"
Team:Calgary/Project/Achievements
From 2014.igem.org
(Difference between revisions)
Fretwell s (Talk | contribs) |
|||
| (3 intermediate revisions not shown) | |||
| Line 8: | Line 8: | ||
<ul> | <ul> | ||
| - | <li>Thoroughly researched our <span class="Orange">target markets</span> and <span class="Orange">differing legislations</span> that could affect our system</li> | + | <li>Thoroughly researched our <span class="Orange"><b>target markets</b></span> and <span class="Orange"><b>differing legislations</b></span> that could affect our system</li> |
| - | <li>Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and <span class="Orange">feasibility</span> of the project</li> | + | |
| - | <li>Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the <span class="Orange">viability</span> of our design and concept</li> | + | <li>Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and <span class="Orange"><b>feasibility</b></span> of the project</li> |
| - | <li>Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with <span class="Orange">local physicians</span></li> | + | |
| - | <li>Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the <span class="Orange">advancement</span> of synthetic biology</li> | + | <li>Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the <span class="Orange"><b>viability</b></span> of our design and concept</li> |
| + | |||
| + | <li>Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with <span class="Orange"><b>local physicians</b></span></li> | ||
| + | <li>Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the <span class="Orange"><b>advancement</b></span> of synthetic biology</li> | ||
</ul> | </ul> | ||
| Line 18: | Line 21: | ||
<ul> | <ul> | ||
| - | <li>Designed and manufactured a <span class="Blue">prototype</span> of informed design based on our biological system</li> | + | <li>Designed and manufactured a <span class="Blue"><b>prototype</b></span> of informed design based on our biological system</li> |
| - | <li><span class="Blue">Cost analysis</span> of our prototype and system to ensure that this project is feasible in developing nations</li> | + | <li><span class="Blue"><b>Cost analysis</b></span> of our prototype and system to ensure that this project is feasible in developing nations</li> |
| - | <li><span class="Blue">Quantified</span> the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor</li> | + | <li><span class="Blue"><b>Quantified</b></span> the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor</li> |
| - | <li><span class="Blue">Programmed</span> an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour</li> | + | <li><span class="Blue"><b>Programmed</b></span> an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour</li> |
| - | <li>Applied circuitry of a heating pad/temperature considerations for <span class="Blue">ideal</span> isothermal PCR conditions</li> | + | <li>Applied circuitry of a heating pad/temperature considerations for <span class="Blue"><b>ideal</b></span> isothermal PCR conditions</li> |
| - | <li>Used Autodesk Maya Software to <span class="Blue">visually model</span> and represent our system</li> | + | <li>Used Autodesk Maya Software to <span class="Blue"><b>visually model</b></span> and represent our system</li> |
| - | <li>Used Solid-works Software to <span class="Blue">model</span> fluid flow analysis for different prototype designs</li> | + | <li>Used Solid-works Software to <span class="Blue"><b>model</b></span> fluid flow analysis for different prototype designs</li> |
</ul> | </ul> | ||
| Line 31: | Line 34: | ||
<ul> | <ul> | ||
| - | <li><span class="Orange">Transformed</span> <i>B. subtilis</i> with a primer product containing 125 bp of | + | <li><span class="Orange"><b>Transformed</b></span> <i>B. subtilis</i> with a primer product containing 125 bp of |
homologous sequence flanking our gene of interest</li> | homologous sequence flanking our gene of interest</li> | ||
| - | <li>Modified and optimized general transformation: <span class="Orange">characterized</span> effect of | + | |
| + | <li>Modified and optimized general transformation: <span class="Orange"><b>characterized</b></span> effect of | ||
changing xylose concentrations, temperature, and shaking</li> | changing xylose concentrations, temperature, and shaking</li> | ||
| - | <li><span class="Orange">Optimization</span> of transformation in small, liquid volume</li> | + | <li><span class="Orange"><b>Optimization</b></span> of transformation in small, liquid volume</li> |
| - | <li><span class="Orange">Sporulated</span> <i>B. subtilis</i></li> | + | <li><span class="Orange"><b>Sporulated</b></span> <i>B. subtilis</i></li> |
| - | <li><span class="Orange">Activated</span> <i>B. subtilis</i> spores back to vegetative state</li> | + | |
| - | <li>Isolated the master regular for competency, <span class="Orange"><i>comK</i></span> from the genome of <i>B. subtilis</i> using PCR and inserted it into a <span class="Orange">Biobrick</span> vector for future application as an iGEM standard part. | + | <li><span class="Orange"><b>Activated</b></span> <i>B. subtilis</i> spores back to vegetative state</li> |
| + | <li>Isolated the master regular for competency, <span class="Orange"><i><b>comK</b></i></span> from the genome of <i>B. subtilis</i> using PCR and inserted it into a <span class="Orange"><b>Biobrick</b></span> vector for future application as an iGEM standard part. | ||
</ul> | </ul> | ||
| Line 45: | Line 50: | ||
<ul> | <ul> | ||
| - | <li>Demonstrated efficacy of <span class="Blue">isothermal PCR</span> to amplify DNA sequences | + | <li>Demonstrated efficacy of <span class="Blue"><b>isothermal PCR</b></span> to amplify DNA sequences |
without the need of a thermocycler, using freeze-dried components</li> | without the need of a thermocycler, using freeze-dried components</li> | ||
<li>Demonstrated ability to amplify target DNA sequence from whole | <li>Demonstrated ability to amplify target DNA sequence from whole | ||
| - | <i>E. coli</i> cells in a <span class="Blue">blood mixture</span></li> | + | <i>E. coli</i> cells in a <span class="Blue"><b>blood mixture</b></span></li> |
| - | <li>Obtained <span class="Blue">specificity</span> in target sequence primers - specific to numerous strains of | + | <li>Obtained <span class="Blue"><b>specificity</b></span> in target sequence primers - specific to numerous strains of |
