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Team:Braunschweig/Achievements-content
From 2014.igem.org
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| - | The iGEM competition, a synthetic biology competition, is based on the usage 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 these parts | + | The iGEM competition, a synthetic biology competition, is based on the usage 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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Revision as of 08:01, 14 October 2014
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Parts
The iGEM competition, a synthetic biology competition, is based on the usage 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 of 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.
- BBa_K1390001 - mmoB
The mmoB gene encodes the regulatory subunit B of the sMMO - BBa_K1390005 - mmoY
The mmoY gene encodes the β subunit of the hydoxylase of the sMMO. - BBa_K1390006 - mmoZ
The mmoZ gene encodes the γ subunit of the hydoxylase of the sMMO. - 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 under improved parts.
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.
- BBa_K1390007 - MMOB-His Generator
- BBa_K1390008 - MMOC-His Generator
- BBa_K1390009 - MMOD-His Generator
- BBa_K1390010 - MMOX-His Generator
- BBa_K1390011 - MMOY-His Generator
- 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_K1390002- mmoC
-
- 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.
- BBa_K1390004 - mmoX
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.
- BBa_B0015 - double terminator
This part was used for termination of translation and worked as expected. - 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. - 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. - pSB1C3 - high copy plasmid (CmR)
This standard plasmid was used for replication and cloning efforts. - 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.
- BBa_K823005 - strong promoter
- BBa_K823012 - Anderson promoter J23115
- BBa_E0240- GFP generator
- BBa_I20260 - Measurement Kit Test of J23101
- 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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