Post on 13-Jul-2020
2
Faculty ofEconomics and Business
The Team
Patterns are everywhere
Evolutionary importance
3
Patterns on a Microscopic Scale
Bacillus subtilis P. vortex
E. coli
4
S. Brown, Simple Genetic Circuit Forms Strips, US San Diego News Center, 2011
Basic Principles
Chemokinesis: Tsr chemoreceptor Leucine as repellent
Cell-Cell Interactions
LuxI, LuxR, Plux: AHL based
Ag43: Aggregation
Motility
CheZ: Motor regulation
5
Double Knockout Strains
6
A B
CMPG
Signaling Cascade for Motility
Migration determined by rotational direction of flagella
7Sarkar MK, Paul K, Blair D , “Chemotaxis signaling protein CheY binds to the rotor protein FliN to control the direction of flagellar rotation in Escherichia coli.” PNAS 107, no. 20 (2010): 9370-9375.
cI
cI
cI42 °C
32 °C
Induction Mechanism
cI
AHL
cI
cI42 °C
32 °C
8
Regulatory Circuit of Cells A
cI
AHL
cI
cI42 °C
32 °C
cI42 °C
32 °C
cI
cI
9
cI
AHL
Leucine
cI
cI
1 2
Regulatory Circuit of Cells A42 °C
32 °C
10
Regulatory Circuit of Cells B
cI
cI
cI42 °C
32 °C
11
Expected Pattern
12
Results: Double Knockout Validation
Replacement of the genes cheZ or tsr in Δtarstrain by Kanamycin casette
cheZ knockout validation: Motility test
13
Δtar ΔtarΔcheZ
Results: CheZ-GFP BioBrick Characterization
14
Results: AHL Biosensor Optimization
Chromobacterium violacein CV026 (cviI gene deficient)
T1 T2 T3
0.10
Co
nce
ntr
atio
nA
HL
(mM
)
0.09
0.08
0.07
0.06
0.05
0.04
0.03
0.02
0.01
0.00
DMSO
Replicates Standard Curve
Concentration AHL (mM)
A5
85
nm
/ A
60
0 n
m
15
Chromobacteria provided by Prof. Peeters, Department of Molecular Imaging and Photonics
Clay Fuqua , Matthew R. Parsek , and E. Peter Greenberg “Regulation of Gene Expression by Cell-to-Cell Communication: Acyl-Homoserine Lactone Quorum Sensing” , Annu. Rev. Genet. (2001) 35:439–68
Measurement Interlab Study
16
D1 BBa_J23117 + BBa_I13504
D2 BBa_J23106 + BBa_I13504
D3 BBa_J23101 + BBa_I13504
Measurement equipement: Prof. Mizuno, Department of Biochemistry and Molecular and Structural BiologyFluorescein: Prof. Johan Hofkens, Department of Molecular Imaging and Photonics
17
ModelingInternal model
Colony level model
Hybrid model
18
Internal Model
Cell A Cell B
Cell A
19
Internal Model
20
Internal Model
21
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Colony Level Model
22
Colony Level Model
𝝏𝑨
𝝏𝒕= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝝏𝑩
𝝏𝒕= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝝏𝑹
𝝏𝒕= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝝏𝑯
𝝏𝒕= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Change in density
Change in concentration
23
Colony Level Model
𝜕𝐴
𝜕𝑡= 𝑫𝒂𝜵
𝟐𝑨 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝑫𝒃𝜵
𝟐𝑩 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝑫𝒓𝜵
𝟐𝑹 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝑫𝒉𝜵
𝟐𝑯+ 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Diffusion
24
Colony Level Model
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝜸𝑨 𝟏 −𝑨
𝒌𝒑
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝜸𝑩 𝟏 −𝑩
𝒌𝒑
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Logistic growth
25
Colony Level Model
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝜵 𝑷 𝑩,𝑯, 𝑹 𝜵𝑹 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Chemotaxis drift
26
Colony Level Model
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝒌𝒓𝑨 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝒌𝒉𝑨 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
Production
27
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝒌𝒍𝒐𝒔𝒔𝑹𝑹
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝒌𝒍𝒐𝒔𝒔𝑯𝑯
Degradation
Colony Level Model
28
Colony Level Model
𝜕𝐴
𝜕𝑡= 𝐷𝑎𝛻
2𝐴 + 𝛾𝐴 1 −𝐴
𝑘𝑝
𝜕𝐵
𝜕𝑡= 𝐷𝑏𝛻
2𝐵 + 𝛻 𝑃 𝐵,𝐻, 𝑅 𝛻𝑅 + 𝛾𝐵 1 −𝐵
𝑘𝑝
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
29
Colony Level Model
30
Colony Level Model
31
Hybrid Model
Benjamin Franz and Radek Erban. Hybrid modelling of individual movement and collective behaviour. Lecture Notes in Mathematics, 2071:129-157, 2013
