UANL Mty Mxico iGEM 2013 the Thermocoli project the speakers the - PowerPoint PPT Presentation

UANL Mty México iGEM 2013 the Thermocoli project

the speakers

the speakers Heber

the speakers Arely Heber

the speakers Porfirio Arely Heber

the black box Information Input Output processing

Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8.

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. Ari E. Friedland, et al. (2009) Science 324:1199-1202

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 JJ Tabor et al. (2010) J Mol Biol 2:315-324

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 JJ Tabor et al. (2010) J Mol Biol 2:315-324 Tamsir A et al. (2010) Cell 00:1–4

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. logic-gates JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 JJ Tabor et al. (2010) J Mol Biol 2:315-324 Tamsir A et al. (2010) Cell 00:1–4

counters Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. logic-gates JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 What is understanding? JJ Tabor et al. (2010) J Mol Biol 2:315-324 Tamsir A et al. (2010) Cell 00:1–4

counters switches Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. logic-gates JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 What is understanding? JJ Tabor et al. (2010) J Mol Biol 2:315-324 Moon et al. (2012) Nature 00:1-5 Tamsir A et al. (2010) Cell 00:1–4

counters switches information processing in living systems Michael B. Elowitz & Stanislas Leibler (2000) Nature 403:335-8. logic-gates JJ Tabor et al. (2009) Cell 137:1272–1281 Ari E. Friedland, et al. (2009) Science 324:1199-1202 What is understanding? JJ Tabor et al. (2010) J Mol Biol 2:315-324 Moon et al. (2012) Nature 00:1-5 Tamsir A et al. (2010) Cell 00:1–4

the central dogma Francis Crick (1956) Ideas on Protein Synthesis

the central dogma Francis Crick (1956) Ideas on Protein Synthesis

the central dogma Francis Crick (1956) Ideas on Protein Synthesis

the central dogma Francis Crick (1956) Ideas on Protein Synthesis

keep it simple INPU INPUT OUTPUT Input 1 Input 2 A B A AND B 0 0 0 0 1 0 1 0 0 1 1 1

keep it simple INPU INPUT OUTPUT Input 1 A B A AND B 0 0 0 0 1 0 Input 2 1 0 0 1 1 1

RNA thermosensors

RNA thermosensors ⤴ ºC

RNA thermosensors ⤴ ºC

no more Chemicals

no more Chemicals

no more Chemicals

Input A C D B E F H I G Metabolite of Interest

Input A C D B E F H I G Metabolite of Interest

Input A C D B E F H I G Metabolite of Interest

Input A C D B E F H I G Metabolite of Interest

Input A C D B E F H I G Metabolite of Interest

Input A C D B E F H I G Metabolite of Interest

synthetic RNA thermosensors 37ºC 32ºC Neupert J, Karcher D, Bock R (2008) Nuc Acids Res, 36:e124

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

obtaining the circuit synthetic DNA

the circuit BBa_K1140002 BBa_K1140006 37ºC BBa_K1140003 37ºC BBa_K1140004

the circuit BBa_K1140002 BBa_K1140006 37ºC

testing temperature responsiveness

testing temperature responsiveness

testing temperature responsiveness two moles of molecular oxygen to form a mature mCherry chromophore, compared to the one mole required for GFP Regmi KC et al. (2013) J Phys Chem B 117:2247 − 2253 Shu X et al. (2006) Biochemistry 45:9639-9647

temperature responsiveness a)control 30ºC b)control 37ºC c)30ºC d)37ºC M1 temperature responsiveness

temperature responsiveness a)control 30ºC b)control 37ºC c)30ºC d)37ºC M1 temperature responsiveness

temperature responsiveness 0.6 ! 0.5 ! its ! ce Unit 0.4 ! orescence 25°C ! Fluorescen 30°C ! 0.3 ! e Flu 37°C ! ive elativ 0.2 ! 42°C ! Rela 0.1 ! 0 ! M1 ! M2 ! M11 ! M12 !

Fitting to gaussian

Fitting to gaussian

Fitting to gaussian

Fitting to gaussian

Fitting to gaussian E. coli DH5 α can grow at a temperature as high as 49 ºC, above...sporadic and not reproducible. Fotadar U (2005) J Basic Microbiol 45:403-4.

Fitting to gaussian E. coli DH5 α can grow at a temperature as high as 49 ºC, above...sporadic and not reproducible. Fotadar U (2005) J Basic Microbiol 45:403-4.

deducing from Gaussian

deducing from Gaussian g n i t l e m T A N R

deducing from Gaussian i n c r e a s e g n d i t d l e e m g r T a d A a N t i R o n

deducing from Gaussian

deducing from Gaussian

deducing from Gaussian 37ºC 37ºC

optimizing methods Utermark J and Karlovsky P (2006) BioTechniques 41:150-154

Input 1 Input 2 Input 2

Input 1 Input 2 Input 2

Input 1 Input 2 Input 2

Input 1 Input 2 Input 2

Input 1 Input 2 0.6 ! 0.5 ! Input 2 its ! ce Unit 0.4 ! orescence 25°C ! Fluorescen 30°C ! 0.3 ! e Flu 37°C ! ive elativ 0.2 ! 42°C ! Rela 0.1 ! 0 ! M1 ! M2 ! M11 ! M12 !

Input 1 Input 2 0.6 ! 0.5 ! Input 2 its ! ce Unit 0.4 ! orescence 25°C ! Fluorescen 30°C ! 0.3 ! e Flu 37°C ! ive elativ 0.2 ! 42°C ! Rela 0.1 ! 0 ! M1 ! M2 ! M11 ! M12 !

Input 1 Input 2 0.6 ! 0.5 ! Input 2 its ! ce Unit 0.4 ! orescence 25°C ! increased degradation Fluorescen 30°C ! 0.3 ! e Flu 37°C ! ive g elativ 0.2 ! n 42°C ! 37ºC Rela i t l e m 0.1 ! T A 0 ! N 37ºC M1 ! M2 ! M11 ! M12 ! R

the lab safety and containment

risk assessment: plasmid stability 35% ! 30% ! pUC57 25% ! plasmid retention (same replication origin as pSB1) 20% ! 15% ! 10% ! 5% ! 0% ! Day 1 ! Day 2 ! Day 3 ! Day 4 ! Day 5 !

risk assessment: ID-tags

approved by COBIO

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People Reached: 14,000 Synbio Rally: 1.35% Talks International Symposium GENOBIOTEC: 13.5% 3 1 C E T O I B O N E G Math modeling course: 1.62% Poster Exhibitions: 4.73% - School Visits - DNA Bannana Extraction Exhibitions Biotech Roundabout: 15.93 SynBio Tunnel: 60.76% - Chemistry Conference - Poster Exposition Workshops Exhibitions GENOBIOTEC - Synthetic Rally

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People Reached: 14,000 Synbio Rally: 1.35% Synthetic Biology Tunnel 2013 Exhibitions International Symposium GENOBIOTEC: Talks 13.5% 3 1 C E T O I B O N E Math modeling course: 1.62% G Poster Exhibitions: 4.73% Exhibitions Biotech Roundabout: 15.93 SynBio Tunnel: 60.76% Workshops GENOBIOTEC

People Reached: 14,000 Synbio Rally: 1.35% Biotechnology Genomics Roundabout 2013 Exhibitions International Symposium GENOBIOTEC: 13.5% Talks 3 1 C E T O I B O N E G Math modeling course: 1.62% Poster Exhibitions: 4.73% Exhibitions Biotech Roundabout: 15.93 SynBio Tunnel: 60.76% Workshops GENOBIOTEC