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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

iGEM UCLA


What is synthetic biology

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

Useful?

  • Bioremediation

  • Energy Sources

  • Medical

  • Systems Biology


Bioremediation

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


The mer operon

The Mer Operon


Deinococcus radiodurans

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


Energy

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.


Shit to energy

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


Runaway

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


Medical

Medical

  • Arteminisin anti-malaria

  • Oncolytic Virus and E.coli


Systems biology

Systems Biology

  • To really know something, you must be able to produce it (synthesize)

  • To a more complete knowledge of biological systems


Igem ucla

iGEM

  • Open design

  • Biobricks / Registry of Parts

  • Your own parts

  • Creativity in science


Berkeley s bacterial networks

Berkeley’s Bacterial Networks


Programmed pattern formation

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


Igem ucla

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


The parts

The parts


Engineering approach

Engineering Approach

  • Circuits

  • Inverters and Oscillators

  • Logic Gates


Modularity

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.


Aspects

Aspects

  • Chemotaxis

  • Signaling / Quorum sensing

  • Gene regulation pathways

  • Engineering


Organizational

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


Consolidation

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


Igem ucla

Wiki

  • Post all papers, slideshows, schematics

  • Post a summary of research every week


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