but can be easily used on a wider scale by the entire iGEM community. To view the knowledge transfer strategy plan, please click the link below.
Knowledge Transfer Strategy

Conclusion

The purpose of this analysis was to understand the relative feasibility of a synthetic biology tool from the perceptions of a scientific and non-scientific community. When devising a marketing strategy, most companies define a technology’s commercial success by its appeal towards investors or its ability to enter a market heavily saturated by other established technologies. Given that most synthetic biology institutions are still at their preliminary phases in terms of commercialization, it is critical that their product is widely accepted and acknowledged by all disciplines that are impacted or will be potentially exposed to the technology.
In the future we hope to take our research and methodologies and present them to the stakeholders discussed within the analysis. Our next steps are to identify institutions and facilities that would benefit from the use of the knowledge transfer strategy and develop sample activities or educational materials that can be used by these facilities to promote the Staphiscope.

References

A.D.A.M Health Solutions. "Methicillin-resistant Staphylococcus Aureus; Community-acquired MRSA (CA-MRSA); Hospital-acquired MRSA (HA-MRSA)." National Center for Biotechnology Information. 9 June 2011. Web. .

"Ethical Issues in Synthetic Biology." Synthetic Biology Project. Web. .

Gaisser, Sibylle, Thomas Reiss, Astrid Lunkes, Kristian Muller, and Hubert Bernauer. "Making the Most of Synthetic Biology : Article : EMBO Reports." Nature Publishing Group : Science Journals, Jobs, and Information. Nature Publishing Group, 2009. Web. .

Herrera, Stephen. "Preparing the World for Synthetic Biology." Technology Review. Jan. 2005. Web. .

The Lancet. "Community-acquired MRSA." 14 Oct. 2006. Web. .

Mitton, Craig, Carol Adair, Emily McKenzie, Scott Patten, and Brenda Waye Perry. "Knowledge Transfer and Exchange: Review and Synthesis of the Literature." University of British Columbia Okanagan and Child and Family Research Institute of BC; University of Calgary; Alberta Mental Health Board. Web. .

Pombo, David. "Community Acquired MRSA." 29 Sept. 2006. Web. .

“Safety and Ethics of Synthetic Life." Organisation for International Dialogue and Conflict Management (Austria). Web. .

Members

Advisors

About UW

OUR TEAM!

OUR UNDERGRADUATES!

Dan Barlow

Ekta Bibra

Angela Biskupovic

Diljot Chhina

Amanda Clarke

Arpita Desai

Jon Eubank

Matt Gingerich

Peter Hong

Kasia Karpinska-Leydier

Jordan Lapointe

Chris Milousis

James Scott

Michel Simard

Brandon Wang

Hilary Yeung

George Zarubin

OUR GRADUATES!

John Heil

Eddie Ma

Andre Masella

Danielle Nash

OUR ADVISORS!

Dr. Brian Ingalls

Dr. Trevor Charles

Dr. Barb Moffatt

Dr. Marc Aucoin

UNIVERSITY OF WATERLOO

University of Waterloo was founded in 1957 and has grown to accommodate 30,000 undergraduate and graduate students, and has become Canada’s leading university in comprehensive learning. Also, the university has consistently been voted as the most innovative, most likely to produce the leaders of tomorrow, and best overall University in Canada for over 18 years (according to Maclean’s Magazine). Waterloo’s reputation is however based on its excellent and pioneering co-op program which offers students a balance of work and school on a per term basis, making it a unique learning experience. The city of Waterloo has recognized University of Waterloo and its students, by meeting its demands in terms of funding and involvement. The University has also opened up two new campuses; the pharmacy building, and the joint McMaster medical building in Kitchener, as well as the architecture building in Cambridge, contributing to not only the city of waterloo but the whole Grand River area.

WATERLOO - KITCHENER COMMUNITY

City of Waterloo mainly revolves around the two universities: University of Waterloo and Laurier University. Waterloo is surrounded by Kitchener and thus, the two cities are known as the twin cities, also referred to as Kitchener - Waterloo. The population of the city of Waterloo is always fluctuating due to temporary residents at Waterloo’s two universities. Total population in 2009 was recorded to be 121, 700; approximately 20,000 of which were temporary post-secondary students. Due to its small size, people in the past have tried to merge the two cities together but have been unsuccessful. As of today, both cities have their own identity and their own separate city governments.

Parts List

UW's parts for 2011.

BBa_K576003 - RNA - Left part of self-excising ribozyme

BBa_K576004 - RNA - Right part of self-excising ribozyme

BBa_K576005 - Reporter - Left part of GFP (GFP 1) with promoter (J23101) and RBS (B0034)

BBa_K576006 - Reporter - Right part of GFP (GFP 2) with transcription terminator

BBa_K576007 - Intermediate - Left part of GFP with left part of self-excising ribozyme attached using RFC 53 construction.

BBa_K576008 - Intermediate - Right part of the self-excising ribozyme attached to the right part of GFP using RFC 53 construction

BBa_K576009 - Intermediate - Lox attached on to BBa_K576005 on the right of the part. Standard assembly (RFC 10) was used for this construction.

BBa_K576010 - Intermediate - Lox attached on to BBa_K576008 on the left of the part. BBa_K576009 or BBa_K576010 can be used depending on your convenience

BBa_K576011 - Reporter - Final construction of the 2011 project. The self-excising ribozyme should be cut out of from the rest of the sequence and thus expressing the full GFP.

BBa_K576012 - Reporter - Negative control of the experiment. The lox recombination site interrupts the GFP expression

BBa_K576013 - Reporter - Positive control of the experiment. Everything in between has been cut out by the self-excising intron and the GFP is fully expressed.

Lab
Notebook

Safety

Lab Notebook 2011

The following entries pertain to the Quantification Project

Tuesday, May 31, 2011

Transformation of BBa_I20260 from iGem Kit Plate 2, Well 17F.

Wednesday, June 1, 20111

Created a frozen stock of I20260

Inoculated BBa_I0500 and BBa_E0240 from frozen stock already made from last year

Thursday, June 2, 20111

Miniprepped and nanodropped I0500, and E0240.

Inoculated I20260 from the frozen stock created the previous day

Friday, June 3, 20111

Digestion Reaction. Digested I0500 with EcoRI and SpeI. Digested E0240 (first sample) with EcoRI and PstI and digested E0240 (second sample) with EcoRI and XbaI.

Miniprepped and nanodropped I20260

Monday, June 6, 20111

Inoculated I20260, I0500 and E0240

Tuesday, June 7, 20111

Miniprepped and nandodropped I20260, and I0500 and E0240 for extra sample

Inoculated E0240

Wednesday June 8, 20111

Digestion reaction. Digested I0500 with EcoRI and SpeI. Digested E0240 (first sample) with EcoRI and PstI and digested E0240 (second sample) with EcoRI and XbaI. Digested I20260 with EcoRI and PstI.

Miniprepped and nanodropped E0240 for back up

Thursday June 9, 20111

Gel extraction of E0240 (EcoRI+XbaI), I0500 (EcoRI+SpeI), E0240 (EcoRI+PstI) and I20260 (EcoRI+PstI). Two samples of each parts were gel extracted.

Nanodropped the samples from Gel extraction. Concentration of I0500 and I20260 were too low.

Inoculated I0500 and I20260

Friday June 10, 20111

Miniprepped I0500 and I20260 and ran digestion reaction. Same enzymes were used as the ones listed above.

Tuesday, June 14, 20111

Gel extraction of I0500, I20260 and the back-up samples of E0240.

Thursday, June 16, 20111

Ligation reaction: Ligated I0500 on to E0240. Ligated I20260 on to pSB1A2 (from E0240)

Monday, June 20, 20111

Transformation of ligated parts (I0500+E0240, and I20260 on pSB1A2). Plated the transformant and incubated overnight

Tuesday, June 21, 20111

Created plates containing 1% arabinose.

Replicated plates containing I20260 colonies on to a different plate with Ampicilin antibiotic. Incubated overnight.

Wednesday, June 22, 2011

Replicated I0500+E0240 to plates containing 1% arabinose. Incubated overnight

Inoculated a single colony from I20260 plate

Thursday, June 23, 2011

Created frozen stock of I20260

Inoculated a single colony from I0500+E0240 plate

Friday, June 24, 2011

Created frozen stock of I0500+E0240

Monday, July 4, 2011

Inoculated the I20260, and I0500+E0240

Created 1M Arabinose solution

Tuesday, July 5, 2011

Made serial dilutions of arabinose solution (from 1M to 1uM).

Diluted the cultures to 0.50 Absorbance at OD600.

Set up experiment for quantification experiment. Refer to the diagram below for how the experiment was setup.

Monday, July 11, 2011

Inoculated the I20260, and I0500+E0240

Created 1M Arabinose solution

Tuesday, July 12, 2011

Another quantification experiment run. Machine failure.

Wednesday, July 13, 2011

Inoculated the I20260, and I0500+E0240

Created 1M Arabinose solution

Thursday, July 14, 2011

Last quantification experiment run.

 The following entries pertain to the Ribozyme Project

Wednesday July 6, 2011

Received 3 of 4 sequences the previous week (IN1, IN2 and GFP2).

A quick spin down UWAT014-3/UWAT014-2 using centrifuge.

Resuspended DNA in 40ul of MQ water (Concentration: 2ug/40ul=1ug/20ul)

Transformed into DH5-alpha (sequences in PUC57).

grown overnight on ampicillin plates.

Resuspension of PSB1C3 in the Spring 2011 distribution kit (Plate 1 well 3A). Contains BBa_J04450.

Resuspension of PSB1C3 in 10ul of MQ water (aspirated), wait approximately 5 minutes.

1ul of resuspension was transformed into DH5-alpha. Grown overnight on plate.

Thursday July 7, 2011

N1 (amp), IN2 (amp), GFP2 (amp) and PSB1C3 (cm) broth cultures innoculated (3 each)..

Friday July 8, 2011

Frozen stock of IN1, IN2 and GFP2 in PUC57 and PSB1C3 backbone made..

Miniprep for IN1, IN2, GFP2 and PUC57 completed:.

Sequences	In1	In2	GFP 2	pSB1C3
260/280	1.85	1.80	1.88	1.86
ng/ul	229.8	236.1	198.6	166.2

GFP1 Sequence(588nt)in PUC57 received from Bio Basic Canada INC..

Tuesday July 12, 2011

Liquid cultures of GFP1 (x2), IN1, IN2, GFP2 and PSB1C3 were innoculated with the appropriate antibiotic in the broth..

Wednesday July 13, 2011

GFP1, IN1, IN2, GFP2 and PSB1C3 were minipreped to isolate plasmid DNA..

Frozen stock of GFP1 made..

Thursday July 14, 2011

GFP1, IN1, IN2, GFP2, PSB1C3 digested with EcoRI and PstI. GFP2 also digested with ndeI..

Innoculation of liquid culture (GFP1, IN1, IN2, GFP2, PSB1C3)..

Friday July 15, 2011

Gel extraction of GFP1, IN1, IN2, GFP2 and PSB1C3. However, the results were not as anticipated..

Miniprep of cultures innoculated yesterday.

Monday July 18, 2011

Cultures were miniprepped, however, GFP1 did not have a sufficient concentration to undergo digestion..

Proceeded with digestion for GFP2 (ndeI), IN1, IN2 and PSBIC3 with EcoRI and PstI..

Innoculation of GFP1 (x4).

Tuesday July 19, 2011

Miniprep and digestion of GFP1..

Gel extraction of each digestion (PSB1C3(x2), GFP1, IN1, IN2, GFP2)..

Wednesday July 20, 2011

Lox resuspended and digested..

Ligation of GFP2, IN1, IN2 and Lox into PSB1C3..

Thursday July 21, 2011

Transformation of GFP2, IN1, IN2 and Lox. Each was plated on cm containing media and grown overnight..

Friday July 22, 2011

All negative plates did not produce colonies..

Growth was good on all positive plates except for IN1, which only produced two main colonies..

Monday July 25, 2011

Gel extraction IN1, IN2 and GFP1, however, GFP1 failed..

Ligation of IN1 and IN2 into PSB1C3..

Tuesday July 26, 2011.

Innoculation of GFP2 into cm containing LB broth tube and lox into amp containing LB broth tube..

Gel extraction did not work (likely a problem with digestion or transformation).

Innoculation x5 of GFP1..

Wednesday July 27, 2011

Frozen stock of GFP2 and lox made.

Miniprep of GFP1 x4 replicates.

Gel extraction of IN1 and IN2 resulted in improved concentrations.

Transformation.

July 30, 2011

Miniprepped GFP 1 and GFP 2.

August 2, 2011

Miniprepped Intron 1 and intron 2..

August 3, 2011

Digestion of GFP 1 and Intron 2 with SacI and EarI.

Digestion of GFP2 and Intron 1 with SacI and SapI.

August 4, 2011

Nothing.

Figuring out unexpected SacI cute site in the middle of pSB1C3 vector.

August 5, 2011

Nothing.

August 6, 2011

Digestion of GFP 1 with Bgl II and Ear I.

Digestion of Intron 1 with Bgl II and Ear I.

Digestion of GFP 1 with Ear I and Pst I.

Digestion of GFP 2 with EarI and Pst I..

Gel extraction of all the samples listed above.

August 7, 2011

Ligation of GFP 1 with Intrton 1 and GFP 1 with GFP 2.

Transformation of the two ligation mixtures listed above.

August 8, 2011

Minipreping Int2, lox and GFP2.

Digestion.

Gel extraction.

August 9, 2011

Miniprepping BBa_K576007.

Digestion.

gel extraction.

August 10, 2011

Ligation and transformation of BBa_K576007 and J61046 to create K576009.

August 11, 2011

Ligation and transformation.

August 12, 2011

Streak plating GFP1-GFP2 (BBa_K576013).

Backbone for RFC arrived and was streaked on cm plate.

August 15th, 2011

Inoculation of a single colony of K371053 into an LB broth

August 16th, 2011

Made frozen stock of K371053

Inoculated K371053 (X3), K576004, and K576006.

August 17th, 2011

Miniprepped K371053(vector), K576004 (insert), and K5756006 (insert).

Standard assembly of the two parts and a vector listed above. Ran gel extraction experiment after.

August 18th, 2011

Ligation and transformation reaction for transferring K576004 and K576006 from pSB1C3 to K371053.

August 19th, 2011

Inoculation of single colonies from the transformed samples from the previous days.

Inoculated K576009

August 22nd, 2011

Created frozen stock and inoculated K576004 and K576006 on K371053

Miniprepped, digested (SpeI and PstI) and gel extracted K576009.

August 23rd, 2011

Miniprepped, digested and gel extracted K576004 (SpeI and PstI) and K576006 (XbaI and PstI) on K371053.

August 24th, 2011

Ligation and transformation of samples prepared on the 23rd.

August 25th, 2011

Single colony for K576008 was picked and inoculated

August 26th, 2011

Created frozen stock of K576008

August 28th, 2011

Inoculated K576008 and K576009 in LB broth containing chloramphenicol

August 29th,2011

miniprepped and digested K576008 and K576009.

August 30th, 2011

Gel extraction of K576008 (insert) and K576009 (vector).

August 31st, 2011

Ligation and transformation of final construction (BBa_K576011)

September 1st-2nd, 2011

No lab work was done.

September 4th, 2011

inoculated K576011 and K576008 in LB broth containing Chloromphenicol antibiotic

September 5th, 2011

Miniprepped, digested (EcoRI and PstI) and gel electrophoresed part K576008 to move the part into pSB1C3 for submission. Questionable band placement; Did not go further with the experiment.

Miniprepped all the intermediate steps, controls and final construction for submission to partsregistry.

September 6th, 2011

Miniprepped, digested and gel extracted part K576008. Confirmed band placement via aPe program. Failed at the final step of the gel extraction process; Wash Solution without ethanol (miniprep solution provided from Biobasic) was added

September 7th, 2011

Miniprepped, digested and gel extracted part K576008.

Septermber 8th, 2011

Ligation and transformation reaction for K576008. Moved K576008 part from the BBa_K371053 to pSB1C3 for submission purposes.

Septermber 9th – 15th, 2011

no lab work was done

September 16th, 2011

Final diagnostic digestion reaction. Digested every intermediate, control and final constructs. BBa_K576003, K576004, K576005, and K576006 were the only parts able to be confirmed. All the other intermediates and constructs have questionable band location. Lab work stopped due to time constraint.

SAFETY

Laboratory Safety

The Ribozyme Project is not expected to raise any research, public or environmental safety concerns other than those normally associated with Biosafety Level 2 organisms, such as Escherichia coli (DH5-alpha), which is classified as very low to moderate. The use of this project is primarily reserved for research and laboratory use, therefore, should not purposefully be exposed to the public or environment except after further testing in its specific applications (such as with particular fusion proteins). Furthermore, the basis of our project is to establish a self-excising sequence (ribozymes), which should limit the expression of any intervening sequences to the RNA level. If the intervening sequence were something of environmental or public relevance (such as antibiotic resistance), the experimental design indicates that the sequence will be removed and, thus, not expressed. This is a relevant contribution of the design in limiting expression to the RNA level, which eases environmental hazard concern upon the accidental release of a GMO containing this biobrick. Therefore, the new biobrick parts submitted should not raise any safety issues.

The necessary facility, equipment and handling procedures associated with Level 2 Biosafety concerns were met:

1.Pipetting aids
2.Biosafety cabinets where applicable
3.Laboratory separated from other activities
4.Biohazard sign
5.Proper safety and disposal equipment, including autoclave
6.Personal protective equipment, worn only in the laboratory
7.Screw-capped tubes and bottles
8.Plastic disposable pasteur pipettes, when necessary

All precautions with respect to recombinant DNA were observed:
1.All waste was autoclaved before being thrown away.
2.Researchers practiced aseptic technique and personal hygiene and safety precautions
3.Procedures likely to generate aerosols are performed in a biosafety cabinet
4.Bench surfaces were disinfected with ethanol.
4.Potentially contaminated waste is separated from general waste

Safety Questions

1. Would the materials used in your project and/or your final product pose: The materials used in the lab are non toxic to health of individuals as well as to the environment. One of the major reagents that is used is GelRed which is used as a substitute for Ethidium Bromide. Gel Red is unable to penetrate into cells and so is a non-mutagenic agent. As well it has the same spectral characteristics as Ethidium Bromide and so has the same effectiveness of use. The project itself is safe even if released into the environment by design or accident since the part being expressed is the Green Fluorescent Protein (GFP). Unless the sequences are mutated, the project poses no risk.
Please explain your responses (whether yes or no) to these questions.
Specifically, are any parts or devices in your project associated with (or known to cause):
- pathogenicity, infectivity, or toxicity? No
- threats to environmental quality? No
- security concerns? No
The parts that are associated with the project this year are at the same level of risk as the any of the regular parts that already exist. All parts are constructed in an antibiotic containing backbone so that accidental release of will pose minimal risk to contaminating other bacterial populations.

2.Under what biosafety provisions will / do you operate?
a.Does your institution have its own biosafety rules and if so what are they? The University of Waterloo had a Bio-Safety plan in place to ensure the proper use to bio-hazardous materials in teaching and research at the university. A more detailed overview of their plans is outlined at the Bio-Safety Website
b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? The laboratories operating at the University of Waterloo have obtained permits from the Bio-Safety Committee in order to perform intended research. Since the Waterloo iGEM team performs all laboratory work in a parent lab under the guidance of the Masters and PhD students of that lab, the projects carried out in the lab are covered by the permits obtained by the parent lab.
c. Will / did you receive any biosafety and/or lab training before beginning your project? If so, describe this training. All lab volunteers are required to take an online training to familiarize themselves with the Biosafety practices of the University of Waterloo. The training is followed up by a quiz ensuring proper understanding of the material. Upon completion of the training and quiz a hands- on lab training is provided under supervision of the parent lab’s PhD student. The hands-on training involves instruction of use of the appropriate equipment that is used in the lab, as well as how to maintain and discard materials in a safe manner.
d. Does your country have national biosafety regulations or guidelines? If so, provide a link to them online if possible. Canada operates under the guidelines set up by the Public Health Agency of Canada. The Agency is the national authority on matters concerning biosafety and biosecurity. Risks to the public are reduced by standardizing controls over activities that involve human pathogenic agents, domestic or imported. While these guidelines are in place the current iGEM project does not involve work with any agents or materials that may pose a risk to humans. The link to the Public Health Agency of Canada is provided below: Public Health Agency of Canada

