http://2010.igem.org/wiki/index.php?title=Special:Contributions/Peteremmrich&feed=atom&limit=50&target=Peteremmrich&year=&month=2010.igem.org - User contributions [en]2024-03-28T18:24:06ZFrom 2010.igem.orgMediaWiki 1.16.5http://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-28T03:43:28Z<p>Peteremmrich: /* Applications */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. To help publicise our conclusions we produced a short video summarising the arguments for openness in research.<br />
<br />
==Futures==<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Cocktail.jpg|caption=Bioluminescent drinks of the future?}}<br />
<br />
We spent a day early in the project imagining how engineered artificial bioluminescence might be used in the future. This workshop, led by [http://www.daisyginsberg.com/ Daisy Ginsberg] from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How would omnipresent bioluminescence affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
We split the team into three groups, each of which went on to explore their own ideas about the future of bioluminescence:<br />
<br />
The first group considered the impact of bacterial lighting at home. If ‘E.colights’ became available for household use how would they be received? What issues would have to be addressed for this to happen? We also considered the markets for other domestic products that might arise as a result and made a mock advert for ‘Bactobang’, an improved antibacterial agent to prevent the escape of bioluminescent synthetic organisms should their container become damaged. We also thought about the possibility of bioluminescence in art and fashion and presented our ideas to the rest of the team.<br />
<br />
The second group envisaged ‘Bright Foods’ where the plants and animals that we eat might be engineered to have different colours of bioluminescence that would give an easily interpretable indication of nutritional content. The brightness of the luminescence would fade over time giving an indication of the freshness of the foodstuffs. This could also add an additional dimension to the experience of eating – perhaps restaurants would serve food in the dark so customers could fully appreciate the aesthetics of their luminescent meal. Food standards agencies might even insist that all food conforms to bioluminescent regulations such that foods with high levels of salt or saturated fat glowed particular colours to indicate this to customers. Perceptions might change such that people come to expect their food to glow and view dark food as spoiled and unappetizing. Bioluminescent cocktails could also become a fashionable drink in upmarket bars.<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Light_polution.jpg|caption=Bioluminescence genes escaping}}<br />
The third group considered how bioluminescence might slowly replace conventional lighting and the issues with intellectual property that this might cause. Initially, artificial bioluminescence could be a novelty – perhaps bioluminescent fish would be a popular pet. As our knowledge of synthetic biology grows, luminescent trees could become a real possibility; the commercial potential in replacing the street lights of the world could lead to strong competition with patents for bioluminescent systems. It could then be difficult to control and police the use of patented genetic systems; if the parts were put into fertile organisms then people might start illegally breeding their own light sources. We also considered containment issues and people’s attitudes towards them. As organisms engineered to be bioluminescent would not pose any considerable threat to public health or the environment, their escape might not be considered a serious issue. The amazement and awe inspired by natural bioluminescence might even <br />
lead to the escape of bioluminescent genes being welcomed by the public of the future – particularly one that had grown accustomed to this form of lighting in their homes and cities.<br />
<br />
==Applications==<br />
[[Image:Home ec pic.jpg|370px|thumb|left|Bioluminescence at home]]<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be more sustainable and environmentally friendly than conventional devices? Were might it be useful? Bioluminescence is 'cold light' and much more efficient than conventional lighting. Despite this we find it unlikely that bioluminescence would completely replace current lighting and instead considered it's applications in remote off grid areas or complementing existing sources. Our biological systems would require only a chemical fuel source so would not be dependant on the electrical grid. Perhaps this fuel could come from waste products be that human waste or food waste. If a photosynthetic organism such as a suitable alga species was used then additional energy could be harnessed from sunlight. We might imagine a system where a bioreactor in the roof of a house - supplied with leftover foodstuffs - could pipe glowing algae through the rooms of the house during the night and across the roof during the day. We also considered the exciting prospect of bioluminescent trees lighting our roads and produced a 3D model of what this might look like as well as researching the [https://2010.igem.org/Team:Cambridge/Tools/Lighting feasibility] of such a project.<br />
<br />
We also considered the prospect of using our light production in [https://2010.igem.org/Team:Cambridge/Tools/microMeasure biosensors] after a talk from [http://practicalaction.org/blog/author/djg/ David Grimshaw] of Practical Action. Dr. Grimshaw has worked with the issues of contamination of water sources with arsenic in Bangladesh and mercury in Nepal. He informed us that local people wished for a portable device that was easy to use such that testing of wells could be performed by members of the community and a quantitative digital readout would be preferable. Light production as an output of a biological circuit could be detected by a sensor in an electrical system to give a digital readout. Our biobricks could bridge the gap between biological and electrical circuits. Further investigation into the practicalities of this led to the development of the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]<br />
<br />
==Knowledge Recycling==<br />
<br />
''"He who receives an idea from me receives it without lessening me, as he who lights his candle at mine receives light without darkening me."'' – Thomas Jefferson<br />
<br />
Sustainability considerations in designing our system also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends? And what can we do to maximise knowledge recycling?<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Recycle.png|caption=}}<br />
We believe the need for openness and sharing of ideas to be of considerable importance to further knowledge, in the iGEM competition and beyond and the information society that we live in makes the sharing of ideas and finding relevant knowledge easier than ever before. The breadth and depth humanity’s current scientific understanding means that it is difficult for any single person to know enough about a particular area to make substantial advances on their own; collaboration is essential. It is not enough to only publicise and publish polished results at the end of a project. Work in progress should be made just as accessible to encourage this collaboration. Making available results from, and information about, experiments that failed is also important. It could prevent someone from wasting time trying exactly the same protocol again and may in fact be an important result in itself (that what was attempted be discovered simply cannot be discovered in that way). <br />
<br />
It is difficult to get research papers published for experiments that do not work, though journals such as the [http://www.jasnh.com/ Journal of Articles in Support of the Null Hypothesis] are changing this. Instead experiment attempts could be documented on wikis or blogs such that they are still available to someone searching the internet for them - this means all the hand work is not wasted, even if the desired results are not obtained. Protocols and techniques are particularly valuable when shared; reproducibility is a central concept to science and standardising protocols is necessary for this. Putting detailed protocols up on sites such as [http://openwetware.org/wiki/Main_Page open wetware] also helps encourage new researchers to get involved the particular field and prevents time and resources being wasted optimising procedures. <br />
<br />
After coming to these conclusions from our discussions we made sure we conducted our research in the light of these ideas. We got our Wiki up as early as possible with our aims and ideas and kept the online lab book updated with our ongoing research. We always endeavoured to be open and honest about exactly the protocols we were using and what results they gave. The [https://2010.igem.org/Team:UNAM-Genomics_Mexico UNAM Genomics, Mexico] team contacted us because of the information on our Wiki and we were able to collaborate with them and help them with part of their project. We were also able to have useful discussions with the [https://2010.igem.org/Team:Edinburgh Edinburgh] team based on information we read on each other’s Wikis. From our thoughts about sharing our findings we decided that we should put effort into publicising our science. Our project will be featured on a documentary to be broadcast on [http://www.arte.tv/fr/70.html ARTE] which will bring a better understanding of synthetic biology to the general public. We also wanted to get a message across to the scientific community; the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson assembly] technique which we performed frequently is not as widely used as we believe it could be so we chose this to publicise and produced a [https://2010.igem.org/Team:Cambridge/Videos music video] to do so. The song has over 3000 views so far and researchers have contacted us for more information about our experience with the technique.<br />
<br />
Many iGEM teams were similarly open with their ideas and results and this helped to foster the culture of collaboration that we believe is important to iGEM. We were however disappointed to see that some teams were less open. Three weeks before the wiki freeze 58 of the 127 teams participating had little more than an abstract on their wiki. This meant we were unable to engage in potentially valuable dialogue because we had little idea about what they were researching. To help encourage future teams and scientists generally to be more open with their work we produced a short video summarising our arguments. Previous iGEM teams have made interesting contributions to the field of human practises which perhaps have not had the desired effect on the way people conduct their science because not enough other scientists have seen them. We hope a short and more light-hearted summary might reach more people and help translate our conclusions into future action.<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-28T03:40:15Z<p>Peteremmrich: /* Applications */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. To help publicise our conclusions we produced a short video summarising the arguments for openness in research.<br />
<br />
==Futures==<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Cocktail.jpg|caption=Bioluminescent drinks of the future?}}<br />
<br />
We spent a day early in the project imagining how engineered artificial bioluminescence might be used in the future. This workshop, led by [http://www.daisyginsberg.com/ Daisy Ginsberg] from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How would omnipresent bioluminescence affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
We split the team into three groups, each of which went on to explore their own ideas about the future of bioluminescence:<br />
<br />
The first group considered the impact of bacterial lighting at home. If ‘E.colights’ became available for household use how would they be received? What issues would have to be addressed for this to happen? We also considered the markets for other domestic products that might arise as a result and made a mock advert for ‘Bactobang’, an improved antibacterial agent to prevent the escape of bioluminescent synthetic organisms should their container become damaged. We also thought about the possibility of bioluminescence in art and fashion and presented our ideas to the rest of the team.<br />
<br />
The second group envisaged ‘Bright Foods’ where the plants and animals that we eat might be engineered to have different colours of bioluminescence that would give an easily interpretable indication of nutritional content. The brightness of the luminescence would fade over time giving an indication of the freshness of the foodstuffs. This could also add an additional dimension to the experience of eating – perhaps restaurants would serve food in the dark so customers could fully appreciate the aesthetics of their luminescent meal. Food standards agencies might even insist that all food conforms to bioluminescent regulations such that foods with high levels of salt or saturated fat glowed particular colours to indicate this to customers. Perceptions might change such that people come to expect their food to glow and view dark food as spoiled and unappetizing. Bioluminescent cocktails could also become a fashionable drink in upmarket bars.<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Light_polution.jpg|caption=Bioluminescence genes escaping}}<br />
The third group considered how bioluminescence might slowly replace conventional lighting and the issues with intellectual property that this might cause. Initially, artificial bioluminescence could be a novelty – perhaps bioluminescent fish would be a popular pet. As our knowledge of synthetic biology grows, luminescent trees could become a real possibility; the commercial potential in replacing the street lights of the world could lead to strong competition with patents for bioluminescent systems. It could then be difficult to control and police the use of patented genetic systems; if the parts were put into fertile organisms then people might start illegally breeding their own light sources. We also considered containment issues and people’s attitudes towards them. As organisms engineered to be bioluminescent would not pose any considerable threat to public health or the environment, their escape might not be considered a serious issue. The amazement and awe inspired by natural bioluminescence might even <br />
lead to the escape of bioluminescent genes being welcomed by the public of the future – particularly one that had grown accustomed to this form of lighting in their homes and cities.<br />
<br />
==Applications==<br />
[[Image:Home ec pic.jpg|370px|thumb|left|Bioluminescence at home]]<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be more sustainable and environmentally friendly than conventional devices? Were might it be useful? Bioluminescence is 'cold light' and much more efficient than conventional lighting. Despite this we find it unlikely that bioluminescence would completely replace current lighting and instead considered it's applications in remote off grid areas or complementing existing sources. Our biological systems would require only a chemical fuel source so would not be dependant on the electrical grid. Perhaps this fuel could come from waste products be that human waste or food waste. If a photosynthetic organism such as a suitable alga species was used then additional energy could be harnessed from sunlight. We might imagine a system where a bioreactor in the roof of a house - supplied with leftover foodstuffs - could pipe glowing algae through the rooms of the house during the night and across the roof during the day. We also considered the exciting prospect of bioluminescent trees lighting our roads and produced a 3D model of what this might look like as well as researching the [https://2010.igem.org/Team:Cambridge/Tools/Lighting feasibility] of such a project.<br />
<br />
We also considered the prospect of using our light production in [[https://2010.igem.org/Team:Cambridge/Tools/microMeasure biosensors]] after a talk from [http://practicalaction.org/blog/author/djg/ David Grimshaw] of Practical Action. Dr. Grimshaw has worked with the issues of contamination of water sources with arsenic in Bangladesh and mercury in Nepal. He informed us that local people wished for a portable device that was easy to use such that testing of wells could be performed by members of the community and a quantitative digital readout would be preferable. Light production as an output of a biological circuit could be detected by a sensor in an electrical system to give a digital readout. Our biobricks could bridge the gap between biological and electrical circuits. Further investigation into the practicalities of this led to the development of the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]<br />
<br />
==Knowledge Recycling==<br />
<br />
''"He who receives an idea from me receives it without lessening me, as he who lights his candle at mine receives light without darkening me."'' – Thomas Jefferson<br />
<br />
Sustainability considerations in designing our system also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends? And what can we do to maximise knowledge recycling?<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Recycle.png|caption=}}<br />
We believe the need for openness and sharing of ideas to be of considerable importance to further knowledge, in the iGEM competition and beyond and the information society that we live in makes the sharing of ideas and finding relevant knowledge easier than ever before. The breadth and depth humanity’s current scientific understanding means that it is difficult for any single person to know enough about a particular area to make substantial advances on their own; collaboration is essential. It is not enough to only publicise and publish polished results at the end of a project. Work in progress should be made just as accessible to encourage this collaboration. Making available results from, and information about, experiments that failed is also important. It could prevent someone from wasting time trying exactly the same protocol again and may in fact be an important result in itself (that what was attempted be discovered simply cannot be discovered in that way). <br />
<br />
It is difficult to get research papers published for experiments that do not work, though journals such as the [http://www.jasnh.com/ Journal of Articles in Support of the Null Hypothesis] are changing this. Instead experiment attempts could be documented on wikis or blogs such that they are still available to someone searching the internet for them - this means all the hand work is not wasted, even if the desired results are not obtained. Protocols and techniques are particularly valuable when shared; reproducibility is a central concept to science and standardising protocols is necessary for this. Putting detailed protocols up on sites such as [http://openwetware.org/wiki/Main_Page open wetware] also helps encourage new researchers to get involved the particular field and prevents time and resources being wasted optimising procedures. <br />
<br />