<i>N. meningititis</i> but not other pathogens including a commensal strain of <i>N. meningititis</i> | <i>N. meningititis</i> but not other pathogens including a commensal strain of <i>N. meningititis</i> | ||
| Line 58: | Line 63: | ||
<ul> | <ul> | ||
| - | <li>Designed composite <span class="Orange">regulatory promoter sequences</span> - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or | + | <li>Designed composite <span class="Orange"><b>regulatory promoter sequences</b></span> - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or |
triplicate repeats for variation in strength of repression</li> | triplicate repeats for variation in strength of repression</li> | ||
| - | <li>Demonstrated <span class="Orange">interaction</span> (i.e. repression) between the reporter gene and repressor gene in <i>E. coli</i></li> | + | <li>Demonstrated <span class="Orange"><b>interaction</b></span> (i.e. repression) between the reporter gene and repressor gene in <i>E. coli</i></li> |
| - | <li>Demonstrated the efficacy of <span class="Orange">homologous recombination</span> in <i>B. subtilis</i> and showed the minimum length of flanking sequences</li> | + | <li>Demonstrated the efficacy of <span class="Orange"><b>homologous recombination</b></span> in <i>B. subtilis</i> and showed the minimum length of flanking sequences</li> |
| - | <li><span class="Orange">Biobricked</span> and submitted the full-length <span class="Orange"><i>lacZ</i></span> gene, previously non-existent in the latest | + | <li><span class="Orange"><b>Biobricked</b></span> and submitted the full-length <span class="Orange"><i><b>lacZ</b></i></span> gene, previously non-existent in the latest |
distribution plates</li> | distribution plates</li> | ||
| - | <li>Constructed a <span class="Orange">reporter operon</span> consisting of a constitutive promoter (Pveg), ribosome binding site, operator (C1434) and reporter ( | + | <li>Constructed a <span class="Orange"><b>reporter operon</b></span> consisting of a constitutive promoter (<i>Pveg</i>), ribosome binding site, operator (C1434) and reporter (<i>lacZ/RFP</i>).</li> |
| - | <li>Constructed a <span class="Orange">complementary repressor operon</span> consisting of a constitutive promoter (Pveg), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.</li> | + | <li>Constructed a <span class="Orange"><b>complementary repressor operon</b></span> consisting of a constitutive promoter (<i>Pveg</i>), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.</li> |
</ul> | </ul> | ||
Latest revision as of 03:12, 18 October 2014
Achievements
Policies and Practices:
- Thoroughly researched our target markets and differing legislations that could affect our system
- Connected with many different experts in the fields of infectious diseases, anti-malarial medications and public health to truly understand the needs and feasibility of the project
- Connected with the foremost authority in low cost diagnostics, Foundation for Innovative New Diagnostics (FIND), to discuss the viability of our design and concept
- Connected with a small village clinic in rural Uganda, which gave an opportunity to see the facility as well as discuss the topic with local physicians
- Featured iGEM and our project on a global stage at the United Nations, in Geneva, and created discussion regarding the advancement of synthetic biology
Modelling:
- Designed and manufactured a prototype of informed design based on our biological system
- Cost analysis of our prototype and system to ensure that this project is feasible in developing nations
- Quantified the visible threshold of detection for several reporters using time-lapsed cell count and absorbance readings, as well as a programmed colour sensor
- Programmed an Arduino UNO microcontroller, colour sensor, and LCD screen to detect colour change among detection chambers, allowing for quantification of the colour
- Applied circuitry of a heating pad/temperature considerations for ideal isothermal PCR conditions
- Used Autodesk Maya Software to visually model and represent our system
- Used Solid-works Software to model fluid flow analysis for different prototype designs
Transformation:
- Transformed B. subtilis with a primer product containing 125 bp of homologous sequence flanking our gene of interest
- Modified and optimized general transformation: characterized effect of changing xylose concentrations, temperature, and shaking
- Optimization of transformation in small, liquid volume
- Sporulated B. subtilis
- Activated B. subtilis spores back to vegetative state
- Isolated the master regular for competency, comK from the genome of B. subtilis using PCR and inserted it into a Biobrick vector for future application as an iGEM standard part.
Sample Preparation:
- Demonstrated efficacy of isothermal PCR to amplify DNA sequences without the need of a thermocycler, using freeze-dried components
- Demonstrated ability to amplify target DNA sequence from whole E. coli cells in a blood mixture
- Obtained specificity in target sequence primers - specific to numerous strains of N. meningititis but not other pathogens including a commensal strain of N. meningititis
Detection/Genetic circuit
- Designed composite regulatory promoter sequences - used to allow repression of a downstream reporter with a specific repressor. Includes 5 variants of repressible promoters in either single or triplicate repeats for variation in strength of repression
- Demonstrated interaction (i.e. repression) between the reporter gene and repressor gene in E. coli
- Demonstrated the efficacy of homologous recombination in B. subtilis and showed the minimum length of flanking sequences
- Biobricked and submitted the full-length lacZ gene, previously non-existent in the latest distribution plates
- Constructed a reporter operon consisting of a constitutive promoter (Pveg), ribosome binding site, operator (C1434) and reporter (lacZ/RFP).
- Constructed a complementary repressor operon consisting of a constitutive promoter (Pveg), ribosome binding site, and repressor pertaining to the operator. Repressor was also flanked with regions homologous to certain sequences within our pathogens of interest.
