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Team:Valencia Biocampus/Achievements
From 2014.igem.org
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<h2>A Golden St2OOL</h2> | <h2>A Golden St2OOL</h2> | ||
<p><p> | <p><p> | ||
| - | We have spent a fruitful –and stressful- summer working on an empirical, mathematical and comprehensive approach on the engineering pillars of SynBio. We have fulfilled the Gold Medal requirements: we have documented our standards that were submitted to the Registry of Biological Parts, and also validated experimentally; the characterization of existing parts has been improved -all the ten BioBricks used in the St2ool project are combinations of existing parts of the registry, and we believe to have performed one of the most complete characterizations of existing Registry parts in terms of stability, standardization and orthogonality. And last but not least, we have developed an original Human Practices approach dealing with Intellectual Property in Synthetic Biology in the context of Responsible Research and Innovation. | + | We have spent a fruitful –and stressful- summer working on an empirical, mathematical and comprehensive approach on the engineering pillars of SynBio.''' We have fulfilled the Gold Medal requirements''': we have documented our standards that were submitted to the Registry of Biological Parts, and also validated experimentally; the characterization of existing parts has been improved -all the ten BioBricks used in the St2ool project are combinations of existing parts of the registry, and we believe to have performed one of the most complete characterizations of existing Registry parts in terms of stability, standardization and orthogonality. And last but not least, we have developed an original Human Practices approach dealing with Intellectual Property in Synthetic Biology in the context of Responsible Research and Innovation. |
<p> | <p> | ||
<h2>Yes, we could</h2> | <h2>Yes, we could</h2> | ||
<p> | <p> | ||
| - | We have performed an unprecedented research effort to determine in detail how biological parts behave under different conditions. We have used several hundreds of Petri dishes and fluorescence –among other- measurements that have allowed us to finely characterize the behavior of ten selected SynBio devices. Our main results are the following:<p> | + | We have performed an '''unprecedented research effort to determine in detail how biological parts behave under different conditions'''. We have used several hundreds of Petri dishes and fluorescence –among other- measurements that have allowed us to finely characterize the behavior of ten selected SynBio devices. Our main results are the following:<p> |
| - | 1.- ''E. coli'' is, as expected, an extremely strong chassis for SynBio, as its is able to survive in a very wide rage of environmental stresses, of which we have tested pH, salt, temperature, Mars-like vacuum. The only factor to which E. coli proved very sensitive to was UV light. By contrast, Biobricks behavior was dependent on environmental conditions: sub-optimal temperatures and vacuum dramatically decreased Biobrick output.<p> | + | 1.- '''''E. coli'' is, as expected, an extremely strong chassis for SynBio''', as its is able to survive in a very wide rage of environmental stresses, of which we have tested pH, salt, temperature, Mars-like vacuum. The only factor to which E. coli proved very sensitive to was UV light. By contrast, '''Biobricks behavior was dependent on environmental conditions''': sub-optimal temperatures and vacuum dramatically decreased Biobrick output.<p> |
| - | 2.- Emergent properties. Even in 2014, many new species are discovered hidden in the jungles of our Planet. Similarly, we have been lucky to report here an unexpected emergent property in the best-known bacterium on Earth: thermal oscillations resulted in a significant increase of ''E. coli'' DH5-alfa growth. We are still finding out how. Surprisingly, fatigue of materials in biology is not always a deleterious process.<p> | + | 2.- '''Emergent properties'''. Even in 2014, many new species are discovered hidden in the jungles of our Planet. Similarly, we have been lucky to report here an unexpected emergent property in the best-known bacterium on Earth: '''thermal oscillations resulted in a significant increase of ''E. coli'' DH5-alfa growth.''' We are still finding out how. Surprisingly, fatigue of materials in biology is not always a deleterious process.<p> |
| - | 3.- Standards not that standard. We were shocked to see only Biobrick 5 behave in a relatively standard way when its output was compared within six different ''E. coli'' strains. Variation in the output was the norm, not the exception in what we expected to be standard parts.<p> | + | 3.- '''Standards not that standard'''. We were shocked to see only Biobrick 5 behave in a relatively standard way when its output was compared within six different ''E. coli'' strains. '''Variation in the output was the norm, not the exception''' in what we expected to be standard parts.<p> |
| - | 4.- Orthogonality, what’s that? We used a range of techniques (fluorimetry, cell citometry, protein electrophoresis and proteomics) to find out whether one of the simplest device combination possible (two different reporter proteins under the control of the same promoter and on the same plasmid) behave in a orthogonal way. The hypothesis was that, if so, the relative outputs should be approximately equal. Again, we found that engineering assumptions could not be validated: co-transformants with two Biobricks displayed an asymmetric behavior indicating a clear lack of orthogonality.<p> | + | 4.- '''Orthogonality, what’s that?''' We used a range of techniques (fluorimetry, cell citometry, protein electrophoresis and proteomics) to find out whether one of the simplest device combination possible (two different reporter proteins under the control of the same promoter and on the same plasmid) behave in a orthogonal way. The hypothesis was that, if so, the relative outputs should be approximately equal. Again, we found that engineering assumptions could not be validated: '''co-transformants with two Biobricks displayed an asymmetric behavior indicating a clear lack of orthogonality.'''<p> |