After coming to these conclusions from our discussions we made sure we conducted our research in the light of these ideas. We got our Wiki up as early as possible with our aims and ideas and kept the online lab book updated with our ongoing research. We always endeavoured to be open and honest about exactly the protocols we were using and what results they gave. The [https://2010.igem.org/Team:UNAM-Genomics_Mexico UNAM Genomics, Mexico] team contacted us because of the information on our Wiki and we were able to collaborate with them and help them with part of their project. We were also able to have useful discussions with the [https://2010.igem.org/Team:Edinburgh Edinburgh] team based on information we read on each other’s Wikis. From our thoughts about sharing our findings we decided that we should put effort into publicising our science. Our project will be featured on a documentary to be broadcast on [http://www.arte.tv/fr/70.html ARTE] which will bring a better understanding of synthetic biology to the general public. We also wanted to get a message across to the scientific community; the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson assembly] technique which we performed frequently is not as widely used as we believe it could be so we chose this to publicise and produced a [https://2010.igem.org/Team:Cambridge/Videos music video] to do so. The song has over 3000 views so far and researchers have contacted us for more information about our experience with the technique.<br />
<br />
Many iGEM teams were similarly open with their ideas and results and this helped to foster the culture of collaboration that we believe is important to iGEM. We were however disappointed to see that some teams were less open. Three weeks before the wiki freeze 58 of the 127 teams participating had little more than an abstract on their wiki. This meant we were unable to engage in potentially valuable dialogue because we had little idea about what they were researching. To help encourage future teams and scientists generally to be more open with their work we produced a short video summarising our arguments. Previous iGEM teams have made interesting contributions to the field of human practises which perhaps have not had the desired effect on the way people conduct their science because not enough other scientists have seen them. We hope a short and more light-hearted summary might reach more people and help translate our conclusions into future action.<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-28T03:35:19Z<p>Peteremmrich: /* Futures */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. To help publicise our conclusions we produced a short video summarising the arguments for openness in research.<br />
<br />
==Futures==<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Cocktail.jpg|caption=Bioluminescent drinks of the future?}}<br />
<br />
We spent a day early in the project imagining how engineered artificial bioluminescence might be used in the future. This workshop, led by [http://www.daisyginsberg.com/ Daisy Ginsberg] from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How would omnipresent bioluminescence affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
We split the team into three groups, each of which went on to explore their own ideas about the future of bioluminescence:<br />
<br />
The first group considered the impact of bacterial lighting at home. If ‘E.colights’ became available for household use how would they be received? What issues would have to be addressed for this to happen? We also considered the markets for other domestic products that might arise as a result and made a mock advert for ‘Bactobang’, an improved antibacterial agent to prevent the escape of bioluminescent synthetic organisms should their container become damaged. We also thought about the possibility of bioluminescence in art and fashion and presented our ideas to the rest of the team.<br />
<br />
The second group envisaged ‘Bright Foods’ where the plants and animals that we eat might be engineered to have different colours of bioluminescence that would give an easily interpretable indication of nutritional content. The brightness of the luminescence would fade over time giving an indication of the freshness of the foodstuffs. This could also add an additional dimension to the experience of eating – perhaps restaurants would serve food in the dark so customers could fully appreciate the aesthetics of their luminescent meal. Food standards agencies might even insist that all food conforms to bioluminescent regulations such that foods with high levels of salt or saturated fat glowed particular colours to indicate this to customers. Perceptions might change such that people come to expect their food to glow and view dark food as spoiled and unappetizing. Bioluminescent cocktails could also become a fashionable drink in upmarket bars.<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Light_polution.jpg|caption=Bioluminescence genes escaping}}<br />
The third group considered how bioluminescence might slowly replace conventional lighting and the issues with intellectual property that this might cause. Initially, artificial bioluminescence could be a novelty – perhaps bioluminescent fish would be a popular pet. As our knowledge of synthetic biology grows, luminescent trees could become a real possibility; the commercial potential in replacing the street lights of the world could lead to strong competition with patents for bioluminescent systems. It could then be difficult to control and police the use of patented genetic systems; if the parts were put into fertile organisms then people might start illegally breeding their own light sources. We also considered containment issues and people’s attitudes towards them. As organisms engineered to be bioluminescent would not pose any considerable threat to public health or the environment, their escape might not be considered a serious issue. The amazement and awe inspired by natural bioluminescence might even <br />
lead to the escape of bioluminescent genes being welcomed by the public of the future – particularly one that had grown accustomed to this form of lighting in their homes and cities.<br />
<br />
==Applications==<br />
[[Image:Home ec pic.jpg|370px|thumb|left|Bioluminescence at home]]<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be more sustainable and environmentally friendly than conventional devices? and where might it be useful? Bioluminescence is 'cold light' and much more efficient than conventional lighting. Despite this we find it unlikely that bioluminescence would completely replace current lighting and instead considered it's applications in remote off grid areas or complementing existing sources. Our biological systems would require only a chemical fuel source so would not be dependant on the electrical grid. Perhaps this fuel could come from waste products be that human waste or food waste. If a photosynthetic organism such as a suitable alga species was used then additional energy could be harnessed from sunlight. We might imagine a system where a bioreactor in the roof of a house - supplied with leftover foodstuffs - could pipe glowing algae through the rooms of the house during the night and across the roof during the day. We also considered the exciting prospect of bioluminescent trees lighting our roads and produced a 3D model of what this might look like as well as researching the [https://2010.igem.org/Team:Cambridge/Tools/Lighting feasibility] of such a project.<br />
<br />
We also considered the prospect of using our light production in biosensors after a talk from [http://practicalaction.org/blog/author/djg/ David Grimshaw] of Practical Action. Dr. Grimshaw has worked with the issues of contamination of water sources with arsenic in Bangladesh and mercury in Nepal. He informed us that local people wished for a portable device that was easy to use such that testing of wells could be performed by members of the community and a quantitative digital readout would be preferable. Light production as an output of a biological circuit could be detected by a sensor in an electrical system to give a digital readout. Our biobricks could bridge the gap between biological and electrical circuits. Further investigation into the practicalities of this led to the development of the [https://2010.igem.org/Team:Cambridge/Tools/Eglometer E.glometer]<br />
<br />
==Knowledge Recycling==<br />
<br />
''"He who receives an idea from me receives it without lessening me, as he who lights his candle at mine receives light without darkening me."'' – Thomas Jefferson<br />
<br />
Sustainability considerations in designing our system also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends? And what can we do to maximise knowledge recycling?<br />
<br />
{{:Team:Cambridge/Templates/RightImage|image=Recycle.png|caption=}}<br />
We believe the need for openness and sharing of ideas to be of considerable importance to further knowledge, in the iGEM competition and beyond and the information society that we live in makes the sharing of ideas and finding relevant knowledge easier than ever before. The breadth and depth humanity’s current scientific understanding means that it is difficult for any single person to know enough about a particular area to make substantial advances on their own; collaboration is essential. It is not enough to only publicise and publish polished results at the end of a project. Work in progress should be made just as accessible to encourage this collaboration. Making available results from, and information about, experiments that failed is also important. It could prevent someone from wasting time trying exactly the same protocol again and may in fact be an important result in itself (that what was attempted be discovered simply cannot be discovered in that way). <br />
<br />
It is difficult to get research papers published for experiments that do not work, though journals such as the [http://www.jasnh.com/ Journal of Articles in Support of the Null Hypothesis] are changing this. Instead experiment attempts could be documented on wikis or blogs such that they are still available to someone searching the internet for them - this means all the hand work is not wasted, even if the desired results are not obtained. Protocols and techniques are particularly valuable when shared; reproducibility is a central concept to science and standardising protocols is necessary for this. Putting detailed protocols up on sites such as [http://openwetware.org/wiki/Main_Page open wetware] also helps encourage new researchers to get involved the particular field and prevents time and resources being wasted optimising procedures. <br />
<br />
After coming to these conclusions from our discussions we made sure we conducted our research in the light of these ideas. We got our Wiki up as early as possible with our aims and ideas and kept the online lab book updated with our ongoing research. We always endeavoured to be open and honest about exactly the protocols we were using and what results they gave. The [https://2010.igem.org/Team:UNAM-Genomics_Mexico UNAM Genomics, Mexico] team contacted us because of the information on our Wiki and we were able to collaborate with them and help them with part of their project. We were also able to have useful discussions with the [https://2010.igem.org/Team:Edinburgh Edinburgh] team based on information we read on each other’s Wikis. From our thoughts about sharing our findings we decided that we should put effort into publicising our science. Our project will be featured on a documentary to be broadcast on [http://www.arte.tv/fr/70.html ARTE] which will bring a better understanding of synthetic biology to the general public. We also wanted to get a message across to the scientific community; the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson assembly] technique which we performed frequently is not as widely used as we believe it could be so we chose this to publicise and produced a [https://2010.igem.org/Team:Cambridge/Videos music video] to do so. The song has over 3000 views so far and researchers have contacted us for more information about our experience with the technique.<br />
<br />
Many iGEM teams were similarly open with their ideas and results and this helped to foster the culture of collaboration that we believe is important to iGEM. We were however disappointed to see that some teams were less open. Three weeks before the wiki freeze 58 of the 127 teams participating had little more than an abstract on their wiki. This meant we were unable to engage in potentially valuable dialogue because we had little idea about what they were researching. To help encourage future teams and scientists generally to be more open with their work we produced a short video summarising our arguments. Previous iGEM teams have made interesting contributions to the field of human practises which perhaps have not had the desired effect on the way people conduct their science because not enough other scientists have seen them. We hope a short and more light-hearted summary might reach more people and help translate our conclusions into future action.<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/File:Cocktail.jpgFile:Cocktail.jpg2010-10-28T03:33:56Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/BioBricksTeam:Cambridge/BioBricks2010-10-28T03:09:34Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Parts submitted}}<br />
The Cambridge iGEM team has submitted 20 parts to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. Many of these parts have been extensively characterised. This data is stored in the Parts Registry, you can click on any BioBrick to view its technical datasheet.<br />
=Featured parts=<br />
<html><br />
<style><br />
td.lefttd{text-align:center; padding-right:20px;}<br />
table.partlist td{padding-bottom:40px;}<br />
<br />
</style><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/TableRowAll|3d=219|image=3/3c/Bulb219.png|title=Red luciferase and LRE operon from L. cruciata under pBAD|description=This part generates the luciferase and luciferin regenerating enzyme proteins from the Japanese firefly, <i>Luciola cruciata</i>, when induced by L-arabinose. The luciferase produced has a point mutation Ser286Asn which gives it a redshifted emission spectrum as compared to wild-type. The sequence of nucleotides is codon optimised for expression in E. coli.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=909|image=a/a6/G28.jpg|title=V. fischeri luxCDABE under pBAD|description=This part generates luxCDABE proteins from the bioluminescent bacterium, <i>Vibrio fischeri</i>, when induced by L-arabinose. The BioBrick produces light from basic metabolites found in E. coli, luxCDE produce the substrate used by luxAB for bioluminescence. The part creates a blue light.}}<br />
<html><br />
</table><br />
</html><br />
=Parts based on bacterial systems=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=902|title=V. fischeri luxCD|description=This is a translational unit designed to produce <i>V. fischeri</i> luxC and luxD genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. Both proteins are part of the fatty aldehyde synthesis pathway. luxC is a reductase and luxD is a acyltransferase. LuxE must also be supplied to complete the pathway for fatty aldehyde synthesis. Such fatty aldehydes are the substrate for the luxAB bacterial luciferase.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=903|title=V. fischeri luxEG|description=This is a translational unit designed to produce <i>V. fischeri</i> luxE and luxG genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. luxE functions as the synthetase creating fatty aldehydes for bioluminescence. LuxG is a flavin reductase. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=905|title=luxCDEG pLambda AB|description=This part constitutively expresses [http://partsregistry.org/wiki/index.php?title=Part:BBa_K216008 the Xenorhabdus luminescens luxAB luciferase] already in the registry. It also features a translational unit for the substrate generating luxCDEG from Vibrio fischeri. This means that only when supplied with PoPs will it produce light output. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=906|title=pBAD luxCDEG pLambda AB|description=This is the same as the part above but was built for testing induction by adding the pBAD promoter, making light inducible by addition of L-arabinose. }}<br />
<html><br />
</table><br />
</html><br />
<br />
=Firefly luciferases=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=101|title=Luciferase from Photinus pyralis with increased substrate affinity|description=This is a translational unit for a mutated and codon-optimised form of the luciferase from the North American firefly, Photinus pyralis. It is described in [http://www.ncbi.nlm.nih.gov/pubmed/17540326 Fujii et al. 2007] as having a 10 times higher substrate affinity and luminescence output compared to wildtype.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=108|title=P.pyralis luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=211|title=L. cruciata luciferase (red mutant)|description=This is a translational unit for a mutant (Ser286Asn) and codon-optimised luciferase from the Japanese firefly, Luciola cruciata. It is deeply red-shifted as compared to wild type. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=218|title=L. cruciata luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferin regenerating enzymes=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=102|title=P. pyralis Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the North American firefly, Photinus pyralis.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=202|title=L. cruciata Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the Japanese firefly, Luciola cruciata.}}<br />
<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferase, LRE operons=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=210|title=Luciola cruciata LRE and luciferase|description=This translational unit combines the luciferin regenerating enzyme (BBa_K325202) and red-shifted luciferase (BBa_K325211) from the Japanese firefly, Luciola cruciata. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=100|title=Photinus pyralis LRE and luciferase|description=This part combines the luciferin regenerating enzyme (BBa_K325102) and luciferase (BBa_K325101) from the North American firefly, Photinus pyralis. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=109|image=a/aa/Rainbow100.png|title=Photinus pyralis LRE and luciferase under pBAD|description=This part is the part above expressed under pBAD for characterisation.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=209|image=b/bc/Rainbow219.png|title=L. cruciata LRE and luciferase (wildtype) under pBAD|description=This part combines the Luciferin Regenerating Enzyme and luciferase from the Japanese firefly, Luciola cruciata. It is expressed under pBAD.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=229|image=e/e9/Rainbow229.png|title=L. cruciata LRE and luciferase (green) under pBAD|description=This is the same as the part above but with a Val239Ile mutation which green-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=239|image=4/4f/Rainbow239.png|title=L. cruciata LRE and luciferase (red) under pBAD|description=This is the same as the part above but instead has a Gly326Ser mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=249|image=d/d1/Rainbow249.png|title=L. cruciata LRE and luciferase (scarlet) under pBAD|description=This is the same as the part above but instead has a His433Tyr mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=4/47/Rainbow259.png|title=L. cruciata LRE and luciferase (yellow) under pBAD|description=This is the same as the part above but instead has a Pro452Ser mutation which shifts its emission spectrum to peak at a yellow wavelength.}}<br />
<br />
<html><br />
</table><br />
</html><br />
<br />
==Summary table==<br />
<groupparts>iGEM010 Cambridge</groupparts><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/File:Bulb219.pngFile:Bulb219.png2010-10-28T03:07:11Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/BioBricksTeam:Cambridge/BioBricks2010-10-28T03:03:11Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Parts submitted}}<br />