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@@ Line 121: / Line 121: @@
          <a href="/Special:MovePage/Team:Waterloo" style="color:white;font-size:8px;float:left;margin-left:10px;">Move</a>
          <a href="/wiki/index.php?title=Talk:Team:Waterloo&amp;action=edit" style="color:white;font-size:8px;float:left;margin-left:10px;">Discussion</a>
-<div id="UWigemlogo" style="float:left;margin-left:50px;"><img src="https://static.igem.org/mediawiki/2010/6/62/IGEMlogo2010.png" alt="UW iGEM logo"></img></div>
+<div id="UWigemlogo" style="float:left;margin-left:0px;"><img src="https://static.igem.org/mediawiki/2011/7/77/Waterrloo_logo_%281%29.png" alt="UW iGEM logo" width ="150" height="90"></img></div>
 <div id="igemLogo" style="float:right;margin-right:250px;"><a href="https://2011.igem.org"><img src="https://static.igem.org/mediawiki/2010/f/fd/IGEM_basic_Logo_white_small_UW.png" alt="Return to iGEM 2011"></img></a></div>
 </div>
@@ Line 159: / Line 159: @@
 <p>
               Introns, self-excising ribozymes, can become a useful tool to create in vivo protein fusions of BioBrick parts. To make this possible, intron sequences are used to flank non-protein parts embedded in coding sequences. An intron sequence with an embedded recombination site is capable of in vivo insertion of a compatible protein fusion part. As an example, a GFP-fusion was created with an intervening lox site that is removed from the final protein using the intron to form a fully functional GFP protein. In vivo protein fusions can be applied to a larger number of modular systems to make complicated expression systems, such as synthetic antibodies or plants capable of Cry-toxin domain shuffling.
-</p><br /><br />
+</p><br/>
-<h3>MODELING</h3>
-<p>
+<br /><br />
-!!!!!!!Write Something Here!!!!!!
+<div><h3>WE WOULD LIKE TO THANK OUR GENEROUS SPONSORS.</h3></div><div id="sponsers" style="width: 90%;margin-left:5%;margin-right:5%;">
-</p>
+<div style="text-align: center;"><br/>
-<br /><br /><br />
+<img src="https://static.igem.org/mediawiki/2010/8/85/SciFac.PNG" alt="Faculty of Science" width="400px" height="200px" style="margin:15px;"></img>
-<div class="innerHeader"><h3>WE WOULD LIKE TO THANK OUR GENEROUS SPONSORS.</h3></div><div id="sponsers" style="width: 90%;margin-left:5%;margin-right:5%;">
+<img src="https://static.igem.org/mediawiki/2010/f/fc/DeptOfBioLogo.png" alt="Department of Biology" width="400px" height="200px" style="margin:15px;"></img><br/>
-<img src="https://static.igem.org/mediawiki/2010/8/85/SciFac.PNG" alt="Faculty of Science"></img>
+<img src="https://static.igem.org/mediawiki/2011/2/27/Engineering-Chemical_web.gif" alt="Faculty of Mathematics" style="width:300px;height:50px;margin:10px;"></img>
-<img src="https://static.igem.org/mediawiki/2010/f/fc/DeptOfBioLogo.png" alt="Department of Biology"></img>
+<img src="http://www.math.uwaterloo.ca/templates/pp/wordmark/math.gif" alt="Faculty of Mathematics" style="width:300px;height:50px;margin:10px;"></img>
-<img src=""></img>
+<img src="https://static.igem.org/mediawiki/2009/9/97/UWiGEMMEF.png" alt="Mathematics Endowment Fund" style="width:300px;height:100px; margin:10px;"></img>
-<img src="https://static.igem.org/mediawiki/2010/9/9e/WEEFLogo.png" alt="WEEF"></img>
+<img src="https://static.igem.org/mediawiki/2010/9/97/SandfordFlemingFoundation.png" alt="SFF" width="150" height="150" style="margin:10px;"></img><br/>
-<img src=""></img>
+<img src="https://static.igem.org/mediawiki/2011/b/b8/FSF_Waterloo.png" alt="FSF" width=150 height=100 style="margin:10px;"></img>
-<img src="https://static.igem.org/mediawiki/2010/9/97/SandfordFlemingFoundation.png" alt="SFF"></img>
+<img src="https://static.igem.org/mediawiki/2011/8/8c/UWaterlooChem-logo.gif" alt="Department of Chemistry" width="20%" height="20%" style="margin:10px;"></img><br/>
+<img src="https://static.igem.org/mediawiki/2010/9/9e/WEEFLogo.png" alt="WEEF" width="100" height="75" style="margin:10px;"></img>
+<img src="https://static.igem.org/mediawiki/2011/1/1f/BBI-LOGO_as_of_Jan_2011.jpg" width="100" height="75" style="margin:10px;"></img></div>
 </div>
                     </div>
@@ Line 219: / Line 221: @@
 <br><h3 style="color:#0077be">1.0 INTRODUCTION</h3>
 <p>
-This design provides a reasonable basis to implement in vivo applications involving RNA level regulatory sequences such as recombination sites. Since recombination sites can interrupt the functional production of a protein, the incorporated ribozyme portions can remove them before the translation phase of gene expression. Functional synthetic antibodies and plants capable of producing domain-shuffled Cry toxins are possible applications. This experimental investigation is a novel tool for producing a wide variety of these compounds with a supplementary regulation step.
+This design provides a reasonable basis to implement in vivo applications involving RNA level regulatory sequences. The fusion proteins produced surpass strictly what is coded in the DNA. As a result of incorporating ribozyme segments in between two halves of the protein coded in the DNA construct, a regulatory sequence (such as a recombination site) could be included. Since recombination sites can interrupt the functional production of a protein if translated fully (resulting in excess amino acids in the polypeptide), the incorporated ribozyme portions remove them before the translation phase of gene expression so that a functional protein is produced. For example, Cry proteins, which account for the insecticidal activity (toxicity) of <i>Bacillus thuringiensis</i>, could be the fusion protein produced for a particular insecticide. Using our experimental design, the sequence containing the code for the Cry protein (at the DNA stage) is split by ribozyme segments containing a recombination site. In this case, the recombination site is the regulatory sequence that will be removed once transcribed into RNA. At the DNA level, recombination (shuffling) will occur, exchanging DNA strand segments. Therefore, when the shuffled DNA sequence is transcribed into RNA, the recombination site is spliced out of the sequence with the ribozymes, and the resulting RNA code is different than that of the un-shuffled code. Consequently, the translated Cry protein is different. This system would oppose pesticide resistance among the target organism.
 </p>
 <br><h4 style="color:#0077be">1.1 A Little Bit About Group 1 Introns</h4>
 <p>
-All group I introns in bacteria have presently been shown to self-splice (with few exceptions) and maintain a conserved secondary structure comprised of a paired element which uses a guanosine (GMP, GDP or GTP) cofactor. Conversely, only a small portion of group II introns have been verified as ribozymes (they are not related to group I introns) and generally have too many regulators to easily work with. It is mainly the structural similarity of these introns that designates them to group II. We will mainly be working with group I introns, such as the phage twort.ORF143.
+All group I introns in bacteria have presently been shown to self-splice (with few exceptions) and maintain a conserved secondary structure comprised of a paired element which uses a guanosine (GMP, GDP or GTP) cofactor. Conversely, only a small portion of group II introns have been verified as ribozymes (they are not related to group I introns) and generally have too many regulators to easily work with. It is mainly the structural similarity of these introns that designates them to group II. We will mainly be working with group I introns, such as the <i>Staphylococcus</i> phage twort.ORF143.
 </p>
 <br><p> Group I introns contain a conserved core region consisting of two helical domains (P4–P6 and P3–P7). Recent studies have demonstrated that the elements required for catalysis are mostly in the P3 to P7 domain. They are ribozymes that consecutively catalyze two trans-esterification reactions that remove themselves from the precursor RNA and ligate the flanking exons. They consist of a universally conserved core region and subgroup-specific peripheral regions, which are not essential for catalysis but are known to cause a reduction in catalytic efficiency if removed. To compensate for this, a high concentration of magnesium ions, spermidine or other chemicals that stabilize RNA structures can be added. Thus, the peripheral regions likely stabilize the structure of the conserved core region, which is essential for catalysis.
@@ Line 232: / Line 234: @@
 The secondary structures, such as P6, formed by group I introns facilitates base pairing between the 5' end of the intron and the 3' end of the exon, as well as generates an internal guide sequence. Additionally, there is a pocket produced to encourage binding of the Guanosine cofactor. The Guanine nucleotide is placed on the first nucleotide of the intron. The 3'OH of Guanosine group nucleophilically attacks and cleaves the bond between the last nucleotide of the first exon and the first nucleotide of the 5' end of the intron; concurrently, trans-esterification occurs between the 3'OH and the 5'phosphorous from the 5' end of the intron. Subsequent conformational rearrangements ensure that the 3'OH of the first exon is placed in proximity of the 3' splice site. In this way, further trans-esterification reactions and splicing occurs.</br>
-<br><img src="https://static.igem.org/mediawiki/2011/e/e7/Transester.png"></img></br>
+<br/><div style="width: 350 px; font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/e/e7/Transester.png" width = "350" height "350" style="padding-bottom:0.5em;" /><br/><i>Retreived June 21, 2011 from Self-Splicing RNAs</i> [1] This diagram shows the trans-esterification reaction and splicing of group I introns from a sequence.</div>
 <br><h4 style="color:#0077be">1.3 Fusion Proteins</h4>
@@ Line 254: / Line 256: @@
 </p>
-<br><img src="https://static.igem.org/mediawiki/2011/thumb/f/f4/Figure1.png/500px-Figure1.png"></img></br>
+<br/><div style="width: 350 px; font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/1/18/Figure2UWigem2011.png" width = "700" height "250" style="padding-bottom:0.5em;" /><br/><b>Figure 2</b> shows the experimental design of the sequence immediately following transcription. It contains a constituent promoter, RBS Ribosome Binding Site), GFP1, IN1, in-frame stop codon, IN2, GFP2 and TT. The dotted lines and scissors indicate that the introns will be spliced out of the sequence at these points, however, the introns are self-excising.</div><br/>
-<br><img src="https://static.igem.org/mediawiki/2011/thumb/b/bc/Figure2.png/500px-Figure2.png"></img></br>
+<br/><div style="width: 350 px; font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/thumb/b/bc/Figure2.png/500px-Figure2.png" width = "600" height "350" style="padding-bottom:0.5em;" /><br/><b>Figure 3</b> is a representative view of the sequence folding in order to catalyze the trans-esterification reaction, however, there are many hairpin loops actually formed. This is the process of post-transcriptional modification. Specifically, Group I intron splicing events utilize a guanosine nucleotide to bind another sequence and dislodge the 5' site, then the cleavage initializes another splicing event with the remaining hydroxyl end to dislodge the rest of the RNA sequence and ligate the remaining exons. The remaining fusion protein code is different than that of the primary transcript.</div><br/>
+<br/><div style="width: 350 px; font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/8/89/Posctrlwat.png" width = "600" height "350" style="padding-bottom:0.5em;" /><br/><b>Figure 4</b> shows a non-disruptive ligation scar and active GFP after the self-excision of IN1 and IN2. This is the modified RNA transcript prior to translation..</div><br/>
 <br><h4 style="color:#0077be">2.2 CONSTRUCTION MAPs AND RFC 53</h4>
-As per RFC 53 convention, enzyme digestions are followed in the particular order outlined below. The standard procedure makes this technique reproducible, therefore, more easily extrapolated to other applications. Compared to other protein fusion methods, this design facilitates additional regulation within necessary guidelines. However, the embedded post-transcriptional modification in this design is a complication to consider in simpler designs where regulation at this level is not necessary. As such, unnecessary bulk in plasmid vectors is known to add to metabolic load.
+As per RFC 53 convention, enzyme digestions are followed in the particular order outlined below. The standard procedure makes this technique reproducible, therefore, more easily extrapolated to other applications. Compared to other protein fusion methods, this design facilitates additional regulation within necessary guidelines. However, the embedded post-transcriptional modification in this design is a complication to consider in simpler designs where regulation at this level is not necessary. As such, unnecessary bulk in plasmid vectors is known to add to metabolic load and decrease replication rate compared to non-plasmid carriers.
-<br><h5 style="color:#0077be">	2.2.1 General Construction Map</h5>
+<br/><h5 style="color:#0077be">	2.2.1 General Construction Map</h5>
 <br><p>
-The following figure graphically shows the laboratory procedure for the experimental design in the form of an enzyme map:
+<b>Figure 5</b> graphically shows the laboratory procedure for the experimental design in the form of an enzyme map:
 </p>
-<br><img src="https://static.igem.org/mediawiki/2011/b/b2/Enzyme_map1.jpg"></img></br>
+<br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/b/b2/Enzyme_map1.jpg"></img></div></br>
 <li><b>K576005</b> contains the first component of GFP (GFP1)</li>
@@ Line 275: / Line 280: @@
 <li><b>K576007</b> contains GFP1 and IN1</li>
 <li><b>K576009</b> contains GFP1, IN1 and lox1</li>
-<li><b><K576011></b> contains the promoter (P), ribosomal binding site (RBS), GFP1, IN1, lox site, IN2, GFP2 and transcriptional terminator (TT). This is the final construct (experimental design).</li>
+<li><b>K576011</b> contains the promoter (P), ribosomal binding sit (RBS), GFP1, IN1, lox site, IN2, GFP2 and transcriptional terminator (TT). This is the final construct (experimental design)</li>
@@ Line 283: / Line 288: @@
 <p>Controls are necessary to prove that the design of this experimental investigation is functional and more practically for comparison of fluorescence in the laboratory. In the positive control, GFP1 and GFP2 flank either RFC25 or RFC53, which will not disrupt translation regardless of the linker. Therefore, fluorescence is expected. The experimental run will ideally show fluorescence resulting from the self-excision of IN1 and IN2.</p>
-<br><img src="https://static.igem.org/mediawiki/2011/thumb/c/c4/Figure5a.png/430px-Figure5a.png"></img></br>
+<br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/thumb/c/c4/Figure5a.png/430px-Figure5a.png" ></img></br>
+<b>Figure 6</b> represents the positive control. For consistency, GFP1 and GFP2 are separated by RFC53 (RFC25 could have also be used), which should not disrupt expression of a functional GFP.</div><br>
-<br><p>In the negative control (using the same constitutive promoter), GFP1 and GFP2, followed by a transcriptional terminator, flank RFC10 (Request For Comments) resulting in a stop-codon-containing scar. No fluorescence is expected for this component (background) because translation is interrupted. This is meant to control for the possibility of a non functional fusion protein. The expectation is that this fusion of GFP1 and GFP2 will not fluoresce, which is a consequence of some fusion protein techniques. Figure 6 shown below details the negative control design:</p></br>
+<br><p>In the negative control (using the same constitutive promoter), GFP1 and GFP2, followed by a transcriptional terminator, flank RFC10 (Request For Comments) resulting in a stop-codon-containing scar. No fluorescence is expected for this component (background) because translation is interrupted. This is meant to control for the possibility of a non functional fusion protein. The expectation is that this fusion of GFP1 and GFP2 will not fluoresce, which is a consequence of some fusion protein techniques. Figure 7 shown below details the negative control design:</p></br>
-<br><img src="https://static.igem.org/mediawiki/2011/thumb/2/2a/Figure4.png/560px-Figure4.png"></img></br>
+<br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/thumb/2/2a/Figure4.png/560px-Figure4.png"></img></br>
+<b>Figure 7</b> is an illustration of the negative control containing the interrupted GFP with an in-frame stop codon, ensuring that it is not expressed. Since this sequence contains no excision sites (Group I introns), we do not expect any modification to this area of the RNA.</div><br>
 <p><br>The figure below shows the construction map for the controls.</br>
-<br><img src="https://static.igem.org/mediawiki/2011/0/08/Enzyme_map3.jpg"></img></br>
+<br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/0/08/Enzyme_map3.jpg"></img></div></br>
 <li><b>K576005</b> contains the first component of GFP (GFP1)</li>
@@ Line 307: / Line 313: @@
 <br><h3  style="color:#0077be">2.3 MAKING THE CONSTRUCT WITH RFC 53</h3>
-<p><br><img src="https://static.igem.org/mediawiki/2011/thumb/2/2f/53.png/500px-53.png"></img></br>
+<p><br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/thumb/2/2f/53.png/500px-53.png"></img></br>
+<b>Figure 9:</b> Making the Construct: Parts were sequenced into PUC57, digested and ligated into PSB1C3.</div><br />
-<br>
+<b>Figure 9</b> is a flow chart of the general work flow involved in the construction of our experimental plasmid, as per RFC53 conventions.<br><br>
 <ol>
 <li>1) The insert is isolated through a series of enzyme digestions. One intron (in blue) is shown here as a representation. The insert is isolated for subsequent ligation.</li>
@@ Line 323: / Line 329: @@
 Although completion of a preliminary version of the final construct was achieved, lack of GFP fluorescence proved suspicion of questionable band placements during second and third stage electrophoresis. Final diagnostic digestion reaction confirmed abnormalities from designed constructs. Testing via digestion was completed for every intermediate, control and final constructs. Consequently, BBa_K576003, K576004, K576005, and K576006 were the only parts able to be confirmed. All the other intermediates and constructs have questionable band location which disrupted final construct fluorescence.
-<p><br><img src="https://static.igem.org/mediawiki/2011/thumb/4/46/Gel916113.jpg/500px-Gel916113.jpg"></img></br>
+<p><br><div style="font-size:90%; text-align:center;"><img src="https://static.igem.org/mediawiki/2011/a/a5/Figure10UWigem2011.png"></img></br>
+<b>Figure 10:</b> shows the diagnostic digestion from September 16, 2011: All subclones shown to be correct, however, positive control not correct. Relative placement of GFPs and INTS required further verification and showed incorrect placement. This accounts for lack of fluorescence in final stage.</div><br>
 <br><p>
 The above electrophoresis picture describes the resultant bands from the diagnostic digestion. Although bands 5, 6 and 7 (sub clones) have been confirmed, the adjacent positive control (band 8) and all GFP and intron digestions are not consistent with the expected patterns. The GFP-INT and GFP-INT-lox constructions (bands 9, 10 and 11) have been verified as inaccurate. The questionable placements of these bands indicate that the cut sites, thus the fragment length and containing sequence, do not match the planned construction. Therefore, it is not likely that they contain functional GFP, introns or lox, which would result in a lack of fluorescence in the final stage of construction. Further testing to reconstruct the contaminated clones is necessary for the functional final product; however, lab work has stopped due to time constraint. A diagnostic digestion at each step is recommended to circumvent any similar issues upon the continuation of this project.
@@ Line 333: / Line 339: @@
 <br><p>
 The biggest advantage of the ribozyme project is the ability to create in vivo protein fusions. These can then be applied to a larger number of modular systems that can be used to make complicated expression systems. One such system is the creation synthetic antibodies. If protein sequences are flanked by intron sequences and then set up along the same stretch of DNA, different combinations of fusion proteins will be created based on how the intron excision occurs. Another system where the ribozyme project can be applied is DNA shuffling experiments. The Cry toxin is used as an effective biopesticide, however for now it has a very small range of insects that it effects. The ways to increase its range would be to change the structure of one of the vital domains so that it is able to recognize a wider spectrum of receptors in the host mid gut cell. To create different variations of this domains an in vivo DNA shuffling experiments using the ribozymes could be carried out.
-<br>
+<br><br />
+<h3 style="color:#0077be">4.0 REFERENCES</h3><br />
-<br/><h3 style="color:#0077be">4.0 REFERENCES</h3>
   Belfort,M., Cech, T., Celander, D., Chandry, P., Heuer, T. (1991). Folding of group I introns from bacteriophage T4 involves internalization of the catalytic core. Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado. 88(24): 11105–11109.
 <br /><br />
@@ Line 374: / Line 379: @@
                              <div class="innerContent">
-<h3 style="color:#0077be">1.0 INTRODUCTION</h3>
+<h3 style="color:#0077be">Motivation and Goals</h3>
-<p>Since the Staphiscope project aims to detect S. aureus at low concentrations, it's important to determine how sensitive the system will be so that it can be adjusted to detect S. aureus at clinically-relevant concentrations. A detector that triggers at too low a concentration may display false positives, while one that triggers at too high a concentration may not give a positive when it should. To achieve the best sensitivity, numerical characterization for the Cambridge's 2009 sensitivity tuners needs to be obtained <i>independent of the promoter used</i>, in order to be combined with models for the AIP detection system and yield a predictive numerical model for Staphiscope. Work toward these ends is ongoing.</p><br>
+<p>This year’s modelling project focused on extending the work done by the modelling team in 2010.</p><br>
+<p>Waterloo’s 2010 iGEM project, "Staphiscope", utilized amplifier parts developed by Cambridge in 2009 to detect low levels of Staph Aureus. These amplifier parts were characterized by the Cambridge team, but only under control of AraC/pBAD promoter, which differed from the promoter used in our 2010 Staphiscope project.</p><br>
-<h3 style="color:#0077be">2.0 BACKGROUND</h3><p>
+<p>In order to characterize the amplifiers, a parameter scan was undertaken to find promoter-independent Hill parameters of each amplifier, consistent with data of full system. However, empirical verification of our results was lacking. This year, we sought to obtain this data, which (in conjunction with Cambridge data and model), would allow us to find Hill parameters for each amplifier.
-The sensitivity of Staphiscope may depend on various factors. For now, analysis has been restricted to just one factor: the choice of part used for the amplifier component of the system. The amplifier will be chosen from one of the 15 amplifiers submitted to the parts registry by Cambridge in 2009. Each amplifier responds uniquely to a given input signal, differing from the others with respect to its activation threshold (amoung a few other parameters less crucial to our analysis). Our goal is to determine which amplifier has an activation threshold in the correct range for the detection of S. aureus in relevant concentrations.</p><br><p>
+</p><br>
+<h3 style="color:#0077be">Model</h3><p>
+<p>To allow for comparison of data, we used the same model as <a href="https://2009.igem.org/Team:Cambridge/Modelling">Cambridge in 2009</a>.</p><br>
