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Michaelmas Term 1 > Systems And Networks In Biology > Flashcards

Systems And Networks In Biology Flashcards

1
Q

Why, in light of the gene-centric view, is it still important for us to study the phenotype?

A
  • knowing the genome does not give much insight into organism or behaviour
  • gives contextual utility to ecological analysis
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2
Q

What is a non-equilibrium dynamical system?

A
  • based on principles of non-equilibrium thermodynamics
  • constrains and drives organisation
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3
Q

What are the components of a non-equilibrium dynamical system?

A
  1. Self-organisation
  2. Self-assembly
  3. Energy
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4
Q

Describe self-assembly

A
  • physical association of molecules into an equilibrium structure
  • properties at the larger scale are defined by properties of the subunit
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5
Q

Describe self-organisation

A
  • non-equilibrium systems that dissipate energy to achieve a dynamic steady state
  • higher (system) level organisation is not explicitly specified by rules
  • robust - can recover from severe perturbation of the system
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6
Q

How does dynamic self-organisation arise ?

A

Spontaneously emerges from a series of (non-linear) local interactions

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7
Q

What is dynamic self-organisation a type of?

A

Spatio-temporal order

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8
Q

What is the central dogma of molecular biology

A

The detailed residue-residue transfer of sequential information

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9
Q

Why is the central dogma wrong?

A

A linear, causal chain does not illustrate the complex network of system interactions across multiple scales that show emergent behaviour

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10
Q

What is the genome?

A

Protein-gene interactions

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11
Q

What is the proteome?

A

Protein-protein interactions?

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12
Q

What is metabolism?

A

Biochemical reactions

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13
Q

Describe a complex system

A
  1. Typically has many interacting components
  2. Non-linear interactions (and feedback loops)
  3. Emergent properties
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14
Q

Give examples of emergent properties

A
  • spontaneous order
  • adaptation
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15
Q

Describe emergent behaviour

A

a property of a system that is not apparent from its component parts in isolation

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16
Q

How does emergent behaviour arise

A

Interactions between the components of when operating together in a system

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17
Q

Examples of complex systems:

A
  1. Collective behaviour
  2. Evolution and adaptation
  3. Game theory
  4. Networks
  5. Nonlinear dynamics
  6. Pattern formation
  7. Systems theory
18
Q

What do complex systems consist of?

A
  1. Complexity
  2. Emergence
  3. Energy
  4. Self-assembly
  5. Self-organisation
19
Q

What was Van Valen’s fitness theory?

A
  • fitness is expansive energy
  • natural selection, at any level or time scale, maximises the expected amount of expansive energy
20
Q

Absolute fitness is defined as

A

Control of trophic energy level (reduced carbon)

21
Q

What is the pro of Van Valen’s fitness definition?

A
  • can be applied to all organisms
  • avoids issues with individuals, clonality, body size, indeterminate growth or expansion
22
Q

What are Dynamic Energy Budget models?

A

The application of Van Valen’s fitness theory at an ecosystem level

23
Q

What is an experimental approach to investigating a complex system?

A
  • mating in yeast under starvation (the shmoos)
  • abstracted network representations
24
Q

How do we use mating in yeast under starvation to investigate complex systems ?

A
  • analysing gene expression patterns using a DNA microarray
  • red = upregulated after pheromone
  • green = downregulated
  • apply probes to array to measure red/green ratio
  • cluster analysis of gene behaviour through gene transcripts
  • repeat transcript analysis in different mutant backgrounds with predictions
25
Q

How are green fluorescently labelled probes made

A

From cDNA library of normal cells

26
Q

How are red fluorescently labelled probes made

A

From cDNA library of cells treated with mating pheromone

27
Q

Results of starved yeast mating investigation

A
  • > 200 transcripts increased in abundance
  • > 200 decrease in abundance
  • 383 genes changed by >3 fold
28
Q

Describe abstract network representations

A
  • Abstract representations of nodes and (directed) edges
  • node degree distributions
  • metabolic flux networks
  • signal transduction networks
  • physical transport networks
  • food webs
29
Q

List abstracted network representations

A
  1. Basic unit
  2. Motifs
  3. Modules
  4. Transcriptional regulatory network
30
Q

Give example of abstracted network representation motifs

A
  1. SIM
  2. MIM
  3. FFL
31
Q

Give an example of a scale-free abstracted network representation

A
  • Yeast metabolism
  • metabolic networks for organisms of all 3 domains of life
32
Q

The phenotype operates as

A

Interconnected networks across multiple levels

33
Q

What are phenotypes

A

Non-equilibrium systems maintained by continuous energy flows

34
Q

Network theory provides

A

One framework to explore high-level concepts across multiple domains

35
Q

What does non-equilibrium mean?

A

Requires constant energy input

36
Q

Give an example of a non-equilibrium system

A

Us!

37
Q

Give an example of a self-organising system

A
  • Microtubules
  • nucleoli
  • lipid-lipid phase
38
Q

Give an example of a non-linear interaction

A

Enhancers/repressors binding to the promoter regions

39
Q

What does the word ‘complicated’ imply?

A

Predictability

40
Q

Described starved yeast

A

Conflict between cell division and shmoo formation pathways

Michaelmas Term 1 (42 decks)

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