The Cambridge iGEM team has submitted 20 parts to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. Many of these parts have been extensively characterised. This data is stored in the Parts Registry, you can click on any BioBrick to view its technical datasheet.<br />
=Featured parts=<br />
<html><br />
<style><br />
td.lefttd{text-align:center; padding-right:20px;}<br />
table.partlist td{padding-bottom:40px;}<br />
<br />
</style><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=a/a6/G28.jpg|title=Red luciferase and LRE operon from L. cruciata under pBAD|description=This part generates the luciferase and luciferin regenerating enzyme proteins from the Japanese firefly, <i>Luciola cruciata</i>, when induced by L-arabinose. The luciferase produced has a point mutation Ser286Asn which gives it a redshifted emission spectrum as compared to wild-type. The sequence of nucleotides is codon optimised for expression in E. coli.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=a/a6/G28.jpg|title=V. fischeri luxCDABE under pBAD|description=This part generates luxCDABE proteins from the bioluminescent bacterium, <i>Vibrio fischeri</i>, when induced by L-arabinose. The BioBrick produces light from basic metabolites found in E. coli, luxCDE produce the substrate used by luxAB for bioluminescence. The part creates a blue light.}}<br />
<html><br />
</table><br />
</html><br />
=Parts based on bacterial systems=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=902|title=V. fischeri luxCD|description=This is a translational unit designed to produce <i>V. fischeri</i> luxC and luxD genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. Both proteins are part of the fatty aldehyde synthesis pathway. luxC is a reductase and luxD is a acyltransferase. LuxE must also be supplied to complete the pathway for fatty aldehyde synthesis. Such fatty aldehydes are the substrate for the luxAB bacterial luciferase.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=903|title=V. fischeri luxEG|description=This is a translational unit designed to produce <i>V. fischeri</i> luxE and luxG genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. luxE functions as the synthetase creating fatty aldehydes for bioluminescence. LuxG is a flavin reductase. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=905|title=luxCDEG pLambda AB|description=This part constitutively expresses [http://partsregistry.org/wiki/index.php?title=Part:BBa_K216008 the Xenorhabdus luminescens luxAB luciferase] already in the registry. It also features a translational unit for the substrate generating luxCDEG from Vibrio fischeri. This means that only when supplied with PoPs will it produce light output. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=906|title=pBAD luxCDEG pLambda AB|description=This is the same as the part above but was built for testing induction by adding the pBAD promoter, making light inducible by addition of L-arabinose. }}<br />
<html><br />
</table><br />
</html><br />
<br />
=Firefly luciferases=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=101|title=Luciferase from Photinus pyralis with increased substrate affinity|description=This is a translational unit for a mutated and codon-optimised form of the luciferase from the North American firefly, Photinus pyralis. It is described in [http://www.ncbi.nlm.nih.gov/pubmed/17540326 Fujii et al. 2007] as having a 10 times higher substrate affinity and luminescence output compared to wildtype.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=108|title=P.pyralis luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=211|title=L. cruciata luciferase (red mutant)|description=This is a translational unit for a mutant (Ser286Asn) and codon-optimised luciferase from the Japanese firefly, Luciola cruciata. It is deeply red-shifted as compared to wild type. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=218|title=L. cruciata luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferin regenerating enzymes=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=102|title=P. pyralis Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the North American firefly, Photinus pyralis.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=202|title=L. cruciata Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the Japanese firefly, Luciola cruciata.}}<br />
<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferase, LRE operons=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=210|title=Luciola cruciata LRE and luciferase|description=This translational unit combines the luciferin regenerating enzyme (BBa_K325202) and red-shifted luciferase (BBa_K325211) from the Japanese firefly, Luciola cruciata. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=100|title=Photinus pyralis LRE and luciferase|description=This part combines the luciferin regenerating enzyme (BBa_K325102) and luciferase (BBa_K325101) from the North American firefly, Photinus pyralis. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=109|image=a/aa/Rainbow100.png|title=Photinus pyralis LRE and luciferase under pBAD|description=This part is the part above expressed under pBAD for characterisation.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=209|image=b/bc/Rainbow219.png|title=L. cruciata LRE and luciferase (wildtype) under pBAD|description=This part combines the Luciferin Regenerating Enzyme and luciferase from the Japanese firefly, Luciola cruciata. It is expressed under pBAD.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=229|image=e/e9/Rainbow229.png|title=L. cruciata LRE and luciferase (green) under pBAD|description=This is the same as the part above but with a Val239Ile mutation which green-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=239|image=4/4f/Rainbow239.png|title=L. cruciata LRE and luciferase (red) under pBAD|description=This is the same as the part above but instead has a Gly326Ser mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=249|image=d/d1/Rainbow249.png|title=L. cruciata LRE and luciferase (scarlet) under pBAD|description=This is the same as the part above but instead has a His433Tyr mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=4/47/Rainbow259.png|title=L. cruciata LRE and luciferase (yellow) under pBAD|description=This is the same as the part above but instead has a Pro452Ser mutation which shifts its emission spectrum to peak at a yellow wavelength.}}<br />
<br />
<html><br />
</table><br />
</html><br />
<br />
==Summary table==<br />
<groupparts>iGEM010 Cambridge</groupparts><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/BioBricksTeam:Cambridge/BioBricks2010-10-28T02:46:02Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Parts submitted}}<br />
The Cambridge iGEM team has submitted 20 parts to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. Many of these parts have been extensively characterised. This data is stored in the Parts Registry, you can click on any BioBrick to view its technical datasheet.<br />
=Featured parts=<br />
<html><br />
<style><br />
td.lefttd{text-align:center; padding-right:20px;}<br />
table.partlist td{padding-bottom:40px;}<br />
<br />
</style><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=219|title=Red luciferase and LRE operon from L. cruciata under pBAD|description=This part generates the luciferase and luciferin regenerating enzyme proteins from the Japanese firefly, <i>Luciola cruciata</i>, when induced by L-arabinose. The luciferase produced has a point mutation Ser286Asn which gives it a redshifted emission spectrum as compared to wild-type. The sequence of nucleotides is codon optimised for expression in E. coli.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=909|title=V. fischeri luxCDABE under pBAD|description=This part generates luxCDABE proteins from the bioluminescent bacterium, <i>Vibrio fischeri</i>, when induced by L-arabinose. The BioBrick produces light from basic metabolites found in E. coli, luxCDE produce the substrate used by luxAB for bioluminescence. The part creates a blue light.}}<br />
<html><br />
</table><br />
</html><br />
=Parts based on bacterial systems=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=902|title=V. fischeri luxCD|description=This is a translational unit designed to produce <i>V. fischeri</i> luxC and luxD genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. Both proteins are part of the fatty aldehyde synthesis pathway. luxC is a reductase and luxD is a acyltransferase. LuxE must also be supplied to complete the pathway for fatty aldehyde synthesis. Such fatty aldehydes are the substrate for the luxAB bacterial luciferase.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=903|title=V. fischeri luxEG|description=This is a translational unit designed to produce <i>V. fischeri</i> luxE and luxG genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. luxE functions as the synthetase creating fatty aldehydes for bioluminescence. LuxG is a flavin reductase. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=905|title=luxCDEG pLambda AB|description=This part constitutively expresses [http://partsregistry.org/wiki/index.php?title=Part:BBa_K216008 the Xenorhabdus luminescens luxAB luciferase] already in the registry. It also features a translational unit for the substrate generating luxCDEG from Vibrio fischeri. This means that only when supplied with PoPs will it produce light output. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=906|title=pBAD luxCDEG pLambda AB|description=This is the same as the part above but was built for testing induction by adding the pBAD promoter, making light inducible by addition of L-arabinose. }}<br />
<html><br />
</table><br />
</html><br />
<br />
=Firefly luciferases=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=101|title=Luciferase from Photinus pyralis with increased substrate affinity|description=This is a translational unit for a mutated and codon-optimised form of the luciferase from the North American firefly, Photinus pyralis. It is described in [http://www.ncbi.nlm.nih.gov/pubmed/17540326 Fujii et al. 2007] as having a 10 times higher substrate affinity and luminescence output compared to wildtype.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=108|title=P.pyralis luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=211|title=L. cruciata luciferase (red mutant)|description=This is a translational unit for a mutant (Ser286Asn) and codon-optimised luciferase from the Japanese firefly, Luciola cruciata. It is deeply red-shifted as compared to wild type. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=218|title=L. cruciata luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferin regenerating enzymes=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=102|title=P. pyralis Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the North American firefly, Photinus pyralis.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=202|title=L. cruciata Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the Japanese firefly, Luciola cruciata.}}<br />
<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferase, LRE operons=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=210|title=Luciola cruciata LRE and luciferase|description=This translational unit combines the luciferin regenerating enzyme (BBa_K325202) and red-shifted luciferase (BBa_K325211) from the Japanese firefly, Luciola cruciata. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=100|image=a/aa/Rainbow100.png|title=Photinus pyralis LRE and luciferase|description=This part combines the luciferin regenerating enzyme (BBa_K325102) and luciferase (BBa_K325101) from the North American firefly, Photinus pyralis. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=109|title=Photinus pyralis LRE and luciferase under pBAD|description=This part is the part above expressed under pBAD for characterisation.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=209|image=b/bc/Rainbow219.png|title=L. cruciata LRE and luciferase (wildtype) under pBAD|description=This part combines the Luciferin Regenerating Enzyme and luciferase from the Japanese firefly, Luciola cruciata. It is expressed under pBAD.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=229|image=e/e9/Rainbow229.png|title=L. cruciata LRE and luciferase (green) under pBAD|description=This is the same as the part above but with a Val239Ile mutation which green-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=239|image=4/4f/Rainbow239.png|title=L. cruciata LRE and luciferase (red) under pBAD|description=This is the same as the part above but instead has a Gly326Ser mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=249|image=d/d1/Rainbow249.png|title=L. cruciata LRE and luciferase (scarlet) under pBAD|description=This is the same as the part above but instead has a His433Tyr mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=4/47/Rainbow259.png|title=L. cruciata LRE and luciferase (yellow) under pBAD|description=This is the same as the part above but instead has a Pro452Ser mutation which shifts its emission spectrum to peak at a yellow wavelength.}}<br />
<br />
<html><br />
</table><br />
</html><br />
<br />
==Summary table==<br />
<groupparts>iGEM010 Cambridge</groupparts><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/BioBricksTeam:Cambridge/BioBricks2010-10-28T02:40:59Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Parts submitted}}<br />
The Cambridge iGEM team has submitted 20 parts to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. Many of these parts have been extensively characterised. This data is stored in the Parts Registry, you can click on any BioBrick to view its technical datasheet.<br />
=Featured parts=<br />
<html><br />
<style><br />
td.lefttd{text-align:center; padding-right:20px;}<br />
table.partlist td{padding-bottom:40px;}<br />
<br />
</style><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=219|title=Red luciferase and LRE operon from L. cruciata under pBAD|description=This part generates the luciferase and luciferin regenerating enzyme proteins from the Japanese firefly, <i>Luciola cruciata</i>, when induced by L-arabinose. The luciferase produced has a point mutation Ser286Asn which gives it a redshifted emission spectrum as compared to wild-type. The sequence of nucleotides is codon optimised for expression in E. coli.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=909|title=V. fischeri luxCDABE under pBAD|description=This part generates luxCDABE proteins from the bioluminescent bacterium, <i>Vibrio fischeri</i>, when induced by L-arabinose. The BioBrick produces light from basic metabolites found in E. coli, luxCDE produce the substrate used by luxAB for bioluminescence. The part creates a blue light.}}<br />
<html><br />
</table><br />
</html><br />
=Parts based on bacterial systems=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=902|title=V. fischeri luxCD|description=This is a translational unit designed to produce <i>V. fischeri</i> luxC and luxD genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. Both proteins are part of the fatty aldehyde synthesis pathway. luxC is a reductase and luxD is a acyltransferase. LuxE must also be supplied to complete the pathway for fatty aldehyde synthesis. Such fatty aldehydes are the substrate for the luxAB bacterial luciferase.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=903|title=V. fischeri luxEG|description=This is a translational unit designed to produce <i>V. fischeri</i> luxE and luxG genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. luxE functions as the synthetase creating fatty aldehydes for bioluminescence. LuxG is a flavin reductase. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=905|title=luxCDEG pLambda AB|description=This part constitutively expresses [http://partsregistry.org/wiki/index.php?title=Part:BBa_K216008 the Xenorhabdus luminescens luxAB luciferase] already in the registry. It also features a translational unit for the substrate generating luxCDEG from Vibrio fischeri. This means that only when supplied with PoPs will it produce light output. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=906|title=pBAD luxCDEG pLambda AB|description=This is the same as the part above but was built for testing induction by adding the pBAD promoter, making light inducible by addition of L-arabinose. }}<br />
<html><br />
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<br />
=Firefly luciferases=<br />
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{{:Team:Cambridge/Templates/Tablerow|3d=101|title=Luciferase from Photinus pyralis with increased substrate affinity|description=This is a translational unit for a mutated and codon-optimised form of the luciferase from the North American firefly, Photinus pyralis. It is described in [http://www.ncbi.nlm.nih.gov/pubmed/17540326 Fujii et al. 2007] as having a 10 times higher substrate affinity and luminescence output compared to wildtype.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=108|title=P.pyralis luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=211|title=L. cruciata luciferase (red mutant)|description=This is a translational unit for a mutant (Ser286Asn) and codon-optimised luciferase from the Japanese firefly, Luciola cruciata. It is deeply red-shifted as compared to wild type. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=218|title=L. cruciata luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
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</html><br />
=Firefly luciferin regenerating enzymes=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=102|title=P. pyralis Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the North American firefly, Photinus pyralis.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=202|title=L. cruciata Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the Japanese firefly, Luciola cruciata.}}<br />
<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferase, LRE operons=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=210|title=Luciola cruciata LRE and luciferase|description=This translational unit combines the luciferin regenerating enzyme (BBa_K325202) and red-shifted luciferase (BBa_K325211) from the Japanese firefly, Luciola cruciata. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/TablerowAll|3d=100|image=a/aa/Rainbow100.png|title=Photinus pyralis LRE and luciferase|description=This part combines the luciferin regenerating enzyme (BBa_K325102) and luciferase (BBa_K325101) from the North American firefly, Photinus pyralis. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=109|title=Photinus pyralis LRE and luciferase under pBAD|description=This part is the part above expressed under pBAD for characterisation.}}<br />
{{:Team:Cambridge/Templates/TablerowAll|3d=209|image=b/bc/Rainbow219.png|title=L. cruciata LRE and luciferase (wildtype) under pBAD|description=This part combines the Luciferin Regenerating Enzyme and luciferase from the Japanese firefly, Luciola cruciata. It is expressed under pBAD.}}<br />
{{:Team:Cambridge/Templates/TablerowAll|3d=229|image=e/e9/Rainbow229.png|title=L. cruciata LRE and luciferase (green) under pBAD|description=This is the same as the part above but with a Val239Ile mutation which green-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TablerowAll|3d=239|image=4/4f/Rainbow239.png|title=L. cruciata LRE and luciferase (red) under pBAD|description=This is the same as the part above but instead has a Gly326Ser mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TablerowAll|3d=249|image=d/d1/Rainbow249.png|title=L. cruciata LRE and luciferase (scarlet) under pBAD|description=This is the same as the part above but instead has a His433Tyr mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=4/47/Rainbow259.png|title=L. cruciata LRE and luciferase (yellow) under pBAD|description=This is the same as the part above but instead has a Pro452Ser mutation which shifts its emission spectrum to peak at a yellow wavelength.}}<br />
