Stochastic simulations!

Size: px
Start display at page:

Download "Stochastic simulations!"

Transcription

1 Stochastic simulations! Application to biomolecular networks! Literature overview

2

3

4 Noise in genetic networks! Origins! How to measure the noise and distinguish between the two sources of noise (intrinsic vs extrinsic)?! What are the molecular processes that produce the most of noise?"! Consequences! How is the noise propagated in gene networks?! How does the noise affect the cellular behavior?!! Control! What are the cellular mechanisms that confer robustness to noise?!

5 Papers! Stochasticity gene expression in a single cell!!elowitz, Levine, Siggia, Swain (2002) Science 297: ! Regulation of noise in the expression of a single gene!!ozdudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Control of stochasticity in eukaryotic gene expression!!raser, O'Shea (2004) Science 304: ! Noise in eukaryotic gene expression!!blake, Kaern, Cantor, Collins (2003) Nature 422: !! Gene regulation at the single-cell level!!rosenfeld, Young, Alon, Swain, Elowitz (2005) Science 307: ! Stochastic kinetic analysis of a developmental pathway bifurcation in phage-λ E. coli cell!!arkin, Ross, McAdams (1998) Genetics 149: ! Multistability in the lactose utilization network of E. coli!!ozbudak, Thaittai, Lim, Shraiman, van Oudenaarden (2004) Nature 427: ! Noise propagation in gene networks!!pedraza, van Oudenaarden (2005) Science 307: !! Ultrasensitivity and noise propagation in a synthetic transcriptional cascade!!hooshangi, Thilberge, Weiss (2005) PNAS 102: ! Engineering stability in gene networks by autoregulation!!becskei, Serrano (2000) Nature 405: 590-3! Design principles of a bacterial signalling network!!kollmann, Lodvok, Bartholomé, Timmer, Sourjik (2005) Nature 438: !

6 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Abstract Clonal populations of cells exhibit substantial phenotypic variation. Such heterogeneity can be essential for many biological processes and is conjectured to arise from stochasticity, or noise, in gene expression. We constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated. Both stochasticity inherent in the biochemical process of gene expression (intrinsic noise) and fluctuations in other cellular components (extrinsic noise) contribute substantially to overall variation. Transcription rate, regulatory dynamics, and genetic factors control the amplitude of noise. These results establish a quantitative foundation for modeling noise in genetic networks and reveal how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.

7 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Goals measuring the noise at the level of single cells discriminate between the intrinsic and extrinsic noise identify genetic factors that control the magnitude of noise E. coli Definitions intrinsic noise: inherent stochasticity of biochemical processes extrinsic noise: fluctuation in other cellular components (number of ribosomes, polymerase, transcriptional regulators, etc): global to a single cell but varies from cell to cell.

8 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Methodology: built strains of Escherichia coli, incorporating the distinguishable cyan (cfp) and yellow (yfp) alleles of green fluorescent protein in the chromosome. Double reporter construction! In each strain, the two reporter genes were controlled by identical promoters. To avoid systematic differences in copy number, the genes are inserted at loci equidistant from, and on opposite sides of the origin of replication. The two fluorescent proteins exhibited statistically equivalent intensity distributions and thus displayed the necessary independence and equivalence to detect noise. Experiment in E. coli! To assess the effect of the strength of the promotor on the level of noise, they use artificial lac repressible promoters: IPTG - laci repressor

9 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Intrinsic vs extrinsic noise no intrinsic noise, only extrinsic noise (A) In absence of intrinsic noise, the 2 fluorescence proteins fluctuate in a correlated manner over time. Thus in each cell the level of the two proteins is equal and appears in yellow (red+green). both intrinsic and extrinsic noise (B) Due to intrinsic noise, the expressin of the 2 proteins become uncorrelated. In this case, at a given time point, some cells will express more one protein (red) and other the other protein (green). This results in a heterogeneous cell population.

