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iGEM UCLA

iGEM UCLA. What is Synthetic Biology?. A) the design and construction of new biological parts, devices, and systems, and B) the re-design of existing, natural biological systems for useful purposes. Useful?. Bioremediation Energy Sources Medical Systems Biology. Bioremediation.

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iGEM UCLA

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  1. iGEM UCLA

  2. What is Synthetic Biology? • A) the design and construction of new biological parts, devices, and systems, and • B) the re-design of existing, natural biological systems for useful purposes.

  3. Useful? • Bioremediation • Energy Sources • Medical • Systems Biology

  4. Bioremediation • Bioremediation can be defined as any process that uses microorganisms, fungi, green plants or their enzymes to return the environment altered by contaminants to its original condition. • Deinococcus radiodurans--the most radiation resistant organism known

  5. The Mer Operon

  6. Deinococcus radiodurans • The most radiation resistant organism known. • Put it together with the mer operon and a toluene metabolizing pathway and… • You have a very effective bioremediating agent, fit to deal with nuclear waste especially. • Change radioactive Hg(II) to environmentally friendly form. • Meshing pathways

  7. Energy • Carbon emissions and fossil fuels • Vs. • Venter et al. reworking the photosynthetic pathway in plants and microbes for cleaner energy production. • Eliminate emissions, fix/capture carbon already there.

  8. Shit to energy! • A Geobacter can cleanup uranium and actually transfer oxidized electrons from biomass, such as sludge directly to anodes. This is a current. • That is directly harnessing electrical energy from organic matter

  9. Runaway • Queasy about the idea of bacteria running rampant? • Venter is also working on how to make minimal genomes that can only survive, in say, the lab? • Or in nuclear canisters

  10. Medical • Arteminisin anti-malaria • Oncolytic Virus and E.coli

  11. Systems Biology • To really know something, you must be able to produce it (synthesize) • To a more complete knowledge of biological systems

  12. iGEM • Open design • Biobricks / Registry of Parts • Your own parts • Creativity in science

  13. Berkeley’s Bacterial Networks

  14. Pattern formation is a hallmark of coordinated cell behaviour in both single and multicellular organisms1, 2, 3. It typically involves cell−cell communication and intracellular signal processing. Here we show a synthetic multicellular system in which genetically engineered 'receiver' cells are programmed to form ring-like patterns of differentiation based on chemical gradients of an acyl-homoserine lactone (AHL) signal that is synthesized by 'sender' cells. In receiver cells, 'band-detect' gene networks respond to user-defined ranges of AHL concentrations. By fusing different fluorescent proteins as outputs of network variants, an initially undifferentiated 'lawn' of receivers is engineered to form a bullseye pattern around a sender colony. Other patterns, such as ellipses and clovers, are achieved by placing senders in different configurations. Experimental and theoretical analyses reveal which kinetic parameters most significantly affect ring development over time. Construction and study of such synthetic multicellular systems can improve our quantitative understanding of naturally occurring developmental processes and may foster applications in tissue engineering, biomaterial fabrication and biosensing. Programmed pattern formation

  15. Activator molecule A1 Activator gene Lac regulator Lactose Urease gene |A| |R| Repressor molecule R1 Ammonia Arsenic (5ppb) LacZ gene Repressor gene R1 Ars regulator 1 Urease enzyme LacZ enzyme Lactic Acid Arsenic (20ppb) Ars regulator 2 Arsenic sensor system diagram 8.5 pH: 7.0 6.0 4.5 A1 binding site Promoter (NH2)2CO + H2O = CO2 + 2NH3 R1 binding site

  16. The parts

  17. Engineering Approach • Circuits • Inverters and Oscillators • Logic Gates

  18. Modularity • Legos make it so you don’t have to reinvent the wheel everytime. • Put a protein generator, a signaling system, an oscillator together and you have a system that can act predictably in large numbers. • The large numbers come from a population of bacteria acting in concert.

  19. Aspects • Chemotaxis • Signaling / Quorum sensing • Gene regulation pathways • Engineering

  20. Organizational • Groups of 3ish • Find a common time • For the first week, present on basic background • The next 3 weeks, dedicate to individual papers. • Short (10-15 minute) presentations to get everyone on the same page

  21. Consolidation • After 4 weeks of presentations, brainstorming within the group • Formulate at least 4 ideas • Come up with schematics and dissect and reference the literature • Present and post on the wiki

  22. Wiki • Post all papers, slideshows, schematics • Post a summary of research every week

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