<br />
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<br />
==Summary table==<br />
<groupparts>iGEM010 Cambridge</groupparts><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/BioBricksTeam:Cambridge/BioBricks2010-10-28T02:35:09Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Parts submitted}}<br />
The Cambridge iGEM team has submitted 20 parts to the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts]. Many of these parts have been extensively characterised. This data is stored in the Parts Registry, you can click on any BioBrick to view its technical datasheet.<br />
=Featured parts=<br />
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<br />
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</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=219|title=Red luciferase and LRE operon from L. cruciata under pBAD|description=This part generates the luciferase and luciferin regenerating enzyme proteins from the Japanese firefly, <i>Luciola cruciata</i>, when induced by L-arabinose. The luciferase produced has a point mutation Ser286Asn which gives it a redshifted emission spectrum as compared to wild-type. The sequence of nucleotides is codon optimised for expression in E. coli.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=909|title=V. fischeri luxCDABE under pBAD|description=This part generates luxCDABE proteins from the bioluminescent bacterium, <i>Vibrio fischeri</i>, when induced by L-arabinose. The BioBrick produces light from basic metabolites found in E. coli, luxCDE produce the substrate used by luxAB for bioluminescence. The part creates a blue light.}}<br />
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=Parts based on bacterial systems=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=902|title=V. fischeri luxCD|description=This is a translational unit designed to produce <i>V. fischeri</i> luxC and luxD genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. Both proteins are part of the fatty aldehyde synthesis pathway. luxC is a reductase and luxD is a acyltransferase. LuxE must also be supplied to complete the pathway for fatty aldehyde synthesis. Such fatty aldehydes are the substrate for the luxAB bacterial luciferase.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=903|title=V. fischeri luxEG|description=This is a translational unit designed to produce <i>V. fischeri</i> luxE and luxG genes when placed under a suitable promoter. The DNA sequence is codon optimised for expression in E. coli. luxE functions as the synthetase creating fatty aldehydes for bioluminescence. LuxG is a flavin reductase. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=905|title=luxCDEG pLambda AB|description=This part constitutively expresses [http://partsregistry.org/wiki/index.php?title=Part:BBa_K216008 the Xenorhabdus luminescens luxAB luciferase] already in the registry. It also features a translational unit for the substrate generating luxCDEG from Vibrio fischeri. This means that only when supplied with PoPs will it produce light output. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=906|title=pBAD luxCDEG pLambda AB|description=This is the same as the part above but was built for testing induction by adding the pBAD promoter, making light inducible by addition of L-arabinose. }}<br />
<html><br />
</table><br />
</html><br />
<br />
=Firefly luciferases=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=101|title=Luciferase from Photinus pyralis with increased substrate affinity|description=This is a translational unit for a mutated and codon-optimised form of the luciferase from the North American firefly, Photinus pyralis. It is described in [http://www.ncbi.nlm.nih.gov/pubmed/17540326 Fujii et al. 2007] as having a 10 times higher substrate affinity and luminescence output compared to wildtype.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=108|title=P.pyralis luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=211|title=L. cruciata luciferase (red mutant)|description=This is a translational unit for a mutant (Ser286Asn) and codon-optimised luciferase from the Japanese firefly, Luciola cruciata. It is deeply red-shifted as compared to wild type. }}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=218|title=L. cruciata luciferase under pBAD|description=This is the same as the part above but placed under the pBAD promoter induced by L-arabinose for characterisation.}}<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferin regenerating enzymes=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=102|title=P. pyralis Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the North American firefly, Photinus pyralis.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=202|title=L. cruciata Luciferin Regenerating Enzyme|description=This is a translational unit for a codon-optimised Luciferin Regenerating Enzyme (LRE) from the Japanese firefly, Luciola cruciata.}}<br />
<br />
<html><br />
</table><br />
</html><br />
=Firefly luciferase, LRE operons=<br />
<html><br />
<table style="background:transparent" class="partlist"><br />
</html><br />
{{:Team:Cambridge/Templates/Tablerow|3d=210|title=Luciola cruciata LRE and luciferase|description=This translational unit combines the luciferin regenerating enzyme (BBa_K325202) and red-shifted luciferase (BBa_K325211) from the Japanese firefly, Luciola cruciata. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=100|image=a/aa/Rainbow100.png|title=Photinus pyralis LRE and luciferase|description=This part combines the luciferin regenerating enzyme (BBa_K325102) and luciferase (BBa_K325101) from the North American firefly, Photinus pyralis. The luciferin regenerating enzyme helps to strengthen and sustain light output.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=109|title=Photinus pyralis LRE and luciferase under pBAD|description=This part is the part above expressed under pBAD for characterisation.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=209|image=b/bc/Rainbow219.png|title=L. cruciata LRE and luciferase (wildtype) under pBAD|description=This part combines the Luciferin Regenerating Enzyme and luciferase from the Japanese firefly, Luciola cruciata. It is expressed under pBAD.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=229|image=e/e9/Rainbow229.png|title=L. cruciata LRE and luciferase (green) under pBAD|description=This is the same as the part above but with a Val239Ile mutation which green-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=239|image=4/4f/Rainbow239.png|title=L. cruciata LRE and luciferase (red) under pBAD|description=This is the same as the part above but instead has a Gly326Ser mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/Tablerow|3d=249|image=d/d1/Rainbow249.png|title=L. cruciata LRE and luciferase (scarlet) under pBAD|description=This is the same as the part above but instead has a His433Tyr mutation which red-shifts its emission spectrum.}}<br />
{{:Team:Cambridge/Templates/TableRowAll|3d=259|image=4/47/Rainbow259.png|title=L. cruciata LRE and luciferase (yellow) under pBAD|description=This is the same as the part above but instead has a Pro452Ser mutation which shifts its emission spectrum to peak at a yellow wavelength.}}<br />
<br />
<html><br />
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</html><br />
<br />
==Summary table==<br />
<groupparts>iGEM010 Cambridge</groupparts><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/File:Rainbow259.pngFile:Rainbow259.png2010-10-28T02:05:55Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow249.pngFile:Rainbow249.png2010-10-28T02:05:02Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow239.pngFile:Rainbow239.png2010-10-28T02:04:33Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow229.pngFile:Rainbow229.png2010-10-28T02:04:14Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow219.pngFile:Rainbow219.png2010-10-28T02:03:48Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow100.pngFile:Rainbow100.png2010-10-28T02:03:06Z<p>Peteremmrich: uploaded a new version of "Image:Rainbow100.png"</p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/File:Rainbow100.pngFile:Rainbow100.png2010-10-28T02:01:53Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/PublicityTeam:Cambridge/Publicity2010-10-27T22:11:33Z<p>Peteremmrich: /* Artist Interest */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Publicity}}<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-Tv.png}}<br />
=Spreading the Word=<br />
As a team we thought it was really imporant to spread the word about iGEM. Synthetic biology is a new and developing field and the world should know about it. We feel it's especially important that synthetic biology is presented in an accessible way to people so that it is embraced by the general public. We also feel it's especially important to promote the open source nature of iGEM in the hope that as the field develops it can adopt these principles. The following are the main ways in which we have been spreading the word about iGEM over the summer. <br />
<br />
===French Documentary on ARTE===<br />
<br />
Through Daisy Ginsberg, we were approached by a French TV crew from the channel [http://www.arte.tv/fr/70.html ARTE] filming a documentary on synthetic biology. They visited us for a day of filming where they recorded us in the lab in the morning and then in the afternoon filmed us as we discussed the human practices and ethical side of synthetic biology, facilited by Daisy's interesting presentation. <br />
<br />
The film crew will also be filming at the jamboree, so look out for them there!<br />
<br />
===Telling Companies About iGEM===<br />
Through the generous sponsorship of all our [[Team:Cambridge/Partners|partners]] we have had the opportunity to spread the word about iGEM. We have written an article for [http://www.sterilin.co.uk/ Sterilin] which will be featured in the next edition of their brochure all about iGEM and the Cambridge team's project this year. <br />
<br />
[http://www.biolegio.com/ Biolegio]'s generous contribution and provision of t-shirts also enabled us to take some amusing photographs to raise iGEM's profile. <br />
<br />
===Gibson Assembly Video===<br />
What started out as an idea to make a Cambridge iGEM band, and to promote the [[Team:Cambridge/Gibson/Introduction|Gibson Assembly]] technique we had been using all summer, materialised into the [[Team:Cambridge/Videos|Gibson Assembly Song]], which is publicly available and has been viewed by over 3000 people so far (24/10/10). A great way to promote having fun in the lab over the summer! Our [[Team:Cambridge/Videos|Bacterial Bubble Lamp]] is also publicly available on youtube.<br />
<br />
===Artist Interest===<br />
We have also been contacted by several artists and designers, including a student from Delft University of Technology, who are interested in the idea of lighting the world with bacterial luminescence. This idea has obviously captured the imagination of many people who are also looking into ways of using this 'living light', as well as the feasiblity and usefulness of using bioluminescence to light our environments.</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-27T21:51:58Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
[[Image:Cambridge_logo.gif|center|500px|University of Cambridge]]<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe, Gos Micklem and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Royal College of Art}}<br />
For tips and ideas on Human Practises and design.<br />
<br />
Special thanks to: Daisy Ginsberg<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
James Slock<br />
<br />
<br />
Laura Rowe<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-27T21:51:44Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
[[Image:Cambridge_logo.gif|center|500px|University of Cambridge]]<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe, Gos Micklem and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Royal College of Art}}<br />
For tips and ideas on Human Practises and design<br />
<br />
Special thanks to: Daisy Ginsberg<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
James Slock<br />
<br />
<br />
Laura Rowe<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Notebook/13Team:Cambridge/Notebook/132010-10-26T23:06:42Z<p>Peteremmrich: </p>
<hr />
<div>By this stage term was about to start and members of the team had very little time. Nevertheless, due to the synthesis dramas described, work had to continue for some time.<br />
<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Monday 4th October}}<br />
<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-MixedPhenotype.jpg}}<br />
Today we received extremely bad news. We had ordered 3 DNA constructs for synthesis by Mr. Gene on 19th August who had said that 98% of sequences of this length would have a turn-around time of 14 business days. We had become increasingly alarmed as time had gone on without the order being completed. We received our first contact from them at this time, informing us that the company was having problem with one of our constructs - luxAB. They said they had split the sequence into three parts and had to start from scratch, and that it might be 3 weeks until we got the sequence. This would take us until just before the Jamboree.<br />
<br />
We moped for a bit and then came up with a plan, we asked them to send the completed sequences as soon as possible. We decided we would attempt to fuse them to the Xenorhabdus luminescens luxAB submitted by last year's Edinburgh team.<br />
<br />
But there was good news as shown by the image on the right. We had believed that a number of our colour changes had failed due to sequencing results. But when we assayed our plates we found that some colonies had the desired phenotype. The plate on the right shows two distinct colour types.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Tuesday 5th October}}<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-LuciferinPlate.jpg}}<br />
We spent much of today moving out of the lab, we also analysed the results of the plate reader experiment. Luciferin can be visualised by its fluorescence under UV light as shown on the right.<br />
{{Team:Cambridge/Templates/Day|Day=Wednesday 6th October}}<br />
Our term proper began today so we were mostly busy but Paul came into the lab.<br />
{{Team:Cambridge/Templates/Day|Day=Thursday 7th October}}<br />
<br />
Ben miniprepped G28 and some of the colour-changed luciferases for sequencing and placed the order.<br />
<br />
Emily and Peter transformed two hns-mutant strains (black and red) with G28 and of Top10 with CD and EG from Mr Gene. In case that didn't work, we should have plenty of DNA left in the tube they sent us.<br />
I'll check in on those tomorrow. The Top10 cells are plated on kanamycin plates. If the transformation works, we can roll out the Gibson assembly. Assemblies to do are:<br />
<br />
CD into Psb1C3<br />
EG into Psb1C3<br />
CD+EG into Psb1C3<br />
pBad+CD+EG into Psb1C3<br />
<br />
<br />
Since the hns-mutants are temperature sensitive, and the Lux operon is as well, we left the plates out on the bench. I used big plates with 300µl of transformed cells to increase the chances of getting some working colonies.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Saturday 9th October}}<br />
<br />
Peter went in to check on the transformation plates today, the CD and EG transformants grew up massively, i.e. hundreds of cultures. There are still a couple of singles, so we should be fine (unless our Soc is contaminated again).<br />
<br />
The hns mutants (termed R28 and K28, if only to abuse Will's naming system) don't show any colonies yet, but that was to be expected. 20°C and all that.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Sunday 10th October}}<br />
<br />
Peter set on liquid colonies of Top10 G28, R28, K28 (the hns mutants) pBad+PP+YFP and pBad+YFP. All of these grew up, but they were rather thin (because shaking incubator < rotation incubator and all the cells sedimented). He left them to grow a bit more and will go and take them out of the incubator tonight.<br />
<br />
There were lots and lots of colonies on the hns-mutant plates, so many to make us doubt our SOC, so Peter plated some out and left the bottle on the bench, but nothing grew over night, so we're probably fine. The K28 plate was grown over quite densely, so it was put in the fridge yesterday. Peter checked both plates for glowth yesterday and couldn't see anything, but today the R28 plate (a hns knockout) glowed quite well, so yay!<br />
<br />
everything is in the fridge now.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Tuesday 12th October}}<br />
<br />
Peter went into the Plants lab and looked at the results of the plate reader. All the strains seem to be growing fine, with quite consistent ODs, Luminescence has fallen off in all of them by now and seems to have leveled out. Three wells, however gave a massive spike at the start, much brighter than all the others. 'Which one?', I hear you ask, 'is it K, the master of quiescence, R, the loveable knockout, or G, the old champion?'<br />
For now, imagine the plate reader hanging off a cliff... <br />
<br />
Can our cells overcome the repression and shine brighter than they ever shone before? Will science happen? Are hns-mutants shite? Tune in to watch the exciting conclusion of Plate Reader: The Reckoning!<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Wednesday 13th October}}<br />
Previously on Plate Reader: The Reckoning<br />
<br />
(title: Based on a true story)<br />
<br />
Paul: "Lets set up the machine to read K28 and R28 brightness at different arabinose concentrations. It's a long shot, but it might just work"<br />
Bill: "You're crazy! we need to run calculations, replicates, controls! We'll need at least 5 days to prepare everything!"<br />
Paul: "You've got 5 minutes"<br />
Bill: "I'll do it in 2"<br />
<br />
(Montage of 72 wells being loaded with three replicates at each concentration and one row of controls, G28 at different arabinose concs and blanks)<br />
<br />
Paul: "Go my mutants! To a brighter future, free from repression!" <br />
<br />
(cut to black, sounds of OD readings)<br />
<br />
And now:<br />
<br />
(dedicated to the lives lost in transformation)<br />
<br />
At the start, K28 seemed a bit disoriented and didn't shine very bright. R28 made and honest effort, but neither could step out of the shadow of G28, which surged to a peak of 3.7 million units of pure awesomeness after a few hours. <br />
<br />
But soon after that, G28's btightness came crashing down. K28 still hadn't quite got to grips with the situation - while growing happily, it didn't seem into the whole glowing business. But what is that? Even though only half as bright as G28 at the start, R28 takes a stand against the fall and maintains its luminescence at a respectable level of 1.7 million Somethings. <br />
<br />
G28 hadlong fallen into darkness, but R28 is still going strong to this hour. K28 went to get a coffee...<br />
<br />
<br />
<br />
Right, like any season finale this gave more questions than answers. My take on all of that would be that H-NS does indeed repress, but is still affected by physiological changes connected with cell density, despite the absence of the Vibrio quorum sensing system. Therefore, expression is reduced after a while and falls off rapidly. In R28, the lux operon is not repressed and keeps glowing away as the cells are growing and slowly changing into stationary phase. The initially lower brightness might be due to greater availability of secondary substrates, like ATP, as Top10 is generally more viable. Another explanation could be that G28 burns out all its resources at the start, while R28 lives at a much slower pace (although the OD values do not show this), but uses a greater proportion of its resources to make light. K28 just sucks.<br />
