Team:Braunschweig/Achievements-content

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The iGEM competition, a synthetic biology competition, is based on the use of BioBricks. BioBricks are biological fragments or parts, comparable to building blocks. Just as building blocks they allow individual use as well as assembly into bigger devices. In iGEM these BioBricks are created, documented and shared between all iGEM teams throughout the competition. Furthermore the number of these parts is steadily increased year by year. All BioBricks are recorded in one single giant catalog: the Registry of Standard Biological Parts. This year we contributed to the registry by submitting new parts, improving existing ones and, of course, using  parts already known to be reliable due to the experiences of teams from past years. All used BioBricks are listed in this page.
The iGEM competition, a synthetic biology competition, is based on the use of BioBricks. BioBricks are biological fragments or parts, comparable to building blocks. Just as building blocks they allow individual use as well as assembly into bigger devices. In iGEM these BioBricks are created, documented and shared between all iGEM teams throughout the competition. Furthermore the number of these parts is steadily increased year by year. All BioBricks are recorded in one single giant catalog: the Registry of Standard Biological Parts. This year we contributed to the registry by submitting new parts, improving existing ones and, of course, using  parts already known to be reliable due to the experiences of teams from past years. All used BioBricks are listed in this page.
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<h2>Our favorite new Part - The climate change killer</h2>
<h2>Our favorite new Part - The climate change killer</h2>
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<li><b><a href="http://parts.igem.org/Part:BBa_K1390012">BBa_K1390012</a> - MMOZ-His Generator</b></li>
<li><b><a href="http://parts.igem.org/Part:BBa_K1390012">BBa_K1390012</a> - MMOZ-His Generator</b></li>
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<h2>Our improved parts</h2>
<h2>Our improved parts</h2>
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<p class="parts"> For further detailed information check our Results Page <!-- LINK! --> and the experience pages of the original part.
<p class="parts"> For further detailed information check our Results Page <!-- LINK! --> and the experience pages of the original part.
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<h2>Used parts</h2>
<h2>Used parts</h2>

Revision as of 10:29, 15 October 2014

E. Cowli - Fighting Climate Change - iGEM 2014 Team Braunschweig

Hier fehlt der header

Parts

Parts-Cow The iGEM competition, a synthetic biology competition, is based on the use of BioBricks. BioBricks are biological fragments or parts, comparable to building blocks. Just as building blocks they allow individual use as well as assembly into bigger devices. In iGEM these BioBricks are created, documented and shared between all iGEM teams throughout the competition. Furthermore the number of these parts is steadily increased year by year. All BioBricks are recorded in one single giant catalog: the Registry of Standard Biological Parts. This year we contributed to the registry by submitting new parts, improving existing ones and, of course, using parts already known to be reliable due to the experiences of teams from past years. All used BioBricks are listed in this page.

Our favorite new Part - The climate change killer

Part: BBa_K1390019 - complete sMMO from Methylococcus capsulatus
This device consists of the six subunits of the soluble methane monooxygenase (sMMO) of Methlyococcus capsulatus (Bath). The expression is controlled by a lacI-regulated promotor BBa_R0011. The sMMO is able to convert methane to methanol using oxygen and NAD(P)H. Apart from the promoter, the BioBrick contains an RBS upstream of each subunit-encoding gene and a double terminator. The construct is therefore ready for expression in E. coli.

Our new parts

sMMO genes

We isolated all genes encoding the different subunits of the sMMO from Methylococcus capsulatus (Bath) and made them compatible with the RFC 10 Assembly Standard.

  1. BBa_K1390001 - mmoB
    The mmoB gene encodes the regulatory subunit B of the sMMO
  2. BBa_K1390005 - mmoY
    The mmoY gene encodes the β subunit of the hydoxylase of the sMMO.
  3. BBa_K1390006 - mmoZ
    The mmoZ gene encodes the γ subunit of the hydoxylase of the sMMO.
  4. BBa_K1390003 - mmoD
    The mmoD gene product might be important for the function of the sMMO, but the exact mechanism is still under investigation.

