Team:DTU-Denmark/Achievements/Medal fulfillings

From 2014.igem.org

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<pageheader>Medal fulfillments</pageheader>
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<li>Participate in the Measurement Interlab Study</li>
<li>Participate in the Measurement Interlab Study</li>
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<li>As participants in the measurement track we have contributed to the <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/Interlab_study">Interlab
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<li>As participants in the measurement track we have contributed to the <a href="https://2014.igem.org/Team:DTU-Denmark/Interlab_form">Interlab
               Study</a>, by transforming GFP expressed from different promoters into <i>E. coli</i> and measure                        
               Study</a>, by transforming GFP expressed from different promoters into <i>E. coli</i> and measure                        
               fluorescence signal with BioLector and FACS.</li>
               fluorescence signal with BioLector and FACS.</li>
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               <li>Furthermore we intended to streamline the <a href="http://parts.igem.org/Promoters/Catalog/Anderson"target="_blank">Anderson promoter library</a> by   
               <li>Furthermore we intended to streamline the <a href="http://parts.igem.org/Promoters/Catalog/Anderson"target="_blank">Anderson promoter library</a> by   
                     transforming promoters formerly present in plasmid J61002 into the iGEM standard
                     transforming promoters formerly present in plasmid J61002 into the iGEM standard
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                 backbone pSB1C3. This includes the promoters J23105, J23110, J23112 and J23116, now registered as <a    href="http://parts.igem.org/Part:BBa_K1330002" Target="_blank">BBa_K1330002</a>, BBa_K1330003, BBa_K1330004 and BBa_K1330005 respectively.
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                 backbone pSB1C3. This includes the promoters J23105, J23110, J23112 and J23116, now registered as <a    href="http://parts.igem.org/Part:BBa_K1330002" Target="_blank">BBa_K1330002</a>, <a href="http://parts.igem.org/Part:BBa_K1330003" Target="_blank">BBa_K1330003</a>, <a href="http://parts.igem.org/Part:BBa_K1330004" Target="_blank">BBa_K1330004</a> and <a href="http://parts.igem.org/Part:BBa_K1330005" Target="_blank">BBa_K1330005</a> respectively.
                 This will be a great advantage for future iGEM teams working with the Anderson promoter Library. </li>
                 This will be a great advantage for future iGEM teams working with the Anderson promoter Library. </li>
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<li>Document the characterization of this part in the Registry.</li>
<li>Document the characterization of this part in the Registry.</li>
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<ul><li>The two Spinach2.1 BioBricks and the corresponding documentation can be found in the Registry with the entries <a href="http://parts.igem.org/Part:BBa_K1330000">BBa_K1330000</a> and <a href="http://parts.igem.org/Part:BBa_K1330001">BBa_K1330001</a>.</li></ul>
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<ul><li>The two Spinach2.1 BioBricks and the corresponding documentation can be found in the Registry with the entries <a href="http://parts.igem.org/Part:BBa_K1330000" Target="-blank">BBa_K1330000</a> and <a href="http://parts.igem.org/Part:BBa_K1330001" Target="-blank">BBa_K1330001</a>.</li></ul>
<li>Submit this new part to the iGEM Parts Registry </li>
<li>Submit this new part to the iGEM Parts Registry </li>
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<li>Demonstrate a substantial improvement over the state of the art in cost, efficiency, precision, resolution, and/or other relevant capabilities of your measurement technique.</li>
<li>Demonstrate a substantial improvement over the state of the art in cost, efficiency, precision, resolution, and/or other relevant capabilities of your measurement technique.</li>
<ul>
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<li>Today promoter activity is measured with the use of GFP which entail several complications, including bleaching effect and uncertainty associated with measuring on protein level. The method developed through our project exterminate these issues by using the spinach RNA-aptamer expressed from the promoter of choice. This allows measurement performed at RNA level thereby eliminating several uncertainties faced when using GFP. With our experimental work and our developed PoPS <a href="https://2014.igem.org/Team:DTU-Denmark/Calculator">calculator</a> we have enabled a new way of measuring promoter activity on RNA-level with the use of Spinach.</li>
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<li>Today promoter activity is measured with the use of GFP which entail several complications, including bleaching effect and uncertainty associated with measuring on protein level. The method developed through our project exterminate these issues by using the spinach RNA-aptamer expressed from the promoter of choice. This allows measurement performed at RNA level thereby eliminating several uncertainties faced when using GFP. With our experimental work and our developed PoPS <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/Calculator">calculator</a> we have enabled a new way of measuring promoter activity on RNA-level with the use of Spinach.</li>
</ul>
</ul>
<li>Increase the ease of accessibility and portability of methods to other laboratories of a new measurement technique of your choosing.</li>
<li>Increase the ease of accessibility and portability of methods to other laboratories of a new measurement technique of your choosing.</li>
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<ul> <li>We have transformed Spinach2.1 into the standard iGEM backbone so it easily can be placed behind any optional promoter. Thereby making a easy, fast and standardized protocol to measure promoter strength on RNA level. With our <a href="https://2014.igem.org/Team:DTU-Denmark/Calculator">calculator</a> we have developed a fast and easy way to convert fluorescence signal into a absolute PoPS value for promoter activity.</li></ul>
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<ul> <li>We have transformed Spinach2.1 into the standard iGEM backbone so it easily can be placed behind any optional promoter. Thereby making a easy, fast and standardized protocol to measure promoter strength on RNA level. With our <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/Calculator">calculator</a> we have developed a fast and easy way to convert fluorescence signal into a absolute PoPS value for promoter activity.</li></ul>
<li>Help any registered iGEM team from another school or institution. </li>
<li>Help any registered iGEM team from another school or institution. </li>
<ul><li>One of our first achievements was hosting a <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/BioBrick_Workshop">BioBrick Workshop</a> in May for the other two danish iGEM teams SDU-Denmark and UNIK Copenhagen. We shared our knowledge within USER cloning and arranged a programme covering three days of workshops with relevant presentations and lab introduction. Thereby helping other teams by giving them some skills, knowledge and techniques useful when developing a great iGEM project. It also served as a good way to start up the projects with the great opportunity for idea development and knowledge exchange among the teams. </li></ul>
<ul><li>One of our first achievements was hosting a <a href="https://2014.igem.org/Team:DTU-Denmark/Achievements/BioBrick_Workshop">BioBrick Workshop</a> in May for the other two danish iGEM teams SDU-Denmark and UNIK Copenhagen. We shared our knowledge within USER cloning and arranged a programme covering three days of workshops with relevant presentations and lab introduction. Thereby helping other teams by giving them some skills, knowledge and techniques useful when developing a great iGEM project. It also served as a good way to start up the projects with the great opportunity for idea development and knowledge exchange among the teams. </li></ul>
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Latest revision as of 00:10, 18 October 2014

