Orkun Soyer

Question 1

How are biological systems dynamic?

Answer 1

• Temporal behaviour/how they change over time, so we will need to monitor these changes over time
• The inputs and outputs vary – so the way the system responds to an input/what the output is can change

Question 2

What are the two types of temporal dynamics?

Answer 2

Linear and non-linear

Question 3

What is the outcome of negative feedback dynamics?

Answer 3

Faster response (to signals) ‘Adaptation’

Question 4

What is the outcome of positive feedback?

Answer 4

Bistability, Switches, Logic Gates, Memory

Question 5

What is the outcome of negative and positive feedback with delay?

Answer 5

Oscillations.

Frequency-based signaling Entrainment

Question 6

Interlocked +/- Feedback with Delay

Answer 6

Robust oscillations

Question 7

What affects the concentration of a transcription factor when there is no regulation?

Answer 7

Expression of the gene will increase the concentration.
General cell growth as it will decrease the concentration through dilution

—> P —>
b a

so:
d[P]/dt = b - a * [P]

Question 8

What affects the concentration of a transcription factor when there is negative autoregulation?

Answer 8

Expression of the gene will increase the concentration.
General cell growth as it will decrease the concentration through dilution
Expression inhibits expression

—> P —>
/b/ a

so:
d[P]/dt = b/1+([P]/K)^n - a * [P]

Question 9

What do steady state and time both depend on?

Answer 9

alpha, the dilution factor

but steady state can be made independent from alpha

Question 10

What would you add if you want to control protein levels in a cell and the time it takes to respond to a stimulus?

Answer 10

Negative feedback loop

Question 11

What gives you a threshold response?

Answer 11

Positive feedback mechanism

Question 12

What is bistability?

Answer 12

When the system has two stable equilibrium states. Something that is bistable can be resting in either of two states

Question 13

How would you study interactions in a sample of multiple communities?

Answer 13

genome sequencing and temporal sampling to see how groups change in response to different conditions
stable isotope tracking involves adding stable isotopes and seeing which groups take it up

Question 14

What can we currently do with microbial communities?

Answer 14

• Extend metabolic capacities
• Make something that can stabilise other things
• Gut treatments – ways of controlling naturally occurring microbial communities
• Biocomputing power
• Create functional materials.

Question 15

What is tractability and what happens when complexity increases?

Answer 15

controllability/measurability, ability to model

and it decreases

Question 16

How many species does the largest constructed community have?

Answer 16

5

Question 17

What are the two ways to engineer synthetic microbial communities?

Answer 17

• Start with a complex community and try to remove species through dilution or increase some species with culture enrichment
• Rational engineering - Put species together one by one. It is more difficult than it sounds because finding common media to promote growth and to make sure they don’t kill each other is hard.

Question 18

What is Chassis?

Answer 18

The under lying biology in which a device or system is implemented. This can be a living organism (host) or an in vitro system for transcription and translation.

Question 19

How do you do rational engineering?

Answer 19

Connect cells with :
Signaling
Physical Interactions
Metabolism

Question 20

How would you analyse a microbial community?

Answer 20

Take sample, extract DNA and sequence the genomes. Combine this with temporal sampling of some sort of metadata like pH or rainfall. Find out of the proportions of certain species increases or decreases in rain vs out of rain.
Species that increase together and decrease together may interact

Question 21

How would you find out which species in a microbial community takes up a compound?

Answer 21

Stable isotope tracking - spike a sample with a heavy isotope

Question 22

Give examples of how we already exploit microbial communities

Answer 22

Gut Microbiome
Biogas reactors
Waste water treatment

Question 23

Why would putting different pathways in different microbes make things more efficient?

Answer 23

You can create different environments for different pathways like high or low pH so microbial communities can be helpful when putting it all in one organism is not feasible.
Spatially organising the microbes can let you marry up different metabolic processes.

Question 24

What are potential things we can do with engineering microbial communities?

Answer 24

• Extend metabolic capacities
• Make something that can stabilise other things
• Gut treatments – ways of controlling naturally occurring microbial communities
• Biocomputing power
• Create functional materials.

Question 25

What are the different possible ways of engineering microbial communities?

Answer 25

Top down = engineer natural microbial communities like gut microbiota of patients to treat linked diseases Bottom up = engineering synthetic communities from scratch, starting with individual species.

Question 26

What compromise has to be made with increasing complexity of microbial communities?

Answer 26

Tractability (ability to control, measure and model) decreases

Question 27

How would rational engineering of synthetic microbial communities work?

Answer 27

Carry out the design, build, test cycle and use signalling to make them interact, physical interactions to have them stick together, or metabolisms so that one species produces something that another species uses

Question 28

Give an example of Signalling-Based Engineering of SMCs

Answer 28

Balagaddé et al 2008: Designed a predator and prey circuit. One produces a toxin and the other produces an antidote so they cannot survive without each other.

Question 29

What is an issue with engineering microbial communities?

Answer 29

Horizontal gene transfer can be a problem so you need to limit it. If one species replicates more quickly than another, how do you control population size? You can run out of ‘wires’ to connect species if you have thousands Evolution – replicating systems can evolve so if you add a costly circuit, mutated bacteria will stop using it. It’s an issue in monocultures too.

Question 30

What are the different types of SMC engineering?

Answer 30

Signalling-based Spatial Metabolism-based

Question 31

Give an example of Spatial Engineering of SMCs

Answer 31

Tsai et al 2009 engineered a mini cellulosome: four engineered yeast strains producing different cellulose-degrading enzymes and their scaffold

Question 32

How would you model spatial interactions in microbial communities

Answer 32

Agent Based Models with Space Spatial Differential Equation (PDEs)

Question 33

How would you model spatial interactions in microbial communities?

Answer 33

Agent Based Models with Space Spatial Differential Equation (PDEs)

Question 34

How many microbial metabolic interactions can you name?

Answer 34

``` Commensalism Amensalism Competition Cooperation Cross-feeding Syntrophy Auxotrophy ```

Question 35

Give an example of auxotropy

Answer 35

Mee et al 2014 14 synthetic amino acid auxotrophies were engineered in ecoli by knocking out biosynthetic enzymes that leads to the different amino acids. Paired up different auxotrophy strains to see if they could sustain each other's growth. Not viable in all amino acids. Some pairs and triplets worked, some didn't. They compared monocultures with communities where one overexpresses amino acid and another cannot. It was also asked whether the communities will stay stable through evolution so they tried adding mutants to see if they would take over - it was evolutionarily stable

Question 36

Give an example of cross feeding

Answer 36

Grosskopf & Soyer et al found that glucose-acetate crossfeeding had evolved in long-term experiment with E. coli - had one large culture and every other day, subcultured it into new media (took a sample to freeze as well). Every new subculture was diluted (added selection pressure)

Question 37

Why is cross feeding the best choice of metabolic interaction?

Answer 37

They are found naturally and are evolutionarily stable. | It has been shown to have increased fitness over WT