The other two sMMO genes can be found in the "improved parts" section.

Our His-tag constructs

We provided each subunit of sMMO with a 6x His-tag. This tag facilitates purification and detection of the recombinant proteins.

  1. BBa_K1390007 - MMOB-His Generator
  2. BBa_K1390008 - MMOC-His Generator
  3. BBa_K1390009 - MMOD-His Generator
  4. BBa_K1390010 - MMOX-His Generator
  5. BBa_K1390011 - MMOY-His Generator
  6. BBa_K1390012 - MMOZ-His Generator

Our improved parts

    • BBa_K1390002- mmoC
      One of three subunits of the sMMO from M. capsulatus (Bath), which serves as a reductase using NADH as an electron donor.
    • Original Part: BBa_K593008 - mmo C
      The original part contains the wrong sequence without any distinct function.
    • Our improvement:
      The new part BBa_K1390002 now contains the original sequence from M. capsulatus (Bath), which was optimized for RFC10 Standard by removing restriction sites.
    • BBa_K1390004 - mmoX
      The mmoX gene encodes the α subunit. The α subunit is one of the three proteins constituting the hydroxylase component of sMMO and houses the active site of the enzyme.
    • Original Parts: BBa_K593004 - mmo X
      The original part contained the sequence of the chromoprotein DsRedExpress instead of the mmoX sequence.
    • Our improvement:
      The new part BBa_K1390004 now contains the original sequence from M. capsulatus (Bath), which was optimized for RFC10 Standard by removing restriction sites.

For further detailed information check our Results Page and the experience pages of the original part.

Used parts

It is one of the basic principles of iGEM to build on the work of prior teams. We adapted this thought of collaborating and sharing when we built our expression constructs. In this process we used the following Standard BioBricks. We found all of these parts reliable and well-documented. These parts were provided in the iGEM 2014 DNA Distribution-Kit. For further information on why we chose exactly these BioBricks check our Results Page.

  1. BBa_B0015 - double terminator
    This part was used for termination of translation and worked as expected.
  2. BBa_B0032 - RBS.3 (medium) -- derivative of BBa_0030
    This part was used as a ribosome binding site. This part is known to show a relatively low strength compared to other standard RBS Bricks.
  3. BBa_R0011 - Promoter (lacI regulated, lambda pL hybrid)
    This IPTG-inducible promoter was used for controlled protein biosynthesis and chosen because of the excellent documentation.
  4. pSB1C3 - high copy plasmid (CmR)
    This standard plasmid was used for replication and cloning efforts.
  5. pSB1A3 - high copy plasmid (AmpR)
    This standard plasmid was used for coexpression with other plasmids.

ILS

We participated in the first international interlab study, and thus helped to characterize the strength of different promoters in collaboration with teams from all over the world. In this measurement study the following BioBricks were used.

  1. BBa_K823005 - strong promoter
  2. BBa_K823012 - Anderson promoter J23115
  3. BBa_E0240- GFP generator
  4. BBa_I20260 - Measurement Kit Test of J23101
  5. BBa_K516032- mRFP protein generator TERM+ RBS+(B0032)