-Empirical characterization of the response curves of each amplifier was carried out by Cambridge. However, in Cambridge's system the amplifiers were under control of the the pBAD promoter, which is not the case in Staphiscope. Therefore, the data gathered by Cambridge is not directly applicable to our system, since in general the response curve of each amplifier will be different under different promoters.</p>
+<p>In this model, araC represses the pBAD promoter in the absence of the inducer, arabinose. When arabinose is present, it binds to araC, preventing repression of the promoter and allowing transcription of reporter (GFP). This situation is modelled by a Hill function; we seek the Hill parameters of this function.</p><br>
-<br><p>
-To obtain a numerical characterization of each amplifier, independent of promoter choice, we are undertaking the task of "reverse engineering" Cambridge's data to extract the parameters describing the amplifiers. A more detailed explanation of our approach first requires a description of the mathematical models relevant to this system.
+<p>Thus, when AraC/pBAD system is induced with arabinose, we expect to see a steady increase of fluorescence from a low level, followed by a plateau of fluorescence at steady state.
+</p><br>
+<h3 style="color:#0077be">Method</h3><p>To measure fluorescence, we closely followed the assay described in the paper <a href="http://www.jbioleng.org/content/3/1/4">"Measuring the activity of BioBrick promoters using an in vivo reference standard"</a>, in the section "Assay of Promoter Collections".</p><br>
+<p>Three cultures were grown overnight at 37 degrees Celsius with spinning at 200 rpm: untransformed BW27783, BW27783 containing BBa_I0500, and BW27783 containing BBa_I20260. These were then diluted 1:100 and regrown for roughly 4 hours under the same conditions. They were then diluted to an OD between 0.05 and 0.09, and regrown for 1 hour, again under the same conditions.</p><br>
+<p>After this, the cultures were diluted into a 96-well plate at 8 different concentrations of inducer (arabinose), ranging from 0 to 6.4 uM. The plate was then incubated in a Wallac Victor3 multi-well fluorimeter at 37 degrees Celsius, and repeating measurements of absorbance and fluorescence were taken at 10 minute intervals, with shaking after each measurement. Untransformed BW27783, at each concentration of arabinose, was used to measure background fluorescence, and wells containing only broth were included to measure background absorbance. The machine settings used were identical to those described in the paper referenced above.</p><br>
+<p>With this data, we aimed to calculate the steady-state per-cell GFP concentration during log-phase growth, for both BBa_I0500 and BBa_I20260 (measurement kit for the standard promoter, J23101). The ratio of these values would then characterize the strength of the AraC/pBAD promoter in units of RPU. The justification for this approach can be found in the supplemental material of the paper referenced above.
 </p>
 <br>
-<h3 style="color:#0077be">3.0 SYSTEM MODEL</h3><p>
+<h3 style="color:#0077be">Results</h3><p>
-The parts characterized by Cambridge consist of a detector (the pBAD/AraC promoter) and one of the fifteen amplifiers. To obtain a mathematical description of the entire system, Cambridge used the following equations to describe the input/output response of these individual components.</p>
+The results of the experiment were anomalous, and considered too unreliable to be conclusive. There was no clear relationship between cell fluorescence and inducer concentration.</p><br>
-<br><p>
+<p>The fluorescence curve did not qualitatively match the predictions of the model; across all concentrations, and for each of the 3 cultures, we observed a high initial fluorescence, with a rapid drop to a lower steady state value. For each culture, this drop in fluorescence aligned well with the growth curve.</p><br>
-<img src="https://static.igem.org/mediawiki/2010/8/8d/Waterloo2010Modelling_Table1.PNG" alt="Table of equations.">
+<p>In addition, the untransformed BW27783 cells exhibited consistently higher fluorescence than cells containing BBa_I0500, which was highly anomalous. Because of this, we could not reliably use these cells to measure background fluorescence.</p><br>
-</p><br><p>
+<p>Below, a sample graph of Total Fluorescence is shown for each of the 3 cultures. These are curves of the total fluorescence for each culture, averaged over 3 replicates for each culture.
-The <a href="https://2009.igem.org/Team:Cambridge/Modelling">Cambridge 2009 modelling page</a> develops these equations in more detail.</p>
+<br><img src="https://static.igem.org/mediawiki/2011/thumb/3/31/UW_2011_Raw_Fluorescence.png/800px-UW_2011_Raw_Fluorescence.png">
-<p>
+</p>
-When these individual component models are strung together, the resulting model of the entire system has a sigmoidal shape. This means the response curve for the entire system can be fit to a Hill function, which is of the form
+<br>
-<img src="https://static.igem.org/mediawiki/2010/b/b2/Hillfunction.gif" alt="(general hill function equation)">.</p><br><p>
+<h3 style="color:#0077be">Discussion</h3><p>It is believed that an error in our strain of BW27783 is most likely responsible for the anomalous qualitative features of our data. This is because for each concentration of inducer, the untransformed BW27783 cells exhibit a fluorescence curve highly similar to that of BW27783 containing BBa_I0500, and yet the untransformed cells should not be expressing GFP.</p><br>
+<p>Prior to the measurement assay, BW27783 cells transformed with BBa_I0500 were plated and examined for fluorescence, both with and without the presence of inducer. The uninduced cells were not found to fluoresce, while the induced cells did fluoresce. The fluorescing cultures were used to make the frozen stock of BBa_I0500 which was used in the measurement assay. This indicates that our untransformed BW27783 should not fluoresce without the presence of inducer. Furthermore, the untransformed BW27783 cells used in the measurement assay were at no point prior to the assay exposed to arabinose.</p><br>
-Note that 4 parameters are required to specify the response curve: increase in rate, basal rate, switch point, and Hill coefficient. These parameters need to be determined empirically, with the exception of the Hill coefficient, which we assume is equal to 2.
+<p>To explain the fluorescence of the untransformed BW27783 in the measurement assay, it is speculated that our strain of BW27783 exhibits a rapid production of GFP in response to even low concentrations of inducer. Experimental error is also a likely source of inaccuracy in the data, although the qualitative features described were consistent across 3 trials of the experiment. Research into these results is still ongoing.
-</p><br><p>
-The detector and amplifier also each have the form of a Hill function, but of course each has its own set of parameters which will differ from the Hill parameters of the overall system.
 </p><br>
-<h3 style="color:#0077be">4.0 EXTRACTING DATA</h3><p>
-Ultimately we seek a numerical characterization of the amplifier part alone. Since we know its response curve has the form of a Hill function, we need only find its four Hill parameters. The following table summarizes the known and desired data.</p>
-<br><p>
-<img src="https://static.igem.org/mediawiki/2010/8/81/Waterloo2010Modelling_Table2.PNG" alt="List of parameters.">
-</p><br><p>
-If all the parameters other than the amplifier parameters are known, the model above together with the response curves of the amplifiers is enough information to extract the desired parameters. Explicitly solving the equations above for the amplifier parameters is difficult; instead, MATLAB's curve fitting toolbox will be used to find the parameters which, when combined with the known parameters and inserted into the equations for Cambridge's overall system, matches the empirical data obtained by Cambridge. This process must be repeated for each of the 15 amplifiers.
-</p><br><p>
-Unfortunately, not all the necessary parameters are known. Some were not measured by Cambridge (those in block 1), but can be found in the literature. However, the Hill parameters for the pBAD/AraC promoter are not known, and must be measured. To do this, an experiment is being designed to characterize this promoter in RPU, but has not yet been carried out.</p>
 </div>
 </div>
              <div id="acmid2sub3" class="aContentMidSub">
 <div class="innerContent">
+<h2 style="color:#0077be">University of Waterloo: iGEM OUTREACH</h2><br />
+The purpose of UW iGEM Outreach has always been and will continue to be the connection between our community and us. To help build a better understanding of synthetic biology, how it has affected the world around us and to create a basic, fundamental knowledge of the subject that can be incorporated into the way we see things. That perspective can be positive or negative, but we aim to provide the baseline knowledge required that will allow our community members to form a fact-based opinion.<br/><br/>
-</div>
+This year, UW iGEM: Outreach focused on designing and running workshops targeted at schoolchildren. We hoped to share our love and passion for biology with tomorrow's future scientists and engineers. We plan to continue building on what we currently have and to eventually develop a complete syllabus for all grade levels. These workshops will be available for download for other educators and enthusiasts interested in their own outreach.<br/><br/>
-            </div>
-            <div id="acmid2sub4" class="aContentMidSub">
-              <div class="innerContent">
-<h3 style="color:#0077be">INTRODUCTION</h3>
-<br><p>
-As synthetic biology expands, as new innovations are made, and pressing world problems are solved, the potential impact synthetic biology will have on the world becomes more evident. Although a primary goal of developers of synthetic biology should be to consider the ethical, societal, safety, environmental, and political impact of the science, we believe that interest should also be paid unto the impact that synthetic biology will have in the business world.
-</p>
-<br><p><b>
-As a group we are most interested in the course of development of synthetic biology in industry; the goal of our project is to try and decipher the path that synthetic biology will forge as it expands in the business world.
-</b></p>
-<br><p>
-Our attempt to answer this question has begun with a comprehensive inquiry into important factors affecting the diffusion of synthetic biology. It is our opinion that before we attempt to make any conclusive statements about the future direction of synthetic biology or the economy as a whole we must have a complete picture of the current landscape of synthetic biology and the markets it could potentially impact.
-</p>
-<br><p>
-This inquiry is intended for use by multiple audiences; particularly scientists and members of business in relevant industries. As scientists it is important to understand the context in which discoveries are made, understanding where world needs lie and how discoveries will impact the world makes for better-informed scientists. Members of the business world should also strive to have an understanding of where the need and rationale for discoveries come from. Although profit is the ultimate endgame a well-informed approach helps to prevent ethical pitfalls and often greater success.
-</p>
-<br><p>
-This analysis looks at both extrinsic and intrinsic factors relating to the development of synthetic biology as a whole. In particular intrinsic factors such as the development of synthetic biology in specific industries (biofuels, pharmaceuticals, and bioremediation) is examined in depth. Important extrinsic factors such as the impact of patenting and open source are also analyzed. With this information we feel we have laid the foundations for a comprehensive inquiry that will allow us to better understand what the expansion of synthetic biology in the business world will resemble.
-</p>
+<h3 style="color:#0077be">Workshop Materials</h3><br/>
+<br/>
+We have submitted two community bricks! One for our Grade 12 workshop and the other for our Engineering Science Quest activity for Grades 3-4. The downloadable material is the same as what you can find here on our wiki page. <br/>
+             -Synthetic Biology and You: <a href="http://openwetware.org/wiki/IGEM_Outreach:Synthetic_Biology_and_You_Interactive_Workshop_%28Gr._11-12%29">Interactive Workshop for Grades 11-12</a><br/>
+             -All About Bacteria: <a href="http://openwetware.org/wiki/IGEM_Outreach:All_About_Bacteria:_How_Clean_Are_Your_Hands%3F">How Clean Are Your Hands?</a><br>
-<br><h3 style="color:#0077be">OPEN SOURCING and Synthetic Biology</h3>
+<br/>
-<br><h4  style="color:#0077be">What is Open Sourcing?</h4>
+<strong>Grades 3-4: All About Bacteria</strong> - <a href="https://static.igem.org/mediawiki/2011/3/36/Grades_3-4_-_All_About_Bacteria.pdf">Outline</a> | <a href="https://static.igem.org/mediawiki/2011/3/3d/Grades_3-4_-_All_About_Bacteria_%28Handout%29.pdf">Handout</a> <em>(Duration: 2-day workshop, 1.5 hours total)</em><br/>
-<br><p>
-What differentiates synthetic biology from biotechnology is that it offers the creation of systems or pathways that would not be found naturally in an organism. Synthetic biologists believe in a standardized system of parts similar to that of electrical engineers having standard circuits and components<sup>1</sup>. This is also similar to how LINUX modules have been combined to create different software. This contrasts the closed-parts strategy where developers use such methods as patent protection and secrecy to gain a competitive advantage over others<sup>2</sup>.
-That is why the Massachusetts Institute of Technology (MIT) has created the initiative for what is known as the “Registry of Standard Biological Parts” where it indexes biological parts that are currently being built. A standard array of modular gene switches or parts that can be found from a common library and can be mixed and matched in various combinations, which is the goal that synthetic biology targets. This is a similar path as what happened twenty years ago when software became standardized and allowed Microsoft to become a monopoly. The issue in the air currently is if this could happen with the synthetic biology industry<sup>3</sup>.
-</p>
-<br><h4 style="color:#0077be">Advantages</h4>
+<Strong>Grades 5-6: All About DNA</strong> - <a href="https://static.igem.org/mediawiki/2011/d/da/Grades_5-6_-_All_About_DNA.pdf">Outline</a> <em>(Duration: 1 hour)</em><br/>
-<br><p>
-Open-sourcing has been an idea that has been the basic foundation of synthetic biology throughout the years. Supporters strongly believe in a world where companies and academia will be able to develop and share parts freely for the advancement of the whole field, not just a singular firm or university<sup>4</sup>.
-</p>
-<br><p>
-A term that is used commonly in this industry is called network effects. This means that the more a product is used, the more attractive it becomes. Over time as each part is used repeatedly on a specific metabolic pathway, especially when in successive experiments, its cost goes down. With the limited data that is available, it is predicted that total project costs could be cut down by 25% after its first successive use. It is also likely that these costs would be cut down several more times until it flattens as with each subsequent experiment more knowledge on that part is gained and intuitively, less errors are made.
-</p>
-<br><p>
-One such example is with Amyris’ artemisinin project that spanned over the length of five years, costing $20 million. It was reported that 95% of the time spent was on finding and fixing unintended interactions between parts.
-</p>
-<br><p>
-Due to the fact that one part must be used in conjunction with other sets of parts gives incentive to companies to create whole libraries. This is very similar to how software companies develop several programs that are able to cover multiple applications. Not only that, but there is opportunity for these companies to make profit by patenting some of these parts and making others openly available due to the strong modularity of the open-parts approach.
-</p>
-<br><p>
-It is expected that companies will have their own individual parts needs. This means that other companies cannot just sit around and wait for another to develop a part. This also gives a type of competitive advantage as companies that share parts will not be losing their, ‘technological edge’ to other competitors. Since different companies have idiosyncratic needs and hence expertise, it proposes that community-based libraries will outperform individual companies. The industry will probably have a large number of small, distinctive customers, meaning that patent licensing will be less attractive and the open-parts initiative more so<sup>5</sup>.
-</p>
-<br><p>
-Normally, the value of a patent depends on the inventor’s initial R&D investment, but with synthetic biology parts it would depend on that as well as how many researchers have subsequently used that part. According to the law, this allows patent owners to capture both sources of value, which can be unfair to society as they must deal with high prices without getting anything more in return. The open-parts initiative sets the price of parts equal to zero, so it is naturally able to solve that problem. There are two incentives that will draw companies to an open-parts initiative. The first would be the opportunity to share R&D investments among multiple firms and secondly the opportunity to produce parts faster due to shared insights<sup>6</sup>.
-</p>
-<br><h4 style="color:#0077be">Barriers and Disadvantages</h4>
+<strong>Grade 12: Synthetic Biology and You</strong> - <a href="https://static.igem.org/mediawiki/2011/b/b4/Waterloo_iGem_Outreach_Materials_for_Download.zip">Materials</a> | <a href="https://static.igem.org/mediawiki/2011/c/cb/SynBio%2C_Biotech_and_You_Part_1.zip">Ppt (part 1)</a> | <a href="https://static.igem.org/mediawiki/2011/1/12/SynBio%2C_Biotech_and_You_Part_2.zip">Ppt (part 2)</a> <em>(Duration: 2-3 hours)</em>
-<br><p>
+<br /><br />
-About twenty years ago when software became standardized, it opened the path for Microsoft to come in, take over the industry and monopolize it. Can something similar potentially happen in the synthetic biology industry? At the moment, synthetic biology is what is called a ‘tipping market’. It is unstable and prone to monopoly. Building on this, the tipping dynamic is indifferent to whether or not the dominant parts constellation is open or closed. If for instance a mature industry is able to grab a hold of these shared parts, it can work towards this open-parts initiative. Though on the other hand, companies, out of necessity will also pay for closed parts, both solutions are equally viable.
+Are you interested in doing any of these activities with kids around this age? Feel free to use any of our materials above and/or contact us at uwigem.outreach.hp@gmail.com. It is an inexpensive, interactive and fun way to have kids involved in genetics, microbiology and synthetic biology at a very early age. And definitely a lot of fun!<br /><br />
-</p>
-<br><p>
-Some other issues include an agreement on standard nomenclature for the parts, therefore when actually designing a database, controversies might come up. As well when collaboration occurs there must be adequate legal infrastructure. This must include a license specifying the rights and duties of members. One of the main legal problems is that gene data is unlike software, it cannot be copyrighted.
-</p>
-<br><p>
-Many pessimists towards the idea say that it is now too late for synthetic biology to use an open-parts collaboration. Now with Amyris’ advancement in the field it seems that this industry might monopolize and follow the path that Microsoft had. The fact that commercial synthetic biology receives so much government support shows a bit of laissez faire attitude. In America’s Department of Energy $350 million biofuel initiative there was no open-parts requirement at all. It is said that at least when Bill Gates cornered the software market he did it with private money<sup>7</sup>.
-</p>
-<br>
+<h3 style="color:#0077be">Events</h3><br/>
-<br>
+We were also fortunate enough this year to have been given the opportunity to run our workshops at two different outreach events, both of which were on a grand  scale. Now, we'd like to share our experiences with you.<br /><br />
-<sup>1</sup>
+<h3 style="color:#0077be">Grade 12 Outreach Workshop: March 25th, 2011</h3><br />
-<a href:"http://heinonline.org/HOL/LandingPage?collection=journals&handle=hein.journals/tlr85&div=50&id=&page">
+The first was an organized Grade 12 workshop aimed at biology students to gain a better understanding of synthetic biology, the industries it has been affecting, career prospects as well as two hands-on activities. Over the planning span of 3 months, this event was organized in close accordance with the Kitchener-Waterloo school board and with the Marketing and Recruitment Co-ordinator for Science at the University of Waterloo. Through the creation of a brochure and meeting with individuals from the school board we had sent out an invitation all across the district for students to come in for our event. Eventually we had gotten more than 85 students to attend, which was great as it was the first time we had implemented this idea. <br /><br />
-http://heinonline.org/HOL/LandingPage?collection=journals&handle=hein.journals/tlr85&div=50&id=&page
+ The next step had then been to recruit interested volunteers for the event so we could have our own students give a helping hand and who shared the same passion of sharing knowledge as we did. In order to facilitate this we had sent out emails, gone to various lectures and talked to students all over campus to get them involved. After recruiting 12 volunteers the brainstorming process had begun. We had wanted to have an interactive workshop where students were not just listening to us talk, but were actually involved in a stimulating activity that they could be excited about.
-</a>
+The first part of our presentation looked into what was synthetic biology, what were Genetically Modified Organisms (GMOs) and what were the positives and negatives of them. Once that was through we started the first event.
-<br/>
+ The first event we had was to talk about our very own Canadian genetically enhanced Yorkshire pig called the EnviroPig™. It has the capability to digest plant phosphate more efficiently than traditional Yorkshire pigs, which do not contain the enzyme to break it down, phytase. This gene can be found in E.coli which had been inserted into a pig embryo to allow it to produce phytase in its salivary glands. This is a real technology in Canada and is currently a very hot topic of debate among many citizens, so we thought it would be ideal to introduce students to the world of biotechnology right in their very own backyards. Once students had been exposed to the information, we had given them a package which we had compiled giving the positives and negatives of societal, technological, ethical, environmental and economical issues. <br /><br />
-<sup>2,3,4,6,7</sup>
+  Of course, it did not end there! Students were then put into groups of 5 and as mentioned above, one of the key goals of UW iGEM Outreach is to allow members of our community to make informed decisions based on facts. Supplied with markers and paper students were to give a 1-2 minute presentation on why they did/did not believe that the EnviroPig™ should continue receiving funding from the government of Canada. The best and most convincing presentation won- we had great discussions from the negative aspects to positive aspects to even a compiled rap song about the EnviroPig™! <br /><br />
-<a href:"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726678/ ">
-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726678/
-</a>
-<br/>
-<sup>5</sup>