<br />
We left the plate reader running. It will be interesting to see how long R28 is able to maintain its light output. Either way, there definitely is a significant influence of H-NS on LuxCDABEG without the original promoter regions, and we can definitely present that as evidence for our codon-usage-change approach. <br />
<br />
Peter bumped into Jim Ajioka today and he asked me to let him know when we are going to do the LRE/spinning down experiment. Are we still going to do that? It would help us a fair bit in showing the efficacy of LRE and how much of the effect depends on liberation of luciferase and how much is actual recycling.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Thursday 14st October}}<br />
<br />
Basically, the sequencing didn't work. There was something wrong with the sample concentrations or something, so even though they say they've repeated the readings they can't get any meaningful results. So we don't yet know if we have successful colour changes yet I'm afraid. BUT, all we need to do is send some more samples off. I'm afraid I'm busy today so can't. Any volunteers? <br />
<br />
Duncan has also asked to remind us all about trying to organise that lab meeting with the supervisors next week. <br />
<br />
{{Team:Cambridge/Templates/Day|Day=Thursday 21st October}}<br />
Will and Peter had a long day in an attempt to do a number of Gibson Assembly operations. The most crucial was to place Edinburgh's luxAB under pBAD and then add our codon optimised CD and EG to it.</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Notebook/13Team:Cambridge/Notebook/132010-10-26T22:24:11Z<p>Peteremmrich: </p>
<hr />
<div>By this stage term was about to start and members of the team had very little time. Nevertheless, due to the synthesis dramas described, work had to continue for some time.<br />
<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Monday 4th October}}<br />
<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-MixedPhenotype.jpg}}<br />
Today we received extremely bad news. We had ordered 3 DNA constructs for synthesis by Mr. Gene on 19th August who had said that 98% of sequences of this length would have a turn-around time of 14 business days. We had become increasingly alarmed as time had gone on without the order being completed. We received our first contact from them at this time, informing us that the company was having problem with one of our constructs - luxAB. They said they had split the sequence into three parts and had to start from scratch, and that it might be 3 weeks until we got the sequence. This would take us until just before the Jamboree.<br />
<br />
We moped for a bit and then came up with a plan, we asked them to send the completed sequences as soon as possible. We decided we would attempt to fuse them to the Xenorhabdus luminescens luxAB submitted by last year's Edinburgh team.<br />
<br />
But there was good news as shown by the image on the right. We had believed that a number of our colour changes had failed due to sequencing results. But when we assayed our plates we found that some colonies had the desired phenotype. The plate on the right shows two distinct colour types.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Tuesday 5th October}}<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-LuciferinPlate.jpg}}<br />
We spent much of today moving out of the lab, we also analysed the results of the plate reader experiment. Luciferin can be visualised by its fluorescence under UV light as shown on the right.<br />
{{Team:Cambridge/Templates/Day|Day=Wednesday 6th October}}<br />
Our term proper began today so we were mostly busy but Paul came into the lab.<br />
{{Team:Cambridge/Templates/Day|Day=Thursday 7th October}}<br />
<br />
Ben miniprepped G28 and some of the colour-changed luciferases for sequencing and placed the order.<br />
<br />
Emily and Peter transformed two hns-mutant strains (black and red) with G28 and of Top10 with CD and EG from Mr Gene. In case that didn't work, we should have plenty of DNA left in the tube they sent us.<br />
I'll check in on those tomorrow. The Top10 cells are plated on kanamycin plates. If the transformation works, we can roll out the Gibson assembly. Assemblies to do are:<br />
<br />
CD into Psb1C3<br />
EG into Psb1C3<br />
CD+EG into Psb1C3<br />
pBad+CD+EG into Psb1C3<br />
<br />
<br />
Since the hns-mutants are temperature sensitive, and the Lux operon is as well, we left the plates out on the bench. I used big plates with 300µl of transformed cells to increase the chances of getting some working colonies.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Saturday 9th October}}<br />
<br />
Peter went in to check on the transformation plates today, the CD and EG transformants grew up massively, i.e. hundreds of cultures. There are still a couple of singles, so we should be fine (unless our Soc is contaminated again).<br />
<br />
The hns mutants (termed R28 and K28, if only to abuse Will's naming system) don't show any colonies yet, but that was to be expected. 20°C and all that.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Sunday 10th October}}<br />
<br />
Peter set on liquid colonies of Top10 G28, R28, K28 (the hns mutants) pBad+PP+YFP and pBad+YFP. All of these grew up, but they were rather thin (because shaking incubator < rotation incubator and all the cells sedimented). He left them to grow a bit more and will go and take them out of the incubator tonight.<br />
<br />
There were lots and lots of colonies on the hns-mutant plates, so many to make us doubt our SOC, so Peter plated some out and left the bottle on the bench, but nothing grew over night, so we're probably fine. The K28 plate was grown over quite densely, so it was put in the fridge yesterday. Peter checked both plates for glowth yesterday and couldn't see anything, but today the R28 plate (a hns knockout) glowed quite well, so yay!<br />
<br />
everything is in the fridge now.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Tuesday 12th October}}<br />
<br />
Peter went into the Plants lab and looked at the results of the plate reader. All the strains seem to be growing fine, with quite consistent ODs, Luminescence has fallen off in all of them by now and seems to have leveled out. Three wells, however gave a massive spike at the start, much brighter than all the others. 'Which one?', I hear you ask, 'is it K, the master of quiescence, R, the loveable knockout, or G, the old champion?'<br />
For now, imagine the plate reader hanging off a cliff... <br />
<br />
Can our cells overcome the repression and shine brighter than they ever shone before? Will science happen? Are hns-mutants shite? Tune in to watch the exciting conclusion of Plate Reader: The Reckoning!<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Tuesday 13th October}}<br />
Previously on Plate Reader: The Reckoning<br />
<br />
(title: Based on a true story)<br />
<br />
Paul: "Lets set up the machine to read K28 and R28 brightness at different arabinose concentrations. It's a long shot, but it might just work"<br />
Bill: "You're crazy! we need to run calculations, replicates, controls! We'll need at least 5 days to prepare everything!"<br />
Paul: "You've got 5 minutes"<br />
Bill: "I'll do it in 2"<br />
<br />
(Montage of 72 wells being loaded with three replicates at each concentration and one row of controls, G28 at different arabinose concs and blanks)<br />
<br />
Paul: "Go my mutants! To a brighter future, free from repression!" <br />
<br />
(cut to black, sounds of OD readings)<br />
<br />
And now:<br />
<br />
(dedicated to the lives lost in transformation)<br />
<br />
At the start, K28 seemed a bit disoriented and didn't shine very bright. R28 made and honest effort, but neither could step out of the shadow of G28, which surged to a peak of 3.7 million units of pure awesomeness after a few hours. <br />
<br />
But soon after that, G28's btightness came crashing down. K28 still hadn't quite got to grips with the situation - while growing happily, it didn't seem into the whole glowing business. But what is that? Even though only half as bright as G28 at the start, R28 takes a stand against the fall and maintains its luminescence at a respectable level of 1.7 million Somethings. <br />
<br />
G28 hadlong fallen into darkness, but R28 is still going strong to this hour. K28 went to get a coffee...<br />
<br />
<br />
<br />
Right, like any season finale this gave more questions than answers. My take on all of that would be that H-NS does indeed repress, but is still affected by physiological changes connected with cell density, despite the absence of the Vibrio quorum sensing system. Therefore, expression is reduced after a while and falls off rapidly. In R28, the lux operon is not repressed and keeps glowing away as the cells are growing and slowly changing into stationary phase. The initially lower brightness might be due to greater availability of secondary substrates, like ATP, as Top10 is generally more viable. Another explanation could be that G28 burns out all its resources at the start, while R28 lives at a much slower pace (although the OD values do not show this), but uses a greater proportion of its resources to make light. K28 just sucks.<br />
<br />
We left the plate reader running. It will be interesting to see how long R28 is able to maintain its light output. Either way, there definitely is a significant influence of H-NS on LuxCDABEG without the original promoter regions, and we can definitely present that as evidence for our codon-usage-change approach. <br />
<br />
Peter bumped into Jim Ajioka today and he asked me to let him know when we are going to do the LRE/spinning down experiment. Are we still going to do that? It would help us a fair bit in showing the efficacy of LRE and how much of the effect depends on liberation of luciferase and how much is actual recycling.<br />
<br />
{{Team:Cambridge/Templates/Day|Day=Thursday 21st October}}<br />
Will and Peter had a long day in an attempt to do a number of Gibson Assembly operations. The most crucial was to place Edinburgh's luxAB under pBAD and then add our codon optimised CD and EG to it.</div>Peteremmrichhttp://2010.igem.org/File:Ribosome.jpgFile:Ribosome.jpg2010-10-26T18:34:35Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Bioluminescence/Bacterial_Codon_optimisationTeam:Cambridge/Bioluminescence/Bacterial Codon optimisation2010-10-26T18:34:05Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Bacterial Codon Optimisation}}<br />
=What is codon usage?=<br />
[[Image:codons.jpg|300px|right|the universal genetic code]]<br />
One of the fascinating features of life is the '''universal genetic code'''. In all known organisms, from bacteria to man, the same triplets of DNA bases code for the same amino acids. However this does not mean that all species encode their genomes in exactly the same way. <br />
The code is ''redundant'': a number of triplets code for the same amino acid. While all species are able to translate any sequence of DNA interchangeably, E. coli prefers to use certain triplets to code for certain amino acids which may be different to the ones we use. This 'preference' is reflected in the levels of tRNA which match such a triplet. In this project we resynthesised a number of genes ''de novo'' and thus were able to codon optimise them for expression in E. coli.<br />
<br />
=Improved translational speed=<br />
[[Image:ribosome.jpg|300px|left|Ribosome translating mRNA]]<br />
Starting with the DNA sequence of the ''Vibrio fischeri'' lux operon found on the NCBI database, we used a number of tools to replace the codons used with the most common codons found in the E.coli genome. To achieve optimal expression of the Lux operon in E.coli, we had the operon re-synthesized after optimising the usage of codons. This conserves the sequence of amino acids in the gene products, but improves the rate of translation, as more common tRNAs are recruited. Codon usage optimization can yield dramatic increases in the expression of foreign genes, especially if they are introduced from less closely related species [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4C8NKCY-3&_user=6094838&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1511316646&_rerunOrigin=scholar.google&_acct=C000053194&_version=1&_urlVersion=0&_userid=6094838&md5=c970323b521fa1ec9d3050d4c4970eb1&searchtype=a Gustafsson et al. 2004]<br />
<br />
=Altered G-C content=<br />
DNA curvature is increased by sequences rich in A-T or G-C pairs. The natural ''V.fischeri'' Lux operon, and especially its intergenic regions, contains stretches rich in A-T, resulting in the curvature that H-NS proteins bind to preferentially. Changing the coding DNA sequence also meant changing the curvature of the DNA, which affects the binding affinity of H-NS proteins. To alleviate the repression that H-NS exerts, we took care to raise the G-C content of intergenic regions and coding sequences (at times resorting to suboptimal codons). According to a computational prediction, this resulted in greatly reduced DNA curvature, and thus hopefully to a reduced affinity for H-NS proteins.<br />
<br />
[[Image:GC_content.png|600px|center| The LuxC coding region before and after codon optimisation. Blue denotes A-T rich regions. Note the reduction in A-T rich stretches after opitmisation]]<br />
<br />
=Differential Expression=<br />
In ''Vibrio fischeri'', LuxA and B are expressed at five times the levels of LuxC, D, E and G. Since all these genes are transcribed on the same mRNA, but have their own Ribosome Binding Sites, this is probably due to differences in codon usage ([http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055 Meighen et al. 1988]). A number of rare codons are found in Lux C, D, E and G, but not in LuxA and B. Since we did not receive the newly synthesised LuxA and B in time, we constructed a new operon using our LuxC, D, E and G, and the LuxAB BioBrick that was put into the registry by the Edinburgh iGEM team 2009 (BBa_216008). These genes originate from Xenorhabdus luminescens. Compared to ''Vibrio fischeri'', there is only limited amino acid identity in the Lux A and B genes (52% and 66% respectively). Yet the literature describes both as using the same substrates. [http://aem.asm.org/cgi/content/abstract/55/10/2607 Schmidt et al. 1989] describe positive complementation test using components from ''V. fisheri'' and ''Xenorhabdus luminescens''. To use foreign genes from two very different donor species in one pathway in E.coli is an exciting test of our understanding of the processes involved in bacterial bioluminescence and of the power of synthetic biology in general.<br />
In this construct, LuxC, D, E and G are codon optimised, but LuxA and B are not. In order to adjust the ratio of gene expression between these genes to the state found in nature, we chose to put LuxA and B under a very strong, phage derived promoter (plambda) to be constitutively expressed. The other genes can now be put under any promoter to create a PoPS-to-light device. In conjunction with an inducible or repressible promoter, this could be used as a reporter device. To test the system, we placed the LuxCDEG under an arabinose induced pbad promoter (BBa_i0500).<br />
<br />
=Parts submitted to the registry=<br />
Ideally we would have submitted a codon-optimised version of the entire Lux operon. Unfortunately Mr Gene, the company we employed for synthesis, still had not completed the order two months after placing, and at the point of the wiki-freeze we still have not received the optimised versions of LuxA and B. In order to complete our aim of creating a PoPs->light device that can be placed under any promoter, we combined the optimised ''Vibrio'' LuxCDEG genes with the Edinburgh 2009 ''Xenorhabdus'' LuxAB. The assembly was achieved using the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson method]. Since we only received LuxCD and LuxEG from Mr Gene two weeks before the documentation deadline, we could not properly characterise these parts. For a complete list of the BioBricks we submitted see the [https://2010.igem.org/Team:Cambridge/BioBricks BioBricks section].<br />
<br />
<br />
Codon optimised bacterial luminescence parts:<br />
<br />
[http://partsregistry.org/Part:BBa_K325902 luxCD (BBa_K325902)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325903 luxEG (BBa_K325903)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325905 CDEG pLambda AB (BBa_K325905)] a PoPs->light device that can be placed under any promoter, hybrid device containing promoterless V. fisheri derived CDEG (optimised) and Xenorhabdus AB under a strong constitutive promoter<br />
<br />
[http://partsregistry.org/Part:BBa_K325906 pbad CDEG pLambda AB (BBa_K325906)] the above part under the arabinose induced pbad promoter<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/VideosTeam:Cambridge/Videos2010-10-26T13:57:15Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Videos}}<br />
The Cambridge iGEM team created a number of videos, published on YouTube to engage both scientists and the general public with our work.<br />
<br />
The '''Gibson Assembly Song''' was designed to promote the technique of Gibson Assembly and received over 3000 views.<br />
<br />
<html><br />
<script type="text/javascript" charset="utf-8"><br />
$(document).ready(function(){<br />
$("a[rel^='prettyPhoto']").prettyPhoto();<br />
});<br />
</script><br />
<div align="center"><object width="640" height="385"><param name="movie" value="http://www.youtube.com/v/WCWjJFU1be8?fs=1&amp;hl=en_GB"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/WCWjJFU1be8?fs=1&amp;hl=en_GB" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="640" height="385"></embed></object></div><br />
</html><br />
<br />
<br />
<br />
The '''Bacterial Bubble lamp''' was intended to show the powerful effect of oxygen on light output and to bridge our far out science with conventional lighting.<br />
<br />
<html><br />
<div align="center"><object width="480" height="385"><param name="movie" value="http://www.youtube.com/v/tUFscEVK5Ks?fs=1&amp;hl=en_GB"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/tUFscEVK5Ks?fs=1&amp;hl=en_GB" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="480" height="385"></embed></object></div></html><br />
<br />
We will soon place our presentation on YouTube so that anyone who didn't get a chance to see it at the jamboree can do so.<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Bioluminescence/G28Team:Cambridge/Bioluminescence/G282010-10-26T04:23:43Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Project Vibrio: The LuxBrick}}<br />
{{:Team:Cambridge/Templates/rightpic|src=Jungle_book.jpg|300px|right|G28 illuminating the Jungle Book}}<br />
{{:Team:Cambridge/Templates/rightpic|src=Space_invader.jpg|400px|right|G28 on a 96 well plate}}<br />
James Slock from King's College, PA kindly provided us with plasmids carrying the genes responsible for bioluminescence in ''V. fischeri''. Using Long-Range PCR, we extracted these genes and assembled them into a new operon. As described in the [https://2010.igem.org/Team:Cambridge/Bioluminescence/Background Background section], The lux operon in ''V. fischeri'' is under tight quorum sensing control. In the absence of LuxR protein and AHL the Lux genes are virtually inactive. In order to relieve this control, we used [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson Assembly] to produce an operon consisting of Lux C, D, A, B, E (in this order, reflecting ''V. fischeri'') under the arabinose-induced promoter pBAD ([http://partsregistry.org/Part:BBa_I0500 BBa_i0500]). We called this construct G28. It caused bright and reproducible light output in the transformed E.coli Top10 cells. This new BioBrick ([http://partsregistry.org/Part:BBa_K325909 BBa_K325909]) can be used as an arabinose->light device and is a very useful part if the aim is to get a high bacterial light output. Many of the images in our [https://2010.igem.org/Team:Cambridge/Photos Photo Gallery] were created using Top10 cell transformed with this part. <br />
