This year, despite of our highly ambitious project, our team achieved goals in several different areas.
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This year our team came up with a highly ambitious project and achieved goals in several different areas.
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We successfully modelled, designed, characterised and entered our IPTG- inducible Filamentous cells BioBrick part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302012 BBa_K302012] in the parts registry.
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We successfully modelled, designed, characterised and submitted our IPTG-inducible Filamentous cells BioBrick part ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K302012 BBa_K302012]).
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We also improved the BioBrick parts Hyperspank [http://partsregistry.org/Part:BBa_K143015 (BBa_K143015)] and Pspac_oid [http://partsregistry.org/Part:BBa_K174004 (BBa_K174004)] to make Hyperspank_oid promoter [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302003 BBa_K302003] rendering it tight regulation.
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We also developed [https://2010.igem.org/Team:Newcastle/E-Science an e-Science Approach to Synthetic Biology] which focuses on workflows in synthetic biology. This work led to the creation of BBF RFC 66.
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We also developed [https://2010.igem.org/Team:Newcastle/E-Science An e-Science Approach to Synthetic Biology].
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We developed the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302018 Subtilin Immunity] BioBrick, which provides immunity against the lantibiotic subtilin, a quorum sensing molecule for our cell population. Subtilin will help to initiate a population-wide response for concrete repair.
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We developed [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302018 Subtilin Immunity] BioBrick part which provides cells immunity against the lantibiotic subtilin, which is also a quorum sensing molecule for our cell population. It will help in initiating a population wide response for initiating concrete repair.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302015 Urease] BioBrick increases urea hydrolysis by increasing arginine and arginase production. Arginase breaks down arginine to form urea and ornithine. The overall increase in urea leads to an increase in urease production which hydrolyses urea into carbonate and ammonium ions which are exported out of the cell. The carbonate ions form a bond with calcium ions in the environment, resulting in the production of calcium carbonate.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302015 Urease] BioBrick part helps in the increasing urea hydrolysis by increasing arginine and arginase production. Arginase breaks down by arginine to form urea and ornithine. The overall incrase in urea leads to incrase in urease production in the cell which hydrolyses urea into carbonate and ammonium ions which are exported out of the cell. The carbonate ions forms a bond with calcium ions provided in the media and forms calcium carbonate.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302016 Swarming] BioBrick would help ''Bacillus subtilis'' 168 to swarm on the concrete surface by producing surfactin to reduce surface tension and by initiating flagellum biosynthesis.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302016 Swarming] BioBrick part would help ''Bacillus subtilis'' 168 to swarm on the concrete surface by producing surfactin to reduce surface tension and by initiating flagellum biosynthesis.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302030 Levan Glue] BoBrick produces Levan glue in the presence of sucrose. The glue will act as a binding agent for the filamentous cells and the calcium carbonate crystals and will also help in filling up the crack thereby preventing corrosion of the steel reinforcements.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302030 Levans Glue] BoBrick part produces Levans glue in the presence of sucrose. The glue will act as a binding agent for the filamentous cells and the calcium carbonate crystals inside the crack and will also help in filling up the crack thereby preventing corrosion of the steel reinforcements.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302035 ''mazEF'' Kill switch] is built around a stable toxin-antitoxin system for ''Bacillus subtilis''. It would kill bacteria in the absence of sucrose thereby helping to make our project environmentally friendly.
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Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302035 ''MazEF'' Kill switch] is a stable toxin-antitoxin system for ''Bacillus subtilis''. It would kill bacteria in the absence of sucrose thereby helping to make our project environmentally friendly.
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In total we designed and entered 31 BioBrick parts in the parts registry.
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We also modelled 2 components of our project viz. [https://2010.igem.org/Team:Newcastle/modelling#Filamentous_cells Filamentous cells] and [https://2010.igem.org/Team:Newcastle/modelling#Calcium_carbonate Urase]. In total we designed and entered 34 BioBrick parts in the parts registry.
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We also took [https://2010.igem.org/Team:Newcastle/solution#Scanning_Electron_Microscope_Images Scanning Electron Microscope photographs] and found some interesting results: photographs of cells trying to fill up the crack, calcium carbonate crystals and Levan glue covering the cells.
# <strike> <span style="color:#8B4513"> '''BRONZE ONE:''' </span></strike> '''We have registered the team,had a great summer, and are looking forward to the Jamboree!'''
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# <strike> <span style="color:#8B4513"> '''BRONZE TWO:''' </span> </strike> Successfully complete and submit a Project Summary form.
# <strike> <span style="color:#8B4513"> '''BRONZE THREE:''' </span></strike> '''We have created and shared a description of our team's project on the iGEM wiki!'''
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# <strike> <span style="color:#8B4513"> '''BRONZE FOUR:''' </span> </strike> '''We plan to present a Poster and Talk at the iGEM Jamboree'''
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# <strike> <span style="color:#8B4513"> '''BRONZE FIVE:''' </span> </strike>Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Parts
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#*Entered information for each new part or device should at least include primary nucleic acid sequence, description of function, authorship, any relevant safety notes, and an acknowledgement of sources and references. E.g. [http://parts.mit.edu/registry/index.php/Part:BBa_J45004 BBa_J45004].