-<a href:"http://www.nature.com/msb/journal/v3/n1/full/msb4100161.html">
-http://www.nature.com/msb/journal/v3/n1/full/msb4100161.html
-</a>
-<br>
+<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2011/e/e5/Watout1.png" width="350" height="270"><img src="https://static.igem.org/mediawiki/2011/d/d6/Outreach2.png" width="350" height="270"><br/><br/></div>
-<br/><h3 style="color:#0077be">PATENTS and Synthetic Biology</h3>
-<br/><p>
-The ideological reasoning behind applying for a patent lies in the fundamental incentive that it would bring forth financial rewards and a sense of monopolistic supremacy in an advancing market. The imposition of patenting technology has been deemed useful in many industries, most notably in electronics. However, it has also brought forth a considerable level of controversial dialogue in determining how historical protocols can be implemented within new technological streams that sometimes question the concept of man-made invention. For example, Craig Venter’s desire in protecting his synthetic cell research methodology gives him a deserving ownership, but his broad patent places a downgrading threat towards the field of synthetic biology. Ironically speaking, patenting is a legal practice that promotes innovation, but imposes a sense of apprehension for those who wish to adapt towards a more open-sourced strategy. This analysis focuses on the implications of introducing patent law to the field of synthetic biology as well as the practicality of gaining rights to a product not developed entirely by man, but with elements  arising from nature.
-</p>
-<br/><h4 style="color:#0077be">Monopolizing Synthetic Biology</h4>
+After the first event we continued on with our presentation. Here we discussed current industries that had been affected by synthetic biology. This incorporated the pharmaceutical and biofuels industries specifically. We discussed how pharmaceuticals had incorporated an aspect known as biosynthesis where they could customize and fine-tune certain pathways using standardized parts in order to provide efficient and precise drug delivery systems. In biofuels we talked about first and second generation biofuels and how the use of synthetic biology has the ability to create a ‘superbug’ to look for corresponding metabolic pathways for yielding ideal results. After this we did the second activity. <br /><br />
-<br/><p>
+The second event that had been implemented was to incorporate what we do in our labs, outside of the lab. Essentially, we wanted to introduce the idea of synthetic biology to students and how it was an extension of what we knew as genetic engineering and consisted of students not just from science but from math, engineering and computer science. The activity called, ‘Design Your Own Pathway’ gave a series of scenarios we had given students with a library of BioBricks to create a certain pathway. Progressively each scenario was harder, more complicated and required the use of multiple BioBricks. The BioBricks that we had used were from the library and were real parts. Essentially this was to enable students to have a feel of how we have a ‘mix and match’ concept when it comes to synthetic biology. The activity had been set up as a relay race, where students in the same teams as the previous activity had to race each other to finish all scenarios. The activity and concept had been such a success that after the workshop teachers had asked to use our activity in their own classrooms.
-The accrued financial and proprietary benefit of monopolizing an idea within a competitive market is indeed an accelerated advantage when a patent is granted. However, many have the misconception that monopolistic proprietorship has a standardized value to any industry it is applied to. For years, Professor John Sulston from the University of Manchester, a believer in promoting an open-source environment in the field of synthetic biology has proposed the implications that would arise should Venter receive approval upon his protocol in developing synthetic organisms.  Sulston states,
+<br /><br />
-</p>
-<br/><p><i>
-"I hope very much these patents won't be accepted because they would bring
-<br/>genetic engineering under the control of the J Craig Venter Institute (JCVI). They would
-<br/>have a monopoly on a whole range of techniques (BBC UK, 2010)."
-</i></p>
-<br><p>
+  <div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2011/9/98/Watout3.png" width="350" height="270"><img src="https://static.igem.org/mediawiki/2011/7/7c/Watout4.png" width="350" height="270"><br/><br/></div>
-The irony in this matter is that the technological industry used the concept of monopolistic competition to drive both innovation and the development of products that would eventually overpower the market leaders. The reason that this concept cannot presently be applied is that synthetic biology is strongly reliant on collaborative construction. Patenting biological parts or processes will not motivate a group of scientists to pursue their research, but cause them to weigh the opportunity costs between their groundbreaking research and the hefty payments they would make to patent holders.
-</p>
-<br><p>
-In the case of Venter’s claim, organizations such as the ETC group believe that Venter’s group is eyeing on a profit making opportunity. Hope Shands of the ETC group states, “The fledgling synthetic biology industry keeps talking about how they’re going to fix climate change – but these sweeping patent claims reveal that the companies are much more focused on securing profits than on human needs” (ETC Group, 2007). The multi-purpose use of a biological methodology would not only give Venter ownership to a scientific methodology, but to a range of applications that could be possible in the chemical, medicinal or environmental industries. Venter reported to Business Week, “If we made an organism that produced fuel that could be the first billion- or trillion-dollar organism. We would definitely patent that whole process” (ETC Group,2007). Many would dispute that this financial and market acquisition would only de-motivate other synthetic biology scientists and facilities to halt their research. But from looking at it from Venter’s perspective, wouldn’t anyone want to reap the rewards on a project that took 15 years and 40 million dollars to reach its success?
-</p>
-<br>
+Finally, we completed the presentation with a discussion of career paths that students could pursue that did not necessarily involve working in a lab. We wanted students to understand that the world of synthetic biology and biotechnology encompasses the involvement of individuals from multiple backgrounds and can penetrate into many different industries. <br /><br />
-<br><h4 style="color:#0077be">Patenting Artificial Life: Is synthetic biology a man-made industry?</h4>
+There was such an interest in our workshop that our prospects for the next one are aimed at more than 150 students. One thing’s for sure, mission accomplished and there’s definitely more to come!
-<p>
+Would you also like to have your own workshop at your high school or university? Please feel free to view the downloadable materials for the presentation and two activities or contact us at uwigem.outreach.hp@gmail.com. <br/><br/>
-As previously noted, synthetic biology encapsulates the field of biotechnology, software and computing. The current patent laws that have been put in place have generally been applicable to all industries individually. However, the field of synthetic biology is an amalgamation of two fields that have faced years of controversial debate in terms of granting or approving patents. The concern lied in the fact that patents related to inventions in biotechnology or software could be broad or narrow, but extensive enough to “hold-up” the concept of innovation and invention (Rai and Boyle, 2007 ).
-</p>
-<br><p>
-Synthetic biology is being renowned as a stream towards the development of artificial life, which for some raises social, ethical and legal concerns. Patent Act 101 states that any subject matter that is found in nature is not deemed as patentable. However, if the product found in nature is modified or transformed to something that is novel and non-obvious, it holds credibility in attaining a patent. Looking at the synthetic cell created by Venter’s team, it is difficult to denote the “man-made” material in his composition. His cell includes a computer generated “minimal genome sequence” that is encapsulated within a bacterial cell (found in nature) and still hosts cellular machinery required to allow the cell to adapt and function within its environment. The modification is within the genome, but even that raises some debate on whether it can be patentable.
-</p>
-<br><p>
-The software industry has always tackled with patenting mathematical and computational algorithms, particularly in concern was their level of broadness. In perspective to the field of synthetic biology, an algorithm is analogous to the creation of novel and modified genetic sequences, which give rise to new metabolic pathways and cellular functionalities. Yet again, the derivation of their new genetic sequence comes from the naturally degenerate genetic code, bringing up the question of whether this is entirely man-made. What is seen here is a disconnect, in that it would be difficult to set  fundamental patenting protocols for the field of synthetic biology, given the legal complications faced in both the field of biology and computing. This is where many may agree that an open-source strategy such as the MIT Registry of Standard Biological Parts would bring forth more progression, versus the time and effort it would take to validate the patentability of a biological part or process.
-</p>
-<br><h4 style="color:#0077be">SWOT Analysis</h4>
-<br><p>
-Below are other indicators to help define the relative benefit of introducing patent law, as well as the long-term threats that may hinder the advancement of research in the field of synthetic biology.
-</p>
-<br><p>
-<b>Strengths</b>
-<br>
-<br>1.Patenting assists in stimulating investment, and secured investments bring forth progression in research. Given that research projects can cost up to hundreds of millions of dollars, patenting synthetic biology technologies would provide a more steady approach in financing the development of an invention.
-<br><br>2.Developers are motivated by reward, which is provided by the successful implementation of patent law
-</p>
-<br><p>
+<br /><br />
-<b>Weaknesses</b>
+<h3 style="color:#0077be">Engineering Science Quest: July-August 2011</h3>
+Founded in 1990, the Engineering Science Quest or ESQ is a not-for-profit program that operates with the goal of exposing children in the Kitchener-Waterloo region to the world of engineering, science and technology through engaging them in a variety of hands-on activities. Promotion is primarily done through workshops in-school but also have satellite programs which reach out to rural and Native communities as well.<br /><br />
+This is not the first time that UW iGEM has been involved in ESQ and we are proud to say that our continued involvement has allowed us to develop a standard set of activities which we are pleased to present to kids ranging from Grades 3-6 with more than 100 students. Currently we are also developing ideas for older kids that are similar to our activities from the Outreach workshop we had in March for Grades 10-12 and for even younger kids from Grades 1-2. Through involvement with managers specifically for ESQ this year we were able to have continual workshops every week from July 11th- August 12th, 2011. This was done with the recruitment of volunteers who again shared the same passion as we did in connecting with our community to facilitate that baseline knowledge; to get students introduced or even extend their knowledge on the world of synthetic biology and biotechnology.<br /><br />
+  The first activity for Grades 3-4 was called, “All About Bacteria: Do You Really Need to Wash Your Hands?” In this activity we introduce kids to the idea of biology, bacteria, synthetic biology, and iGEM. We also introduce them to basic ideas of sanitary techniques and tools used in a standard lab such as petri plates, agar, swabs etc. and how to layout an experiment; what is your hypothesis, results and conclusions? Once we discuss these basic concepts we allow the kids to take a swab of their hand and plate it on half of a petri dish. They then clean their hands with sanitizer and swab the other half of the petri dish. They then receive another petri dish where they can swab other places to find other ‘neat’ bacteria that may be lying around on the floor, counters, door knobs or wherever else they want (except up their nose, in their eyes, ears or mouth!). At this point and throughout the activity, interaction with the kids is key, as they always have stories or thoughts and experiences that are enlightening to share- even to us university students. <br /><br />
+<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2011/1/1c/Watout5.png" width="350" height="270"><img src="https://static.igem.org/mediawiki/2011/2/25/Watout6.png" width="350" height="270"><br/><br/></div>
+ Once we explain what incubation is, we allow kids to come in the next day and see all the different types of bacteria that may have grown on their petri plates and come up with conclusions from the results they have seen. We provide them with a record sheet where they are able to write down what they saw such as; morphology, colour, its surface and even elevation. To be able to interact with kids at such a young age and to introduce them to concepts which students are normally exposed to in higher grades, allows them to explore a part of their world that they never knew existed. Building curiosity at a basal level helps us connect with our community and bridge the gap towards making more informed decisions.
+<br /><br />
+The second activity for Grades 5-6 was called, “DNA Extraction from Your Cheeks”. This activity centers around the idea of DNA, where it is found, what it looks like and how every living organism contains very similar genomes, proteins and enzymes. There were four steps to this process, first to collect cheek cells, second to burst cells open to release DNA, third to separate DNA from proteins and debris and finally isolate the concentrated DNA. Kids obtain a cup of Gatorade containing a saline solution and swish the drink in their mouth for about a minute while gently chewing on their cheek cells. Then detergent is added to the test tube and meat tenderizer is added and the tube is inverted gently a couple of times. Cold rubbing alcohol is then added with a pipette which should allow the DNA to be visible. Then kids   transfer the DNA into a PCR tube where they can hang it on a string to make a really neat necklace. <br /><br />
+<div style="text-align: center;"><img src="https://static.igem.org/mediawiki/2011/6/6c/Watout7.png" width="350" height="270"><img src="https://static.igem.org/mediawiki/2011/2/2c/Watout8.png" width="350" height="270"><br/><br/></div>
+Kids were keen and interested in these activities, especially learning about various different concepts that they had not yet been exposed to. “Who knew that DNA could come out of your own cheeks?” was the idea we wanted to pass along- that every living organism contains DNA. From bacteria to animals.
+<br /><br />
+Are you interested in doing these activities with kids around this age? Feel free to contact us at uwigem.outreach.hp@gmail.com. It is an inexpensive, interactive and fun way to have kids involved in genetics, microbiology and synthetic biology at a very early age.
+<br /><br />
+</div>
+            </div>
+            <div id="acmid2sub4" class="aContentMidSub">
+              <div class="innerContent">
+<h2 style="color:#0077be">Introduction</h2><br>
+Synthetic Biology has been perceived as a field of science that has introduced tools, concepts and technologies which are sometimes sociologically and ethically insupportable. The non-scientific community has developed a stigma against the application of various synthetic biology technologies. The problem does not lie within the technology, but by an institution’s poorly executed strategy in educating the prospective end user about the relative benefit of its product. At times, the rate of technological advancements in the bioengineering industry surpasses the end-user’s ability to understand the necessity of the technology.<br><br>
+The science behind these synthetic biology tools has been the current driver in instilling a sense of appeal and intrigue within the scientific community. However, it is critical that the institutions that develop these technologies educate the non-scientific community of the importance and benefit of these tools to help relieve these evolving stigmas.<br><br>
+This year, the University of Waterloo’s Human Practices team’s focus was to develop a marketing strategy for their 2010 design project, the Staphiscope. The Staphiscope is an enhancement to the existing conventional plating methods that are used to detect Methicillin Resistant Staphylococus Aureus.<br><br>
+<b>The scope of the analysis includes:</b><br><br>.
+<li>What is the selling point of the product? What differentiates the Staphiscope from what already exists and is accepted by the non-scientific community?</li>
+<li>Does the concept of competition exist within synthetic biology? If so, how does an institution market the Staphiscope to optimize their opportunities for growth?</li>
+<li>How can the marketing strategy approach be differentiated to ensure that both the scientific and non-scientific community are exposed to the relative benefits of the Staphiscope?</li>
+<li>How do we channels the knowledge and learnings acquired within the synthetic biology industry and channel it to other stakeholders that will prospectively be impacted by the technology?</li><br>
+The purpose of the analysis is to ensure that the scientific industry understands the importance of bridging the scientific theory of a product to its economic feasibility. Moreover, it encourages institutions who participate in developing synthetic biology technologies to align their perception of a revolutionary design to what will be socially acknowledged by a non-scientific community.<br><br>
+<h3>What is the Staphiscope?</h3><br>
+Methicilin resistant Staphylococcus aureus (MRSA) are bacteria whose presence has been quite problematic in terms of human pathogenic infections. Since its discovery in the 1880s, Staphylococcus aureus has been the known cause for several kinds of minor skin, and major post-surgical infections. Prior to 1940, mortality rates in relation to this pathogenic organism reached 80% (Deurenberg and Stobberingh, 2008.) The first wave of resistant S. aureus came two years after the introduction of penicillin for medicinal practice in 1940. In less than twenty years, most of the S. aureus strains known to man were unaffected by the antibiotic. In the late 1950s, a penicillinase-resistant penicillin was brought forth to the medicinal market; this was methicilin (Deurenberg and Stobberingh, 2008.) The bacterium's subsequent resistance to methicilin came two years after its introduction in 1959. The mecA gene responsible for methicillin resistance is also to blame for the organisms’ desensitization to several classes of antibiotics (Deurenberg and Stobberingh, 2008). This has led to the creation of the term: MRSA, now commonly used worldwide.<br><br>
+While an MRSA infection is much like a S. aureus infection, the difference comes in the lack of sensitivity of the MRSA to several classes of antibiotics. This makes MRSA infections a serious threat in both health and economical aspects.<br><br>
+The infection could be easily transferred directly (through regular skin-to-skin contact), as well as indirectly (through contamination of surfaces). The ease with which infection could occur, as well as the high mortality rate involved with the infection, make MRSA a serious threat to the health of patients worldwide (Durai et al., 2010.)
+There are only a few methods, which currently exit for MRSA screening. These are plating, liquid-broth inoculation, and PCR (polymerase chain reaction) assays. While these will be discussed in further detail later on in the report, it is important to note that these methods could be costly and time consuming, and could sometimes present incorrect results (Durai et al., 2010.)<br><br>
+In 2010, the International Genetically Engineered team at the university of Waterloo had been working on a method which can be used in supplement to the already-existing ones for the detection of MRSA infections. It is a proof of concept for diagnosing the presence of Staphylococcus aureus in an infection site before it has had the chance to create an infection. This synthetic biology–based diagnostic method will take advantage of the quorum sensing mechanism of Staphylococcus aureus, and utilize Escherichia coli as the sensor and reporter.
+ For more information with regards to the Design of the Staphiscope please see the University of Waterloo’s 2010 iGEM Page: <a href="https://2010.igem.org/Team:Waterloo">https://2010.igem.org/Team:Waterloo</a><br><br>
+<h3>Who are the “Competitors”?</h3><br>
+Treatment of an S. aureus infection is of extreme importance, as outcomes can range from simple pustules to death. Early detection and treatment of S. aureus carriers can reduce healthcare costs and greatly improve the health of the patient. There are only a few methods currently available to hospitals for the diagnosis of S. aureus infection. These methods are time consuming, expensive and, in some cases, not very reliable.
+The purpose of the Staphiscope is to provide the option of accelerating the method of detecting S. aureus, without compromising reliability. It will be a particularly useful tool in speeding up the conventional methods of serial plating.<br><br>
+The following section analyzes the current products on the market and compares them to the Staphiscope.<br><br>
+<h4>BD GeneOhm StaphSR</h4><br>
+<div style="text-align:center;"><img src="https://static.igem.org/mediawiki/2011/b/b1/Sectionanalysis_uw2011.png"></img></div><br>
+ Traditional culture methods for the detection of S. aureus are usually 2-3 days. The new BD GeneOhm™ StaphSR delivers a diagnosis in less than 2 hours, using rapid real-time PCR. Also, it can simultaneously detect and differentiate Methicillin-Resistant S. aureus and S. aureus from a positive result (blood culture). Currently under development are additional specimen claims – nasal and wound samples. Nasal claim will be able to determine colonization status and the wound claim will add to the rapid identification of positively infected patients. Obtaining positive results in a timely fashion aids clinicians in the prevention and control of infections.
+<br><br>
+<h3>Method</h3><br>
+Specimen is prepared by transferring an aliquot of positive blood culture into a buffer team and then vortexed at high speed.<br><br>
+Cell suspension is lysed (via vortex and centrifuge) and heated. Then the lysis is cooled.
+Molecular reagents are reconstituted and the sample undergoes PCR.
+Results are obtained in about 1 hour.
+<br><br>
+<h3>References</h3><br>
+"BD - GeneOhm - Products." BD: Medical Supplies, Devices and Technology; Laboratory Products; Antibodies. BD, 2011. Web. 23 July 2011. <a href="http://www.bd.com/geneohm/english/products/idi_staphsr.asp"><http://www.bd.com/geneohm/english/products/idi_staphsr.asp>.</a><br><br>
+<h3>GenoType MRSA</h3>
+Genotype MRSA uses DNA Strip Technology to identify both S. aureus and S. epidermidis cultures. Therefore, coagulase-positive and coagulase-negative staphylococci are differentiated. Simultaenously, the product can also detect Methicillin-Resistant S. aureus and S. aureus , which is incredibly important for therapeutic purposes. The test is performed from an overnight culture and guarantees results in only 4 hours.<br><br>
+<h3>Method</h3> <br><br>