| - | 5.- Bridging gaps in IP. We wanted to contribute to the IP controversy in a new way. We propose a marriage between the concepts of Responsible Research and Innovation and the Diverse Ecology scenario, being the former a key tool to choose within the multiple ecology of IP forms. We have contributed to that goal by creating dictionaries of SynBio terms for lawyers, and of legal terms for Synthetic Biologists, and by making a politically incorrect proposal: why not using Maths to help experts on IP take their decisions?<p> | + | 5.- '''Bridging gaps in IP'''. We wanted to contribute to the IP controversy in a new way. '''We propose a marriage between the concepts of Responsible Research and Innovation and the Diverse Ecology scenario''', being the former a key tool to choose within the multiple ecology of IP forms. We have contributed to that goal by creating '''dictionaries''' of SynBio terms for lawyers, and of legal terms for Synthetic Biologists, and by making a politically incorrect proposal: '''why not using Maths to help experts on IP take their decisions?'''<p> |
| - | 6.- On weakness and strength. Our experimental results and modeling analysis confirm that engineering pillars cannot be taken for granted in SynBio. A new bioprospection point of view is thus needed. | + | 6.- '''On weakness and strength'''. Our experimental results and modeling analysis confirm that engineering pillars cannot be taken for granted in SynBio. A new bioprospection point of view is thus needed. W'''e have developed a DNA extraction robot “The Tool”''' to help us carry out a functional metagenomic approach directed at identifying natural DNA parts with particularly standard and stable behaviors. If engineering assumptions are not met by the Biobricks we tested, let’s isolate/build new ones with the desired properties. |
<p> | <p> | ||
<h2>Beyond scientific achievements</h2> | <h2>Beyond scientific achievements</h2> | ||
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"I never use a piano stool. I always use a drum stool. Because I feel that when you're down there, you're playing in that way you're supposed to. I like to be above it." | "I never use a piano stool. I always use a drum stool. Because I feel that when you're down there, you're playing in that way you're supposed to. I like to be above it." | ||
<p> | <p> | ||
| - | Jamie Cullum | + | '''Jamie Cullum''' |
</div> | </div> | ||
</html> | </html> | ||
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Revision as of 15:52, 12 October 2014
Achievements
A Golden St2OOL
We have spent a fruitful –and stressful- summer working on an empirical, mathematical and comprehensive approach on the engineering pillars of SynBio.''' We have fulfilled the Gold Medal requirements''': we have documented our standards that were submitted to the Registry of Biological Parts, and also validated experimentally; the characterization of existing parts has been improved -all the ten BioBricks used in the St2ool project are combinations of existing parts of the registry, and we believe to have performed one of the most complete characterizations of existing Registry parts in terms of stability, standardization and orthogonality. And last but not least, we have developed an original Human Practices approach dealing with Intellectual Property in Synthetic Biology in the context of Responsible Research and Innovation.
Yes, we could
We have performed an '''unprecedented research effort to determine in detail how biological parts behave under different conditions'''. We have used several hundreds of Petri dishes and fluorescence –among other- measurements that have allowed us to finely characterize the behavior of ten selected SynBio devices. Our main results are the following:
1.- '''''E. coli'' is, as expected, an extremely strong chassis for SynBio''', as its is able to survive in a very wide rage of environmental stresses, of which we have tested pH, salt, temperature, Mars-like vacuum. The only factor to which E. coli proved very sensitive to was UV light. By contrast, '''Biobricks behavior was dependent on environmental conditions''': sub-optimal temperatures and vacuum dramatically decreased Biobrick output.
2.- '''Emergent properties'''. Even in 2014, many new species are discovered hidden in the jungles of our Planet. Similarly, we have been lucky to report here an unexpected emergent property in the best-known bacterium on Earth: '''thermal oscillations resulted in a significant increase of ''E. coli'' DH5-alfa growth.''' We are still finding out how. Surprisingly, fatigue of materials in biology is not always a deleterious process.
3.- '''Standards not that standard'''. We were shocked to see only Biobrick 5 behave in a relatively standard way when its output was compared within six different ''E. coli'' strains. '''Variation in the output was the norm, not the exception''' in what we expected to be standard parts.
4.- '''Orthogonality, what’s that?''' We used a range of techniques (fluorimetry, cell citometry, protein electrophoresis and proteomics) to find out whether one of the simplest device combination possible (two different reporter proteins under the control of the same promoter and on the same plasmid) behave in a orthogonal way. The hypothesis was that, if so, the relative outputs should be approximately equal. Again, we found that engineering assumptions could not be validated: '''co-transformants with two Biobricks displayed an asymmetric behavior indicating a clear lack of orthogonality.'''
5.- '''Bridging gaps in IP'''. We wanted to contribute to the IP controversy in a new way. '''We propose a marriage between the concepts of Responsible Research and Innovation and the Diverse Ecology scenario''', being the former a key tool to choose within the multiple ecology of IP forms. We have contributed to that goal by creating '''dictionaries''' of SynBio terms for lawyers, and of legal terms for Synthetic Biologists, and by making a politically incorrect proposal: '''why not using Maths to help experts on IP take their decisions?'''
6.- '''On weakness and strength'''. Our experimental results and modeling analysis confirm that engineering pillars cannot be taken for granted in SynBio. A new bioprospection point of view is thus needed. W'''e have developed a DNA extraction robot “The Tool”''' to help us carry out a functional metagenomic approach directed at identifying natural DNA parts with particularly standard and stable behaviors. If engineering assumptions are not met by the Biobricks we tested, let’s isolate/build new ones with the desired properties.
Beyond scientific achievements
We really had fun! In our “Art & More section” you’ll find Paula’s great watercolors for the wiki, the poster and the presentation; Kristie’s epigenetic music interpreted as what she calls “genomic serialism”; and videos such as the YMCA parody “The St2OOL is going to i.G.E.M.”
And finally, the St2OOL quote
"I never use a piano stool. I always use a drum stool. Because I feel that when you're down there, you're playing in that way you're supposed to. I like to be above it."'''Jamie Cullum'''