<br />
=h-ns mutants=<br />
To test the theory that H-NS proteins repress the Lux genes by interacting with their coding regions, we transformed two E.coli mutant strains with this construct and measured their light output. The strains we used were GM230 hns-205::Tn10, which has a C-terminal deletion in the H-NS gene and BW25113 Δhns::kan, a strain from a knockout library. In the literature, h-ns mutant strains have been described as producing much brighter luminescence than wild type strains. While we could not reproduce a higher peak brightness, it was apparent that the knockout strain maintained its light output for much longer than wild type, which showed a steep reduction in brightness upon entering stationary phase. This phenomenon (Abrupt Decline in Luciferase Activity - or ADLA) has been described by [http://www.springerlink.com/content/w73k840k27866462/fulltext.pdf Koga et al. 2004]. However, this paper suggests that the effect of H-NS on luminescence is not due to expression of the lux genes, but occurs indirectly via the cell's redox pool, in particular the availability of FMNH2.<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T04:20:52Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
[[Image:Cambridge_logo.gif|center|500px|University of Cambridge]]<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe, Gos Micklem and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
James Slock<br />
<br />
<br />
Laura Rowe<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-26T04:18:24Z<p>Peteremmrich: /* Futures */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-Photobacterium_plate.JPG|caption=One of the plates of <i>V. phosphoreum</i> we prepared.}}<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. <br />
<br />
==Futures==<br />
We spent one day early in the project imagining how engineered artificial bioluminescence might be used in the future. This workshop, led by Daisy Ginsberg from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How would omnipresent bioluminescence affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
We split the team into three groups, each of which went on to explore their own ideas about the future of bioluminescence:<br />
<br />
==Applications==<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be better than conventional devices in this area? and where might it be useful? We also considered the prospect of using our light production in biosensors (after a talk from 'Practical Action'*). Coupled with a light sensor our parts could provide a bridge between biological and electrical circuits. <br />
<br />
==Knowledge Recycling==<br />
Sustainability considerations in end design also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends?<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Gibson/RFCTeam:Cambridge/Gibson/RFC2010-10-26T03:47:26Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Gibson Assembly: RFC}}<br />
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-RFC.JPG|caption=RFC-57, submitted by the Cambridge team}}<br />
The BioBrick foundation uses documents known as [http://bbf.openwetware.org/RFC.html RFC]s to document standard techniques in synthetic biology. Until now no such RFC existed for Gibson Assembly. The Cambridge team created such a document, providing standard protocols for the technique.<br />
<br />
<br />
Gibson assembly allows joining any sequences using appropriate overlaps. As no restriction enzymes are used, this assembly method technically does not require the assembled parts to be in BioBrick format. It must however be emphasised that it is still necessary to comply with existing RFCs in terms of prefixes, suffixes and illegal sites for all new parts that are entered into the registry. Gibson assembly can be used as an alternative to BioBrick Standard Assembly, while retaining full backwards compatibility. <br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Gibson/RFCTeam:Cambridge/Gibson/RFC2010-10-26T03:41:02Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Gibson Assembly: RFC}}<br />
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-RFC.JPG|caption=RFC-57, submitted by the Cambridge team}}<br />
The BioBrick foundation uses documents known as [http://bbf.openwetware.org/RFC.html RFC]s to document standard techniques in synthetic biology. Until now no such RFC existed for Gibson Assembly. The Cambridge team created such a document, providing standard protocols for the technique.<br />
<br />
<br />
Gibson assembly allows joining any sequences using appropriate overlaps. As no restriction enzymes are used, this assembly method technically does not require the assembled parts to be in BioBrick format. It must however be emphasised that it is still necessary to ensure compatibility with existing RFCs in terms of prefixes, suffixes and illegal sites. Gibson assembly can be used to produce fully backwards compatible parts.<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Gibson/MechanismTeam:Cambridge/Gibson/Mechanism2010-10-26T03:13:29Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Gibson Assembly: Mechanism}}<br />
<br />
Gibson Assembly is a means to join overlapping DNA sequences, technically it does not describe the way in which these sequences are created. However since this will be of importance to iGEM teams, we will briefly discuss this.<br />
<br />
===Creating overlapping DNA sequences===<br />
Overlapping DNA sequences can be created by PCR. We can add twenty base-pairs to the end of a sequence by using a primer which runs as follows from 5' to 3'.<br />
<br />
[[Image:PCR.png|500px|center|template extension using primers]]<br />
<br />
By using two ~40nt oligonucleotides as primers, we can add 20 bp of sequence A to sequence B and 20 bp of sequence B to sequence A. We are then ready to use Gibson Assembly. The Cambridge team have developed [http://www.gibthon.org/ Gibthon] to help you design primers for Gibson Assembly. The tool allows you to put in two sequences and choose 20bp of each to get a 40bp primer; it then analyses the melting temperature and secondary structure of this primer.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/a/a3/Cambridge-Gib1.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
== Gibson Assembly==<br />
Gibson Assembly master mix contains 3 enzymes:<br />
* T5 exonuclease<br />
* Phusion polymerase<br />
* Taq ligase<br />
<br />
The Gibson reaction relies on the action of the T5 exonuclease - this chews back at the 5' ends of both pieces of DNA<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/b5/Cambridge-Gib2.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/bf/Cambridge-Gib3.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Once it has chewed back far enough A-T G-C base pairing allows the two pieces to bind together.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/5/57/Cambridge-Gib5.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/1/1f/Cambridge-Gib6.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
We now have a single piece of DNA but it is not physically ligated together, it is merely held together by hydrogen bonding, also there are gaps in both single strands.<br />
<br />
Phusion is a DNA polymerase that repairs these gaps. It extends from the 3' end, so it does not interfere with T5 exonuclease which is acting at 5' ends.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/8f/Cambridge-Gib7.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Now we have DNA with no missing fragments but there is still a break in the phosphodiester bonds in the backbones of both single strands of DNA. This is corrected when Taq ligase action forms this bond.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/82/Cambridge-Gib8.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
And finally we have our finished piece of DNA. <br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/6/62/Cambridge-Gib9.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Gibson/MechanismTeam:Cambridge/Gibson/Mechanism2010-10-26T03:11:08Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Gibson Assembly: Mechanism}}<br />
<br />
Gibson Assembly is a means to join overlapping DNA sequences, technically it does not describe the way in which these sequences are created. However since this will be of importance to iGEM teams, we will briefly discuss this.<br />
<br />
===Creating overlapping DNA sequences===<br />
Overlapping DNA sequences can be created by PCR. We can add twenty base-pairs to the end of a sequence by using a primer which runs as follows from 5' to 3'.<br />
<pre><br />
20 bp of sequence to add -> 20 bp of template to anneal to.<br />
</pre><br />
By using two such primers we can add 20 bp of sequence A to sequence B and 20 bp of sequence B to sequence A. We are then ready to use Gibson Assembly. The Cambridge team have developed [http://www.gibthon.org/ Gibthon] to help you design primers for Gibson Assembly. The tool allows you to put in two sequences and choose 20bp of each to get a 40bp primer; it then analyses the melting temperature and secondary structure of this primer.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/a/a3/Cambridge-Gib1.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
== Gibson Assembly==<br />
Gibson Assembly master mix contains 3 enzymes:<br />
* T5 exonuclease<br />
* Phusion polymerase<br />
* Taq ligase<br />
<br />
The Gibson reaction relies on the action of the T5 exonuclease - this chews back at the 5' ends of both pieces of DNA<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/b5/Cambridge-Gib2.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/bf/Cambridge-Gib3.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Once it has chewed back far enough A-T G-C base pairing allows the two pieces to bind together.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/5/57/Cambridge-Gib5.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/1/1f/Cambridge-Gib6.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
We now have a single piece of DNA but it is not physically ligated together, it is merely held together by hydrogen bonding, also there are gaps in both single strands.<br />
<br />
Phusion is a DNA polymerase that repairs these gaps. It extends from the 3' end, so it does not interfere with T5 exonuclease which is acting at 5' ends.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/8f/Cambridge-Gib7.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Now we have DNA with no missing fragments but there is still a break in the phosphodiester bonds in the backbones of both single strands of DNA. This is corrected when Taq ligase action forms this bond.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/82/Cambridge-Gib8.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
And finally we have our finished piece of DNA. <br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/6/62/Cambridge-Gib9.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Gibson/MechanismTeam:Cambridge/Gibson/Mechanism2010-10-26T03:10:29Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Gibson Assembly: Mechanism}}<br />
<br />
Gibson Assembly is a means to join overlapping DNA sequences, technically it does not describe the way in which these sequences are created. However since this will be of importance to iGEM teams, we will briefly discuss this.<br />
<br />
===Creating overlapping DNA sequences===<br />
Overlapping DNA sequences can be created by PCR. We can add twenty base-pairs to the end of a sequence by using a primer which runs as follows from 5' to 3'.<br />
<pre><br />
20 bp of sequence to add -> 20 bp of template to anneal to.<br />
</pre><br />
By using two such primers we can add 20 bp of sequence A to sequence B and 20 bp of sequence B to sequence A. We are then ready to use Gibson Assembly. The Cambridge team have developed [http://www.gibthon.org/ Gibthon] to help you design primers for Gibson Assembly. The tool allows you to put in two sequences and choose 20bp of each to get a 40bp primer; it then analyses the melting temperature and secondary structure of this primer.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/a/a3/PCR.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
== Gibson Assembly==<br />
Gibson Assembly master mix contains 3 enzymes:<br />
* T5 exonuclease<br />
* Phusion polymerase<br />
* Taq ligase<br />
<br />
The Gibson reaction relies on the action of the T5 exonuclease - this chews back at the 5' ends of both pieces of DNA<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/b5/Cambridge-Gib2.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/b/bf/Cambridge-Gib3.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Once it has chewed back far enough A-T G-C base pairing allows the two pieces to bind together.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/5/57/Cambridge-Gib5.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/1/1f/Cambridge-Gib6.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
We now have a single piece of DNA but it is not physically ligated together, it is merely held together by hydrogen bonding, also there are gaps in both single strands.<br />
<br />
Phusion is a DNA polymerase that repairs these gaps. It extends from the 3' end, so it does not interfere with T5 exonuclease which is acting at 5' ends.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/8f/Cambridge-Gib7.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
Now we have DNA with no missing fragments but there is still a break in the phosphodiester bonds in the backbones of both single strands of DNA. This is corrected when Taq ligase action forms this bond.<br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/8/82/Cambridge-Gib8.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
And finally we have our finished piece of DNA. <br />
<br />
<html><div style="text-align:center"><img src="https://static.igem.org/mediawiki/2010/6/62/Cambridge-Gib9.png" style="border:1px solid gray; margin-top:20px; margin-bottom:20px;"></div></html><br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/File:PCR.pngFile:PCR.png2010-10-26T03:09:24Z<p>Peteremmrich: Using oligonucleotides to isolate and extend a template DNA by PCR. This can be used to create the overlaps of ~40bp, that are needed for Gibson Assembly.</p>
<hr />
<div>Using oligonucleotides to isolate and extend a template DNA by PCR. This can be used to create the overlaps of ~40bp, that are needed for Gibson Assembly.</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/TheTeamTeam:Cambridge/TheTeam2010-10-26T03:03:43Z<p>Peteremmrich: /* Students */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Meet the Team}}<br />
<br />
<html><br />
<br />
<div style="float:right"><br />
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</html><br />
=Students=<br />
<html><img src="https://static.igem.org/mediawiki/2010/9/95/CambridgeTeamAnja.jpg" style="float:left; padding-right:10px" /></html><br />
{{:Team:Cambridge/Templates/Nolineheader|header=Anja Hohmann}}<br />
:Anja is a biochemist. She likes singing along to 'Fireflies', is extremely efficient and makes sure our lab book is always kept up to date.<br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/3/3c/CambridgeTeamBen.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Ben Reeve}}<br />
:Ben is a molecular biologist. He is the Hacky Sack-master, loves the word 'epic' and brought the beats to the Gibson Assembly song. <br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/9/93/CambridgeTeamBill.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Bill Collins}}<br />
:Bill is a control engineer. He is the creator of Gibthon and always happy to assist with helpful advice: 'Get a Mac!'.<br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/7/7e/CambridgeTeamEmily.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Emily Knott}}<br />
:Emily is a mechanical engineer. She will happily sing to you about Gibson Assembly. Alternatively, she might teach you the dance moves to 'Blame it on the Boogie'. <br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/7/70/56q23864732.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Hannah Copley}}<br />
:Hannah is a medic. She initated the 'wiki morning turns into afternoon turns into day turns into weekend' and was the only one to remember dress-up friday. <br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/4/4f/CambridgeTeamPaul.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Paul Masset}}<br />
:Paul is a systems engineer. He is in charge of characterising our BioBricks, but generally found rowing on the river. <br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/e/e1/CambridgeTeamPeter.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Peter Emmrich}}<br />
:Peter is a plant scientist. He is the team's personal photographer, an instigator of party games and likes plastering the lab with motivational posters.<br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/4/47/CambridgeTeamTheo.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Theo Sanderson}}<br />
:Theo is a geneticist. He makes good videos, funny faces and wins every fast walk competition.<br />
<br />
<br />
<html><img src="https://static.igem.org/mediawiki/2010/1/19/CambridgeTeamWill2.jpg" style="float:left; padding-right:10px" /></html><br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Will Handley}}<br />
:Will is a physicist. He is our expert in oligo design, but can regularly be found juggling with all sorts of laboratory equipment.<br />
<br />
=Mission Statement=<br />
:As a team of scientists and engineers from very diverse backgrounds we aim to create an environment in which every member is able to apply his or her unique talents and knowledge to the fullest. We will document our literature research as well as our experimental work on the wiki and the online labbook. We will make new content available as soon as possible. To make our work more relevant and transparent we will clearly distinguish between theoretical designs, mathematical simulations and physically designed biological systems, and include measurements where appropriate.<br />
<br />
==Share and Enjoy==<br />
:In the Open Source spirit of iGEM, we will try to make our ideas, the progress of our work and our results as open as possible. This requires honesty about which parts of our project succeeded, which ones yielded ambiguous results and which ideas had to be abandoned. We believe that such transparency will make our project more useful for future iGEM teams and researchers.<br />
:Although iGEM takes the form of a competition, all our work is ultimately a collaboration to create a registry that will act as a firm foundation supporting the scientists and engineers of the future.<br />
:Therefore, we would love to collaborate with other current iGEM teams working on related projects. If you think parts of our work could be useful to you, please get in contact and we will see how we can help. Conversely, if you have any resources or knowledge that you believe could help us, please let us know!<br />
<br />
==Attribution==<br />
Unless otherwise indicated, all work presented on this wiki is the sole work of the iGEM team members listed above. We are also extremely grateful for the help of the following advisors and instructors.<br />
<br />
=Advisors=<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Jim Haseloff}}<br />
<br />
Dr Haseloff is a lecturer and group leader in the Department of Plant Sciences investigating biological engineering of plant systems. <br />