+Culture is isolated from a sample or a primary culture is used.<br>
+DNA is extracted via methods producing amplifiable DNA from bacteria (for example     QIAamp DNA Mini Kit from Qiagen).<br>
+Nucleic acids are selectively replicated in an amplification reaction. In the next step, the amplicons are chemically denatured, since detection on the DNA•STRIP® is done using single-stranded DNA.
+During the conjugate reaction, the specifically bound amplicon is marked with the enzyme alkaline phosphatase and is then made visible in a colorimetric detection reaction.
+In this way, a specific banding pattern develops on the DNA•STRIP®. Using a test-specific evaluation template, the test result can be read out quickly and clearly.
+<h3>References</h3><br>
+"GenoType® MRSA | Identification of MRSA from Cultured Material." Hain Lifescience | Ihr Partner in Der Modernen Labordiagnostik. Hain Lifescience, 2011. Web. 23 July 2011. <a href="http://www.hain-lifescience.de/en/products/microbiology/mrsa/genotype-mrsa.html"<http://www.hain-lifescience.de/en/products/microbiology/mrsa/genotype-mrsa.html>.</a><br><br>
+"DNA•STRIP® Technology." Hain Lifescience | Ihr Partner in Der Modernen Labordiagnostik. Hain Lifescience, 2011. Web. 23 July 2011. <a href="http://www.hain-lifescience.de/en/technologies/dnastrip.html"><http://www.hain-lifescience.de/en/technologies/dnastrip.html>.</a><br><br>
+<h3>Brilliance Agar</h3><br>
+<div><img src="https://static.igem.org/mediawiki/2011/9/93/Brillianceagar_uw2011.png"></img></div><br>
+ Brilliance Agar is a chromogenic screening plate used for the diagnosis of Methicillin-Resistant S. aureus. It uses a novel chromogen to show a blue colour when Methicillin-Resistant S. aureus phosphatase activity. For sensitivity, it contains antibacterial compounds which inhibit growth of various competitor bacteria. This product has high sensitivity and specificity, which minimizes healthcare costs. However, results are presumptive and would need to be confirmed. Organisms with atypical resistance can give false negative results.<br><br>
+<h3>Method</h3><br>
+Patient is inoculated using a screening swab or an isolated colony or liquid suspension is used.
+Sample is plated on Brilliance Agar. Plates are incubated at 37 ºC.
+Results are obtained in 18 hours. Methicillin-Resistant S. aureus grows as denim blue colonies.<br><br>
+<h3>References</h3><br>
+"Brilliance MRSA AGAR." Oxoid - Worldclass Manufacturer of Dehydrated Culture Media and Diagnostics Products. Oxoid, 2010. Web. 23 July 2011. <a href="http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=PO1162"><http://www.oxoid.com/UK/blue/prod_detail/prod_detail.asp?pr=PO1162>.</a><br><br>
+<h4>Competitive Analysis Matrix</h4><br><br>
+<div style="text-align:center;"><img src="https://static.igem.org/mediawiki/2011/3/39/Matrix2_UW2011.png"></img></div>
+<br><br>
+<h4>Rating Scale</h4>
 <br>
-<br>1.The field of synthetic biology is different in the sense that innovation is not promoted through attaining proprietary rights to an entire process or genome, but through the collaborative use of fine, functional and specific biological parts
+<div style="text-align:center;"><img src="https://static.igem.org/mediawiki/2011/a/a8/Matrix_UW2011.png"></img></div>
-<br><br>2.Synthetic biology is multidisciplinary as it incorporates the field of biotechnology and computing, each has their own sets of legal rights, restrictions, and pitfalls
-<br><br>3.In addition, lawyers would require a more extensive level of knowledge and proficiency in both fields
-<br><br>4.Sometimes, hundreds of parts are necessary for the composition of one biological machine, and attaining rights to each part would create what is called to be a "patent thicket" (Rutz, 2009). Attaining rights to so many parts does not only hinder innovation, but is time-consuming and costly
-</p>
-<br><p>
+<br><br>
-<b>Opportunities</b>
+<h3>Methodology for Rating Scale</h3><br>
-<br><br>1.Patents add value, reputation and credibility to an invention. Although this legal concept is frowned upon in the R&D field, it brings a source of financial opportunity that would bring forth strategic partnerships and lump some funding to further progress research. At an economic perspective, patenting would be useful in advancing one's research.
+The Competitive Analysis Matrix uses a format that divides the product’s market profile into several categories, providing a framework that ensures all issues are considered.  Each category is scored in the course of the ratings process (using a numerical scoring system). Products are scored 1 through 27; those facing greater competitive threats would wind up with an overall low market profile score. Please note that ratings represent, in the end, an opinion. Please note, thorough assessment of each product’s market profile requires a broader framework, involving a comprehensive review of the product’s competitive position.<br><br>
-<br><br>2.Patenting requires thorough documentation and characterization of each aspect of the part, streamlined patenting protocols could add standardization to the part development process
+<h3>Conclusions</h3><br>
-</p>
+Based on a comparison and competitive analysis of the Staphiscope and the three major detection products on the market, the Staphiscope was found to have the highest market profile score. It uniquely scored highest in reliability and ease of use. Although all products on the market signify great innovation in the field, Staphiscope has great potential to gain market share.<br><br>
+<div style="text-align:center"><img src="https://static.igem.org/mediawiki/2011/d/dd/Staphimarketanalysis_uw2011.png"></img></div><br>
+ <div style="text-align:center; font-size:90%;">Porter’s Five Forces analysis</div><br><br>
+<h3>Marketing Strategy</h3><br>
+Pitching the Staphiscope to a Research and Development Company
+When pitching the Staphiscope to the R&D industry, it is of paramount importance to establish its competitive advantage over traditional methods for S. aureus detection. To have a competitive advantage, a product or company must excel in at least one of the three following categories while remaining equal to its competitors in the others (Szarka, 2010):<br><br>
+<li>Market access</li>
+<li>Infrastructure</li>
+<li>Technology</li><br>
+Market access refers to how easily the target demographic can get the product. Even a revolutionary technology can be hampered by a lack of market access. Infrastructure is related to whether or not a supply chain exists, as well as facilities for production and distribution. The third point, technology, is where the Staphiscope excels; its superior technology is what will separate it from competitors. Other selling points of the Staphiscope include its speed, efficiency, and room for expansion (could this technique be applied to other cases?). Conversely, there are also barriers that must be overcome when pitching to the R&D industry; namely, one must avoid falling prey to “not invented here” syndrome (Szarka, 2010). This term applies to the mindset some companies have of only trusting in-house innovation, and can be difficult to alter. Other barriers include the lacking of Staphiscope use on a commercial scale, and public perception regarding E. coli. While the latter issue can be combated via a public awareness campaign, the former is simply a fact of any innovative technology.<br>
+Companies such as Amyris Biotechnologies and Codon Devices have attempted to commercialize in the field of synthetic biology. Their experiences provide valuable lessons that can applied to the Staphiscope (Wilan, 2005). The most relevant of these is that patent protection should be a serious concern when developing a novel technology, especially in such a burgeoning and competitive field. Consolidating IP ownership and control early is equally important, as doing so will prevent a lack of unified vision from stalling the Staphiscope’s progress. Of course, there are a plethora of patent and IP issues surrounding the field of synthetic biology that must be dealt with before or during the commercialization process. Chief amongst these is the scope of protection that can be provided to new technologies (Chugh  Sakushyma, 2009). Additionally, looking for a pharmaceutical partner can help ease the transition into commercialization.<br>
+It is important to realize that commercialization is a multi-year effort. As such, it can be beneficial to develop a commercialization plan (Office of Technology Transfer). This plan gives a general outline of what information the R&D industry will be looking for when it comes time to make a pitch. Details about market size and growth rates, predicted sales figures for the first five years, licensing agreements and more can all prove invaluable when attempting to bring a product to market.  Preparedness in regards to this information can make the difference between a successful pitch and an unsuccessful one.<br>
+In summary, pitching the Staphiscope to the R&D industry is a complex process that must be handled correctly to ensure its successful commercialization.<br><br>
+<h3>References</h3><br>
+Office of Technology Transfer. Argonne National Laboratory. “Commercialization Plan Worksheet”. <a href="http://www.anl.gov/techtransfer/pdf/LicensingQuestionaire1-0.pdf">http://www.anl.gov/techtransfer/pdf/LicensingQuestionaire1-0.pdf</a><br><br>
+Wilan, K.H. Nature Publishing Group. 2005. “Commercializing synthetic biology”. <a href="http://www.nature.com/bioent/startup/072005/full/bioent870.html">http://www.nature.com/bioent/startup/072005/full/bioent870.html</a><br><br>
+Chugh, A., Saukshyma, T. 2009. “Commercializing synthetic biology: Socio-ethical concerns and challenges under intellectual property regime”. <a href="http://stopogm.net/webfm_send/315">http://stopogm.net/webfm_send/315</a><br><br>
+Szarka, M. “Adventures in Commercialization”. 2010. <a href="http://webcast.utm.utoronto.ca/1/watch/515.aspx">http://webcast.utm.utoronto.ca/1/watch/515.aspx</a><br><br>
+<h3>How Do We Achieve Public Acceptance?</h3><br>
+For years, it has been believed that the prevalence of MRSA infections has resided within the walls of either a hospital or health care facility. Due to understated hygienic practices, a modified and relatively more virulent strain of Staphylococcus Aureus has also threatened several community based settings. In addition to Hospital Acquired MRSA, general health practitioners must also take into account the occurrence of community acquired MRSA.
+It is important to educate the public about the applications and relative benefit of the Staphiscope. Thus, there needs to be a channel of communication that allows for a transfer of knowledge between the scientific and non-scientific community. <br><br>
+<h3>Who Do We Want To Educate?</h3><br>
+Given that MRSA may not only be spread within a hospital but also within the community, there are quite a few demographics that would gain value in understanding the benefit of the Staphiscope.<br><br>
+<h3>Hospital Setting</h3><br>
+At least 2% of patients in hospitals or health-care facilities are likely to carry a strain of Staphylococcus Aureus that is resistant to antibiotics such as Methicillin. The following individuals are susceptible in contracting an MRSA infection: <br><br>
+<li>Individuals who have weak immune systems</li>
+<li>People receiving kidney dialysis or cancer treatments</li>
+<li>Individuals who have been hospitalized or have had surgery over the past year</li><br>
+<h3>MRSA within the Community</h3> <br><br>
+Patients who are discharged may have an inactive form of MRSA that remains colonized in their system. Thus, those who live within the community are still at risk of acquiring and suffering from antibiotic resistant Staph infections that are relatively more virulent. MRSA has been detected and acquired by healthy people in both institutionalized and individual based settings. The following individuals are susceptible in contracting MRSA in the community:<br><br>
+<li>Day-care facilities or facilities in which equipment of personal items are shared</li>
+<li>Military bases</li>
+<li>Individuals who get tattoos</li><br><br>
+<h3>The Strategy</h3><br>
+In the field of synthetic biology, there is an unrecognized paradox that hinders the level of interdisciplinary communication between the scientific and non-scientific community. The stigmas built outside the realms of a scientific community grow at a greater rate than a scientist’s ability to answer the plethora of questions surrounding the regulation, safety and potentiality of these synthetic biology technologies.
+Another problem lies in a scientific institution’s inclination to address the ethical concerns surrounding their synthetic biology technology or process. Generally an individual who has not be previously exposed to the field, will construct an ethical judgement proceeding the phase where a company is about to commercialize their product. At this critical stage of a company’s product plan, stakeholders are reluctant in addressing these ethical concerns as it may discourage their ability to advance and innovate their existing technology.
+Regardless of the threats that these ethical judgments have previously imposed, there is a necessity in developing an approach in which the end result is an internationally renowned sense of public acceptance and support.
+“Without public support and understanding of research into synthetic biology, both funding and regulation are unlikely to support significant scientific advances” (Gaisser, et. al, 2009).
+To address this issue, an expert committee in Europe supported by the New and Emerging Science and Technology programme set out a roadmap that outlines the four interconnected attributes that will instil a sense of public acceptance within the non-scientific community. These four attributes are:<br><br>
+<li>Scientific Milestones</li>
+<li>Knowledge Transfer</li>
+<li>Funding</li>
+<li>Regulation</li><br><br>
+This roadmap outlines that without the implementation of a knowledge transfer strategy, there is limited confidence attaining in achievements under the other three key areas of the model. Scientific milestones would not be achievable without a sustained level of funding provided through other groups impacted by the prospective commercialization of these synthetic biology tools. Moreover, regulation of synthetic biology tools is influenced by the ethically themed perceptions created by both the scientific and non-scientific community.<br>
+The knowledge transfer strategy would be an interdisciplinary model that would impact the following stakeholders:<br><br>
+<li>Natural and Social Scientists</li>
+<li>Engineers</li>
+<li>Industry Representatives</li>
+<li>Non-governmental organizations</li>
+<li>Non-scientific community (ie. hospital staff, hospital patients and members within institutionalized settings)</li>
+<li>Decision makers (ie. potential investors)</li>
+<li>Funding Agencies</li> <br><br>
+<h3>Knowledge Transfer Strategy</h3><br><br>
+In this context, knowledge transfer is the exchange of research knowledge between the institution producing the synthetic biology technology and their target end-user. The purpose of the knowledge transfer strategy is to develop a communication platform between all stakeholders to mitigate the unsourced perceptions, bias’ and stigmas against the field of synthetic biology. Moreover, it is better to develop an interdisciplinary team at the early stages of the technology development phases versus segregating the two communities until the technology is prospectively in its commercialization phase. <br><br>
+<h3>Method</h3><br>
+The following are examples of methods that can be used by the synthetic biology industry in promoting tools such as the Staphiscope to its potential end-users (ie. individuals within hospitals and community facilities)<br><br>
+<li>Development of an interdisciplinary network that consists of synthetic biologists, engineers, potential investors, and the general public</li>
+<li>Sustainable dialogue between all stakeholders within the interdisciplinary network. This can be achieved through:
+Workshops that aim in exchanging information to individuals that will benefit from the application of the Staphiscope in either a hospital or community based setting</li>
+<li>Educational materials that are specifically tailored to the different parties that could be impacted by the commercialization of the StaphiScope (ie. Hospital Microbiologists, Patients, and the General Public)</li>
+<li>Incorporating the General Public and other stakeholders at the research phase of the technology development process. This results in a mutual benefit to both the institution as well as the end-user in that they are able to collaboratively discuss the ethical feasibility of the technology.</li>
+<li>Use of knowledge broker- A knowledge broker is essentially an intermediary resource that assists in translating research knowledge to information that is comprehensible to a member that is not from the field of synthetic biology. An individual that has attained perceptions, knowledge and experiences from the scientific, business and social field is best suited to convey the importance of the Staphiscope to the stakeholders that have been listed above.</li><li>Partnerships between Synthetic Biology institutions and hospitals or other community based facilities.</li> <br><br>
-<br><p>
+Synthetic biologists must consider the importance of implementing an approach to help relieve the prospective stigmas that could potentially impact the relative success of their technology. The general public plays an influential role in the innovation capabilities of these synthetic biology technologies. Thus it is critical that these synthetic biology institutions involve the public and create awareness of their technologies at all stages of the research and development stage. Integrating a strategy that incorporates the exchange of knowledge  is a fundamental leverage that would help create an aura of public acceptance and support all dimensions of the synthetic biology roadmap.<br><br>
-<b>Threats</b>
-<br><br>1.European patent law states that "iventions of commercial exploitation to morality are omitted from patentable rights" (Rutz, 2009).  The general public fears that if rights to a biological process or part are give they may be abused.  Examples are biological warfare or the unintentional release of pathogenic organisms.
-<br><br>2."Patent sharks and trolls" (Rutz , 2009) may find it simple to file lawsuits against such patents. •On the other side of the coin, some have claimed that finding a patent application for a biological part is similar to finding a needle in a haystack. Moreover, it is not the job of a scientist to be rummaging around in identifying his legal rights to using a biological part, nor should his time be consumed by understanding the patenting process relevant to his field.
-</p>
-<br><h4 style="color:#0077be">Conclusion</h4>
+<h3>Human Practices Commercialization Toolkit</h3><br>
-<br><p>
-The concept of patenting makes scientists cringe at the thought that their research and advancements would be diminished by the monopolistic power held by the broad patent holders within synthetic biology. There is currently no established set of specific protocols for patenting products in synthetic biology. Moreover, the attempt to blend the patent laws applicable to a range of disciplines to one as intricate as synthetic biology is difficult. Additionally, companies who wish to have a formalized process in examining and submitting processes would have to understand that a large number of additional resources would be needed to accommodate for the labour intensive, time consuming and costly process of patenting such biological parts. So the underlying question is that what is of greater value in today’s market, leading innovation through open-source strategies or banking on profit-making opportunities by securing an idea with a patent?
-</p>
-<br><h3 style="color:#0077be">INDUSTRY ANALYSIS</h3>
+Following the Regional Jamboree, the Human Practices team began to develop the tools, templates and models that would assist a synthetic biology community and its associate stakeholders to understand the commercialization process. More importantly, our aim is to develop informational material that would achieve the integration of a knowledge transfer strategy in the field of synthetic biology. By streamlining the knowledge transfer strategy throughout each stage of the commercialization process, we are able to achieve a paralleled level of communication between the scientific and non-scientific community. Below is a sample of the toolkit our team has developed.<br><br>
-<br><p>
-Before we attempt to understand the impact of synthetic biology on the business world as a whole, we must first understand what kind of an impact it will have on specific sectors. The goal of the industry analysis was to pick specific industries that we felt would be heavily impacted by the emergence of synthetic biology and attempted to understand their current situation as well as opportunities and threats facing each industry.
-</p>
+<h4>The Commercialization Road Map</h4><br>
-<br><h4 style="color:#0077be">Biofuel Industry</h4>
+The University of Waterloo Human Practices Team has devised a commercialization road map specific to the field of synthetic biology. The purpose of this road map is to outline the different stages of the technology development process. More importantly, it indicates what initiatives must be completed at each stage, who needs to be involved, and the strategies that can be utilized to attain the intended end-goal; <b>A Scientific Milestone</b>. To view the road map please click the link below.<br>
-<br><p>
-The oil industry has become an integral part of the society we live in for, transportation, food, healthcare, and communication. However, there is a dire need for alternative sources of energy and the world is beginning to turn towards biofuels for support in this area. Although there is immense promise in this area there is also many challenges to overcome such as reliance on environmental factors and adequate feedstocks. Although emergence of biofuels created through synthetic biology does not have the market potential to shift the whole method of biofuel production, politicians are optimistic that it has the potential to make an impact and have therefore taken measures to support the infrastructure of its’ development. The emergence of a viable synthetic biology biofuel would serve to excel the development of synthetic biology, particularly on the business stage.
-</p>
-<br><h4 style="color:#0077be">Pharmaceutical Industry</h4>
+<a href="https://static.igem.org/mediawiki/2011/4/48/HP_Roadmap_Waterloo.pdf">Synthetic Biology Commercialization Roadmap</a> <br><br>
-<br><p>
-Our knowledge of diseases and treatments has advanced to an exciting point as has society’s perception of health problems and issues. However, as fast as our knowledge advances, diseases like H1N1 and HIV provide a pressure for the pharmaceutical industry to advance further and faster. In addition, aging populations and growing urban centres poise pharmaceutical companies for significant and meaningful innovation over the coming decades. The pharmaceutical industry is expected to grow to an $800 billion industry by 2011, expanding as a global force. Thus, synthetic biology, although faced with challenges in terms of legal and social concerns, is poised to have a significant impact on the pharmaceutical industry. Not only is there promise for curative treatments that would change how we view illnesses like HIV, there promises to be significant implications in the social, technological, and political realms. Unanswered questions about the handling of intellectual property issues will challenge the development of synthetic biology in the pharmaceutical industry as will ethical, safety, and political issues.
-</p>
-<br><h4 style="color:#0077be">Bio-remediation Industry</h4>
+<h4> The Knowledge Transfer Strategy Action Plan </h4><br>
