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