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

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

Jan 02, 2024 286 likes •1.11k views

UANL Mty Mxico 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

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UANL Mty México

iGEM 2013

the Thermocoli project

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the speakers

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the speakers

Heber

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the speakers

Heber Arely

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the speakers

Heber Arely Porfirio

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Input Output

the black box

Information processing

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

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

counters

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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

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

counters

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

counters

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

counters

logic-gates

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

counters

logic-gates

What is understanding?

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

switches counters

logic-gates

Moon et al. (2012) Nature 00:1-5

What is understanding?

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

switches counters

logic-gates

Moon et al. (2012) Nature 00:1-5

What is understanding?

information processing in living systems

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the central dogma

Francis Crick (1956) Ideas on Protein Synthesis

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the central dogma

Francis Crick (1956) Ideas on Protein Synthesis

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the central dogma

Francis Crick (1956) Ideas on Protein Synthesis

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the central dogma

Francis Crick (1956) Ideas on Protein Synthesis

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Input 1 Input 2

keep it simple

INPU INPUT OUTPUT A B A AND B 1 1 1 1 1

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Input 1 Input 2

keep it simple

INPU INPUT OUTPUT A B A AND B 1 1 1 1 1

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RNA thermosensors

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RNA thermosensors

⤴ ºC

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RNA thermosensors

⤴ ºC

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no more Chemicals

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no more Chemicals

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no more Chemicals

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Input

H E D C I G F B A

Metabolite

  • f Interest
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Input

H E D C I G F B A

Metabolite

  • f Interest
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Input

H E D C I G F B A

Metabolite

  • f Interest
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Input

H E D C I G F B A

Metabolite

  • f Interest
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Input

H E D C I G F B A

Metabolite

  • f Interest
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Input

H E D C I G F B A

Metabolite

  • f Interest
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synthetic RNA thermosensors

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

32ºC

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the circuit

BBa_K1140003 BBa_K1140006 BBa_K1140004 BBa_K1140002

37ºC 37ºC

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the circuit

BBa_K1140003 BBa_K1140006 BBa_K1140004 BBa_K1140002

37ºC 37ºC

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the circuit

BBa_K1140003 BBa_K1140006 BBa_K1140004 BBa_K1140002

37ºC 37ºC

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the circuit

BBa_K1140003 BBa_K1140006 BBa_K1140004 BBa_K1140002

37ºC 37ºC

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the circuit

BBa_K1140003 BBa_K1140006 BBa_K1140004 BBa_K1140002

37ºC 37ºC

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  • btaining the circuit

synthetic DNA

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the circuit

BBa_K1140006 BBa_K1140004 BBa_K1140002 BBa_K1140003

37ºC 37ºC

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the circuit

BBa_K1140006 BBa_K1140002

37ºC

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testing temperature responsiveness

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testing temperature responsiveness

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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

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

temperature responsiveness

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

temperature responsiveness

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0! 0.1! 0.2! 0.3! 0.4! 0.5! 0.6!

M1! M2! M11! M12! Rela elativ ive e Flu Fluorescen

  • rescence

ce Unit its!

25°C! 30°C! 37°C! 42°C!

temperature responsiveness

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Fitting to gaussian

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Fitting to gaussian

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Fitting to gaussian

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Fitting to gaussian

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Fitting to gaussian

  • E. coli DH5α can grow at a

temperature as high as 49 ºC, above...sporadic and not reproducible.

Fotadar U (2005) J Basic Microbiol 45:403-4.

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Fitting to gaussian

  • E. coli DH5α can grow at a

temperature as high as 49 ºC, above...sporadic and not reproducible.

Fotadar U (2005) J Basic Microbiol 45:403-4.

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deducing from Gaussian

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R N A T m e l t i n g

deducing from Gaussian

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i n c r e a s e d d e g r a d a t i

  • n

R N A T m e l t i n g

deducing from Gaussian

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deducing from Gaussian

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deducing from Gaussian

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deducing from Gaussian

37ºC 37ºC

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  • ptimizing methods

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

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Input 1 Input 2 Input 2

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Input 1 Input 2 Input 2

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Input 1 Input 2 Input 2

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Input 1 Input 2 Input 2

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Input 1 Input 2 Input 2

0! 0.1! 0.2! 0.3! 0.4! 0.5! 0.6!

M1! M2! M11! M12! Rela elativ ive e Flu Fluorescen

  • rescence

ce Unit its!

25°C! 30°C! 37°C! 42°C!

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Input 1 Input 2 Input 2

0! 0.1! 0.2! 0.3! 0.4! 0.5! 0.6!

M1! M2! M11! M12! Rela elativ ive e Flu Fluorescen

  • rescence

ce Unit its!

25°C! 30°C! 37°C! 42°C!

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Input 1 Input 2 Input 2

0! 0.1! 0.2! 0.3! 0.4! 0.5! 0.6!

M1! M2! M11! M12! Rela elativ ive e Flu Fluorescen

  • rescence

ce Unit its!

25°C! 30°C! 37°C! 42°C!

increased degradation R N A T m e l t i n g

37ºC 37ºC

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the lab safety and containment

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risk assessment: plasmid stability

0%! 5%! 10%! 15%! 20%! 25%! 30%! 35%! Day 1! Day 2! Day 3! Day 4! Day 5!

pUC57 (same replication origin as pSB1)

plasmid retention

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risk assessment: ID-tags

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approved by COBIO

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People Reached: 14,000

Math modeling course: 1.62%

Poster Exhibitions: 4.73%

Exhibitions

G E N O B I O T E C 1 3

Talks Workshops Exhibitions

GENOBIOTEC Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Human Practices

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People Reached: 14,000

Synbio Rally: 1.35% Math modeling course: 1.62% International Symposium Genobiotec13: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Exhibitions

G E N O B I O T E C 1 3

Talks Workshops Exhibitions

GENOBIOTEC

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SLIDE 76

People Reached: 14,000

Exhibitions

G E N O B I O T E C 1 3

Workshops Exhibitions

GENOBIOTEC Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Talks

  • School Visits
  • DNA Bannana Extraction
  • Chemistry Conference
  • Poster Exposition
  • Synthetic Rally
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People Reached: 14,000

Exhibitions

G E N O B I O T E C 1 3

Exhibitions

GENOBIOTEC

Talks

Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Workshops

  • Math Modelling Course
  • SynBio UANL 2013
  • SynBio CIDEB 2012
  • SynBio CIDEB 2013
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People Reached: 14,000

Exhibitions

G E N O B I O T E C 1 3

GENOBIOTEC

Talks Workshops

Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Exhibitions Synthetic Biology Tunnel 2013

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People Reached: 14,000

Exhibitions

G E N O B I O T E C 1 3

GENOBIOTEC

Talks Workshops

Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

Exhibitions

Biotechnology Genomics Roundabout 2013

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SLIDE 80

People Reached: 14,000

Exhibitions

G E N O B I O T E C 1 3

Talks Exhibitions

Synbio Rally: 1.35%

Math modeling course: 1.62% International Symposium GENOBIOTEC: 13.5% Poster Exhibitions: 4.73% Biotech Roundabout: 15.93 SynBio Tunnel: 60.76%

GENOBIOTEC

INTERNATIONAL SYMPOSIUM

Pamela Silver Timothy Lu Eric Davidson

Caroline Ajo-Franklin Julio Collado Vidés Mauricio Antunes Octavio Mondragón

Michael Leavell Rubén Morones James Ferrell

Peng Yin

Gerd Moe-Behrens
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students instructors & advisors