-<br><p>
-Unlike other industries, bio-remediation is an industry that has incorporated the use of genetic engineering and synthetic biology since the 1970’s. Based on the research conducted, there is a definitive understanding that this field poses an optimistic approach in achieving results that are environmentally friendly and cost-effective. The major setback with the field of bio-remediation is the intricacy of the techniques that are involved. Aside from the general publics qualms about bio-remediation procedures, even the scientific community does not have a holistic understanding of how the processes within bio-remediation work, or how to optimize a microbe’s “oil-eating” activity based on its metabolic characteristics. Most say that bio-remediation is a cost effective technique in treating vast oil spills, but it seems that investors and economists have not incorporated the cost of time and labour required in mastering the techniques involved. Once these techniques have established, there is a definite opportunity for this field to overpower the current invasive chemical processes that are being used as a last desperate resort in treating these environmental disasters.
-</p>
-<br><p>
+The University of Waterloo Human Practices Team has devised a knowledge transfer strategy to help parallel the level of communication between the scientific and non-scientific community. This document outlines the strategies that are currently being used or proposed at the University of Waterloo but can be easily used on a wider scale by the entire iGEM community. To view the knowledge transfer strategy plan, please click the link below.<br>
-The project wiki contains a condensed overview of the industry analyses, if you are interested in learning more be sure to check out the complete industry analysis.
-</p>
-<br><h3 style="color:#0077be">Conclusions and Outlook</h3>
+<a href="https://static.igem.org/mediawiki/2011/4/48/KT_strategy_Waterloo.pdf">Knowledge Transfer Strategy </a><br><br>
-<br><p>
-After conducting this research into the current and future position of synthetic biology particularly in the context of the business world, we are optimistic about the course that it will take. There are significant hurdles to overcome but overall there is a sense that synthetic biology will impart a positive impact not only in terms of specific products but also in terms of micro and macroeconomic impact.
-</p>
-<br><p>
-In this inquiry we have attempted to understand some of the important issues facing synthetic biology from a business perspective. In the future we hope to take our work a step further; we hope to take our knowledge, thoughts, and questions into the business world. Through interaction with business owners, scientists, legal specialists, and other stakeholders we hope to disseminate our findings and build on them. In the future we will continue to focus on our goal of deciphering the path that synthetic biology will take as it emerges in the business world.
-</p>
-<br><h3 style="color:#0077be">References</h3>
-<p>
-<br>1)Rai A, Boyle J (2007) Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons. PLoS Biol 5(3): e58. doi:10.1371/journal.pbio.0050058
-<br><br>2)Barrett, Margaret. Intellectual Property. 2nd ed. New York: Aspen Online, 2008. 33-34
-<br><br>3)Dickinson, Boonsri. "Will Patents Give Craig Venter a Monopoly over Synthetic Life? - SmartPlanet." SmartPlanet - We Make You Smarter - People, Business & Technology. 28 May 2010. Web. 26 Oct. 2010. <http://www.smartplanet.com/technology/blog/science-scope/will-patents-give-craig-venter-a-monopoly-over-synthetic-life/1949/>.
-<br><br>4)"Artificial Life: Patent Pending | The Economist." The Economist - World News, Politics, Economics, Business & Finance. 14 June 2007. Web. 26 Oct. 2010. <http://www.economist.com/node/9333408?story_id=9333408>.
-<br><br>5)"Postnote: Synthetic Biology." Parliamentary Office of Science and Technology, Jan. 2008. Web. <http://www.parliament.uk/documents/post/postpn298.pdf>.
-<br><br>6)Rutz, Berthold. "Synthetic Biology and Patents : A European Perspective." Nature Publishing Group : Science Journals, Jobs, and Information. 2009. Web. 26 Oct. 2010. <http://www.nature.com/embor/journal/v10/n1s/full/embor2009131.html>.
-<br><br>7)Joachim, Henkel, and Maurer Stephen. "The Economics of Synthetic Biology." Molecular Systems Biology. Nature Publishing Group, 5 June 2007. Web. 26 Oct. 2010. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1911203/>.
-<br><br>8)Ghosh, Pallab. "BBC News - Synthetic Life Patents 'damaging'" BBC - Homepage. 24 May 2010. Web. 26 Oct. 2010. <http://www.bbc.co.uk/news/10150685>.
-<br><br>9)Ball, Philip. "Biology News: The Patent Threat to Designer Biology." BioEd Online. 22 June 2007. Web. 26 Oct. 2010. <http://www.bioedonline.org/news/news.cfm?art=3404>.
-<br><br>10)ETC Group. "Extreme Monopoly: Venter's Team Makes Vast Patent Grab on Synthetic Genomes | ETC Group." 8 Dec. 2007. Web. 26 Oct. 2010. <http://www.etcgroup.org/en/node/665>.
-<br><br>11)Hammond, John, and Robert Gunderman. "The Limited Monopoly- Patent Law 101: What Is Patentable?" The Rochester Journal, June-July 2007. Web. 25 Oct. 2010. <http://www.patenteducation.com/images/200706_Limited_Monopoly_-_35_USC_101.pdf>.
-</p>
-<br>
-<br>
+<h4>Conclusion</h4><br>
+The purpose of this analysis was to understand the relative feasibility of a synthetic biology tool from the perceptions of a scientific and non-scientific community. When devising a marketing strategy, most companies define a technology’s commercial success by its appeal towards investors or its ability to enter a market heavily saturated by other established technologies. Given that most synthetic biology institutions are still at their preliminary phases in terms of commercialization, it is critical that their product is widely accepted and acknowledged by all disciplines that are impacted or will be potentially exposed to the technology.<br>
+In the future we hope to take our research and methodologies and present them to the stakeholders discussed within the analysis.  Our next steps are to identify institutions and facilities that would benefit from the use of the knowledge transfer strategy and develop sample activities or educational materials that can be used by these facilities to promote the Staphiscope. <br><br>
+<h3>References </h3><br>
+A.D.A.M Health Solutions. "Methicillin-resistant Staphylococcus Aureus; Community-acquired MRSA (CA-MRSA); Hospital-acquired MRSA (HA-MRSA)." National Center for Biotechnology Information. 9 June 2011. Web. <a href="http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0004520/"><http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0004520/>.</a> <br><br>
+"Ethical Issues in Synthetic Biology." Synthetic Biology Project. Web. <a href="http://www.synbioproject.org/events/archive/ethical_issues_in_synthetic_biology/"><http://www.synbioproject.org/events/archive/ethical_issues_in_synthetic_biology/>.</a><br><br>
+Gaisser, Sibylle, Thomas Reiss, Astrid Lunkes, Kristian Muller, and Hubert Bernauer. "Making the Most of Synthetic Biology : Article : EMBO Reports." Nature Publishing Group : Science Journals, Jobs, and Information. Nature Publishing Group, 2009. Web. <a href="http://www.nature.com/embor/journal/v10/n1s/full/embor2009118.html"><http://www.nature.com/embor/journal/v10/n1s/full/embor2009118.html>.</a><br> <br>
+Herrera, Stephen. "Preparing the World for Synthetic Biology." Technology Review. Jan. 2005. Web. <a href="http://www.technologyreview.com/printer_friendly_article.aspx?id=14077"><http://www.technologyreview.com/printer_friendly_article.aspx?id=14077>. </a><br><br>
+The Lancet. "Community-acquired MRSA." 14 Oct. 2006. Web.<a href="http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(06)69557-3/fulltext"> <http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(06)69557-3/fulltext>. </a><br><br>
+Mitton, Craig, Carol Adair, Emily McKenzie, Scott Patten, and Brenda Waye Perry. "Knowledge Transfer and Exchange: Review and Synthesis of the Literature." University of British Columbia Okanagan and Child and Family Research Institute of BC; University of Calgary; Alberta Mental Health Board. Web. <a href="http://cre-premus.uwaterloo.ca/~cre-msd3/Attachment/KTE_evaluation.pdf"><http://cre-premus.uwaterloo.ca/~cre-msd3/Attachment/KTE_evaluation.pdf>.</a><br> <br>
+Pombo, David. "Community Acquired MRSA." 29 Sept. 2006. Web. <a href="http://www.acponline.org/about_acp/chapters/ut/mtg_outline06_pombo.pdf"><http://www.acponline.org/about_acp/chapters/ut/mtg_outline06_pombo.pdf>.</a><br> <br>
+“Safety and Ethics of Synthetic Life." Organisation for International Dialogue and Conflict Management (Austria). Web. <a href="http://www.synbiosafe.eu/uploads/pdf/Synbiosafe.pdf"><http://www.synbiosafe.eu/uploads/pdf/Synbiosafe.pdf>.</a><br>
                </div>
              </div>
@@ Line 652: / Line 693: @@
 <div class="innerContent">
 <div class="innerHeader"><h2>OUR TEAM!</h2></div>
-<img src="https://static.igem.org/mediawiki/2010/7/76/Teamfotobanner.JPG" alt="Team Photo" style="margin:50px;float:left">
+<img src="https://static.igem.org/mediawiki/2011/7/72/Waterlooteam2011.png" width = "800" height = "566.66666" alt="Team Photo" style="margin:50px;float:center">
 <div class="innerHeader"><h2>OUR UNDERGRADUATES!</h2></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/2/2d/Teamprofile23_UW.jpg" alt="Dan"></img><br />Dan Barlow</div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/e/e6/Teamprofile08_UW.jpg" alt="Ekta"></img><br />Ekta Bibra</div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/e/e1/AngelaUW2011%28200x160%29.jpg" alt="Angela"></img><br />Angela Biskupovic</div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/5/50/Igemheadshot.jpg" alt="Diljot"></img>Diljot Chhina</div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/0/05/Screen_Shot_2011-09-29_at_12.20.05_AM.png" alt="Amanda", width="160" height="200">Amanda Clarke</img></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/d/de/Teamprofile02_UW.jpg" alt="Arpita"></img><br />Arpita Desai</div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/a/ab/Teamprofile24_UW.JPG" alt="Jon"></img><br />Jon Eubank</div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/c/ca/Teamprofile07_UW.jpg" alt="Matt">Matt Gingerich</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/a/a6/Teamprofile28_UW.png" alt="Billy">Billy Khan</div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/b/b0/Screen_Shot_2011-09-29_at_12.15.05_AM.png" alt="Peter", width="160" height="200">Peter Hong</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2009/f/f7/Teamprofile13_UW.jpg" alt="Leah">Leah Kocsis</img></div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/8/87/Kasiawaterloo.jpg" alt="Kasia", width="160" height="200">Kasia Karpinska-Leydier</img></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/f/fb/Teamprofile29_UW.jpg" alt="Jordan"></img>Jordan Lapointe</div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2009/1/15/Teamprofile03_UW.jpg" alt="Cveta">Cveta Manassieva</img></div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/4/47/Screen_Shot_2011-09-29_at_12.15.26_AM.png" alt="Chris", width="160" height="200">Chris Milousis</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/f/f3/Teamprofile25_UW.jpg" alt="Dawson"></img> Dawson Overton</div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/3/37/Screen_Shot_2011-09-29_at_12.16.04_AM.png" alt="James", width = "160" height = "200">James Scott</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/e/ef/Teamprofile11_UW.JPG" alt="Mariko">Mariko Ozawa</img></div>
+<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2011/8/83/Screen_Shot_2011-09-29_at_12.15.37_AM.png" alt=Michel", width = "160" height = "200">Michel Simard</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/1/11/Teamprofile09_UW.jpg" alt="James">James Scott</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2009/b/b6/Teamprofile12_UW.jpg" alt="Alice">Alice Qi</img></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2009/4/49/Teamprofile14_UW.jpg" alt="Brandon">Brandon Wang</img></div>
-<div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/6/66/Teamprofile06_UW.jpg" alt="Fiona">Fiona Whelan</img></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2009/4/4a/Teamprofile15_UW.jpg" alt="Hilary">Hilary Yeung</img></div>
 <div class="teamProfile"><img src="https://static.igem.org/mediawiki/2010/9/97/Teamprofile04_UW.JPG" alt="George">George Zarubin</img></div>
@@ Line 737: / Line 777: @@
              <div id="acmid4sub1" class="aContentMidSub">
                 <div id="parts">
-<h3>UW's parts for 2010.</h3>
+<h3>UW's parts for 2011.</h3>
 <br />
-<a href="http://partsregistry.org/Part:BBa_K359002">BBa_K359002</a>   -    Signalling       - Agr quorum sensing sensor/generator, FepA pore, with P2 + reporter<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576003">BBa_K576003</a>   -    RNA       - Left part of self-excising ribozyme<br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359003">BBa_K359003</a>   -    Reporter         - Agr P2 with RFP<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576004">BBa_K576004</a>   -    RNA         - Right part of self-excising ribozyme<br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359006">BBa_K359006 </a>  -    Intermediate     - AIP sensor and generator<br />
+<a href="http://partsregistry.org/Part:BBa_K576005">BBa_K576005 </a>  -    Reporter     - Left part of GFP (GFP 1) with promoter (J23101) and RBS (B0034)<br/><br/>
+<a href="http://partsregistry.org/Part:BBa_K576006">BBa_K576006</a>   -    Reporter     - Right part of GFP (GFP 2) with transcription terminator <br /><br/>
-S. aureus oligopeptide-based quorum sensing system into a BioBrick-compatible signalling mechanism including the AIP sensor and generator of AIP (auto-inducer peptide).<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576007">BBa_K576007</a>   -    Intermediate     - Left part of GFP with left part of self-excising ribozyme attached using RFC 53 construction.<br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359007">BBa_K359007</a>   -    Intermediate     - AIP sensor with FepA pore<br />
+<a href="http://partsregistry.org/Part:BBa_K576008">BBa_K576008</a>   -    Intermediate     - Right part of the self-excising ribozyme attached to the right part of GFP using RFC 53 construction<br /><br/>
-This part includes the S.aureus Agr quorum sensing sensor which recognizes the oligopeptide. The FepA pore allows for the oligopeptide to diffuse through the outer-membrane<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576009">BBa_K576009 </a>  -    Intermediate - Lox attached on to BBa_K576005 on the right of the part. Standard assembly (RFC 10) was used for this construction.<br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359008">BBa_K359008</a>   -    Intermediate     - AIP generator and sensor, with an added RFP reporter<br />
+<a href="http://partsregistry.org/Part:BBa_K576010">BBa_K576010 </a>  -    Intermediate - Lox attached on to BBa_K576008 on the left of the part. BBa_K576009 or BBa_K576010 can be used depending on your convenience<br /><br />
-Generates an AIP signal, senses it and produces an RFP signal with an Excitation peak: 584 nm and Emission peak: 607 nm<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576011">BBa_K576011</a>  -   Reporter - Final construction of the 2011 project. The self-excising ribozyme should be cut out of from the rest of the sequence and thus expressing the full GFP.<br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359009">BBa_K359009</a>   -    Intermediate     - AIP sensor and consequent RFP reporter; contains FepA permeability pore<br />This part includes the S.aureus Agr quorum sensing sensor which recognizes the oligopeptide. The FepA pore allows for the oligopeptide to diffuse through the outer-membrane. Consequent RFP signal is produced, with an Excitation peak: 584 nm and Emission peak: 607 nm<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576012">BBa_K576012 </a>  -    Reporter - Negative control of the experiment. The lox recombination site interrupts the GFP expression <br /><br />
-<a href="http://partsregistry.org/Part:BBa_K359201">BBa_K359201 </a>  -    Plasmid Backbone - pSB3K3-S-rbsRFP-P<br /><br />
+<a href="http://partsregistry.org/Part:BBa_K576013">BBa_K576013 </a>  -    Reporter - Positive control of the experiment. Everything in between has been cut out by the self-excising intron and the GFP is fully expressed. <br /><br />
                 </div>
              </div>
@@ Line 787: / Line 827: @@
              <div id="acmid5sub1" class="aContentMidSub">
 <div class="innerContent">
-<h3 style="color:#0077be">Lab Notebook 2010</h3>
+<h3>Lab Notebook 2011</h3><br/>
-<br />
+<b>The following entries pertain to the Quantification Project</b><br/><br/>
-<h4>Monday, May 10</h4>
-<br />
-<p>
-We're still working on 2009 project. We just found out that the donor strain sequence lacks att site and oriT. Inoculated liquid broth in order to obtain colonies for conjugation. The tubes were as follows:
-</p><br />
-.DH5α λ rifr attB CT from old patch on rif25, amp100, tet10 (aka RAT)<br />
-.DH5α rifr attB CT from old patch on RAT<br /><br />
-<p>Also, we inoculated the Landing Pad Strain cells into liquid broth.</p><br />
-<h4>Tuesday, May 11</h4><br />
+<h5>Tuesday, May 31, 2011</h5>
-<p>
+<li>Transformation of BBa_I20260 from iGem Kit Plate 2, Well 17F.</li><br/>
-Tubes incubated from yesterday were taken out. All showed no growth. All tubes are to be re-innoculated. Tubes #1 and # 2 were re-done using an old plate and different colonies of the old patch.
-</p><br />
-<p>
-Several dilutions were prepared in order to determine which concentration is best for spread-plating. Dilutions prepared were as follows: e-2, e-4, e-5, e-6, e-7, e-8
-</p><br />
-<p>
-Prepared liquid and solid media, and learned how to use autoclave.
-</p><br />
-<p>
-Made more plates (Rif/Amp/Tet/Sm)
-</p><br />
-<h4>Wednesday, May 12</h4><br />
-<p>
-All tubes incubated yesterday showed growth. Miniprepped the samples.
-</p><br />
-<p>
-As relating to the dilutions, results were as follows
-</p><br />
-<p>
-e-8 = very little growth e-7 = some growth e-6 = highly populated
-</p><br />
-<p>
-Conjugation experiment was attempted (tri-parental mating). This included Donor (DH5alpha), Recipient (MM294A), Helper(MT616)
-</p><br />
-<p>
-Inoculated Landing Pad Strain from frozen stock.
-</p><br />
-<h4>Thursday, May 13</h4><br />
-<p>
-We prepared X-alpha-gal plates and streaked MM294A on them. We would be expecting white.rosy colonies. Nanodropped the samples which were minirepped yesterday (incubations of plates listed on Monday, May 10.)
-</p><br />
-<h4>Friday, May 14</h4><br />
+<h5>Wednesday, June 1, 20111</h5>
-<p>
+<li>Created a frozen stock of I20260</li>
-The x-alpha-gal plates showed no good results - none of the colonies were rosy.
+<li>Inoculated BBa_I0500 and BBa_E0240 from frozen stock already made from last year</li><br/>
-</p><br />
-<p>
-Learned how to do REs digestions properly (did several examples on paper, and in the lab.)
-</p>
-<br />
-<h4>Monday, May 17</h4>
-<p>
-Planned how to do a restriction digest followed by ligation procedure for the donor strain. Discussed the different purposes for restriction digests: diagnostic (to check if you have the plasmid you expect) and for cloning (to isolate desired DNA).
-</p><br />
-<h4>Tuesday, May 18</h4><br />
-<p>
-LPS Analysis W.R.T SacB : LPS was cut with with EcorI & run on 0.8% agarose gel for 45 minutes at 90V to analyze for truncated sacB
-</p><br />
-<p>
-Results: Three distinct bands were found. Therefore, the truncated sacB was not present in the LPS. If sacB were present four bands would have appeared after digestion.
-</p><br />
-<h4>Wednesday, May 19</h4>
-<p>
-PCR of DS Right Plank was performed: The right flank was inserted into DS right flank=Pst site, attB, oriT, MPH 1103
-</p><br />
-<p>
-PFB 9009 was mini prepped(LPS) and nanodropped.
-</p><br />
-<p>
-Nanodrop results of PFB 9009 Mini - prep:
-</p>
-SAMPLE------------>Concentration(ng/µL)----->260/280 <br />
-PFB9009-1--------->21.4.....................>1.75 <br />
-PFB9009-2--------->24.0.....................>1.91 <br />
-PFB9009-3--------->12.9.....................>1.58<br /><br />
-<h4>Thursday, May 20</h4><br />
+<h5>Thursday, June 2, 20111</h5>
+<li>Miniprepped and nanodropped I0500, and E0240.</li>
+<li>Inoculated I20260 from the frozen stock created the previous day</li><br/>
-<p>
+<h5>Friday, June 3, 20111</h5>
-Performed a double digest of PFB 9009-2 with FSPI & NdeI to excise and extract rouge transposase gene.
+<li>Digestion Reaction. Digested I0500 with EcoRI and SpeI. Digested E0240 (first sample) with EcoRI and PstI and digested E0240 (second sample) with EcoRI and XbaI.</li>
-Gel extracted the LPS and DS fragements
+<li>Miniprepped and nanodropped I20260</li><br/>
-LPS: 0.125g DS: 0.0947g
-</p><br />
-<p>
-Dissolved in Buffer to obtain 500µL of LPS and 378µL of DS and extracted the DNA following the protocol from "forEZ-10" kit.</p><br />
-<h4>Friday, May 21</h4><br />
+<h5>Monday, June 6, 20111</h5>
-<p>
+<li>Inoculated I20260, I0500 and E0240</li><br/>
-Performed a ligation reaction of LPS to circularize it
-Nanodropped the samples. Results recorded below:</p><br />
-LPS Concentration: 2.06ng/µL 260/280: 5.6 DNA: 224ng<br />
-DS Concentration: 1.95ng/µL 260/280: 7.1 DNA: 284ng<br /><br />
+<h5>Tuesday, June 7, 20111</h5>
-<p>
+<li>Miniprepped and nandodropped I20260, and I0500 and E0240 for extra sample</li>
-The solutions were speed-vaced on high for 10 mins to increase concentration.
+<li>Inoculated E0240</li><br/>
-</p><br />
-<h4>Monday, May 24</h4><br />
+<h5>Wednesday June 8, 20111</h5>
-<p>
+<li>Digestion reaction. Digested I0500 with EcoRI and SpeI. Digested E0240 (first sample) with EcoRI and PstI and digested E0240 (second sample) with EcoRI and XbaI. Digested I20260 with EcoRI and PstI.</li>
-Prepared agar plates and agar bottles</p>
+<li>Miniprepped and nanodropped E0240 for back up</li><br/>
-<p>
-organized everything in the lab and the freezer so that it was easily accessible</p>
-<p>Construction tree was revised and updated</p><br />
-<h4>Tuesday, May 25</h4><br />
+<h5>Thursday June 9, 20111</h5>
+<li>Gel extraction of E0240 (EcoRI+XbaI), I0500 (EcoRI+SpeI), E0240 (EcoRI+PstI) and I20260 (EcoRI+PstI). Two samples of each parts were gel extracted.</li>
+<li>Nanodropped the samples from Gel extraction. Concentration of I0500 and I20260 were too low.</li>
+<li>Inoculated I0500 and I20260</li><br/>
-Planned and carried out ligation of DS right flank + DS2(blunt ends)
+<h5>Friday June 10, 20111</h5>
-Started transformation of LPS and DS
+<li>Miniprepped I0500 and I20260 and ran digestion reaction. Same enzymes were used as the ones listed above.</li><br/>
-Note: The desktop cooler has been left out for undefined amount of time (approx. 3 hours). However, it should be okay.
-<br />
-<h4>Wednesday, May 26</h4><br />
-<p>
-Transformation results: LPS did not grow. Therefore, reverted to double digest.</p>
-<p>Started double digest of LPS with PspI and NdeI</p>
-<p>Repeated transformation (using more DNA this time)</p><br />
-<h4>Thursday, May 27</h4><br />
-<p>
-Transformation results (pFB10, Km + Sm):</p>
-negative control: no growth<br />
-Positive control: lots of small colonies (approx. 70)<br />
-Therefore transformation was sucessful. <br /><br />
-<h4>Friday, May 28</h4><br />
-Performed a diagnostic digest on DS with PstI + NsPI<br />
+<h5>Tuesday, June 14, 20111</h5>
-Results: Failed. NO 274 fragment was present but 120 fragment was present.<br /><br />
+<li>Gel extraction of I0500, I20260 and the back-up samples of E0240.</li><br/>
-This will be attempted again.<br />
+<h5>Thursday, June 16, 20111</h5>
-Troubleshooting: Ladder will be added in higher concentration and no loading dye will be added for better resolution.<br />
+<li>Ligation reaction: Ligated I0500 on to E0240. Ligated I20260 on to pSB1A2 (from E0240)</li><br/>
-Integrase strain was inoculated into Tc10 LB broth<br /><br />