10 Stochastic gene expression in a single cell!! Elowitz, Levine, Siggia, Swain (2002) Science 297: Results WT + laci (repressed) WT + laci + IPTG (derepressed) WT + ΔRecA + laci + IPTG no intrinsic noise, only extrinsic noise both intrinsic and extrinsic noise! Control of gene expression another WT + laci LacI deleted LacI under the control of the repressilator

11 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Quantification of noise The amount of a given protein varies from cell to cell Noise strength defined as: η = variance (gene expression) mean (gene expression) = σ x 2 < x > Orthogonal contributions: η tot 2 = η int 2 + η ext 2 M22 = quite strain (wild type)" D22 = noisy strain (deletion of reca gene)"

12 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! M22 wild type! Quantification of noise D22 fully induced" (no LacI repressor)" ΔrecA! These results show that: the contribution of extrinsic noise is larger than the contribution of intrinsic noise and suggest that: the level of noise is controlled: - by expression level - by genetic background Expression level controled by IPTG

13 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Experiments with various genetic backgrounds The level of noise is similar in most strains, but one, D22, which displays about 2x the amount of noise. This is due to the deletion of the RecA gene, involved in DNA repair.

14 Stochastic gene expression in a single cell! Elowitz, Levine, Siggia, Swain (2002) Science 297: ! Conclusions Using a two-reporter method, it is possible to measure and to distinguish extrinsic vs intrinsic noise. The relative contributions of extrinsic and intrinsic components to the total noise vary with expression level, but the contribution of extrinsic noise is usually much larger than the contribution of intrinsic noise. An increase of noise may arise from transient copy number differences between parts of the chromosomes (cf. increase of noise in ΔRecA mutant). The stochastic nature of gene expression gives rise to noise in protein levels, and hence creates heterogeneity in a clonal population. For the theory see: Swain, Elowitz, Siggia (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. PNAS 99: "

15 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Abstract Stochastic mechanisms are ubiquitous in biological systems. Biochemical reactions that involve small numbers of molecules are intrinsically noisy, being dominated by large concentration fluctuations. This intrinsic noise has been implicated in the random lysis/lysogeny decision of bacteriophage-lambda, in the loss of synchrony of circadian clocks and in the decrease of precision of cell signals. We sought to quantitatively investigate the extent to which the occurrence of molecular fluctuations within single cells (biochemical noise) could explain the variation of gene expression levels between cells in a genetically identical population (phenotypic noise). We have isolated the biochemical contribution to phenotypic noise from that of other noise sources by carrying out a series of differential measurements. We varied independently the rates of transcription and translation of a single fluorescent reporter gene in the chromosome of Bacillus subtilis, and we quantitatively measured the resulting changes in the phenotypic noise characteristics. We report that of these two parameters, increased translational efficiency is the predominant source of increased phenotypic noise. This effect is consistent with a stochastic model of gene expression in which proteins are produced in random and sharp bursts. Our results thus provide the first direct experimental evidence of the biochemical origin of phenotypic noise, demonstrating that the level of phenotypic variation in an isogenic population can be regulated by genetic parameters.

16 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Goals quantify the relative contribution of transcription and translation to noise B. subtilis assess the effect of efficiency of transcription and translation to noise measure fluorescent reporter gene at single cell level in Bacillus subtilis develop a stochastic model of gene expression

17 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Methodology Experiment in bacillus subtilis = expression level Translational and transcriptional mutants

18 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! translational mutants transcriptional mutants translational + transcriptional mutants

19 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Theoretical model! mrna protein average number of proteins synthesized per mrna transcript low transcription rate high translation rate => high variability mean level of protein and standard deviation (noise) high transcription rate low translation rate => low variability

20 Regulation of noise in the expression of a single gene! Ozbudak, Thattai, Kurtser, Grossman, van Oudenaarden (2002) Nat Genet 31: 69-73! Conclusions By genetic mutations, it is possible to control transcription and translation efficiency and to study the relative contribution of these two processes to the noise. Both experiments and theory shows that noise strength is more sensitive to variation in translational efficiency than to the rate of transcription This led the authors to suggest that fast transcription followed by inefficient translation results in lower noise in protein levels. The control of noise comes at the energetic cost of producing few proteins from numerous mrna. high noise" low noise" Fig. from Raser & O'Shea (2005)" For additional theoretical results see: Thattai, van Oudenaarden (2002) Intrinsic noise in gene regulatory networks. PNAS 98: "

21 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Abstract Noise, or random fluctuations, in gene expression may produce variability in cellular behavior. To measure the noise intrinsic to eukaryotic gene expression, we quantified the differences in expression of two alleles in a diploid cell. We found that such noise is gene-specific and not dependent on the regulatory pathway or absolute rate of expression. We propose a model in which the balance between promoter activation and transcription influences the variability in messenger RNA levels. To confirm the predictions of our model, we identified both cis- and trans-acting mutations that alter the noise of gene expression. These mutations suggest that noise is an evolvable trait that can be optimized to balance fidelity and diversity in eukaryotic gene expression.