Technical University of Denmark

Medal fulfillments
Since the 2014 DTU iGEM team is signed up in the Measurement Track we have specific medal requirements to fulfill. These are listed below together with our contributions. Some of the requirements have not yet been fulfilled, e.g. presenting our poster, but will be fulfilled at the Giant Jamboree.

Bronze Medal Requirements

The following 6 goals have been achieved or are going to be fulfilled at the final Giant Jamboree:
  1. Team registration
    • We are officially registered as a team representing the Technical University of Denmark in the iGEM 2014 competition. Visit our official team page for more information.
  2. Complete Judging form.
    • Our completed judging form can be found here
  3. Team Wiki.
    • We created this Wiki to communicate our project to our surroundings. Navigate around and discover how we have evolved the project in and outside the laboratory.
  4. Present a poster and a talk at the iGEM Jamboree.
    • We look very much forward to present our product after half a years hard work with a lot of experiences and fun.
  5. Participate in the Measurement Interlab Study
    • As participants in the measurement track we have contributed to the Interlab Study, by transforming GFP expressed from different promoters into E. coli and measure fluorescence signal with BioLector and FACS.
  6. Document at least one new standard BioBrick Part central to your project
    • We have submitted two novel BioBricks essential for our project to the iGEM Registry. This includes the Spinach2.1 in pSB1C3 backbone with and without a terminator. In the submitted BioBrick we have introduced two point mutations in the Spinach2 to remove an internal SpeI restriction site from the original sequence, resulting in Spinach2.1. The parts have been validated by sequencing and demonstrated to be expressed and bind to the fluorophore DFHBI-1T in E. coli. These two parts are registered as BBa_K1330000 and BBa_K1330001 and they are listed at our parts wiki page.
    • Furthermore we intended to streamline the Anderson promoter library by transforming promoters formerly present in plasmid J61002 into the iGEM standard backbone pSB1C3. This includes the promoters J23105, J23110, J23112 and J23116, now registered as BBa_K1330002, BBa_K1330003, BBa_K1330004 and BBa_K1330005 respectively. This will be a great advantage for future iGEM teams working with the Anderson promoter Library.