-<h4>Monday, May 31</h4><br />
-Miniprepped and nanodropped DS<br />
+<h5>Monday, June 20, 20111</h5>
-Results:<br /><br />
+<li>Transformation of ligated parts (I0500+E0240, and I20260 on pSB1A2). Plated the transformant and incubated overnight</li><br/>
-SAMPLE 1<br />
+<h5>Tuesday, June 21, 20111</h5>
-CONENTRATION: 110.14ng/µL<br />
+<li>Created plates containing 1% arabinose.</li>
-/280: 2.02<br /><br />
+<li>Replicated plates containing I20260 colonies on to a different plate with Ampicilin antibiotic. Incubated overnight.</li><br/>
-SAMPLE 2<br />
-CONENTRATION:127.85µL<br />
-/280: 1.06<br /><br />
-SAMPLE 3<br />
-CONENTRATION:105.89ng/µL<br />
-/280: 1.07<br /><br />
-SAMPLE 4<br />
-CONENTRATION:189.74ng/µL<br />
-/280: 2.03<br /><br />
-SAMPLE 5<br />
-CONENTRATION:152.01ng/µL<br />
-/280: 1.05<br /><br />
-Planned out next day's activities regarding DS<br /><br />
-<h4>Tuesday, June 1</h4><br />
-Retried to do a diagnostic gel of DS with PstI & NstI with a fragment known to have approx. 100bp(old DS with no right flank)
+<h5>Wednesday, June 22, 2011</h5>
-FAILED. No alkaline phosphotase was added to DS when digested with restriction enzymes<br />
+<li>Replicated I0500+E0240 to plates containing 1% arabinose. Incubated overnight</li>
-Started a RE digest of mini-prep DS plasmid to be re-ligated with right flank construct. Nanodropped the digested right flank sample.<br /><br />
+<li>Inoculated a single colony from I20260 plate</li><br/>
-Concentration: 7.8ng/µL<br />
-/280: 4.29<br /><br />
-The concentration indicates that we can not use this sample because majority is not DNA.<br />
-Therefore, must PCR the right flank again using the "spring 2010" PCR program<br />
-PCR products were digested with Mph1103 & PstI<br />
-DS was digested with right flank with Mph1103(AvaIII) & PstI to prep for insertion into DS plasmid.<br />
-Two bands were present for positive controls#2(both samples). These bands were extracted and purified.<br />
-TUBE WEIGHTS<br /><br />
-Sample 1:0.1633g<br />
+<h5>Thursday, June 23, 2011</h5>
-Sample 2:1.0477g (did not show bands).<br /><br />
+<li>Created frozen stock of I20260</li>
-NANODROP RESULTS<br /><br />
+<li>Inoculated a single colony from I0500+E0240 plate</li><br/>
-Insert<br /><br />
+<h5>Friday, June 24, 2011</h5>
+<li>Created frozen stock of I0500+E0240</li><br/>
-Concentration: 15.9ng/µL<br />
+<h5>Monday, July 4, 2011</h5>
-/280: 1.61<br /><br />
+<li>Inoculated the I20260, and I0500+E0240</li>
-Vector<br /><br />
+<li>Created 1M Arabinose solution</li><br/>
-Concentration: 8.4<br />
+<h5>Tuesday, July 5, 2011</h5>
-/280: 2.23<br /><br />
+<li>Made serial dilutions of arabinose solution (from 1M to 1uM).</li>
-<h4>Wednesday, June 2</h4><br />
+<li>Diluted the cultures to 0.50 Absorbance at OD600.</li>
+<li>Set up experiment for quantification experiment. Refer to the diagram below for how the experiment was setup.</li><br/>
-Digested DS vector with PstI so that right flank can be inserted. Added SAP to avoid re-ligation with itself.<br />
+<img src="https://static.igem.org/mediawiki/2011/f/f8/Waterloo_Quantification.png" width= "500" height="250"></img>
-Ligated DS vector with Right flank insert<br />
+<br/><br/>
-Transformed newly improved DS(hoepfully, with right flank) into component DH5α<br />
-Discussed possible ligation results<br /><br />
-<h4>Thursday, June 3</h4><br />
-Innoculated S. aureus into LB media for the purpose of collecting AIP sipernatant<br />
-After collecting staph supernatant wanted to test for the effect of adding supernatant to E.coli cultures<br /><br /><br />
-<h4>Friday, June 4</h4><br />
-Innoculated DH5α into AIP supernatant<br />
-made 3 x 5mL tubes of AIP supernatant<br />
-innoculated with DH5α (strain box #1, #41)<br />
-Results from transformation(previous day): No growth of LPS 10 on Km/Sm plates. No clear red color on Rig/Km but good growth observed. Left in the 37˚C incubator over the weekend.<br /><br />
-<h4>Monday. June 7</h4><br />
-Performed another attempt at digestion of diagnostic Nsp/Pst on DS -- FAILED<br />
-Researched and wrote protocols for experiments to be carried out within the week<br />
-Learned how to use DNA from kit<br /><br />
-<h4>Tuesday, June 8</h4><br />
-A new batch of competent cells were made.<br />
-Their competency will be tested by transforming DS in.<br /><br />
-<h4>Wednesday, June 9</h4><br />
-The streaks of putative LPS 10 still showed no red.<br />
-Sensetivity was checked for melibrose. The same patches were streaked(#5,8,26)
-on minimal melibrose.<br /><br />
-If anything grows: ALARM! Also, there are suspicious parts on #5 streak, worth restreaking onto another.<br /><br />
-<h4>Thursday, June 10</h4><br />
-Rif/Km plates were made<br />
-Rif stock was made by dissolving 0.25g into 10mL DM50<br />
-Prepared everything needed for outreach event<br />
-pJET-Right Flank for DS (Donor Strain) has been miniprepped, put in -20C freezer. The streak plates of LPS10 from various sources still show no red colour. Could cutting out the fragment (pFB09->pFB10) messed something up?<br /><br />
-<h4>Friday, June 11</h4><br />
-Tried to cut and gel extract the fragment. Failed, probably due to low Gel Red dye. Will be getting more dye soon. Can try scraping the walls and adding all of it to the gel Monday.<br /><br />
-<h4>Monday, June 14</h4><br />
-Tried to do PstI + Mph1103I digestion again. Failed several times.<br />
-Wednesday will do 10uL diagnostics with BglII on the remaining pJET minipreps; looking for ~200bp fragment. Also will do spectrophotometry of DH5-alpha pre-DS and DH5-alpha blank hourly at 600 and 640 nm.<br /><br />
-<h4>Tuesday, June 15</h4><br />
-Updated construction tree. Drew one out and many copies were made.<br />
-Attended a club meeting and updated all volunteers with what was happening.<br />
-Engineers were given a short biology course to help understand the project better<br /><br />
-<h4>Wednesday, June 16</h4><br />
-Checked concept of absorption RFP estimation<br />
-inoculated with loop (approximate the same aount) HiRFP = pSB1A2 - BBa_K093012 (+ L. flank, can be neglected)(J23118 driven E1010)<br />
-The purpose of this was to check for consistency of A589/A640 on DH5α and useage of that to check consistency of A584-blank / A640<br /><br />
-<h4>Thursday, June 17</h4><br />
-Gel extracted the fresh right flank PCR product (yes, AGAIN). Tomorrow will check on gel for presence along with "control PCR product" from cloneJET kit.<br /><br />
-The parts in DH5 have been inoculated into liquid media to be miniprepped tomorrow.<br /><br />
-The RFP measurements on cuvete absorption spec Ultrospec 2000 suggest that sensitivity is too low to pick out RFP. <br />Should try on Bioscreen C plate reader.<br /><br />
-Planning the assembly should be started tomorrow.<br /><br />
-<h4>Friday, June 18</h4><br />
-Parts miniprepped. right flank PCR ligated into pJET and transformed. To be inoculated to liquid Monday.<br /><br />
-<h4>Monday, June 21</h4><br />
-created a final list of parts to be transformed<br />
-Do not have: K206000, K206001, J23151 and J23150<br />
-All the DNA was transformed into DH5α competent cells<br />
-Results of transformation: most plates grew but with very few small colonies. The plates were put back in the incubator for a few hours and checked later. All had at least a few colonies.<br />
-These were innoculated into liquid LB and incubated overnight at 37˚C<br /><br />
-<h4>Tuesday, June 22</h4><br />
-Was Done:<br /><br />
-Tried diagnostic with Mph1103I alone and PstI alone. The results are here. Wells are as follow<br />
--2 PstI<br />
--1 PstI<br />
--1 PstI<br />
-Ladder Fermentas 1kb plus<br />
--2 Mph1103I<br />
--1 Mph1103I<br />
--1 Mph1103I<br /><br />
-The evidence hints on presence of PstI site on pJET; without first well showing it is quite non-conclusive.<br />
-Red clone of LPS10 strain was found in the fridge and confirmed by X-gal to be MM294A as DH3-alpha is lacZ-. Hooray. <br />Was patched on Kan and Kan+Strept 48-numbered background plates by Corey and Diana.<br /><br />
-To Be Done:<br /><br />
-Talk to people who use Bioscreen C plate reader.<br />
-See if pJET sequence has PstI site(s).<br />
-Cut out right flank with PstI and Mph1103I and run gel preparatively, gel extract the fragment of ~150bp.<br />
-Ligate that fragment into pDS (donor strain plasmid) cut with PstI+SAP.<br />
-Transform that ligation into DH5-alpha.<br />
-From LPS10 patch plates pick the colonies that did not grow on strept or grew poorly, streak on Kan and check on sucrose media (just streak) with empty DH5-alpha as control.<br /><br />
-<h4>Wednesday, June 23</h4><br />
-Was done:<br /><br />
-Looked at pJET for PstI. Yes there is one, at position 5. This means that in Mph1103I+PstI digestion we expect fragments of of 153bp (the one we want) and 371bp (the one we don't care about).<br />
-Spread 70 µL of red LPS10 on X-alpha-gal+rif+kan.<br />
-Streaked red LPS10 on sucrose LB side by side with empty DH5-alpha<br />
-no streptomycin sensitive patches detected<br />
-Mph1103I PstI digestion preparative was done, gel was stained overnight.<br />
-pDS was linearized with PstI<br /><br />
-<h4>Thursday, June 24</h4><br />
-LPS10: sucrose sensitivity not detected; X-alpha-gal plate is mostly blue, only few white colonies, without a sign of red. Should leave x plate in the fridge and hope for colour<br />
-Two attempts to cut out right flank with Mph1103I and PstI were perfmored. Both attempts are to be quantified using nanodrop and pipette, and concentrated on the Speedvac, requantified with pipette.<br /><br />
-<h4>Friday, June 25</h4><br />
-Second attempt of Mph-Pst cut out has been ligated into its proper place in pDS. incubate and pray. Tschüs.<br /><br />
-<h4>Monday, June 28</h4><br />
-PstI+SpeI digest (wells 4 and 5) suggest ligation failure of right flank into pDS.<br /><br />
-<h4>Tuesday, June 29</h4><br />
-Transformed J23107 (constitutive promoter) into DH5α<br />
-Results: colonies grew, some rosie<br />
-These were inoculated and miniprepped<br />
-All parts were sent out for sequencing<br /><br />
-<h4>Wednesday, June 30</h4>
-<br />
-Digested RF with PstI.<br />
-Result: No RF fragment, but PstI- PstI fragment is there<br /><br />
-<h4>Thursday, July 1</h4><br />
-Attended board meeting and updated everyone on what was going on<br />
-Made LB plates<br /><br />
-<h4>Friday, July 2</h4><br />
-Autoclaved 0.8% saline and swabs<br />
-make 70% ethanol<br />
-stocked up pipettes<br /><br />
-<h4>Monday, July 5</h4><br />
-Inoculated J23107 in LB and incubated overnight in 37C<br />
-Inoculated received parts( K206001, I746201, I746001, K20600 onto Amp plates to incubate overnight in the 37C. It will be inoculated in LB tommorow<br /><br />
-<h4>Tuesday, July 6</h4><br />
-inoculated the cultures into LB and will mini-prep tommorow<br /><br />
-<h4>Wednesday, July 7</h4><br />
-Mini-prepped the parts that were inoculated yesterday<br />
-These were to be sequenced<br />
-Made glycerol stock of parts to be sequenced<br /><br />
-<h4>Thursday, July 8</h4><br />
-pIET - rf has been transformed and grew up to nearly lawn coverage o/N. 50uL DH5a comp + 5uL supercoiled plasmid were used. The negative control was clear. The transformants were inoculated into 16 LB tubes + Amp, without purification.<br />
-attempted to assemble the measkit.<br /><br />
-<h4>Friday, July 9</h4><br />
-Nanodropped the following samples:<br />
-J23107 - COnstitutive promoter<br />
-I74601 - AIP sensor<br />
-- AIP generator<br />
-I746201 - FepA<br />
-I7466104 - AgrA P<br />
-K206000 - pBAD strong<br />
-K2066001 - pBAD weak<br />
-I13458 - pBAD<br />
-I13453 - AraC<br />
-J23102 - constitutive promoter<br />
-E1010 - RFP CDS<br />
-J23101 - Constitutive promoter<br />
-I13507 - RFP + RBS +TT<br /><br />
-<h4>Monday, July 12</h4><br />
-Made frozen stock of all the cultures from friday<br />
-Made DMSO stocks : wanted 7% DMSO and 14% LB --> Made it by mixing 1.68mL of DMSO and 10.32LB<br /><br />
-<h4>Wednesday, July 13</h4><br />
-miniprepped all parts from strain box #2 and nanodropped them. Results are listed below:<br />
-I746104 : 100.1ng/uL , 2.16<br />
-J23107 : 149.3ng/uL , 2.01<br />
-I746201 : 139.7ng/uL , 2.00<br />
-I746001 : 185.9ng/uL , 1.96<br />
-I746101 : 104.3ng/uL , 2.08<br />
-J23102 : 319.4ng/uL , 1.94<br />
-I13453 : 139.2ng/uL , 2.01<br />
-I13507: 61.0ng/uL , 2.10<br />
-K0206000 : 155.1ng/uL , 1.60<br />
-I13958 : 155.7ng/uL , 2.03<br />
-J23101 : 262.8ng/uL , 2.00<br />
-E1010 : 99.1ng/uL , 2.05<br /><br />
-<h4>Thursday, July 14</h4><br />
-Added J23107 promoter to I746101 and I746001 (AIP sensor and AIP generator)<br />
-Ran gel electrophesis and gel extracted J23107 ( approx. 3kB fragment)<br />
-Cut J23107 with SpeI and PstI & I746101 and I746001 with XbaI and PstI and ligated into vector<br />
-Transformed and miniprepped.<br /><br />
-<h4>Friday, July 15</h4><br />
-Strain list made public with the link<br />
-I20260 on pSB3K3 inocluated into Kanamycin LB<br />
-strain list is updated with 2010 parts added yesterday<br />
-J23101 on J61002 from frozen stock is inoculated into Ampicilin LB<br />
-Transformed I0500 from 2010/plate3/20B into DH5-alpha, plated on Kanamycin LB Agar<br />
-inoculated all recent parts on strain list (except E1010) to fill up plasmid -20 stocks<br />
-The primary constructs of AIP sender and reciever has been cut, extracted and set ligated (O/N, 16 °C) to J23107.<br /><br />
-<h4>Monday, July 18</h4><br />
-Inocluated pSB2K3-I0500 into Kan-LB<br /><br />
-<h4>Tuesday, July 19</h4><br />
-Performed preparative digestions of J23101 cut with EcoRI + PstI & PSB3K3 also with EcoRI + PstI<br />
-These parts were ran on gel and gel extracted:<br />
-J23101 : 0.0515g<br />
-PSB3K3 : 0.0259g<br />
-Results were not that great. There was not enough DNA and bands were too faint. Also, ladder ran a little funny, may have been overloaded. We will need to redigest. This time a diagnostic gel will be run to see what went wrong.<br /><br />
-<h4>Wednesday, July 20</h4><br />
-LPS: Cveta is looking at the pFB10 sequence<br />
-Dan is looking at Parts Sequences<br />
-DS: hunting for 153bp fragment on larger scale with new batch of Mph1103I enzyme<br />
-Quantification: constructing pSB3K3-J23101-RFP by E+P digest<br />
-Assembly: Stage 1 is assembled but not checked by diagnostic digest. Broth inoculated for miniprep, growing.<br /><br />
-<h4>Thursday, July 21</h4><br />
-DS ligation: three attempts were made with different tubes of competent cells each. Attempts:<br />
--ve ctrl failed<br />
--ve ctrl ok, many colonies still on the transformant plate. 4 larger colonies were pathced and broth-inoculated.<br />
-rd attempt made today, spread on amp plate, growing<br />
-pSB3K3-J23101-RFP construct inoculated from streak plate into broth. two streakplates are in the fridge.<br />
-gel was ran. wells:<br />
-Ladder (Fermentas 1kb plus, as always)<br />
-Preparative digest of J23107+I746101 construct<br />
-Same<br />
-Undigested control for preprative digest above<br />
-Ladder<br />
-Diagnostic digest of J23107+I746101 construct<br />
-Undigested control for diagnostic above<br />
-pSB2K3-I0500 (part from the kit)<br />
-wells 5,6,7 and 8 pic is here, the other half of the gel was exposed to UV only to cut out the top band from well 2 and 3 to be gel-extracted.<br />
-pSB3K3-J23101-RFP was already inoculated into broth by Leah yesterday. Dan miniprepped that and the remaining culture of I0500. George made frozen stock #106 out of pSB3K3-J23101-RFP<br /><br />
-This is the diagnostic gel we ran on the vector (J23107 + I746001). The bands are as follows:<br />
-ladder<br />
-digest with (EcoRI and XbaI)<br />
-Negative control (no restriction enzymes)<br />
-Digest again (left over from preparative, since I had to increase the volume and it didnt all fit into the well)<br />
-The preparative looked the same. respective band excised+extracted.<br /><br />
-<h4>Friday, July 22</h4><br />
-DS lig 3 failed (abundant growth on both plates<br />
-miniprepped DS lig 2 (4 of them) and another culture of 3K3 RFP J23101.<br /><br />
-<h4>Tuesday, July 27</h4><br />
-Ran the /NspI+PstI digestions on gel (2uL + 0.5uL PstI + 0.5uL NspI + 2uL FD buff + 15 uL water)<br />
-Ladder<br />
-DS clone 1<br />
-DS clone 2<br />
-DS clone 3<br />
-DS clone 4<br />
-pSB1A2 (I746104 part)<br />
-Prepped parts list has been updated. The sequencing confirmations are still to come from Dan Barlow.<br />
-BW27783 recieved from UBC, inocluated into liquid culture.<br /><br />
-<h4>Wednesday, July 28</h4><br />
-Made frozen stock of BW27783 #107<br />
-digestion of 3K3-J23101-RFP preparative: (7uL DNA + 1uL EcoRI + 1 uL SpeI + 2uL FD Green Buff. + 9 uL water); diag (3 uL DNA + 0.5 EcoRI + 0.5uL SpeI + 1uL FD Green Buff. + 5uL water) pic of diag<br />
-digestion of 2K3-I0500 preparative: (7uL DNA + 1uL EcoRI + 1 uL SpeI + 2uL FD Green Buff. + 9 uL water); diag (3 uL DNA + 0.5 EcoRI + 0.5uL SpeI + 1uL FD Green Buff. + 5uL water) pic of diag the lower, 1200bp band is the target<br /><br />
-<h4>Thursday, July 29</h4><br />
-pFB10 inoculated into broth, Km+Sm<br />
-pFB10 streaked on Sm and Sm+Suc10%.<br />
-Transformed K359201-I0500 ligation, plated on Km agar.<br />
-FepA-Sensor construct was being miniprepped by Leah<br />
-Sensor-Generator construct inoculated into LB.<br /><br />
-<h4>Friday, July 30</h4><br />
-Planned for the upcoming week<br />
-Worked on the construction tree<br />
-Prepared for Outreach lab event<br /><br />
-<h4>Tuesday, August 3</h4><br />
-Sucrose sensitivity of pFB10 confirmed.<br />
-inoculated broth with 6 different colonies of K359201-I0500.<br />
-Finding source of microplates. According to this, the clear plates are even better than clear-bottom-black ones.<br />
-K201-I500 construct miniprepped, digested E+P, ran on gel:<br />
-Sample 1-1<br />
-Sample 1-2<br />
-Sample 2-1<br />
-Sample 2-2<br />
-Sample 3-1<br />
-Sample 3-2<br />
-Ladder<br />
-linky<br />
-matches expected results (from ApE) ideally.<br /><br />
-<h4>Wednesday, August 4</h4><br />
-plates for ESQ activity poured<br />
-~10mL of 10% L-arabinose stock created from Charles lab supplies (used 1g). Used protocol from OpenWetWare for creating stock.<br /><br />
-<h4>Thursday, August 5</h4><br />
-Made 0.2% arabinose LB agar plates.<br />
-Streaked K359201-I0500 construct on an Ara-LB plate.<br /><br />
-<h4>Friday, August 6</h4><br />
-DH5-allpha with K359201-I0500 shows no red phenotype.<br />
-Transformed ligation of P2-RFP (I746104+I13507)<br /><br />
-<h4>Monday, August 9 - Friday, August 13</h4><br />
-All attempts to transform that P2-RFP has failed<br />
-Autoclaved<br />
-baffled fasks with 50mL LB (freshly prepared, measured out with graduated cylinder)<br />
-two jars of µfuge tubes<br />
-mL 0.1M MgCl2<br />
-GSA bottles<br />
-LPS: Inoculated 5 different cultures of pFB9010 into Km/Sm LB liquid media, as well as into blank LB media. These are needed in order to continue with the Landing Pad Project from 2009. The cultures will be used to make frozen stocks of the plasmid, as well as minipreps for future work. Results will be seen tomorrow. Previous attempts to grow the pFB9010 plasmid containing cells have been unsuccessful – although the inoculation is from Km/Sm patches, no growth has previous been observed in Km/Sm liquid cultures.<br />
-Amp plates were tested by using two plates – one Amp and the other Blank. On them were plated MT616 and DS plasmid. DS plasmid is Amp resistant, MT616 is not. Results to be seen tomorrow.<br /><br />
-<h4>Monday, August 16</h4><br />
-Missed the exponential phase for the comp cell prep, deferred till tomorrow.<br />
-LPS: There was no growth in the Km/Sm liquid cultures but there was growth in the blank cultures.<br />
-LPS: Two plates of pFB9010 have been recovered. In order to solve ambiguity, liquid cultures of Km and Sm were inoculated from plate 1 (most used). Also, plates of Km, Sm, Km/Sm were streaked with each of the 5 patches from each of plates 1 and 2 (where plate 2 is Sm only for some reason…although it should be both). This should solve which of the resistances is not functional. Results tomorrow.<br /><br />
-<h4>Tuesday, August 17</h4><br />
-Assembly: Nonodropping of both J23107 and I13507 stocks was performed. Digestion of J23107 with PstI and SpeI was unsuccessful. The 0.8% Agarose gel showed that the plasmid was not cut, since the uncut control beside it yielded the same bands.<br />
-Assembly: Digestion of I13507 with PstI and XbaI was successful, although the bands were slightly off as related to the ladder. Suggestion was made that Gene Ladder Plus should be ran as 2uL of solution + 8ul of water. Also, it has ran fast before, so beware. Bands expected are 883 and 2057 (from I13507 in pSB1A2 plasmid). 883 was taken (appeared at around 1000, however), since it is an insert. The bands were gel purified and stored at -20 C.<br /><br />
-<h4>August 18</h4><br />
-digested and gel extracted I13453/E+X and I13458/E+S<br />
-made 30 plates for ESQ activity<br />
-performed half of competent cell procedure, let incubate on ice in 4°C O/N<br />
-Results from yesterday were as follow:<br />
-Growth from both pFB9010 plates on Km and Sm, but not on Km/Sm.<br />
-Liquid cultures showed growth in Km, but not in Sm.<br />
-Not sure what this means at the moment, so further tests need to be done.<br />
-Transform remainders of pFB9010 stored at -20 C (nanodrop, transform)<br />
-Try digestion of J23107 again – did not work AGAIN! Will attempt another time but with another lab’s REs, SAP and buffer.<br />
-If digestion works, ligate with I13507. – did not work =(<br /><br />
-<h4>August 19</h4><br />
-Digestion of J23107 was re-done using REs, Buffer and SAP from another lab (except for SpeI, since it was not available from anyone else.) This did not work either.<br />
-We think that maybe there is something wrong with the J23107 miniprepped stock in the -20C fridge, so we will make a new one. Took J23107 from frozen stock and streaked onto an Amp100 plate, as well as inoculated into Amp100 liquid culture. This will be miniprepped tomorrow.<br />
-Set ligation of I13458+I13453<br /><br />
-<h4>August 20</h4><br />
-Miniprepped J23107<br />
-Nanodropped and digested – SUCCESSFUL!!!!<br />
-Gel Purified and Nanodropped<br />
-Concentration according to nanodropping is ~ 1ng/ul = way too low.<br />
-More J23107 and I13507 will be inoculated over the weekend, and will be minirepped and digested on Monday.<br />
-Regarding LPS, took a Km20 plate which yielded good results, and inoculated it into the following liquid cultures.<br />
-Km20, Km10, Km20/Sm100, Km20/Sm50,Km10/Sm100,Km10/Sm50, Sm50, Sm100.<br />
-This was done to ensure that the concentration of Sm or Km is not too high in the liquid cultures (mass transfer accounts for erroneously high concentration in comparison to solid agar on plates.)<br /><br />
-<h4>August 22</h4><br />
-Results from inoculations of various Km/Sm concentrations were as follows:<br />
-Contents	 Results<br />
-Km10	 +++ (red precipitate on the bottom)<br />
-Km20	 +++ (red precipitate on the bottom)<br />
-Sm50	 +++(very little white-ish red precipitate on the bottom)<br />
-Sm100	 -/+ (looks little bit cloudier than regular LB, but that could be due to re-suspension of the patches, since it was taken from a patch, not from a single colony)<br />
-Km10/Sm50	 +++ (red precipitate on the bottom)<br />
-Km10/Sm100	 +++ (no red precipitate on the bottom)<br />
-Km20/Sm50	 -/+ (looks little bit cloudier than regular LB, but that could be due to re-suspension of the patches, since it was taken from a patch, not from a single colony)<br />
-Km20/Sm100	 -/+ (looks little bit cloudier than regular LB, but that could be due to re-suspension of the patches, since it was taken from a patch, not from a single colony)<br />
-This probably means that while the resistances are present in the genome, they are not expressed very strongly. Will attempt to grow colonies on plates with reduced Sm/Km. After, will attempt triparental mating again.<br />