22 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Goals measure noise in eukaryots (yeast) at the single cell level. S. cerevisiae assess gene and regulatory specificity (experiments with different promoters) develop a model for gene expression

23 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Double reporter construction! Experiment in S. cerevisiae! use a similar methodology as Elowitz et al (2002). construct diploid strains that express both cyan and yellow fluorescence proteins from identical promoters (Here is shown PHO5 which is controlled by the level of phosphate, Pi). The 2 reporter genes are inserted at the same locus on homologous chromosomes.

24 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! time after Pi starvation YFP (red) and CFP (green) fluorescence micrographs YFP and CFP values for each cell during a time course after induction of PHO5 by phosphate starvation. time Total, extrinsic, and intrinsic noise strength as a function of the population mean These results show that extrinsic noise is the dominant source of noise. (as reported for bacteria by Elowitz et al 2002)

25 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! ADH1! Experiments with different promoters:! total ( extrinsic) noise! The level of total noise ( extrinsic noise) does not depend on the promoter. PHO84! Origin of extrinsic noise: GAL1! cell size? cell shape? PHO84! => use flow cytometry to isolate subpopulations of cells that are homogeneous in size and shape => found that extrinsic noise is a bit decreased but still the dominant source of noise.

26 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! GAL1! Experiment with different promoters:! intrinsic noise! PHO84! GAL1 promoter! PHO84 promoter" PHO5 promoter! controled by Gal4p" controled by the same activator (Pho4p)" Observation! PHO5" GAL1 promoter" PHO84 promoter" PHO5 promoter" low intrinsic noise" large intrinsic noise at low epression rate" The level of intrinsic noise depends on the promoter and on the expression rate.

27 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Theoretical model!! Comparison of various models of gene activation! Numerical simulations done with the Gillespie algorithm Slow promoter activation/deactivation, fast transcription Ex: slow chromatin remodeling Slow activation/ fast deactivation, fast transcription Ex: nucleosome sliding, DNA looping Fast promoter activation/deactivation, slow transcription Ex: rapid binding/unbinding of a transcriptional activator

28 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Theoretical model!! Comparison of various models of gene activation! The noise strength profile of PHO5 is similar to the prediction made for case I (see panel D) when the promoter activation rate is changed (see green curve)." " Prediction:" The noise generation in PHO5 is dependent on the rate of a slow upstream promoter transition."! Predicted consequences! - a decrease of transcriptional efficiency (k m ) leads to a reduction of the noise." - a decrease of promoter activation (k a ) leads to an increase of the noise. "

29 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! complexes involved in chromatin remodeling transcription efficiency mutations in UAS mutations in snf6, arp8, gcn mutations in TATA box This confirms that a decrease of promoter activation (k a ) leads to an increase of the noise." This confirms that a decrease transcriptional efficiency (k m ) leads to a reduction of the noise."

30 Control of stochasticity in eukaryotic gene expression! Raser, O'Shea (2004) Science 304: ! Conclusions The two-reporter technique used by Elowitz et al (2002) to distinguish intrinsic and extrinsic noise in bacteria can be applied to eukaryots (here: yeast). Extrinsic noise is predominant over intrinsic noise. Total noise ( extrinsic) is not gene-specific, but intrinsic noise is gene-specific. high noise" low noise" Intrinsic noise does not depend on the regulatory pathway, neither on absolute rate of expression. Fig. from Raser & O'Shea (2005)" Intrinsic noise depends on the rate of a slow upstream promoter transition, such as chromatin remodeling

31 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Abstract Transcription in eukaryotic cells has been described as quantal, with pulses of messenger RNA produced in a probabilistic manner. This description reflects the inherently stochastic nature of gene expression, known to be a major factor in the heterogeneous response of individual cells within a clonal population to an inducing stimulus. Here we show in Saccharomyces cerevisiae that stochasticity (noise) arising from transcription contributes significantly to the level of heterogeneity within a eukaryotic clonal population, in contrast to observations in prokaryotes, and that such noise can be modulated at the translational level. We use a stochastic model of transcription initiation specific to eukaryotes to show that pulsatile mrna production, through reinitiation, is crucial for the dependence of noise on transcriptional efficiency, highlighting a key difference between eukaryotic and prokaryotic sources of noise. Furthermore, we explore the propagation of noise in a gene cascade network and demonstrate experimentally that increased noise in the transcription of a regulatory protein leads to increased cell-cell variability in the target gene output, resulting in prolonged bistable expression states. This result has implications for the role of noise in phenotypic variation and cellular differentiation.