Silver Medal Requirements

In addition to the bronze medal requirements the requirements for silver medal have been achieved as stated below.
  1. Experimentally validate that at least one new BioBrick Part works as expected:
    • The Spinach2 fragments has been transformed into E. coli. Original Spinach2 and Spinach2.1 containing two point mutations to remove an internal SpeI restriction site, have been demonstrated to fluoresce at equal levels. Spinach2.1 can be applied in our developed method for measuring promoter activity. The parts have been demonstrated to fluoresce only after addition of the fluorophore DFHBI-1T. Furthermore the fluorophore was proved not to cause significant fluorescence signal without the spinach. See our experimental results for more information. This validates that the novel BioBrick works as we expected, and thereby we have opened up for our new new method for measurement of absolute promoter activities with the Spinach technology.
  2. Document the characterization of this part in the Registry.
    • The two Spinach2.1 BioBricks and the corresponding documentation can be found in the Registry with the entries BBa_K1330000 and BBa_K1330001.
  3. Submit this new part to the iGEM Parts Registry
    • Our parts have been submitted 2014.09.30
  4. Articulate at least one question within ethics, sustainability, social justice, safety, security, or intellectual property rights etc, encountered by your team, and describe how your team considered the(se) question(s) within your project.
    • As team we participated in a workshop on ethics hosted by the UNIK_Copenhagen iGEM’14 team. This led to an essay dealing with the several questions on ethics within our project.
      • What ethical issues should be considered regarding our project and synthetic biology in general?
      • How can these issues be approached?
    • Furthermore we have been dealing with laboratory safety since we find that essential for a good project. We have chosen to make a checklist on how to maintain good laboratory safety. This is targeted towards our defined Policy and Practices target group (Danish elite high school students) since they do not yet have well developed laboratory safety routines.


Gold medal requirements

3 of the 4 Gold medal criteria have been achieved
  1. Demonstrate a substantial improvement over the state of the art in cost, efficiency, precision, resolution, and/or other relevant capabilities of your measurement technique.
    • Today promoter activity is measured with the use of GFP which entail several complications, including bleaching effect and uncertainty associated with measuring on protein level. The method developed through our project exterminate these issues by using the spinach RNA-aptamer expressed from the promoter of choice. This allows measurement performed at RNA level thereby eliminating several uncertainties faced when using GFP. With our experimental work and our developed PoPS calculator we have enabled a new way of measuring promoter activity on RNA-level with the use of Spinach.
  2. Increase the ease of accessibility and portability of methods to other laboratories of a new measurement technique of your choosing.
    • We have transformed Spinach2.1 into the standard iGEM backbone so it easily can be placed behind any optional promoter. Thereby making a easy, fast and standardized protocol to measure promoter strength on RNA level. With our calculator we have developed a fast and easy way to convert fluorescence signal into a absolute PoPS value for promoter activity.
  3. Help any registered iGEM team from another school or institution.
    • One of our first achievements was hosting a BioBrick Workshop in May for the other two danish iGEM teams SDU-Denmark and UNIK Copenhagen. We shared our knowledge within USER cloning and arranged a programme covering three days of workshops with relevant presentations and lab introduction. Thereby helping other teams by giving them some skills, knowledge and techniques useful when developing a great iGEM project. It also served as a good way to start up the projects with the great opportunity for idea development and knowledge exchange among the teams.


Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
+45 45 25 25 25
dtuigem14@gmail.com .

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