uOttawas 2013 Project Pulse generator uOttawas 2013 Project Primer - - PowerPoint PPT Presentation

▶
uottawa s 2013 project
SMART_READER_LITE
LIVE PREVIEW

uOttawas 2013 Project Pulse generator uOttawas 2013 Project Primer - - PowerPoint PPT Presentation

Feb 07, 2023 38 likes •672 views

uOttawas 2013 Project Pulse generator uOttawas 2013 Project Primer designer uOttawas 2013 Project Childrens book Accomplishments Constructed the first synthetic pulse generator in yeast Collaborated with the University of

slide-1
SLIDE 1
slide-2
SLIDE 2

Pulse generator

uOttawa’s 2013 Project

slide-3
SLIDE 3

Primer designer

uOttawa’s 2013 Project

slide-4
SLIDE 4

Children’s book

uOttawa’s 2013 Project

slide-5
SLIDE 5

Accomplishments

uOttawa 2013

Constructed the first synthetic pulse generator in yeast Collaborated with the University of Waterloo Mathematically modeled the synthetic network Produced numerous novel functional BioBricks Created a primer-generating web application Wrote the first ever iGEM children’s book

slide-6
SLIDE 6

Synthetic pulse generator

slide-7
SLIDE 7

The incoherent feedforward loop

uOttawa 2013

slide-8
SLIDE 8

Temporal pulse generation

uOttawa 2013

Concentration

slide-9
SLIDE 9

Temporal pulse generation

uOttawa 2013

Concentration

slide-10
SLIDE 10

Temporal pulse generation

uOttawa 2013

Concentration

slide-11
SLIDE 11

Temporal pulse generation

uOttawa 2013

Concentration

slide-12
SLIDE 12

Network Design

uOttawa 2013

slide-13
SLIDE 13

Network Design

uOttawa 2013

slide-14
SLIDE 14

No temporal pulse is observed

uOttawa 2013

slide-15
SLIDE 15

Sigmoidal gene activation

uOttawa 2013

  • Sigmoidal response
slide-16
SLIDE 16

Sigmoidal gene activation

uOttawa 2013

  • Sigmoidal response

TIME

slide-17
SLIDE 17

Negative autoregulation linearizes dose response

uOttawa 2013

  • Sigmoidal response

TIME

slide-18
SLIDE 18

Negative autoregulation linearizes dose response

uOttawa 2013

  • Sigmoidal response
  • Linear response

TIME TIME

slide-19
SLIDE 19

Mechanism of negative autoregulation

uOttawa 2013

slide-20
SLIDE 20

Mechanism of negative autoregulation

uOttawa 2013

slide-21
SLIDE 21

Mechanism of negative autoregulation

uOttawa 2013

slide-22
SLIDE 22

Collaboration with uWaterloo

uOttawa 2013

slide-23
SLIDE 23

Model shows pulse generation

uOttawa 2013 Time (min) Concentration

slide-24
SLIDE 24

Experimental data exhibits a transient pulse in sfGFP in both cases

uOttawa 2013

slide-25
SLIDE 25

Experimental data exhibits a transient pulse in sfGFP in both cases

uOttawa 2013

slide-26
SLIDE 26

Linearization is observed

uOttawa 2013

0.6 0.7 0.8 0.9 1 1.1 1.2 1 1.5 2 2.5 3 3.5 4 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 sfGFP Fluoresecnce (AU) BFP Fluorescence (AU) Time (h)

BFP sfGFP

slide-27
SLIDE 27

Fold-change response

uOttawa 2013

slide-28
SLIDE 28

Model exhibits functional fold-change response

uOttawa 2013 Time (mins) Variation in rate of production Concentration

slide-29
SLIDE 29

Network versatility

uOttawa 2013

slide-30
SLIDE 30

Toxic molecule detection

uOttawa 2013

slide-31
SLIDE 31

BBa_K1164004: pTRE-LX

uOttawa 2013

slide-32
SLIDE 32

BBa_K1164004: pTRE-LX Characterization

uOttawa 2013

0.5 1 1.5 2 2.5 3 3.5 4 2 4 6 8 10

GFP Fluorescence (AU) IPTG (mM)

slide-33
SLIDE 33

BBa_K1164004: pTRE-LX Characterization

uOttawa 2013

0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 25 50 75 100

GFP Fluorescence (AU) ATc (ng/mL)

slide-34
SLIDE 34

Bricklayer Web Application

slide-35
SLIDE 35

Bricklayer Application

PCR based assembly means designing primers.

