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Third International Workshop on Machine Learning in Systems Biology

Synthetic Biology Achievements And Future Prospects

author: Roman Jerala, Laboratory of Biotechnology, National Institute of Chemistry Slovenia

Description

Synthetic biology, which combines engineering approach in biological systems is getting a strong momentum due to the recent technological advances, which allow us to manipulate the genetic information at an unprecedented scale. Currently synthetic biology is exploiting its potentials and advantages but also bottlenecks. We will review some success stories of synthetic biology in different field of applications, such as medicine, energy and materials. Medical applications of synthetic biology are some of the most promising areas of synthetic biology, particularly for the alternative methods of drug production, biosensors and also different therapeutic applications. Recent developments in our understanding of cellular signaling and host-pathogen interactions provide the opportunity for new types of medical intervention, where we can utilize parts of the existing or reengineer signaling responses connected to various pathological conditions. Knowledge of the ways that microbes use to avoid the human immune response allows us to devise approach to bypass those microbial strategies. We will look at three different applications of synthetic biology, which involve reengineering of cell signaling pathways, which we have prepared for the international genetically engineered machines competition in years 2006-2008. We have designed and demonstrated proof of the concept of antiviral detection and defense system based on essential viral functions that is independent on mutations and a synthetic vaccine that activates both innate and adaptive immune response.

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Slides
0:00 Synthetic Biologyachievements and future prospects
1:00 Synthetic Biology
1:54 Different approaches of synthetic biology
2:42 Modularity and hierachical organization
3:32 DNA as the cellular program
4:36 Foundations for the development of Synthetic biology
5:24 DNA sequence determination
6:07 Pace in the last years
7:00 Chemical synthesis of DNA
7:46 Potential areas of application of synthetic biology
8:04 Renewable sources of energy
9:59 Biomimetic materials
11:20 Microbial production of raw materials
12:56 Information processing
13:39 Synthetic gene networks that count
14:26 Bio-photolitography University
15:06 Synthesis of antimalarial drug
16:09 Transfer of the biosynthetic pathway into bacteria using synthetic biology
17:02 Medical applications ofsynthetic biology
17:32 Engineering mammalian cells
18:13 Synthetic cell signaling pathway
19:04 iGEM
20:11 iGEM 2008
20:14 Teams Registred fot iGEM 2009
20:24 Therapeutic targets ofHIVlife cycle
21:12 Problems with antiviral therapy
22:00 Requirements for the effective synthetic antiviral device
22:49 FUNCTION 1:Viral attachment causes receptor heterodimers
23:34 Detection of heterodimer formation based on reconstitution of split proteins
24:13 Split TEV protease-based viral detector
25:37 FUNCTION 2: HIV protease activity
25:57 Viral detectionbased on HIV protease activity
26:33 Localization-based switch of T7 RNA polymeraseactivation
26:55 Model of the anti-HIV defense device
27:24 Experimental results
27:48 HIV causes release of the GFP reporter from the membrane
28:39 HIV protease causes translocation of fluorescent reporter into the nucleus
29:04 Integration of two steps: Split TEV-T7-based cell activation Control + gp120
29:28 HIV protease-based cell activation
29:54 Effectors for antiviral defense
30:24 Apoptotic caspase-3expression triggered by HIV protease
30:33 function-based mutation-independent
31:21 Helicobacter pylori
32:49 Master of disguise
34:17 TLR receptors sense the presence of bacteria
34:29 TLRs and their agonists
34:43 Chimeric flagellin - 1
35:29 Chimeric flagellin - 2
35:54 Multiepitope
36:08 Implementation
36:43 Implementation 1Protein vaccine
37:02 Implementation 2 DNA vaccine - 1
37:36 Implementation 2 DNA vaccine - 2
38:03 in vivo efficiency of the vaccine
38:31 Colocalization of antigen and TLR activation
38:43 TLR signaling
38:58 TLR signaling activates antigen processing
39:52 Constitutively active antigen-TLR fusion
40:10 Modular composition of vaccine in track 2
40:30 The function of TLR-fusion vaccine
40:40 TLR4 activation
40:53 Modulating localization
41:12 Signaling network of TLR-fusion vaccine
42:00 Immune response
42:45 TLR Signaling pathway - 1
43:34 TLR Signaling pathway - 2
43:39 TLR signal pathway involves a complex signaling network
44:19 “All Paths lead through MyD88”
44:45 Modification of signaling network
45:32 Domain structure of MyD88
45:46 Dominant negative MyD88 inhibition
46:03 Simplified model of TLR signaling - 1
46:32 Simplified model of TLR signaling - 2
46:37 Normal cellular response to repeated stimulus
46:41 Insertion of a negative feedback loop
47:06 Response to repeated stimulus in cells with inserted feedback device
47:20 Results
47:43 Slovenian team 2006
47:56 Slovenian team 2007
48:03 iGEM 2008 winners
48:11 Current bottlenecks of SB
49:11 The Future of synthetic biology
49:59 Slovenian teams 2006-2008

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