Post on 10-Jun-2020
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7.81J/8.591J/9.531J
Systems Biology‘modeling biological networks’
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Introducing ...
Lectures: Recitations:
TR 1:00 -2:30 PM W 4:00 - 5:00 PMRm. 6-120 Rm. 26-204
Alexander van Oudenaarden Bernardo PandoRm. 13-2008 Rm. 13-2042avano@mit.edu bpando@mit.edu
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Take-home Exams:
Exam 1 due 10/03/06 15 %Exam 2 due 10/19/06 15 %Exam 3 due 11/02/06 15 %Exam 4 due 11/14/06 15 %Exam 5 due 11/28/06 15 %Final due 12/12/06 25 %
Final Problem Set will be a take-home PSbroadly covering the course material
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Text books: none
Handouts will be available on-line
Good reference (biology textbook):Molecular biology of the cellAlberts et al.
Matlab will be used intensively during thecourse, make sure you known (or learn) howto use it (necessary for problem sets)
Web-page: web.mit.edu/biophysics/sbio(contains all course materials)
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Intrinsic challenge of this class:
mixed audience with wildly different backgrounds
⇒ read up on your biology or math if needed
⇒ recitations (W 4PM, Rm. 26-204) are intended to close the gaps and prepare for homework
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Systems Biology ?
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Systems Biology ≈ Network Biology
GOAL: develop a quantitative understanding of the biological functionof genetic and biochemical networks
gene A
gene C
gene E
gene B
gene D
gene F
INPUT
OUTPUT
- function of gene product A-F can be known in detail but this is notsufficient to reveal the biological function of the INPUT-OUTPUT relation
- a system approach (looking beyond one gene/protein) is necessary toreveal the biological function of this whole network
- what is the function of the individual interactions (feedbacks andfeedforwards) in the context of the entire network ? 8
Three levels of complexity
I Systems Microbiology (~14 Lectures)
‘The cell as a well-stirred biochemical reactor’
II Systems Cell Biology (~8 Lectures)
‘The cell as a compartmentalized system withconcentration gradients’
III Systems Developmental Biology (~3 Lectures)
‘The cell in a social context communicating withneighboring cells’
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I Systems Microbiology (14 Lectures)
‘The cell as a well-stirred biochemical reactor’
L1 IntroductionL2 Chemical kinetics, Equilibrium binding, cooperativityL3 Lambda phageL4 Stability analysisL5-6 Genetic switchesL7 E. coli chemotaxisL8 Fine-tuned versus robust modelsL9 Receptor clusteringL10-11 Stochastic chemical kineticsL12-13 Genetic oscillatorsL14 Circadian rhythms
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I Systems Microbiology (14 Lectures)
‘The cell as a well-stirred biochemical reactor’
L1 IntroductionL2 Chemical kinetics, Equilibrium binding, cooperativityL3 Lambda phageL4 Stability analysisL5-6 Genetic switchesL7 E. coli chemotaxisL8 Fine-tuned versus robust modelsL9 Receptor clusteringL10-11 Stochastic chemical kineticsL12-13 Genetic oscillatorsL14 Circadian rhythms
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Introduction phage biology
Excellent book:
A genetic switch by Mark Ptashne
Phage genome:48512 base pairs ~ 12 kB‘phage.jpg’ ~ 10 kB
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The central dogma defines three major groups of biomolecules (biopolymers):
1. DNA (passive library, 6×109 bp, 2 m/cell,75×1012 cells/human, total length150×1012 m/human ~ 1000 rsun-earth)
2. RNA (‘passive’ intermediate)3. Proteins (active work horses)
The fourth (and final) group consists ofso-called ‘small molecules’.
4. Small molecules (sugars, hormones,vitamines, ‘substrates’ etc.)
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The lysis-lysogeny decision:
As the phage genome is injectedphage genes are transcribed andtranslated by using the host’smachinery.