Lots of primers.

uOttawa 2013

slide-36
SLIDE 36

uOttawa 2013

Early Version of Primer Generator

slide-37
SLIDE 37

uOttawa 2013

slide-38
SLIDE 38

uOttawa 2013

slide-39
SLIDE 39

Bricklayer Application

uOttawa 2013

slide-40
SLIDE 40

Bricklayer Application

uOttawa 2013

slide-41
SLIDE 41

Bricklayer Application

uOttawa 2013

slide-42
SLIDE 42

Bricklayer Application

uOttawa 2013

slide-43
SLIDE 43

Bricklayer Application

Spend less time designing primers. Spend more time designing networks.

uOttawa 2013

slide-44
SLIDE 44

Children’s Book

slide-45
SLIDE 45

Human Practices

uOttawa 2013

Developing a Foundation:

slide-46
SLIDE 46

Human Practices

Our Approach:

uOttawa 2013

How do we complete this?...

Provide accurate information Create a foundation based on knowledge Engage today’s youth

slide-47
SLIDE 47

Human Practices

A Children’s Book!

  • Mr. Cool’s Microscopic Adventures

uOttawa 2013

slide-48
SLIDE 48

uOttawa 2013

slide-49
SLIDE 49

Human Practices

uOttawa 2013

Scalability:

  • Global audience
  • Digital avenues for cross-

platform sharing

– High resolution audiovisual book – Audiobook

  • Registered ISBN
  • Available at three Ottawa Public

Library locations

slide-50
SLIDE 50

Human Practices

So, how do we target

  • ur initial audience,

children?

uOttawa 2013

slide-51
SLIDE 51

Human Practices

In-class Workshops:

  • Students in grades 3-4 (n=24)
  • DNA, protein function, and applications of

synthetic biology

uOttawa 2013

slide-52
SLIDE 52

Human Practices

Workshop Results: What is DNA?

uOttawa 2013

slide-53
SLIDE 53

Human Practices

Workshop Results: What is Synthetic Biology?

uOttawa 2013

slide-54
SLIDE 54

Human Practices

Summary:

  • Wrote, illustrated, and published Mr. Cool’s

Microscopic Adventures

  • Demonstrated scalability of project
  • Provided workshops on synthetic

biology to youth

  • Created a foundation of knowledge

that is statistically supported

uOttawa 2013

slide-55
SLIDE 55

Thank you!

uOttawa 2013 Thanks to the members of the Kærn Lab:

  • Dr. Mads Kærn
  • Afnan Azizi
  • Daniel Charlebois
  • Daniel Jedrysiak
  • Hilary Phenix
  • Ian Roney
  • Mila Tepliakova

Thanks to:

  • Dr. Gábor Balázsi (University of Texas)
  • Dr. David Eide (University of Wisconsin-

Madison)

  • Dr. Tom Ellis (Imperial College)
  • Dr. Michael Knop (ZMBH University of

Heidelberg)

slide-56
SLIDE 56

Questions?

uOttawa 2013

slide-57
SLIDE 57

Supplementary Materials

uOttawa 2013

15 30 45 60 75 90 105

0.2 0.4 0.6 0.8 1 1.2 1.4 3 6 9

ATc (ng/mL) sfGFP Fluorescence (AU)

IPTG (mM)

1.4-1.5 1.2-1.4 1-1.2 0.8-1 0.6-0.8 0.4-0.6 0.2-0.4 0-0.2

  • - Ctrl in IPTG & ATc gradient
slide-58
SLIDE 58

Supplementary Figures

uOttawa 2013 Time (mins) Concentration

  • - Ctrl in IPTG & ATc gradient
slide-59
SLIDE 59

Transcription formulas

uOttawa 2013

slide-60
SLIDE 60

Transcription formulas

uOttawa 2013

slide-61
SLIDE 61

Translation formula

uOttawa 2013

slide-62
SLIDE 62

Protein in nucleus

uOttawa 2013

slide-63
SLIDE 63

Control equations

uOttawa 2013