32 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Goals assess the contribution of transcriptional noise to the heterogeneity of a clonal population examine the pulsatile nature of mrna production and the transcriptional efficiency explore the propagation of noise in a gene cascade network develop a model for gene expression

33 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Experiment in S. cerevisiae! Genetic construction with 2 transcriptional controls: fluorescence GAL (direct activator) and ATc (inhibitor of the TetR inhibitor) Transient response Time induction by 0.2% gal Inductions by GAL or ATc induce differential responses. induction by 40 ng /ml ATc The mode of transcriptional control has a significant influence on the response to the inducer and on the level of noise.

34 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Experiment: effect of transcriptional and translational efficiency on the noise! 28% transcription full transcription Controled by ATc or GAL Controled by mutation in codons (by keeping the same aa sequence) The level of noise in eukaryotic gene expression is influenced by transcription and by the mode of transcriptional regulation

35 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Stochastic model for eukaryotic transcription! reinitiation PC1 = inactive (or silenced) promoter PC2 = intermediate complex (TBP + some TF bound) PC3 = preinitiation complex (TBP + all TF bound) RC1 & RC2 = different repressed promoter configurations Numerical simulations done with the Gillespie algorithm proba to produce a transcript is constant ATc (k 3f is ATc-dependent) GAL (k 1f and k 1b are GAL-dependent) Simulations of the model demonstrate that pulsatile mrna production (resulting from transcriptional reinitiation) is required to reproduce the experimental observations.

36 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Experiment: cascading noise in a gene network! fluorescence level of noise at P GAL10 high level of noise low level of noise level of noise at P ADH1 induction by high level of atc low level of noise high level of noise induction by low level of atc Downstream effects of noise can have profound phenotypic consequences, drastically affecting the stability of gene expression

37 Noise in eukaryotic gene expression! Blake, Kaern, Cantor, Collins (2003) Nature 422: ! Conclusions In eukaryots, the mode of transcriptional control can have a marked effect on the response to the noise. In eukaryots, noise arising from transcription contributes more than noise generated at the translational level (in contrast to observations in prokaryots - cf. Ozdudak et al, 2002). Downstream effects of noise can have profound phenotypic consequences, drastically affecting the stability of gene expression.

38 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Abstract The genetic and biochemical networks which underlie such things as homeostasis in metabolism and the developmental programs of living cells, must withstand considerable variations and random perturbations of biochemical parameters. These occur as transient changes in, for example, transcription, translation, and RNA and protein degradation. The intensity and duration of these perturbations differ between cells in a population. The unique state of cells, and thus the diversity in a population, is owing to the different environmental stimuli the individual cells experience and the inherent stochastic nature of biochemical processes (for example, refs 5 and 6). It has been proposed, but not demonstrated, that autoregulatory, negative feedback loops in gene circuits provide stability, thereby limiting the range over which the concentrations of network components fluctuate. Here we have designed and constructed simple gene circuits consisting of a regulator and transcriptional repressor modules in Escherichia coli and we show the gain of stability produced by negative feedback.

39 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Role of auto-regulations in genetic networks: Model and simulation Evolution equation unregulated free promoter RNA pol k b G + P D G* k a "active" gene k p =k a /k b auto-regulated k b G + P D G* k a k p =k a /k b In these equations, k I is the promoter isomerization rate (i.e. fraction of promoter that can be transcribed?), a is the proportionality constant between the mrna and protein concentration, n is the gene copy number, and k deg is the degradation rate These equations are obtained by applying the quasi-steady state assumption on the binding/unbinding steps of RNA polymerase (P) and of the repressor (R) to the gene promoter (G) and by assuming that G+G*+G R =1. G + R D G R free promoter inhibitor k u k b "inactive" gene k r =k b /k u

40 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Role of auto-regulations in genetic networks: Model and simulation Evolution equation Stability analysis Stochastic simulation are carried out by applied random perturbation at constant time intervals. A stochastic simulation using for ex. the Gillespie algorithm would have been more appropriate...