Which set of phage proteins areexpressed determines the fate of thephage: lysis or lysogeny
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The lysis-lysogeny decision is a genetic switch
RNAp RNAp
only ‘space’ for one RNA polymerase (mutual exclusion)16
Single repressor dimer bound - three cases:
I Negative control, dimer binding to OR2 inhibitsRNAp binding to right PR promoter.
Positive control, dimer binding to OR2 enhancesRNAp binding to left PRM promoter.
cI transcript
more repressor monomers
more repressor dimers
inhibition
activation
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II Negative control, dimer binding to OR1 inhibitsRNAp binding to right PR promoter.
Negative control, dimer binding to OR1 inhibitsRNAp binding to left PRM promoter (too distant).
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III Negative control, dimer binding to OR3 inhibitsRNAp binding to left PRM promoter.
Positive control, dimer binding to OR3 allowsRNAp binding to right PR promoter.
Cro transcript
more Cro monomers
more Cro dimers
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Repressor-DNA binding is highly cooperative
intrinsic association constants:KOR1 ~ 10 KOR2 ~ 10 KOR3
However KOR2* >> KOR2 (positive cooperativity)
cI OFF Cro OFF
cI ON
cI OFF
Cro OFF
Cro OFF20
Flipping the switch by UV:
In lysogenic state, [repressor]is maintained at constant levelby negative feedback(“chemo-stat”)
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UV radiation induces SOS response (DNA damage)protein RecA becomes specific protease for λ repressor
after cleavage monomers cannot dimerize anymore,[repressor dimers] decreases,when all repressors vacate DNA, Cro gene switches on.
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other lytic genes
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Cooperative effects make sharp switch(‘well defined’ decision)
Note: several layers of cooperativity:dimerization, cooperative repressor binding
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I Systems Microbiology (14 Lectures)
‘The cell as a well-stirred biochemical reactor’
L1 IntroductionL2 Chemical kinetics, Equilibrium binding, cooperativityL3 Lambda phageL4 Stability analysisL5-6 Genetic switchesL7 E. coli chemotaxisL8 Fine-tuned versus robust modelsL9 Receptor clusteringL10-11 Stochastic chemical kineticsL12-13 Genetic oscillatorsL14 Circadian rhythms
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The Flagellum
> 40 genes involved
1000 H+ / rotation
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Absence of chemical attractant
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Presence of chemical attractant
chemical gradient sensed in a temporal manner30
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Chemotaxis of Escherichia coli
CW rotation: ‘tumbles’CCW rotation: ‘runs’
absence aspartate gradient random walk (diffusion)presence aspartate gradient biased random walk towards
aspartate source
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Chemotactic pathway in E. coli.
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Correlation of receptor methylation with behavioral response.
Adaptation:
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fast
slowinterm
ediate
What is the simplest mathematical modelthat is consistent with the biology andreproduces the experiments ?
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I Systems Microbiology (14 Lectures)
‘The cell as a well-stirred biochemical reactor’
L1 IntroductionL2 Chemical kinetics, Equilibrium binding, cooperativityL3 Lambda phageL4 Stability analysisL5-6 Genetic switchesL7 E. coli chemotaxisL8 Fine-tuned versus robust modelsL9 Receptor clusteringL10-11 Stochastic chemical kineticsL12-13 Genetic oscillatorsL14 Circadian rhythms
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37Kondo et al. PNAS (1994) 38
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The circadian clock consists of only 3 proteins:KaiA, KaiB and KaiC
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Circadian Oscillations inSingle Cells
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The circadian clock consists of only 3 proteins and can bereconstituted in vitro
Kondo et al. (2005) 42
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Modeling the cell cycle
45http://www.mpf.biol.vt.edu/research/budding_yeast_model 46
II Systems Cell Biology (8 Lectures)
‘The cell as a compartmentalized system withconcentration gradients’
L15 Diffusion, Fick’s equations, boundary and initial conditionsL16 Local excitation, global inhibition theoryL17-18 Models for eukaryotic gradient sensingL19-20 Center finding algorithmsL21-22 Modeling cytoskeleton dynamics
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II Systems Cell Biology (8 Lectures)
‘The cell as a compartmentalized system withconcentration gradients’
L15 Diffusion, Fick’s equations, boundary and initial conditionsL16 Local excitation, global inhibition theoryL17-18 Models for eukaryotic gradient sensingL19-20 Center finding algorithmsL21-22 Modeling cytoskeleton dynamics
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Eukaryotic Chemotaxis
How is this different from E. coli chemotaxis ?
