UTACCEL 2010 Adventures in Biotechnology Graham Cromar

Drew Endy on Synthetic Biology Available here:

Synthetic Biology Automated Sequencing (reading dna) Polymerase Chain reaction (writing dna) Recombinant DNA (restriciton enzymes and ligation) It’s not what you make it’s how you make it. Abstraction Standards Automated construction (made to order dna) A new process for engineering biological systems An approach to engineering biology Genetic Engineering (last 30 years) atagtacc Synthetic Biology

Recombinant DNA Restriction enzymes In nature these proteins provide a defense to protect bacteria by cutting foreign DNA into pieces. This cutting activity is specific to certain short sequences of DNA letters. We call this the “restriction site”. There are many different restriction enzymes that all cut DNA at different sequences of letters. All are commercially available. Ligation A process which repairs breaks in cut DNA using the enzyme, DNA ligase. Together, these allow us to create new DNA sequences by “cut and paste”

EcoRI

PCR Polymerase Chain Reaction Using a heat cycler and all the molecules and enzymes needed to make DNA we can do this process in a test tube making many many copied of our new piece of DNA. This is called “DNA amplification” ATGCCGATGCCG TACGGCTACGGC ATCCCGATCCCG TAGGGCTAGGGC A a ATGCCGATGCCG TACGGCTACGGC ATGCCGATGCCG TACGGCTACGGC aa ATCCCGATCCCG TAGGGCTAGGGC A ATCCCGATCCCG TAGGGCTAGGGC A

Cloning and Transformation

Progress! Automated Sequencing (reading dna) Polymerase Chain reaction (writing dna) Recombinant DNA (restriciton enzymes and ligation) Abstraction Standards Automated construction (made to order dna) Genetic Engineering (last 30 years) Synthetic Biology

Science vs. Engineering A Scientist discovers that which exists; an Engineer creates that which never was. -- Theodore von Karman Biology is the nanotechnology which works Small core of standard parts Real world complexity catabolismanabolism Design information Abstraction reduces complexity by hiding details. Allows for specialization and better reliability

Standardization abstraction hierarchy modularity standardization isolation, separation of concerns flexibility Powerful tools of engineering design Simplified thinking about interfaces Reusable Parts Contracts and commercial access Independent evolution of components Facile comparison of results Role of standards in engineering

Standard Repository of Biological Parts Standard components & interfaces Standard composition Standard function & interfaces Standard measurements Standard chassis Several Standards The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems. The parts catalogue can be found at: Types of devices Examples of parts Promoters Terminators Ribosome binding sites Protein coding regions Protein generators Reporters Inverters Receivers and senders Measurement devices Part:BBa_K Coding A shell-forming protein known as "encapsulin", which we derived from the TM0785 plasmid in T. maritima

iGEM Asia has these 38 teams ArtScienceBangaloreCBNU-KoreaArtScienceBangaloreCBNU-Korea ChibaECUST-ShanghaiChibaECUST-Shanghai HKU-Hong_KongHKUSTHKU-Hong_KongHKUST HokkaidoU_JapanHong_Kong-CUHKHokkaidoU_JapanHong_Kong-CUHK IBB-PuneIBB-Pune IITBombayIIT_Delhi_1 IIT_MadrasIITBombayIIT_Delhi_1IIT_Madras KAIST-KoreaKIT-KyotoKorea_U_SeoulKAIST-KoreaKIT-KyotoKorea_U_Seoul KyotoKyoto Macquarie_AustraliaMonash_AustraliaMacquarie_AustraliaMonash_Australia NCTU_Formosa NYMU-TaipeiNCTU_FormosaNYMU-Taipei OsakaPekingOsakaPeking RMIT_AustraliaSJTU-BioX-ShanghaiRMIT_AustraliaSJTU-BioX-Shanghai TianjinTokyo-NoKoGenTokyo_MetropolitanTokyo_Tech TsinghuaTzuChiU_FormosaTsinghuaTzuChiU_Formosa UQ_AustraliaUSTCUQ_AustraliaUSTC USTC_SoftwareUT-TokyoUSTC_SoftwareUT-Tokyo XMU-ChinaZJU-ChinaXMU-ChinaZJU-China Fudan-Shanghai SJTU-Oncology-Shanghai International Genetically Engineered Machine Competition Student teams are given a kit of biological parts at the beginning of the summer from the Registry of Standard Biological Parts. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells.

Applications

Engineering bacterial microcompartments to make biochemical reactions more efficient G. Cromar, D. Wong, K. Zhan, Y. Leung, M. Gao, S. Hung, F. Raja and J. Parkinson Fully described at:

What would you do? Group Exercise: Poster tour Working in teams of three, use the large paper to create a ‘poster’ describing your ideas of what to make if you could write the genetic code. Can you think of three constructive projects? Three destructive projects? When done tour the posters of the other groups to see their ideas.