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#*Teams are currently expected to design and contribute standard biological parts that conform to the accepted BioBrick standards for physical assembly. Non-BioBrick parts will not be recognized by iGEM 2010 judges unless they have [[Judging#BioBrick_standard_variance_requests | specific approval]]. The two specific BioBrick physical assembly schemes that the judges will recognize by default are (i) Tom Knight's [http://dspace.mit.edu/handle/1721.1/21168 original assembly standard] and (ii) Ira Phillips [http://dspace.mit.edu/handle/1721.1/32535 fusion assembly standard].
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#**[Special Note. A discussion has been initiated by the BioBricks Standards Working Group to consider updating the BioBrick assembly standard in time for June 1. Check back for any updates on acceptable BioBrick assembly standards.]
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#*Any new Devices that are based on gene expression are expected to conform to the PoPS device boundary standard. See chapter 3 of the book, [http://openwetware.org/wiki/Adventures Adventures in Synthetic Biology], for more information about common signal carriers and PoPS.
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#*''' We have entered details of the parts we are using into the registry.'''
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# <strike> <span style="color:#8B4513"> '''BRONZE SIX:''' </span></strike> Submit DNA for at least one new BioBrick Part or Device to the Registry of Parts.
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#*The submitted DNA must be associated with a Part or Device for which you have entered information describing the part or device, and must conform to the BioBrick standards for Parts or Devices (see above).
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#*'''IPTG-inducible filamentous cell formation part has had DNA sent to the registry'''
The requirements to earn a Silver Medal, in addition to the Bronze Medal requirements, are:
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# <strike> <span style="color:#808080"> '''SILVER ONE:''' </span> </strike> Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as '''[[Team:Newcastle/Filamentous_Cells#Characterisation| Characterisation of the IPTG-inducible filamentous cell formation part]]'''
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# <strike> <span style="color:#808080"> '''SILVER TWO:''' </span> </strike> Characterize the operation of at least one new BioBrick Part or Device and enter this information on the Parts or Device page via the Registry of Parts '''[http://partsregistry.org/Part:BBa_K302012:Experience| IPTG-inducible filamentous cell formation part: BBa_K302012]'''
The requirements to earn a Gold Medal, in addition to the Silver Medal requirements, are any one OR more of the following:
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# <strike> <span style="color:#DAA520"> '''GOLD ONE:''' </span> </strike>Characterize or improve an existing BioBrick Part or Device and enter this information back on the Registry '''[http://partsregistry.org/Part:BBa_K302003 BBa_K302003].'''
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# <span style="color:#DAA520"> '''GOLD TWO:''' </span> Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.
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# <strike> <span style="color:#DAA520"> '''GOLD THREE:''' </span> </strike> Develop and document a new technical standard that supports the (i) design of BioBrick Parts or Devices, or (ii) construction of BioBrick Parts or Devices, or (iii) characterization of BioBrick Parts or Devices, or (iv) analysis, modeling, and simulation of BioBrick Parts or Devices, or (v) sharing BioBrick Parts or Devices, either via physical DNA or as information via the internet.[[Team:Newcastle/E-Science|'''We investigate the benefits of an e-Science approach, with a focus on workflows, to synthetic biology''']].
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# <span style="color:#DAA520"> '''GOLD FOUR:''' </span> Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.
This year our team came up with a highly ambitious project and achieved goals in several different areas.
We successfully modelled, designed, characterised and submitted our IPTG-inducible Filamentous cells BioBrick part ([http://partsregistry.org/wiki/index.php?title=Part:BBa_K302012 BBa_K302012]).
We developed the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302018 Subtilin Immunity] BioBrick, which provides immunity against the lantibiotic subtilin, a quorum sensing molecule for our cell population. Subtilin will help to initiate a population-wide response for concrete repair.
Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302015 Urease] BioBrick increases urea hydrolysis by increasing arginine and arginase production. Arginase breaks down arginine to form urea and ornithine. The overall increase in urea leads to an increase in urease production which hydrolyses urea into carbonate and ammonium ions which are exported out of the cell. The carbonate ions form a bond with calcium ions in the environment, resulting in the production of calcium carbonate.
Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302016 Swarming] BioBrick would help Bacillus subtilis 168 to swarm on the concrete surface by producing surfactin to reduce surface tension and by initiating flagellum biosynthesis.
Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302030 Levan Glue] BoBrick produces Levan glue in the presence of sucrose. The glue will act as a binding agent for the filamentous cells and the calcium carbonate crystals and will also help in filling up the crack thereby preventing corrosion of the steel reinforcements.
Our [http://partsregistry.org/wiki/index.php?title=Part:BBa_K302035 mazEF Kill switch] is built around a stable toxin-antitoxin system for Bacillus subtilis. It would kill bacteria in the absence of sucrose thereby helping to make our project environmentally friendly.
In total we designed and entered 31 BioBrick parts in the parts registry.
We also took Scanning Electron Microscope photographs and found some interesting results: photographs of cells trying to fill up the crack, calcium carbonate crystals and Levan glue covering the cells.
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