temporal versus spatial sensing
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cyclic AMP (cAMP) is an attractantfor Dictyostelium (social amoeba)
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cyclic AMP (cAMP) is an attractantfor Dictyostelium (social amoeba)
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uniform step in cAMP
cAMP gradient
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Response of Dictyostelium to cAMP
initialdistributiont ~ 3 s
steady-statedistributiont ∞
uniform stepin cAMP
uniform and transient polarized and persistent
cAMP gradient
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Response of Dictyostelium to pulsed cAMP
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geometry of cell: circularinside cytoplasm: well-stirredinside membrane: diffusion-limited
GFP-PH binds special lipids in membrane:PIP2 and PIP3
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The molecules in the model:
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II Systems Cell Biology (8 Lectures)
‘The cell as a compartmentalized system withconcentration gradients’
L15 Diffusion, Fick’s equations, boundary and initial conditionsL16 Local excitation, global inhibition theoryL17-18 Models for eukaryotic gradient sensingL19-20 Center finding algorithmsL21-22 Modeling cytoskeleton dynamics
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how to find the middle ofa cell ?
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Most of MinE accumulates at the rim of this tube, in the shapeof a ring (the E ring). The rim of the MinC/D tube andassociated E ring move from a central position to the cellpole until both the tube and ring vanish. Meanwhile, a newMinC/D tube and associated E ring form in the opposite cellhalf, and the process repeats, resulting in a pole-to-poleoscillation cycle of the division inhibitor.A full cycle takes about 50 s.
minEminC/D
59gfp-minC
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GFP-minD
61gfp-minE is localizedin a ring
minEminD
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gfp-minE
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Recent results demonstratethat the min proteins assemble in
helices
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II Systems Cell Biology (8 Lectures)
‘The cell as a compartmentalized system withconcentration gradients’
L15 Diffusion, Fick’s equations, boundary and initial conditionsL16 Local excitation, global inhibition theoryL17-18 Models for eukaryotic gradient sensingL19-20 Center finding algorithmsL21-22 Modeling cytoskeleton dynamics
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Center finding in an eukaryotic cell: fission yeastThe importance of the cytoskeleton
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Microtubules
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Microtubules
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kinesin is a molecular motor that runs to the plus end of a MT72
dynein is a molecular motor that runs to the minus end of a MT
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Black tetra
Movies !74
III Systems Developmental Biology (3 Lectures)
‘The cell in a social context communicating withneighboring cells’
L23 Quorum sensingL24-25 Drosophila development
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III Systems Developmental Biology (3 Lectures)
‘The cell in a social context communicating withneighboring cells’
L23 Quorum sensingL24-25 Drosophila development
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major advantage ofDrosphila:
each stripe in theembryo correspondsto certain body partsin adult fly
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egg (contains maternal components,maternal effects, onlydetermined by mother)
zygote (contains DNAfrom father and mother,zygotic effects)
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nuclei formplasma membrane
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radioactive labeled RNA reveals localizationat pole
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interpreting the bicoid gradient (createdby maternal effects) by zygotic effect(gene expression by embryo itself)
hunchback is a zygotic effect !
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hunchback readsthe bicoid gradient
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Center finding in the Drosophila embryo
bicoid
hunchback86
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I Systems Microbiology (14 Lectures)
‘The cell as a well-stirred biochemical reactor’
L1 IntroductionL2 Chemical kinetics, Equilibrium binding, cooperativityL3 Lambda phageL4 Stability analysisL5-6 Genetic switchesL7 E. coli chemotaxisL8 Fine-tuned versus robust modelsL9 Receptor clusteringL10-11 Stochastic chemical kineticsL12-13 Genetic oscillatorsL14 Circadian rhythms