<br />
[http://www.plantsci.cam.ac.uk/Haseloff/ http://www.plantsci.cam.ac.uk/Haseloff/]<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Jim Ajioka}}<br />
<br />
Dr Ajioka is a senior lecturer and group leader in the Department of Pathology working on host-parasite interactions during the infection of warm-blooded animals with the intracellular pathogen Toxoplasma gondii. <br />
<br />
http://www.path.cam.ac.uk/research/investigators/ajioka/<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Duncan Rowe}}<br />
<br />
Dr Rowe is a laboratory manager and teaching technician in the Department of Genetics with research and development experience in recombinant and synthetic DNA technology, cloning, drug target identification and therapeutic protein expression in bacteria.<br />
<br />
http://www.gen.cam.ac.uk/research/personal/rowe/rowe.html<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Gos Micklem}}<br />
<br />
Dr Micklem is director of the Cambridge Computational Biology Institute as well as a group leader in the Department of Genetics interested in bioinformatics and the analysis of small RNAs. <br />
<br />
http://www.gen.cam.ac.uk/research/micklem.html<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=PJ Steiner}}<br />
<br />
PJ is a Ph.D. student in Dr Haseloff's Lab.<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Fernan Federici}}<br />
<br />
Fernan is a PostDoc in Dr Haseloff's lab.<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=James Brown}}<br />
<br />
James is a Ph.D. student Dr Haseloff's lab.<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader2|header=Shuna Gould}}<br />
<br />
Shuna works in Dr Ajioka's lab and was a member of the Cambridge iGEM Team 2009.<br />
<br />
http://labrat.fieldofscience.com/<br />
==Contact us==<br />
You can reach the team by [mailto:info@cambridgeigem.org email]. We will get back to you as soon as we can.<br />
<br />
<br />
<br />
<html><br />
</div><br />
</html><br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-26T03:01:00Z<p>Peteremmrich: /* Futures */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-Photobacterium_plate.JPG|caption=One of the plates of <i>V. phosphoreum</i> we prepared.}}<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. <br />
<br />
==Futures==<br />
We spent one day early in the project imagining how engineered artificial bioluminescence might be used in the future. This workshop, led by Daisy Ginsberg from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How would omnipresent bioluminescence affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
==Applications==<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be better than conventional devices in this area? and where might it be useful? We also considered the prospect of using our light production in biosensors (after a talk from 'Practical Action'*). Coupled with a light sensor our parts could provide a bridge between biological and electrical circuits. <br />
<br />
==Knowledge Recycling==<br />
Sustainability considerations in end design also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends?<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Human_PracticesTeam:Cambridge/Human Practices2010-10-26T02:59:52Z<p>Peteremmrich: /* Futures */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#fb5c2b|title=Human Practices}}<br />
{{:Team:Cambridge/Templates/RightImage|image=Cambridge-Photobacterium_plate.JPG|caption=One of the plates of <i>V. phosphoreum</i> we prepared.}}<br />
Human practises encompasses the social ethical and legal considerations of our work. We imagined how our particular project might impact on peoples lives as well as thinking about the wider issues of the way we practise our science and share our findings. <br />
<br />
==Futures==<br />
We spent one day early in the project imagining how engineered artificial bioluminescence might be used in the future. This Workshop, led by Daisy Ginsberg from the Royal College of Arts, made us think about where research into bioluminescence might one day bring us. How is omnipresent bioluminescence going to affect the way we perceive light in our living environment? Will engineered bioluminescence find its way into consumer products or remain in highly specialised applications and novelty items? Bioluminescent light has a broad spectrum and is emitted volumetrically. How can we use these different qualities of light compared to conventional sources for art, design and architecture?<br />
<br />
==Applications==<br />
Our thoughts on using biological light sources led us to consider the concept of sustainability. Would our lighting be better than conventional devices in this area? and where might it be useful? We also considered the prospect of using our light production in biosensors (after a talk from 'Practical Action'*). Coupled with a light sensor our parts could provide a bridge between biological and electrical circuits. <br />
<br />
==Knowledge Recycling==<br />
Sustainability considerations in end design also led us to consider the sustainability of the way we conduct our research. The theme of recycling echoed strongly throughout or project due to the desire to recycle luciferin substrate in project firefly and more generally with considerations of minimising the environmental impact of our work. Recycling of physical materials is vital for sustainability but do we treat our intellectual property in the same way? Do we give the ideas we have the maximum chance of being taken forward and used to promote further thought rather than reaching intellectual dead ends?<br />
<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T02:11:13Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
[[Image:Cambridge_logo.gif|center|500px|University of Cambridge]]<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe, Gos Micklem and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T02:10:49Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
[[Image:Cambridge_logo.gif|center|500px|University of Cambridge]]<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe, Gos Micklem and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T02:06:27Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
[[Image:Cambridge_logo.gif|center|600px|University of Cambridge]]<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Bioluminescence/Bacterial_Codon_optimisationTeam:Cambridge/Bioluminescence/Bacterial Codon optimisation2010-10-26T02:04:52Z<p>Peteremmrich: /* What is codon usage? */</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Bacterial Codon Optimisation}}<br />
=What is codon usage?=<br />
[[Image:codons.jpg|300px|right|the universal genetic code]]<br />
One of the fascinating features of life is the '''universal genetic code'''. In all known organisms, from bacteria to man, the same triplets of DNA bases code for the same amino acids. However this does not mean that all species encode their genomes in exactly the same way. <br />
The code is ''redundant'': a number of triplets code for the same amino acid. While all species are able to translate any sequence of DNA interchangeably, E. coli prefers to use certain triplets to code for certain amino acids which may be different to the ones we use. This 'preference' is reflected in the levels of tRNA which match such a triplet. In this project we resynthesised a number of genes ''de novo'' and thus were able to codon optimise them for expression in E. coli.<br />
<br />
=Improved translational speed=<br />
Starting with the DNA sequence of the ''Vibrio fischeri'' lux operon found on the NCBI database, we used a number of tools to replace the codons used with the most common codons found in the E.coli genome. To achieve optimal expression of the Lux operon in E.coli, we had the operon re-synthesized after optimising the usage of codons. This conserves the sequence of amino acids in the gene products, but improves the rate of translation, as more common tRNAs are recruited. Codon usage optimization can yield dramatic increases in the expression of foreign genes, especially if they are introduced from less closely related species [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4C8NKCY-3&_user=6094838&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1511316646&_rerunOrigin=scholar.google&_acct=C000053194&_version=1&_urlVersion=0&_userid=6094838&md5=c970323b521fa1ec9d3050d4c4970eb1&searchtype=a Gustafsson et al. 2004]<br />
<br />
=Altered G-C content=<br />
DNA curvature is increased by sequences rich in A-T or G-C pairs. The natural ''V.fischeri'' Lux operon, and especially its intergenic regions, contains stretches rich in A-T, resulting in the curvature that H-NS proteins bind to preferentially. Changing the coding DNA sequence also meant changing the curvature of the DNA, which affects the binding affinity of H-NS proteins. To alleviate the repression that H-NS exerts, we took care to raise the G-C content of intergenic regions and coding sequences (at times resorting to suboptimal codons). According to a computational prediction, this resulted in greatly reduced DNA curvature, and thus hopefully to a reduced affinity for H-NS proteins.<br />
<br />
[[Image:GC_content.png|600px|center| The LuxC coding region before and after codon optimisation. Blue denotes A-T rich regions. Note the reduction in A-T rich stretches after opitmisation]]<br />
<br />
=Differential Expression=<br />
In ''Vibrio fischeri'', LuxA and B are expressed at five times the levels of LuxC, D, E and G. Since all these genes are transcribed on the same mRNA, but have their own Ribosome Binding Sites, this is probably due to differences in codon usage ([http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055 Meighen et al. 1988]). A number of rare codons are found in Lux C, D, E and G, but not in LuxA and B. Since we did not receive the newly synthesised LuxA and B in time, we constructed a new operon using our LuxC, D, E and G, and the LuxAB BioBrick that was put into the registry by the Edinburgh iGEM team 2009 (BBa_216008). These genes originate from Xenorhabdus luminescens. Compared to ''Vibrio fischeri'', there is only limited amino acid identity in the Lux A and B genes (52% and 66% respectively). Yet the literature describes both as using the same substrates. [http://aem.asm.org/cgi/content/abstract/55/10/2607 Schmidt et al. 1989] describe positive complementation test using components from ''V. fisheri'' and ''Xenorhabdus luminescens''. To use foreign genes from two very different donor species in one pathway in E.coli is an exciting test of our understanding of the processes involved in bacterial bioluminescence and of the power of synthetic biology in general.<br />
In this construct, LuxC, D, E and G are codon optimised, but LuxA and B are not. In order to adjust the ratio of gene expression between these genes to the state found in nature, we chose to put LuxA and B under a very strong, phage derived promoter (plambda) to be constitutively expressed. The other genes can now be put under any promoter to create a PoPS-to-light device. In conjunction with an inducible or repressible promoter, this could be used as a reporter device. To test the system, we placed the LuxCDEG under an arabinose induced pbad promoter (BBa_i0500).<br />
<br />
=Parts submitted to the registry=<br />
Ideally we would have submitted a codon-optimised version of the entire Lux operon. Unfortunately Mr Gene, the company we employed for synthesis, still had not completed the order two months after placing, and at the point of the wiki-freeze we still have not received the optimised versions of LuxA and B. In order to complete our aim of creating a PoPs->light device that can be placed under any promoter, we combined the optimised ''Vibrio'' LuxCDEG genes with the Edinburgh 2009 ''Xenorhabdus'' LuxAB. The assembly was achieved using the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson method]. Since we only received LuxCD and LuxEG from Mr Gene two weeks before the documentation deadline, we could not properly characterise these parts. For a complete list of the BioBricks we submitted see the [https://2010.igem.org/Team:Cambridge/BioBricks BioBricks section].<br />
<br />
<br />
Codon optimised bacterial luminescence parts:<br />
<br />
[http://partsregistry.org/Part:BBa_K325902 luxCD (BBa_K325902)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325903 luxEG (BBa_K325903)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325905 CDEG pLambda AB (BBa_K325905)] a PoPs->light device that can be placed under any promoter, hybrid device containing promoterless V. fisheri derived CDEG (optimised) and Xenorhabdus AB under a strong constitutive promoter<br />
<br />
[http://partsregistry.org/Part:BBa_K325906 pbad CDEG pLambda AB (BBa_K325906)] the above part under the arabinose induced pbad promoter<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Bioluminescence/Bacterial_Codon_optimisationTeam:Cambridge/Bioluminescence/Bacterial Codon optimisation2010-10-26T02:04:18Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Bacterial Codon Optimisation}}<br />
=What is codon usage?=<br />
[[Image:GC_content.png|300px|right|the universal genetic code]]<br />
One of the fascinating features of life is the '''universal genetic code'''. In all known organisms, from bacteria to man, the same triplets of DNA bases code for the same amino acids. However this does not mean that all species encode their genomes in exactly the same way. <br />
The code is ''redundant'': a number of triplets code for the same amino acid. While all species are able to translate any sequence of DNA interchangeably, E. coli prefers to use certain triplets to code for certain amino acids which may be different to the ones we use. This 'preference' is reflected in the levels of tRNA which match such a triplet. In this project we resynthesised a number of genes ''de novo'' and thus were able to codon optimise them for expression in E. coli.<br />
<br />
=Improved translational speed=<br />
Starting with the DNA sequence of the ''Vibrio fischeri'' lux operon found on the NCBI database, we used a number of tools to replace the codons used with the most common codons found in the E.coli genome. To achieve optimal expression of the Lux operon in E.coli, we had the operon re-synthesized after optimising the usage of codons. This conserves the sequence of amino acids in the gene products, but improves the rate of translation, as more common tRNAs are recruited. Codon usage optimization can yield dramatic increases in the expression of foreign genes, especially if they are introduced from less closely related species [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4C8NKCY-3&_user=6094838&_coverDate=07%2F31%2F2004&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1511316646&_rerunOrigin=scholar.google&_acct=C000053194&_version=1&_urlVersion=0&_userid=6094838&md5=c970323b521fa1ec9d3050d4c4970eb1&searchtype=a Gustafsson et al. 2004]<br />
<br />
=Altered G-C content=<br />
DNA curvature is increased by sequences rich in A-T or G-C pairs. The natural ''V.fischeri'' Lux operon, and especially its intergenic regions, contains stretches rich in A-T, resulting in the curvature that H-NS proteins bind to preferentially. Changing the coding DNA sequence also meant changing the curvature of the DNA, which affects the binding affinity of H-NS proteins. To alleviate the repression that H-NS exerts, we took care to raise the G-C content of intergenic regions and coding sequences (at times resorting to suboptimal codons). According to a computational prediction, this resulted in greatly reduced DNA curvature, and thus hopefully to a reduced affinity for H-NS proteins.<br />
<br />
[[Image:GC_content.png|600px|center| The LuxC coding region before and after codon optimisation. Blue denotes A-T rich regions. Note the reduction in A-T rich stretches after opitmisation]]<br />
<br />
=Differential Expression=<br />
In ''Vibrio fischeri'', LuxA and B are expressed at five times the levels of LuxC, D, E and G. Since all these genes are transcribed on the same mRNA, but have their own Ribosome Binding Sites, this is probably due to differences in codon usage ([http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055 Meighen et al. 1988]). A number of rare codons are found in Lux C, D, E and G, but not in LuxA and B. Since we did not receive the newly synthesised LuxA and B in time, we constructed a new operon using our LuxC, D, E and G, and the LuxAB BioBrick that was put into the registry by the Edinburgh iGEM team 2009 (BBa_216008). These genes originate from Xenorhabdus luminescens. Compared to ''Vibrio fischeri'', there is only limited amino acid identity in the Lux A and B genes (52% and 66% respectively). Yet the literature describes both as using the same substrates. [http://aem.asm.org/cgi/content/abstract/55/10/2607 Schmidt et al. 1989] describe positive complementation test using components from ''V. fisheri'' and ''Xenorhabdus luminescens''. To use foreign genes from two very different donor species in one pathway in E.coli is an exciting test of our understanding of the processes involved in bacterial bioluminescence and of the power of synthetic biology in general.<br />
In this construct, LuxC, D, E and G are codon optimised, but LuxA and B are not. In order to adjust the ratio of gene expression between these genes to the state found in nature, we chose to put LuxA and B under a very strong, phage derived promoter (plambda) to be constitutively expressed. The other genes can now be put under any promoter to create a PoPS-to-light device. In conjunction with an inducible or repressible promoter, this could be used as a reporter device. To test the system, we placed the LuxCDEG under an arabinose induced pbad promoter (BBa_i0500).<br />
<br />
=Parts submitted to the registry=<br />
Ideally we would have submitted a codon-optimised version of the entire Lux operon. Unfortunately Mr Gene, the company we employed for synthesis, still had not completed the order two months after placing, and at the point of the wiki-freeze we still have not received the optimised versions of LuxA and B. In order to complete our aim of creating a PoPs->light device that can be placed under any promoter, we combined the optimised ''Vibrio'' LuxCDEG genes with the Edinburgh 2009 ''Xenorhabdus'' LuxAB. The assembly was achieved using the [https://2010.igem.org/Team:Cambridge/Gibson/Introduction Gibson method]. Since we only received LuxCD and LuxEG from Mr Gene two weeks before the documentation deadline, we could not properly characterise these parts. For a complete list of the BioBricks we submitted see the [https://2010.igem.org/Team:Cambridge/BioBricks BioBricks section].<br />
<br />
<br />
Codon optimised bacterial luminescence parts:<br />
<br />
[http://partsregistry.org/Part:BBa_K325902 luxCD (BBa_K325902)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325903 luxEG (BBa_K325903)] derived from V. fischeri, but optimised for E.coli<br />
<br />
[http://partsregistry.org/Part:BBa_K325905 CDEG pLambda AB (BBa_K325905)] a PoPs->light device that can be placed under any promoter, hybrid device containing promoterless V. fisheri derived CDEG (optimised) and Xenorhabdus AB under a strong constitutive promoter<br />
<br />
[http://partsregistry.org/Part:BBa_K325906 pbad CDEG pLambda AB (BBa_K325906)] the above part under the arabinose induced pbad promoter<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/File:Cambridge_logo.gifFile:Cambridge logo.gif2010-10-26T02:04:05Z<p>Peteremmrich: </p>
<hr />
<div></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/iGEM_TeamsTeam:Cambridge/iGEM Teams2010-10-26T02:01:00Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Collaboration with iGEM Teams}}<br />