Overview

Part Name Nickname Part Type Short Description Lenght [bp]
♥ BBa_K1390019 complete MMO of Methylococcus capsulatus Device sMMO 5298
A BBa_K1390001 mmoB Protein_Domain Regulator of the sMMO 426
A BBa_K1390002 mmoC Protein_Domain Reductase for the sMMO 1047
A BBa_K1390003 mmoD Protein_Domain unknown function 312
A BBa_K1390004 mmoX Protein_Domain α subunit of the sMMO 1584
A BBa_K1390005 mmoY Protein_Domain β subunit of the sMMO 1170
A BBa_K1390006 mmoZ Protein_Domain γ subunit of the sMMO 513
A BBa_K1390007 MMOB-His Generator Generator Device for expression of His-tagged mmoB 662
A BBa_K1390008 MMOC-His Generator Generator Device for expression of His-tagged mmoC 1283
A BBa_K1390009 MMOD-His Generator Generator Device for expression of His-tagged mmoD 548
A BBa_K1390010 MMOX-His Generator Generator Device for expression of His-tagged mmoX 1820
A BBa_K1390011 MMOY-His Generator Generator Device for expression of His-tagged mmoY 1406
A BBa_K1390012 MMOZ-His Generator Generator Device for expression of His-tagged mmoZ 749
A BBa_K593008 mmoC Coding Reductase for the sMMO 1584
A BBa_K593004 mmoX Coding α subunit of the sMMO 1584
U BBa_K1390013 mmoB-His Protein_Domain His-tagged version of mmoB 444
U BBa_K1390014 mmoC-His Protein_Domain His-tagged version of mmoC 1065
U BBa_K1390015 mmoD-His Protein_Domain His-tagged version of mmoD 330
U BBa_K1390016 mmoX-His Protein_Domain His-tagged version of mmoX 1602
U BBa_K1390017 mmoY-His Protein_Domain His-tagged version of mmoY 1188
U BBa_K1390018 mmoZ-His Protein_Domain His-tagged version of mmoZ 531
A BBa_B0015 TT Terminator double terminator (B0010-B0012) 129
A BBa_B0032 weak RBS RBS RBS.3 (medium) -- derivative of BBa_0030 13
A BBa_R0011 lacI+pl Regulatory Promoter (lacI regulated, lambda pL hybrid) 55
A pSB1C3 high copy plasmid (CmR) Plasmid_Backbone High copy BioBrick assembly plasmid 2070
A pSB1A3 high copy plasmid (AmpR) Plasmid_Backbone High copy BioBrick assembly plasmid 2155
A BBa_K823005 strong ILS promoter Regulatory Anderson promoter J23101 35
A BBa_K823012 weak ILS promoter Regulatory Anderson promoter J23115 35
A BBa_E0240 GFP report Reporter GFP generator 876
A BBa_I20260 GFP constuct Measurement Measurement Kit Test of J23101 919
A BBa_K516032 RFP report Reporter mRFP protein generator TERM+ RBS+(B0032) 862

Medal Requirements

Bronze

Team registration.
Complete Judging form.
Team Wiki.
Present a poster and a talk at the iGEM Jamboree.
The description of each project must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.
Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). A new application of and outstanding documentation (quantitative data showing the Part’s/ Device’s function) of a previously existing BioBrick part in the “Experience” section of that BioBrick's Registry entry also counts. Please note you must submit this new part to the iGEM Parts Registry.
See BBa_K1390019.

Silver

Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.
See BBa_K1390007, BBa_K1390008, BBa_K1390009, BBa_K1390010, BBa_K1390011, BBa_K1390012.
Document the characterization of this part in the “Main Page” section of that Part’s/Device’s Registry entry.
See BBa_K1390007, BBa_K1390008, BBa_K1390009, BBa_K1390010, BBa_K1390011, BBa_K1390012.
Submit this new part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).
See BBa_K1390007, BBa_K1390008, BBa_K1390009, BBa_K1390010, BBa_K1390011, BBa_K1390012.
Your project may have implications for the environment, security, safety and ethics and/or ownership and sharing. Describe one or more ways in which these or other broader implications have been taken into consideration in the design and execution of your project.
See our Safety Section.

Gold

Improve the function of an existing BioBrick Part or Device (created by another team or your own institution in a previous year), enter this information in the Registry (in the “Experience” section of that BioBrick’s Registry entry), create a new registry page for the improved part, and submit this part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).
The part BBa_K593008 was improved to the new part BBa_K1390002.
The part BBa_K593004 was improved to the new part BBa_K1390004.
Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.

iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Describe an approach that your team used to address at least one of these questions. Evaluate your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.
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