Team:TUDelft/Achievements

=Achievements= This is a short list summarizing the most important goals that we achieved during the project, subdivided in differnt modules. For more information on specific achievements use the links to navigate to the corresponding webpage. Please also visit the Deliverables section.

Conjugation System
Verification and Characterization of Wild R751
 * Determination of wild R751 conjugation efficiency.

Verification and Characterization of trbK entry exclusion protein
 * Design and test of a a method to prevent back propagation of the signal by expressing trbK. This allows receiver side control over communication.

Verification and Characterization of Conjugation Testing Plasmid 1
 * A conjugation test was done using our conjugation protocol to verify that Conjugation Testing Plasmid 1 was transmitted during conjugation.

R751 Gene Knockouts
 * A third attempt to knockout oriTR and trbK is currently in progress using the Quick & Easy Conditional Knock Out Kit - FRT from Gene Bridges.

more

Self Destructive Plasmid
I-SceI restriction site
 * construction and verification of the I-SceI homing endonuclease restriction site BBa_K175027.

Restriction site plus reporter
 * construction of an anhydrotetracyclin inducible GFP-LVA reporter gene combined with the I-SceI restriction site: BBa_K175044.

Characterization of I-SceI biobricks
 * determination that BBa_K142200 and all parts containing it encode for an I-SceI homing endonuclease that has an LVA degradation tag attached to it, possibly preventing normal functioning.
 * determination that BBa_K142205 (IPTG inducible I-SceI generator) actually encodes for BBa_K142207 (medium constitutive T4 DNA Ligase generator).

construction of the real BBa_K142205 
 * construction of a part called BBa_K175041 that is identical to the intended sequence of BBa_K142205.

Time-Delay Device
Synthetic Transcriptional Cascade
 * Assembly of plasmid 1 and 2 (K175046) and 2 (K175047).
 * Partial confirmation of sequence of both plasmids.
 * Transformation in Escherichia coli
 * Confirmation of both biobrick individual functionality.
 * Characterization of the plasmids 1 and 2 by fluorescence experiments... more

Biosynthetic AND gate
 * Successful assembly of parts K175023 and K175024 which correspond to Plasmid 1 and 2 of the Biosynthetic AND gate section respectively.
 * Electroporation of plasmid 1 and 2 into Escherichia coli TOP10 cells... more

Lock and Key Library
 * Construction of an algorithm capable to generate locks (cis regulation) for different ribosome binding sites (RBS’s) and their correspond key (trans).
 * Online lock and key generator derived from the algorithm.
 * Construction of four DNA sequences in biobrick format and pSB1A3 plasmid backbone which encode lock for medium RBS (K175031), key for the lock of medium RBS (K175032), lock for weak RBS (K175029) or key for the lock of weak RBS (K175030).
 * Assembly of two composed biobricks (K175034 and K175035), designed to test the functionality of the lock/key pairs constructed.
 * Assembly of two GFP generators under the control of PLacI with weak RBS (K175033) or medium RBS (K175048)... more

Modeling
Synthetic Transcriptional Cascade
 * Construction of a model used to provide the delay team with design guidelines which would maximize the delay time, to asses the affect of parameter variation on the delay time and to determine areas of instability in the parameter space.
 * A sensitivity analysis was done on the system. This looked at how variations in each parameter would influence the delay time.
 * Corroboration of a stable system by determining the Jacobian of the system of ODEs analytically.
 * Identification of best suitable parameters ranges for a desired time-delay device.
 * Based on the results of the simulations, a series of recommendations were given to the delay team to aid them in choosing parts which would maximize the delay time.

Conjugation Modeling


 * The development and documentation of a new model for conjugation systems. This kind of model represents a complete novelty within iGEM framework.

Ethics
Literature research Survey
 * Identification and description of the main ethical issues and concerns in synthetic biology. more
 * Illustration of the main ethical issues in clear frameworks, which can be build on in further research.
 * Recognition of the issues that need specific attention: ethical discussions concerning the top-down (reductionist) approach towards understanding living systems and the bottom-up approach of enhancing/creating biological systems.
 * Elaborate characterization of the omitted issues concerning reductionism and the bottom-up approach in synthetic biology. more
 * Construction of a comprehensive survey mainly focusing on the issues and possible consequences emerging from the reductionist and bottom-up approach as applied in biology, including questions on evolution, life, risks and the research of Craig Venter. more
 * Successful conduction of the survey among 242 people involved in synthetic biology from over 20 different countries, including 168 iGEM participants and 60 supervisors/advisors.
 * Extensive elaboration of the results, both qualitatively and quantitatively. more
 * Integration of a detailed outline of conclusions and recommendations based on the literature research and the survey results. more

Communication

 * We published articles in university newsletters and magazines.
 * Till now we had a good cooperation with our sponsors. We published articles in newsletter of the companies which sponsor our team. Some of our sponsors asked us to present our results after the Jamboree.
 * We created a platform among university magazines and newsletters to write articles about our project after the Jamboree.
 * We attracted attention at our department for our participation to the competition.