32
Hybrid Model
𝑑𝑥𝐴𝑖 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝑑𝑥𝐵𝑖 = 2𝐷𝑏𝑑𝑊 − 𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
33
Hybrid Model
𝒅𝒙𝑨𝒊 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝒅𝒙𝑩𝒊 = 2𝐷𝑏𝑑𝑊 − 𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
Displacement
34
Hybrid Model
𝑑𝑥𝐴𝑖 = 𝟐𝑫𝒂𝒅𝑾+1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝑑𝑥𝐵𝑖 = 𝟐𝑫𝒃𝒅𝑾−𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
Random step ( diffusion)
35
Hybrid Model
𝑑𝑥𝐴𝑖 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝑑𝑥𝐵𝑖 = 2𝐷𝑏𝑑𝑊 −𝑫𝒃𝟏
𝑹𝜵 𝑹 𝒅𝒕 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
Chemotaxis step ( chemotaxis drift)
36
Hybrid Model
𝑑𝑥𝐴𝑖 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝒋
𝑨\{𝒊}𝒅𝑬𝒑,𝒂𝒕𝒕𝒓
𝒅𝒓𝒆𝒊𝒋 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝑑𝑥𝐵𝑖 = 2𝐷𝑏𝑑𝑊 − 𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
Cell-cell attraction
37
Hybrid Model
𝑑𝑥𝐴𝑖 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝒋
𝑩𝒅𝑬𝒑,𝒓𝒆𝒑
𝒅𝒓𝒆𝒊𝒋 𝑑𝑡
𝑑𝑥𝐵𝑖 = 2𝐷𝑏𝑑𝑊 − 𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝒋
𝑨∪𝑩\{𝒊}𝒅𝑬𝒑,𝒓𝒆𝒑
𝒅𝒓𝒆𝒊𝒋 𝑑𝑡
Cell-cell repulsion
38
Hybrid Model
𝑑𝑥𝐴𝑖 = 2𝐷𝑎𝑑𝑊 +1
𝛾
𝑗
𝐴\{𝑖}𝑑𝐸𝑝,𝑎𝑡𝑡𝑟
𝑑𝑟𝑒𝑖𝑗 +
𝑗
𝐵𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝑑𝑥𝐵𝑖 = 2𝐷𝑏𝑑𝑊 − 𝐷𝑏1
𝑅𝛻 𝑅 𝑑𝑡 +
1
𝛾
𝑗
𝐴∪𝐵\{𝑖}𝑑𝐸𝑝,𝑟𝑒𝑝
𝑑𝑟𝑒𝑖𝑗 𝑑𝑡
𝜕𝑅
𝜕𝑡= 𝐷𝑟𝛻
2𝑅 + 𝑘𝑟𝐴 − 𝑘𝑙𝑜𝑠𝑠𝑅𝑅
𝜕𝐻
𝜕𝑡= 𝐷ℎ𝛻
2𝐻 + 𝑘ℎ𝐴 − 𝑘𝑙𝑜𝑠𝑠𝐻𝐻
39
Hybrid Model
40
Hybrid Model
41
Future Applications
Spot E.Shape
Tumorformation
Miniature electrical circuits
Bio-composite materials
Bone replacement
Biocomposite, patterned bacterial calcification hip replacements: A business analysis
MacMillan & McGrath, Harvard Business Review ©
42
Public Perception of Synthetic Biology (BE)Respondents defining synthetic
biology
Do you approve synthetic biology in general?
Education
43
44
Strains - The Card Game
Symposium
• 5 iGEM teams: KU Leuven, Bonn, Amsterdam, Paris-Saclay & Eindhoven
• National & international keynote speakers
• Guests from 6 different countries
• Ethical debate45
Collaborations
46
Diffusion model using COMSOL Multiphysics
Wiki
47
Conclusions
48
Acknowledgements
49
Prof. Robben Department of Biochemistry andMolecular and Structural Biology
Scientific and advisory help
Prof. Mizuno Department of Biochemistry andMolecular and Structural Biology
Scientific help on fluorescent proteins andvisualization
Prof. Hofkens Department of Molecular Imaging and Photonics
Provided us with fluorescein
Prof. Michiels Centre of Microbial and Plant Genetics
Advice with respect to AHL detection
Prof. Peeters Centre of Microbial and Plant Genetics
Provided us withChromobacteriumviolaceum
Natalie Verstraeten Centre of Microbial and Plant Genetics
Provided us with 3 Keiostrains
Prof. Desair Centre of Microbial and Plant Genetics
Helped with leucinedetection
Wet lab
50
Prof. Roose Department of Computer Science Advice on coding andmathematics
Prof. Ramon, Tim Odenthal
Department of Mechatronics, Biostatistics and Sensors
Advice on cell-cellinteractions in hybridmodel
Prof. De Maeyer Department of Biochemistry, Molecular and Structural Biology
Access to the FlemishSupercomputer Centre
VSCentrum Flemish Supercomputer Centre Supercomputer
ICTS ICTS KU Leuven Supercomputing servers
Prof. Michiels Centre of Microbial and Plant Genetics
Advice on cell growth
Prof. Mizuno Department of Biochemistry andMolecular and Structural Biology
Advice on cell-cellinteractions in hybridmodel
Dry lab
Acknowledgements
51
Advisors
Supervisor
Oscar Torres, Yves Peeters, Iris Govaerts, Veerle De Wever & ex-iGEMmers
Katarzyna Malczewska
PromoterProf. Johan Robben
AcknowledgementsSymposium
Keynote speakers Vera van Noort, Victor Dillard, Yves Peeters, prof. Sebastian Maerkl
Ethical debateexpert panel
Prof. Bart De Moor, Prof. Johan Robben, Dr. Stijn Bruers, Prof. Vera van Noort & Victor Dillard
Ethical debatemoderator
Prof. Piet Van der Meer