-innoculated J23107 into 5 liquid Amp 100 cultures, ready to be miniprepped tomorrow (Monday)
-prepared Km10/Sm50, Km10/Sm100, Km20/Sm50, Km20/Sm100 plates and streaked pFB9010 on them. Results to be seen tomorrow. This was done, since liquid versus solid media has been giving varying results with this project.<br /><br />
-<h4>August 23</h4><br />
-There is no growth on any of the pFB9010 plates (with varying conentrations of Km and Sm)<br />
-Miniprepped and nanodropped J23107 (concentrations are written on the tubes)<br />
-Digested J23107 with PstI and SpeI<br />
-Ran diagnostic + preparative gel<br />
-Gel extracted<br />
-Digested I13507 with PstI and XbaI<br />
-Ran diagnostic + preparative gel<br /><br />
-<h4>August 25</h4><br />
-Digestion of I13507 with PstI and XbaI could not be performed yesterday, so will be performed today<br />
-Ran diagnostic + preparative gel<br />
-gel extracted<br /><br />
-<h4>August 26</h4>
-Concentrated samples of digested J23107 (digestion was done with SAP) and I13507.<br />
-Performed ligation (added ATP)<br /><br />
-<h4>August 27</h4><br />
-Ligation was ran on gel (big mistake....should have just went along with transformation right away, since results could not be seen on the gel)<br /><br />
-<h4>August 30</h4><br />
-Performed digest of J23107 again, except used FD Buffer instead of Green FD Buffer<br />
-Ran on gel<br />
-Sample appears as a smudge (potential contamination)<br />
-Performed digestion of I13507 again, using FD buffer instead of FD buffer green.<br />
-Ran on gel<br />
-Could not see digest.<br />
-Transformed ligation of “58+53” (quantification work)<br /><br />
-<h4>Tuesday, August 31 - Friday, September 3</h4><br />
-Performed digest of J23107 and I13507 AGAIN! This time, SAP was not added to the vector digest (usually, if it is a double digest, you don’t really need to add SAP. It helps in the case that one of the REs does not cut). WORKED!!!<br />
-Transformed the ligation of J23107 and I13507<br />
-Using 50µL of competent cells, 20µL of ligation reaction and 15µL of CaCl2(100mM solution)<br /><br />
-<h4>September 6 - September 10</h4><br />
-Orientation week<br /><br />
-<h4>September 13 - September, 17</h4><br />
-First Lab meeting for Fall 2010<br />
-created a new iGEM active lab & a new thread of e-mail to keep everyone updated on lab work done daily<br />
-Innoculated I746104 and I13507 into liquid broth (3 different ones)<br /><br />
-<h4>Monday, September 20 - Wednesday, September 22</h4><br />
-Planned for Jamboree<br />
-Assessed previous work done and decided and what will be done for the competition<br />
-Organized a new schedule to get the work done accordingly for the jamboree<br />
-Miniprepped I746104 and I13507<br /><br />
-<h4>September 23</h4><br />
-. Nanodropped samples of I746104 and I13507. Results are as follow:<br /><br />
-I13507 - [102 ng/ul] 260/280 = 1.87 <br />
-I746104 (1) - [168.8 ng/ul] 260/280 = 1.81 <br />
-I746104 (2) - [158.8 ng/ul] 260/280 = 1.82<br /><br />
-Calculations for digestions: need 617.9 ng of insert, 300ng of vector.<br /><br />
-. Digests:<br /><br />
-I746104 with SpeI and PstI 3ul I746104 1ul Pst 1ul Spe 2ul FD Green Buffer 12ul Nucl. Free Water 1ul SAP<br />
-This was done in duplicate. Control: 1.5 ul I746104 without REs; 10uL reaction.<br />
-I13507 with XbaI and PstI 7ul I13057 1uL PstI 1uL XbaI 2uL FD Buffer Green 9uL Nucl. free water<br />
-control: 3ul of DNA, no REs, 10ul reaction.<br />
-. Left to incubate for an hour @ 37C<br />
-. Gel purified using protocol for purification from enzymatic reactions (used 60uL of Elution buffer for non-controls, 30ul for controls)<br />
-. Speed vac for 10 minutes on high.<br /> 6. Nanodropped<br />
-I746104 (1) - 9.7 ng/uL <br />
-I746104 (2) - 8.7 ng/uL <br />
-I746104 (3) - 5.5 ng/uL<br />
-I13507 (1) - 14.1 ng/uL<br /> I13507 (2) - 21.3 ng/uL<br /> I13507 (contaol) - 14.0 ng/uL<br /><br />
-. Ligation<br /><br />
-Vector 8uL<br />
-Insert 6.5 uL<br />
-X lig buff 2.5uL<br />
-ligase 1.5 uL<br />
-ATP 1uL<br />
-Nucl. free water 6<br />
-total: 25.5 uL<br /><br />
-The two I13507 were mixed, and 6.5 uL were taken from each into the 3 aliquots of I746104. Why is there 3 aliquots, when there was only 2 to begin with, you ask? Because Cveta lose the label on one of them, and couldn't tell which were the actual digests and which was the control.<br />
-To fix this grave mistake:Cveta saved 2uL from each of the three tubes so we can run a gel tomorrow and find out which is which. If you are doing anything with the tubes, please ensure the labelling does not change.
-Left to ligate at 16C in PCR machine.<br /><br />
-<h4>September 24</h4><br />
-Ligation of K359003 and I13507 was completed, plated on Amp100 and incubated overnight at 37˚C<br /><br />
-<h4>September 25</h4><br />
-Informed the lab volunteers of work done over the summer<br />
-Shared the following with them:<br />
-The Handbook<br /><br />
-In Brochure form (please print with Acrobat Reader in the "short" duplex format, or otherwise I am not responsible for wasted paper)<br />
-<h4>September 26</h4><br />
-checked the I746104 digestions that went into ligation by gel, #1 is apparently a control.<br />
-Transformed and plated the ligation (putative 003).<br /><br />
-<h4>September 27</h4><br />
-Incubated Amp100 K359003 plates grew well. Some bright pink colonies were visible, others were white.<br />
-Two aliquots of ligation #2 and #3 were prepared<br />
-pink colonies from each plate were inoculated from each plate into separate liquid broths of Amp50.<br /><br />
-<h4>September 28</h4><br />
-Miniprepped the 6 separate tubes, nanodropped, written concentration on side of the tube and stuck in second green box (the one labeled "2010 Parts Kit 2", disregard the meaning of that name), so it is easier to find.<br /><br />
-<h4>September 29</h4><br />
-clones were digested using the following gel layout:<br />
-: Ladder (2uL + 8uL MQ) <br />
-: clone #1 /E+P<br />
-: clone #2 /E+P <br />
-: clone #3 /E+P<br />
-: clone #4 /E+P <br />
-: clone #5 /E+P <br />
-: clone #6 /E+P<br />
-: I13507 /E+P<br /><br />
-<h4>October 1</h4><br />
-Attempted to make K359009, K359008, K359008 (3A), and K359009 (3A)<br />
-A was not sucessful<br />
-K359008 : obtained from K359006 and K359003<br />
-K359009 : obtained from K359007 and K359003<br />
-Samples were digested, ligated and incubated for over 2 hours at 37˚C<br />
-All 4 samples were purified directly from the enzymatic reaction<br />
-Samples were nanodropped<br />
-SAMPLE ---> CONCENTRATION---> 260/280<br />
-K359003 --> 13.5ng/µL ---> 1.57
-<br />
-K359006 --> 13.8ng/µL ---> 1.90
-<br />
-K359003 --> 7.4ng/µL ---> 1.21
-<br />
-K359007 --> 45.7ng/µL ---> 1.78<br /><br />
-<h4>October 2</h4><br />
-. Digests<br />
+<h5>Monday, July 11, 2011</h5>
-Sad news of the day: SpeI is not heat inactivatable (sp?). Some NEB heat inactivatable SpeI was found, so we shall try that one later.<br />
+<li>Inoculated the I20260, and I0500+E0240</li>
+<li>Created 1M Arabinose solution</li><br/>
-a. Digests # 1 to make K359008 003 cut with XbaI and EcoRI 006 cut with SpeI and EcoRI<br />
+<h5>Tuesday, July 12, 2011</h5>
+<li>Another quantification experiment run. Machine failure.</li><br/>
-b. Digest # 2 to make K359009 003 cut with XbaI and EcoRI 007 cut with SpeI and EcoRI<br /><br />
+<h5>Wednesday, July 13, 2011</h5>
+<li>Inoculated the I20260, and I0500+E0240</li>
+<li>Created 1M Arabinose solution</li><br/>
-. Ligations The above digests were set for ligation. Two aliquots were made for each (but there was barely anything for the second one.) A -ve and +ve control were also included, where -ve = no DNA, +ve = Amp resistant plasmid lying around. Left tubes in PCR machine overnight at 16C.<br /><br />
+<h5>Thursday, July 14, 2011</h5>
+<li>Last quantification experiment run.</li><br/><br/><br/>
-<h4>October 3</h4><br />
-Transformed and plated the tubes from yesterday on Amp. They were left in the 37C incubator overnight.<br />
+ <b>The following entries pertain to the Ribozyme Project</b><br/><br/>
+<h5>Wednesday July 6, 2011</h5>
+<li>Received 3 of 4 sequences the previous week (IN1, IN2 and GFP2).</li>
+<li>A quick spin down UWAT014-3/UWAT014-2 using centrifuge.</li>
+<li>Resuspended DNA in 40ul of MQ water (Concentration: 2ug/40ul=1ug/20ul)</li>
+<li>Transformed into DH5-alpha (sequences in PUC57).</li>
+<li>grown overnight on ampicillin plates.</li>
+<li>Resuspension of PSB1C3 in the Spring 2011 distribution kit (Plate 1 well 3A). Contains BBa_J04450.</li>
+<li>Resuspension of PSB1C3 in 10ul of MQ water (aspirated), wait approximately 5 minutes.</li>
+<li>1ul of resuspension was transformed into DH5-alpha. Grown overnight on plate.</li><br/>
-Reinnoculated DB 3.1<br /><br />
+<h5>Thursday July 7, 2011</h5>
-<h4>October 4</h4><br />
+<li>N1 (amp), IN2 (amp), GFP2 (amp) and PSB1C3 (cm) broth cultures innoculated (3 each)..</li><br/>
+<h5>Friday July 8, 2011</h5>
+<li>Frozen stock of IN1, IN2 and GFP2 in PUC57 and PSB1C3 backbone made..</li>
+<li>Miniprep for IN1, IN2, GFP2 and PUC57 completed:.</li><br/>
-Researched what to do if we ran out of linearized plasmid pSB1c3<br />
+<table border="1">
-http://partsregistry.org/Help:Protocols/Linearized_Plasmid_Backbones<br />
+<tr><td><b>Sequences</b></td><td><b>In1</b></td><td><b>In2</b></td><td><b>GFP 2</b></td><td><b>pSB1C3</b></td></tr>
+<tr><td><b>260/280</b></td><td>1.85</td><td>1.80</td><td>1.88</td><td>1.86</td></tr>
+<tr><td><b>ng/ul</b></td><td>229.8</td><td>236.1</td><td>198.6</td><td>166.2</td></tr></table><br/>
+<li>GFP1 Sequence(588nt)in PUC57 received from Bio Basic Canada INC..</li><br/>
+<h5>Tuesday July 12, 2011</h5>
+<li>Liquid cultures of GFP1 (x2), IN1, IN2, GFP2 and PSB1C3 were innoculated with the appropriate antibiotic in the broth..</li><br/>
+<h5>Wednesday July 13, 2011</h5>
+<li>GFP1, IN1, IN2, GFP2 and PSB1C3 were minipreped to isolate plasmid DNA..</li>
+<li>Frozen stock of GFP1 made..</li><br/>
+<h5>Thursday July 14, 2011</h5>
+<li>GFP1, IN1, IN2, GFP2, PSB1C3 digested with EcoRI and PstI. GFP2 also digested with ndeI..</li>
+<li>Innoculation of liquid culture (GFP1, IN1, IN2, GFP2, PSB1C3)..</li><br/>
+<h5>Friday July 15, 2011</h5>
+<li>Gel extraction of GFP1, IN1, IN2, GFP2 and PSB1C3. However, the results were not as anticipated..</li>
+<li>Miniprep of cultures innoculated yesterday.</li><br/>
+<h5>Monday July 18, 2011</h5>
+<li>Cultures were miniprepped, however, GFP1 did not have a sufficient concentration to undergo digestion..</li>
+<li>Proceeded with digestion for GFP2 (ndeI), IN1, IN2 and PSBIC3 with EcoRI and PstI..</li>
+<li>Innoculation of GFP1 (x4).</li><br/>
+<h5>Tuesday July 19, 2011</h5>
+<li>Miniprep and digestion of GFP1..</li>
+<li>Gel extraction of each digestion (PSB1C3(x2), GFP1, IN1, IN2, GFP2)..</li><br/>
+<h5>Wednesday July 20, 2011</h5>
+<li>Lox resuspended and digested..</li>
+<li>Ligation of GFP2, IN1, IN2 and Lox into PSB1C3..</li><br/>
+<h5>Thursday July 21, 2011</h5>
+<li>Transformation of GFP2, IN1, IN2 and Lox. Each was plated on cm containing media and grown overnight..</li><br/>
+<h5>Friday July 22, 2011</h5>
+<li>All negative plates did not produce colonies..</li>
+<li>Growth was good on all positive plates except for IN1, which only produced two main colonies..</li><br/>
+<h5>Monday July 25, 2011</h5>
+<li>Gel extraction IN1, IN2 and GFP1, however, GFP1 failed..</li>
+<li>Ligation of IN1 and IN2 into PSB1C3..</li><br/>
+<h5>Tuesday July 26, 2011.</h5>
+<li>Innoculation of GFP2 into cm containing LB broth tube and lox into amp containing LB broth tube..</li>
+<li>Gel extraction did not work (likely a problem with digestion or transformation).</li>
+<li>Innoculation x5 of GFP1..</li><br/>
+<h5>Wednesday July 27, 2011</h5>
+<li>Frozen stock of GFP2 and lox made.</li>
+<li>Miniprep of GFP1 x4 replicates.</li>
+<li>Gel extraction of IN1 and IN2 resulted in improved concentrations.</li>
+<li>Transformation.</li><br/>
+<h5>July 30, 2011</h5>
+<li>Miniprepped GFP 1 and GFP 2.</li><br/>
+<h5>August 2, 2011</h5>
+<li>Miniprepped Intron 1 and intron 2..</li><br/>
+<h5>August 3, 2011</h5>
+<li>Digestion of GFP 1 and Intron 2 with SacI and EarI.</li>
+<li>Digestion of GFP2 and Intron 1 with SacI and SapI.</li><br/>
+<h5>August 4, 2011</h5>
+<li>Nothing.</li>
+<li>Figuring out unexpected SacI cute site in the middle of pSB1C3 vector.</li><br/>
+<h5>August 5, 2011</h5>
+<li>Nothing.</li><br/>
+<h5>August 6, 2011</h5>
+<li>Digestion of GFP 1 with Bgl II and Ear I.</li>
+<li>Digestion of Intron 1 with Bgl II and Ear I.</li>
+<li>Digestion of GFP 1 with Ear I and Pst I.</li>
+<li>Digestion of GFP 2 with EarI and Pst I..</li>
+<li>Gel extraction of all the samples listed above.</li><br/>
+<h5>August 7, 2011</h5>
+<li>Ligation of GFP 1 with Intrton 1 and GFP 1 with GFP 2.</li>
+<li>Transformation of the two ligation mixtures listed above.</li><br/>
+<h5>August 8, 2011</h5>
+<li>Minipreping Int2, lox and GFP2.</li>
+<li>Digestion.</li>
+<li>Gel extraction.</li><br/>
+<h5>August 9, 2011</h5>
+<li>Miniprepping BBa_K576007.</li>
+<li>Digestion.</li>
+<li>gel extraction.</li><br/>
+<h5>August 10, 2011</h5>
+<li>Ligation and transformation of BBa_K576007 and J61046 to create K576009.</li><br/>
+<h5>August 11, 2011</h5>
+<li>Ligation and transformation.</li><br/>
+<h5>August 12, 2011</h5>
+<li>Streak plating GFP1-GFP2 (BBa_K576013).</li>
+<li>Backbone for RFC arrived and was streaked on cm plate.</li><br/>
+<h5>August 15th, 2011</h5>
+<li>Inoculation of a single colony of K371053 into an LB broth</li><br/>
-http://partsregistry.org/Help:Spring_2010_DNA_distribution<br />
+<h5>August 16th, 2011</h5>
-Decided to leave 3A alone for now<br />
+<li>Made frozen stock of K371053</li>
-http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly<br /><br />
+<li>Inoculated K371053 (X3), K576004, and K576006.</li><br/>
-<h4>October 5</h4><br />
-Checked on the plates from Saturday:<br /><br />
+<h5>August 17th, 2011</h5>
+<li>Miniprepped K371053(vector), K576004 (insert),  and K5756006 (insert).</li>
+<li>Standard assembly of the two parts and a vector listed above. Ran gel extraction experiment after.</li><br/>
--ve ctrl : no growth<br />
+<h5>August 18th, 2011</h5>
-+ve ctrl: no growth<br />
+<li>Ligation and transformation reaction for transferring K576004 and K576006 from pSB1C3 to K371053.</li><br/>
--1: contaminated<br />
--2: some rosy colonies and white ones. inoculated 5 rosy ones into tubes, but they were so close to each other, I also made one streak plate as backup<br />
--1: few rosy (and white) colonies<br />
--2: (white), rosy and bright red. went for bright red, 5 tubes, 2 streak plates<br />
-DB3.1 reinoculated (again)<br />
-LEFT:<br /><br />
-tubes on shaker<br />
+<h5>August 19th, 2011</h5>
-plates in fridge<br />
+<li>Inoculation of single colonies from the transformed samples from the previous days.</li>
-plates in incubator<br /><br />
+<li>Inoculated K576009</li><br/>
-<h4>October 6</h4><br />
-Transformed the DB3.1 :<br />
+<h5>August 22nd, 2011</h5>
-<a href="http://partsregistry.org/Help:Spring_2010_DNA_distribution pSB1C3-BBa_P1010 from Spring 2009 Distribution Plate 1 Well 5E">
+<li>Created frozen stock and inoculated K576004 and K576006 on K371053</li>
-http://partsregistry.org/Help:Spring_2010_DNA_distribution pSB1C3-BBa_P1010 from Spring 2009 Distribution Plate 1 Well 5E</a><br /><br />
+<li>Miniprepped, digested (SpeI and PstI) and gel extracted K576009.</li><br/>
-plate 1 was obtained,<br />
+<h5>August 23rd, 2011</h5>
-uL MQ was pipetted into Well 5E and all was transfered to a microfuge tube. *labelled: 2009-1-5E, pSB1C3-P1010
+<li>Miniprepped, digested and gel extracted K576004 (SpeI and PstI) and K576006 (XbaI and PstI) on K371053. </li><br/>
-mL of DB3.1 culture was pipetted into microfuge tube. Spun down (~12,000rpm/2 min), decanted and kept on ice. This was repeated twice with 1mL of CaCl2 but spun down in the fridge with the glass door.<br />
-uL of CaCl2 + 2uL of DNA from the 5E well were added and tube was kept on ice for 30 mintues.<br />
-Transformation was proceeded as would normally be done using the protocol.<br /><br />
-<h4>October 7</h4><br />
-Transformation Results: FAILED. No growth on positive control or negative control.<br />
+<h5>August 24th, 2011</h5>
-Reinnoculated DB3.1 culture. Transformation will be reattempted.<br /><br />
+<li>Ligation and transformation of samples prepared on the 23rd. </li><br/>
-<h4>October 8</h4><br />
+<h5>August 25th, 2011</h5>
+<li>Single colony for K576008 was picked and inoculated</li><br/>
-Attempted transformation again using same protocol as before.<br />
+<h5>August 26th, 2011</h5>
-DIGESTION OF 008 & 009 PERFORMED AS INDICATED BELOW:<br />
+<li>Created frozen stock of K576008</li><br/>
--4,5(older prep),7(newer prep) will be digested E+P and ran on gel :<br />
-Ladder<br />
--4 /E+P<br />
--5 /E+P<br />
--7 /E+P<br />
-/E+P<br />
--4 undigested<br />
--5 undigested<br />
--7 undigested<br /><br />
-<h4>Monday, October 11</h4><br />
-Transformation FAILED. This will not be redone. To be discussed in weekly meeting on thursday.<br />
+<h5>August 28th, 2011</h5>
--5 was speedvaced,digested with E+P and ran on gel<br />
+<li>Inoculated K576008 and K576009 in LB broth containing chloramphenicol</li><br/>
-Worked on updating the Wiki and presentation<br /><br />
-<h4>Tuesday, October 12</h4><br />
+<h5>August 29th,2011</h5>
+<li>miniprepped and digested K576008 and K576009.</li><br/>
-Analyzed results from gel on friday:<br />
+<h5>August 30th, 2011</h5>
-Ladder: yeah.<br />
+<li>Gel extraction of K576008 (insert) and K576009 (vector). </li><br/>
--4 /E+P: ladder contamination?<br />
--5 /E+P:<br />
--7 /E+P: the most probable, don't ask me what is in the lowest band<br />
-/E+P: overkill amount, had to have lower exposure to view<br />
--5 undigested: looks fine for undigested<br />
--5 E+P: see above<br />
-/E+P: overkill<br /><br />
-<h4>Wednesday, October 13</h4><br />
-Worked to complete Human practices section<br />
+<h5>August 31st, 2011</h5>
-Individual photos of active team members were gathered with a small blurb about each person for wiki<br />
+<li>Ligation and transformation of final construction (BBa_K576011)</li><br/>
-Worked on updating Quantification for the lab wiki & the SVG tree<br />
-<h4>Thursday, October 14</h4><br />
+<h5>September 1st-2nd, 2011</h5>
+<li>No lab work was done.</li><br/>
-Board meeting: updated on work done in all sections, upcoming work plans made<br />
+<h5>September 4th, 2011</h5>
-Weekly Lab meeting: shared information from board meeting with the rest of the members and accordindly, created an agenda:<br />
+<li>inoculated K576011 and K576008 in LB broth containing Chloromphenicol antibiotic</li><br/>
-Wiki: all due Saturday morning by 12 pm (Oct 23)<br />
-Lab:<br />
-Some intro (very general)<br />
-Quantification: (by Monday, Oct 18)<br />
-Construction tree- SVG (by Monday, Oct 18)<br /><br />
-<h4>Monday, October 18</h4><br />
-Team photos taken<br />
+<h5>September 5th, 2011</h5>
-Looked through our fridge and freezer. Put all relevant microfuge tubes into the "2010 Parts Kit 2" green box.<br />
+<li>Miniprepped, digested (EcoRI and PstI) and gel electrophoresed part K576008 to move the part into pSB1C3 for submission. Questionable band placement; Did not go further with the experiment.</li>
-Could not find 006, nor 007 but did find 008 and 009 and so,inoculated 3 tubes for each.<br />
+<li>Miniprepped all the intermediate steps, controls and final construction for submission to partsregistry.</li><br/>
-Digested parts 003, 006, 007, 008, 009 and pSB1C3 with E + P. Purified these digests and then left them over night in part + pSB1C3 ligations. Also, made 3 inoculations of pSB1C3 and 2 inoculations each of 009/008 (total of 7). These are all on the shaker.<br /><br />
-<h4>Tuesday, October 19</h4><br />
-Miniprepped pSB1C3/008/009 (9 tubes in total) from the incubator.This is required in the case that the transformations are unsuccessful,so that we can start over.<br />
+<h5>September 6th, 2011</h5>
-Nanodropped them and results are as follows:<br />
+<li>Miniprepped, digested and gel extracted part K576008. Confirmed band placement via aPe program. Failed at the final step of the gel extraction process; Wash Solution without ethanol (miniprep solution provided from Biobasic) was added </li><br/>
-pSB1C3 - 1<br />
-CONCENTRATION: 48.7ng/uL<br />
-/280 1.96<br />
-pSB1C3 - 2<br />
-CONCENTRATION: 185ng/uL<br />
-/280 1.91<br />
-pSB1C3 - 3<br />
-CONCENTRATION: 58.4ng/uL<br />
-/280 1.93<br />
--1<br />
-CONCENTRATION: 59.8ng/uL<br />
-/280 1.75<br />
--2<br />
-CONCENTRATION: 131.7ng/uL<br />
-/280 1.86<br />
--1<br />
-CONCENTRATION: 121.7ng/uL<br />
-/280 1.95<br />
--2<br />
-CONCENTRATION: 209.0ng/uL<br />
-/280 1.92<br />
-Transformed all 5 ligations, which were in the PCR machine, in DH5alpha on to Cm plates. Stored the remainder of the ligations in Parts Kit #2, green box in freezer.<br />
-Made media broth - 200mL, placed into 5ml tubes and autoclaved.<br /><br />
-<h4>Wednesday, October 20</h4><br />
+<h5>September 7th, 2011</h5>
+<li>Miniprepped, digested and gel extracted part K576008. </li><br/>
-Ligated 006 into pSB1C3..? RESULTS: TO BE UPDATED<br />
+<h5>Septermber 8th, 2011</h5>
-Cut out the RFP which is currently with the pSB1C3 (5 tubes labelled pSB1C3 contain that plasmid plus an RFP biobrick.<br /> We need to cut out the RFP biobrick and leave just the plasmid for ourselves.<br />
+<li>Ligation and transformation reaction for K576008. Moved K576008 part from the BBa_K371053 to pSB1C3 for submission purposes.</li><br/>
-Need to do the insertions of the biobricks into the desired plasmid (pSB1C3).<br /><br />
-<h4>Thursday, October 21</h4><br />
-Worked to complete Human Practices section<br />
+<h5>Septermber 9th – 15th, 2011</h5>
-Continued work on Jamboree Presentation. Work will be continued on the weekend.<br />
+<li>no lab work was done</li><br/>
-streaked and inoculated into liquid media.<br /><br />
-<h4>Friday, October 22</h4><br />
-Miniprepped the inoculations from yesterday and nanodropped them. Results are as follows:<br />
+<h5>September 16th, 2011</h5>
-These need to digested and shipped off to Boston.<br />
+<li>Final diagnostic digestion reaction. Digested every intermediate, control and final constructs. BBa_K576003, K576004, K576005, and K576006 were the only parts able to be confirmed. All the other intermediates and constructs have questionable band location. Lab work stopped due to time constraint. </li><br/><br/>
-Still need have lots of work pendning for the presentation and other administrative work that will be worked on the weekend and carried over for next week.<br /><br />
 </div>
@@ Line 1,688: / Line 1,123: @@
 <br/>The parts that are associated with the project this year are at the same level of risk as the any of the regular parts that already exist. All parts are constructed in an antibiotic containing backbone so that accidental release of will pose minimal risk to contaminating other bacterial populations.
 <p>
-<br>2.<b>Under what biosafety provisions will / do you operate?</b>
+<br>2.<b>Under what biosafety provisions will / do you operate?</b><br/>
 <b>a.Does your institution have its own biosafety rules and if so what are they?</b> The University of Waterloo had a Bio-Safety plan in place to ensure the proper use to bio-hazardous materials in teaching and research at the university. A more detailed overview of their plans is outlined at the <a href="http://www.safetyoffice.uwaterloo.ca/hse/bio_safety/bsc.html">Bio-Safety Website</a>
 <br/><b>b. Does your institution have an Institutional Biosafety Committee or equivalent group? If yes, have you discussed your project with them? </b>The laboratories operating at the University of Waterloo have obtained permits from the Bio-Safety Committee in order to perform intended research. Since the Waterloo iGEM team performs all laboratory work in a parent lab under the guidance of the Masters and PhD students of that lab, the projects carried out in the lab are covered by the permits obtained by the parent lab.