As a team we thought that it was very important to work together with other teams, since iGEM is an effort to build a registry of parts together, as well as a competition. We respectfully disagree with teams who work on their wiki behind the scenes and then upload it days before the deadline. We think that collaboration is fostered if all teams can see how each other are progressing and ask for help from an appropriate team. As it happened, our openness allowed Mexico to ask us for some of our constructs and fostered an extensive collaboration.<br />
=Teams=<br />
==Sheffield iGEM==<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-Sheffield.jpg}}<br />
The Sheffield team needed an additional sample of pSB1C3, we were able to send them a stab.<br />
<html><p style="clear:both">&nbsp;</p></html><br />
==UNAM Genomics Mexico==<br />
{{:Team:Cambridge/Templates/rightpic|src=Cambridge-Mexico.jpg}}<br />
At the beginning of the Summer we established a collaboration with the team from the National Autonomous University of Mexico. When they had problems measuring any light output we sent them our constructs, which gave them more success. We also shared protocols for best measurement techniques.<br />
<br />
{{:Team:Cambridge/Templates/footer}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T02:00:05Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
<br />
Department of Biochemistry<br />
<br />
Department of Engineering<br />
<br />
School of Technology<br />
<br />
School of Biological Sciences<br />
<br />
<br />
for their invaluable support in teaching and resources<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T01:59:36Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe and David Summers<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Further Thanks to:}}<br />
<br />
Department of Physiology, Development and Neuroscience<br />
Department of Biochemistry<br />
Department of Engineering<br />
School of Technology<br />
School of Biological Sciences<br />
<br />
for their invaluable support in teaching and resources<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T01:56:20Z<p>Peteremmrich: </p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
We would like to thank the following departments of the University of Cambridge for their generous support with money and material, facilites and advice.<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Plant Sciences}}<br />
For letting us use the spacious Teaching Lab over the summer and enduring our abuse of expensive lab equipment. Thank you for providing lots of advice on techniques and helping us to balance imagination and feasibility. <br />
<br />
Special thanks to: Jim Haseloff, James Brown, Fernan Federici, PJ Steiner and Barbara Landamore. <br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Genetics}}<br />
For advice on scientific background and smooth logistics.<br />
<br />
Special thanks to: Duncan Rowe and David Summers<br />
<br />
{{:Team:Cambridge/Templates/Nolineheader|header=Department of Pathology}}<br />
For providing us with a new home after the start of term and practical help. <br />
<br />
Special thanks to: Jim Ajioka and Shuna Gould<br />
<br />
<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/DepartmentsTeam:Cambridge/Departments2010-10-26T01:30:49Z<p>Peteremmrich: New page: {{:Team:Cambridge/Templates/headerMinimalprototype}} {{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}} {{:Team:Cambridge/Templates/footerMinimal}}</p>
<hr />
<div>{{:Team:Cambridge/Templates/headerMinimalprototype}}<br />
{{:Team:Cambridge/Templates/headerbar|colour=#386abc|title=Departmental Support}}<br />
<br />
{{:Team:Cambridge/Templates/footerMinimal}}</div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Templates/headerMinimalprototypeTeam:Cambridge/Templates/headerMinimalprototype2010-10-26T01:21:29Z<p>Peteremmrich: </p>
<hr />
<div>__NOTOC__<html lang="en"> <br />
<head> <br />
<br />
<script type="text/javascript"><br />
<br />
var _gaq = _gaq || [];<br />
_gaq.push(['_setAccount', 'UA-65298-13']);<br />
_gaq.push(['_trackPageview']);<br />
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var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;<br />
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);<br />
})();<br />
<br />
</script><br />
<style><br />
h2{color:#96d446; }<br />
h1, h2, h3, h4, h5{font-family:"Vollkorn"; font-size:200%; line-height:35px; border-bottom:0; margin-bottom:5px; border-top:1px dotted #e3e3e3; margin-top:10px; padding-top:30px; font-weight:normal;}<br />
h2.noline{ border-top:0; margin-top:0; padding-top:0; margin-bottom:0; line-height:20px; padding-top:2px; font-size:20px;}<br />
h2.topheader{border-top:0; padding-top:0; margin-top:5px;}<br />
<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script> <br />
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$('.left-menu ul')[0].innerHTML="<li><a href=\"https://2010.igem.org\" style=\"font-weight:bold; text-transform:none\">iGEM HQ</a></li>"+$('.left-menu ul')[0].innerHTML;<br />
$(function() {<br />
$('ul.llmenu').lavaLamp({ speed: 300, autoReturn: false , target:'li'});<br />
});<br />
$(function(){<br />
$('ul#accmenu').accordion({<br />
header:'.head',<br />
fillSpace:false,<br />
autoHeight:false,<br />
navigation:true,<br />
animated: 'easeslide'})<br />
});<br />
</script><br />
<script type="text/javascript" src="/Team:Cambridge/lightbox/js?action=raw"></script><br />
<br />
<link href='http://fonts.googleapis.com/css?family=Vollkorn:regular,bold&subset=latin' rel='stylesheet' type='text/css'><br />
<style><br />
/**<br />
* jQuery lightBox plugin<br />
* This jQuery plugin was inspired and based on Lightbox 2 by Lokesh Dhakar (http://www.huddletogether.com/projects/lightbox2/)<br />
* and adapted to me for use like a plugin from jQuery.<br />
* @name jquery-lightbox-0.5.css<br />
* @author Leandro Vieira Pinho - http://leandrovieira.com<br />
* @version 0.5<br />
* @date April 11, 2008<br />
* @category jQuery plugin<br />
* @copyright (c) 2008 Leandro Vieira Pinho (leandrovieira.com)<br />
* @license CCAttribution-ShareAlike 2.5 Brazil - http://creativecommons.org/licenses/by-sa/2.5/br/deed.en_US<br />
* @example Visit http://leandrovieira.com/projects/jquery/lightbox/ for more informations about this jQuery plugin<br />
*/<br />
#jquery-overlay {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
z-index: 90;<br />
width: 100%;<br />
height: 500px;<br />
}<br />
#jquery-lightbox {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
width: 100%;<br />
z-index: 100;<br />
text-align: center;<br />
line-height: 0;<br />
}<br />
#jquery-lightbox a img { border: none; }<br />
#lightbox-container-image-box {<br />
position: relative;<br />
background-color: #fff;<br />
width: 250px;<br />
height: 250px;<br />
margin: 0 auto;<br />
}<br />
#lightbox-container-image { padding: 10px; }<br />
#lightbox-loading {<br />
position: absolute;<br />
top: 40%;<br />
left: 0%;<br />
height: 25%;<br />
width: 100%;<br />
text-align: center;<br />
line-height: 0;<br />
}<br />
#lightbox-nav {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
height: 100%;<br />
width: 100%;<br />
z-index: 10;<br />
}<br />
#lightbox-container-image-box > #lightbox-nav { left: 0; }<br />
#lightbox-nav a { outline: none;}<br />
#lightbox-nav-btnPrev, #lightbox-nav-btnNext {<br />
width: 49%;<br />
height: 100%;<br />
zoom: 1;<br />
display: block;<br />
}<br />
#lightbox-nav-btnPrev { <br />
left: 0; <br />
float: left;<br />
}<br />
#lightbox-nav-btnNext { <br />
right: 0; <br />
float: right;<br />
}<br />
#lightbox-container-image-data-box {<br />
font: 10px Verdana, Helvetica, sans-serif;<br />
background-color: #fff;<br />
margin: 0 auto;<br />
line-height: 1.4em;<br />
overflow: auto;<br />
width: 100%;<br />
padding: 0 10px 0;<br />
}<br />
#lightbox-container-image-data {<br />
padding: 0 10px; <br />
color: #666; <br />
}<br />
#lightbox-container-image-data #lightbox-image-details { <br />
width: 70%; <br />
float: left; <br />
text-align: left; <br />
} <br />
#lightbox-image-details-caption { font-weight: bold; }<br />
#lightbox-image-details-currentNumber {<br />
display: block; <br />
clear: left; <br />
padding-bottom: 1.0em; <br />
} <br />
#lightbox-secNav-btnClose {<br />
width: 66px; <br />
float: right;<br />
padding-bottom: 0.7em; <br />
}<br />
<br />
</style> <br />
<script><br />
$(document).ready(function() {<br />
$('a.lightbox').lightBox(); // Select all links with lightbox class<br />
$('a.image').each(function(idx, item) { <br />
var src = item.firstChild.src;<br />
src=src.replace(/wiki\/images\/thumb\/(.+)\/(.+)\/(.+)\/(.+)\..../,"wiki/images/$1/$2/$3");<br />
item.href=src;<br />
});<br />
$('a.image').lightBox();<br />
});<br />
</script><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="http://www.srcf.ucam.org/~wac26/iGEM/css/camgemw.css" /><br />
<br />
</head> <br />
<body> <br />
<style><br />
body{background-image:url('https://static.igem.org/mediawiki/2010/a/a9/Cam-Theoback.png');<br />
background-position:top center;<br />
background-repeat:repeat-y<br />
}<br />
<br />
</style><br />
<div id="wrap"> <br />
<div id="header"><img align="center" style="margin-bottom:0px; padding:0;" src="https://static.igem.org/mediawiki/2010/d/d4/CamBillHeaderSq.png" usemap="#headermap"> </div> <br />
<map name="headermap"><br />
<area shape="rect" coords="10,30,250,240" href="https://2010.igem.org/Team:Cambridge" /><br />
<area shape="rect" coords="888,177,942,201" href="http://www.flickr.com/people/roberts87/" /><br />
</map><br />
<div id="left"> <br />
<br />
<ul id="accmenu"><br />
<li><a class="head" href="#"> Introduction</a><br />
<ul class="llmenu llmenublue"><br />
<li><a href="/Team:Cambridge">Home</a></li><br />
<br />
<br />
<li><a href="/Team:Cambridge/TheTeam">Meet the Team</a></li><br />
<br />
<li><a href="/Team:Cambridge/Photos">Photo Gallery</a></li><br />
<li><a href="/Team:Cambridge/Videos">Videos</a></li><br />
<li><a href="/Team:Cambridge/BioBricks">BioBrick Parts</a></li><br />
<br />
<br />
</ul><br />
</li><br />
<li><a class="head" href="#">Project Firefly</a><br />
<ul class="llmenu llmenugreen"><br />
<li><a href="/Team:Cambridge/Bioluminescence">Introduction</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Background_Firefly">Background</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Colour">Coloured outputs</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Luciferin_Regeneration">Luciferin recovery</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Firefly_Modelling">Modelling</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="head" href="#">Project Vibrio</a><br />
<ul class="llmenu llmenublue"><br />
<li><a href="/Team:Cambridge/Bioluminescence/Bacterial_Luciferases">Introduction</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Background">Background</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/G28">The LuxBrick</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Bacterial_Codon_optimisation">Codon optimisation</a></li><br />
<li><a href="/Team:Cambridge/Bioluminescence/Vibrio_Modelling">Modelling</a></li><br />
</ul><br />
</li><br />
<li><a class="head" href="#">Tools</a><br />
<ul class="llmenu llmenured"><br />
<li><a href="/Team:Cambridge/Tools/Gibson">Gibthon</a></li><br />
<li><a href="/Team:Cambridge/Tools/GenBank">BioBrick → GenBank</a></li><br />
<li><a href="/Team:Cambridge/Tools/Ligate">Ligation Calculator</a></li><br />
<li><a href="/Team:Cambridge/Tools/Eglometer">The E.glometer</a></li><br />
<br />
</ul><br />
</li><br />
<li><a class="head" href="#">Gibson Assembly</a><br />
<ul class="llmenu llmenublue"><br />
<li><a href="/Team:Cambridge/Gibson/Introduction">Introduction</a></li><br />
<li><a href="/Team:Cambridge/Gibson/Mechanism">How it works</a></li><br />
<li><a href="/Team:Cambridge/Gibson/Protocol">Protocol</a></li><br />
<li><a href="/Team:Cambridge/Gibson/RFC">RFC</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="head" href="#">Considerations</a><br />
<ul class="llmenu llmenublue"><br />
<li><a href="/Team:Cambridge/Human_Practices">Human Practices</a></li><br />
<li><a href="/Team:Cambridge/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="head" href="/Team:Cambridge/Notebook/Week1">Notebook</a><br />
<ul class="llmenu llmenuyellow"><br />
<li><a href="/Team:Cambridge/Notebook/Summary">Summary</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week1">Week 1</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week2">Week 2</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week3">Week 3</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week4">Week 4</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week5">Week 5</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week6">Week 6</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week7">Week 7</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week8">Week 8</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week9">Week 9</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week10">Week 10</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week11">Week 11</a></li><br />
<li><a href="/Team:Cambridge/Notebook/Week12">Week 12</a></li><br />
<li><a href="/Team:Cambridge/Notebook/FurtherWork">Beyond Week 12</a></li><br />
<br />
<li><a href="/Team:Cambridge/Protocols">Protocols</a> </li><br />
</ul><br />
</li><br />
<br />
<br />
<br />
<li><a class="head" href="#">Future applications</a><br />
<ul class="llmenu llmenured"><br />
<li><a href="/Team:Cambridge/Tools/microMeasure">Biosensors</a></li><br />
<li><a href="/Team:Cambridge/Tools/Lighting">Lighting</a></li><br />
<li><a href="/Team:Cambridge/References/ProjectBioluminescence">Link sharing</a></li><br />
</ul><br />
</li><br />
<br />
<br />
<li><a href="/Team:Cambridge/Partners" class="head">Our Partners</a><br />
<ul class="llmenu llmenublue"><br />
<li><a href="/Team:Cambridge/Partners">Sponsors</a> </li><br />
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<li><a href="/Team:Cambridge/Departments">University</a> </li><br />
<li><a href="/Team:Cambridge/Publicity">Publicity</a> </li><br />
<br />
</ul> </li><br />
<br />
</ul><br />
<br />
</p><br />
</div> <br />
<div id="right"></div>Peteremmrichhttp://2010.igem.org/Team:Cambridge/Templates/headerMinimalprototypeTeam:Cambridge/Templates/headerMinimalprototype2010-10-26T01:20:49Z<p>Peteremmrich: </p>
<hr />
<div>__NOTOC__<html lang="en"> <br />
<head> <br />
<br />
<script type="text/javascript"><br />
<br />
var _gaq = _gaq || [];<br />
_gaq.push(['_setAccount', 'UA-65298-13']);<br />
_gaq.push(['_trackPageview']);<br />
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var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;<br />
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var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);<br />
})();<br />
<br />
</script><br />
<style><br />
h2{color:#96d446; }<br />
h1, h2, h3, h4, h5{font-family:"Vollkorn"; font-size:200%; line-height:35px; border-bottom:0; margin-bottom:5px; border-top:1px dotted #e3e3e3; margin-top:10px; padding-top:30px; font-weight:normal;}<br />
h2.noline{ border-top:0; margin-top:0; padding-top:0; margin-bottom:0; line-height:20px; padding-top:2px; font-size:20px;}<br />
h2.topheader{border-top:0; padding-top:0; margin-top:5px;}<br />
<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"></script> <br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.2/jquery-ui.js"></script><br />
<script type='text/javascript' src='http://www.srcf.ucam.org/~wac26/iGEM/jquery.lavalamp-1.3.4b.js'></script><br />
<script type='text/javascript' src='http://www.srcf.ucam.org/~wac26/iGEM/jquery.easing.1.3.js'></script><br />
<script type='text/javascript' src='https://2010.igem.org/Team:Cambridge/prettyphoto?ctype=text/javascript&action=raw'></script><br />
<link href='https://2010.igem.org/Team:Cambridge/prettyphotocss?ctype=text/css&action=raw' rel='stylesheet' type='text/css' /><br />
<link href='http://fonts.googleapis.com/css?family=Nobile:regular,bold' rel='stylesheet' type='text/css'><br />
<br />
<script type="text/javascript"> <br />
$('.left-menu ul')[0].innerHTML="<li><a href=\"https://2010.igem.org\" style=\"font-weight:bold; text-transform:none\">iGEM HQ</a></li>"+$('.left-menu ul')[0].innerHTML;<br />
$(function() {<br />
$('ul.llmenu').lavaLamp({ speed: 300, autoReturn: false , target:'li'});<br />
});<br />
$(function(){<br />
$('ul#accmenu').accordion({<br />
header:'.head',<br />
fillSpace:false,<br />
autoHeight:false,<br />
navigation:true,<br />
animated: 'easeslide'})<br />
});<br />
</script><br />
<script type="text/javascript" src="/Team:Cambridge/lightbox/js?action=raw"></script><br />
<br />
<link href='http://fonts.googleapis.com/css?family=Vollkorn:regular,bold&subset=latin' rel='stylesheet' type='text/css'><br />
<style><br />
/**<br />
* jQuery lightBox plugin<br />
* This jQuery plugin was inspired and based on Lightbox 2 by Lokesh Dhakar (http://www.huddletogether.com/projects/lightbox2/)<br />
* and adapted to me for use like a plugin from jQuery.<br />
* @name jquery-lightbox-0.5.css<br />
* @author Leandro Vieira Pinho - http://leandrovieira.com<br />
* @version 0.5<br />
* @date April 11, 2008<br />
* @category jQuery plugin<br />
* @copyright (c) 2008 Leandro Vieira Pinho (leandrovieira.com)<br />
* @license CCAttribution-ShareAlike 2.5 Brazil - http://creativecommons.org/licenses/by-sa/2.5/br/deed.en_US<br />
* @example Visit http://leandrovieira.com/projects/jquery/lightbox/ for more informations about this jQuery plugin<br />
*/<br />
#jquery-overlay {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
z-index: 90;<br />
width: 100%;<br />
height: 500px;<br />
}<br />
#jquery-lightbox {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
width: 100%;<br />
z-index: 100;<br />
text-align: center;<br />
line-height: 0;<br />
}<br />
#jquery-lightbox a img { border: none; }<br />
#lightbox-container-image-box {<br />
position: relative;<br />
background-color: #fff;<br />
width: 250px;<br />
height: 250px;<br />
margin: 0 auto;<br />
}<br />
#lightbox-container-image { padding: 10px; }<br />
#lightbox-loading {<br />
position: absolute;<br />
top: 40%;<br />
left: 0%;<br />
height: 25%;<br />
width: 100%;<br />
text-align: center;<br />
line-height: 0;<br />
}<br />
#lightbox-nav {<br />
position: absolute;<br />
top: 0;<br />
left: 0;<br />
height: 100%;<br />
width: 100%;<br />
z-index: 10;<br />
}<br />
#lightbox-container-image-box > #lightbox-nav { left: 0; }<br />
#lightbox-nav a { outline: none;}<br />
#lightbox-nav-btnPrev, #lightbox-nav-btnNext {<br />
width: 49%;<br />
height: 100%;<br />
zoom: 1;<br />
display: block;<br />
}<br />
#lightbox-nav-btnPrev { <br />
left: 0; <br />
float: left;<br />
}<br />
#lightbox-nav-btnNext { <br />
right: 0; <br />
float: right;<br />
}<br />
#lightbox-container-image-data-box {<br />
font: 10px Verdana, Helvetica, sans-serif;<br />
background-color: #fff;<br />
margin: 0 auto;<br />
line-height: 1.4em;<br />
overflow: auto;<br />
width: 100%;<br />
padding: 0 10px 0;<br />
}<br />
#lightbox-container-image-data {<br />
padding: 0 10px; <br />
color: #666; <br />
}<br />
#lightbox-container-image-data #lightbox-image-details { <br />
width: 70%; <br />
float: left; <br />
text-align: left; <br />
} <br />
#lightbox-image-details-caption { font-weight: bold; }<br />
#lightbox-image-details-currentNumber {<br />
display: block; <br />
clear: left; <br />
padding-bottom: 1.0em; <br />
} <br />
#lightbox-secNav-btnClose {<br />
width: 66px; <br />
float: right;<br />
padding-bottom: 0.7em; <br />
}<br />
<br />
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<div id="right"></div>Peteremmrichhttp://2010.igem.org/File:Codons.jpgFile:Codons.jpg2010-10-26T01:07:08Z<p>Peteremmrich: the universal genetic code</p>
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<div>the universal genetic code</div>Peteremmrich