41 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Role of auto-regulations in genetic networks: Experiment in E. coli Auto-regulatory system P TetR - TetR - GFP construction Here, the TetR repressor is mutated (Y42A) in the DNA binding domain. Here, the TetR binding sites have been replaced by the LacI binding sites. Noise can be attenuated by negative auto-regulation

42 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Role of auto-regulations in genetic networks: Experiment in E. coli Time course after induction (by different concentrations of atc) High variability is observed in both short and long term after induction

43 Engineering stability in gene networks by autoregulation! Becskei, Serrano (2000) Nature 405: 590-3! Conclusions Negative feedback loops in gene circuits (and autoregulation in particular) provide stability (robustness to noise). The experimental results obained here are consistent with the prediction of a simple model of gene expression. (It would however be interesting to run "real" high noise" low noise" stochastic simulations of the same model...) Fig. from Raser & O'Shea (2005)"

44 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade! Hooshangi, Thilberge, Weiss (2005) PNAS 102: ! Abstract The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic networks. Here, we report the construction of synthetic transcriptional cascades comprising one, two, and three repression stages. These model systems enable us to analyze sensitivity and noise propagation as a function of network complexity. We demonstrate experimentally steady-state switching behavior that becomes sharper with longer cascades. The regulatory mechanisms that confer this ultrasensitive response both attenuate and amplify phenotypical variations depending on the system's input conditions. Although noise attenuation allows the cascade to act as a low-pass filter by rejecting short-lived perturbations in input conditions, noise amplification results in loss of synchrony among a cell population. The experimental results demonstrating the above network properties correlate well with simulations of a simple mathematical model of the system.

45 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade! Hooshangi, Thilberge, Weiss (2005) PNAS 102: ! Experiment in E. coli: construction of 3 synthetic transcriptional cascades: atc = inducer = control parameter, prevents the repression by tetr

46 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade! Hooshangi, Thilberge, Weiss (2005) PNAS 102: ! (circuit 1) (circuit 2) (circuit 3) Experiment Experiment Model (3) (1) (2) (3) (2) (1) The noise is more marked during the transition, especially in circuit (3). Longer cascade amplify cell-to-cell variability in the intermediate regions.

47 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade! Hooshangi, Thilberge, Weiss (2005) PNAS 102: ! What is the role of long cascades? Delay in the response Low-pass filter: response to long-pulse pertubation (1) atc added (3) atc (2) short-pulse perturbation 5 min (2) (1) (3) atc removed (1) (2) long-pulse perturbation (1) (2) atc 45 min (3) (3)

48 Ultrasensitivity and noise propagation in a synthetic transcriptional cascade! Hooshangi, Thilberge, Weiss (2005) PNAS 102: ! Conclusions Noise (and consequently cell-to-cell variability) is amplified at transition in long cascades. Synchronization of cell responses is diminished for longer cascades. Long cascade can induce delay in the response Long cascade act as low pass-filter => Trade-off between robustness to noise and function The results are consistent with the prediction of a simple mathematical model

49 ...much work must be done to understand how cellular processes behave robustly in the presence of underlying stochasticity. Such work often requires a non-traditional collaboration between mathematicians, physicists, and in vivo experimentalists

50 References! Raj A, Van Oudenaarden A (2008) Nature, nurture, or chance: stochastic gene expression and its consequences, Cell 135:216 Äì26. Sanchez A, Golding I (2013) Genetic determinants and cellular constraints in noisy gene expression. Science. 342: Eldar A, Elowitz MB (2010) Functional roles for noise in genetic circuits. Nature. 467: Raser JM, O'Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309: Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 6: Munsky B, Neuert G, van Oudenaarden A (2012) Using gene expression noise to understand gene regulation. Science. 336:183-7.

Stochastic simulations

Stochastic simulations Stochastic simulations Application to molecular networks Literature overview Noise in genetic networks Origins How to measure and distinguish between the two types of noise (intrinsic vs extrinsic)? What

More information

the noisy gene Biology of the Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB)

the noisy gene Biology of the Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB) Biology of the the noisy gene Universidad Autónoma de Madrid Jan 2008 Juan F. Poyatos Spanish National Biotechnology Centre (CNB) day III: noisy bacteria - Regulation of noise (B. subtilis) - Intrinsic/Extrinsic

More information

STOCHASTICITY IN GENE EXPRESSION: FROM THEORIES TO PHENOTYPES

STOCHASTICITY IN GENE EXPRESSION: FROM THEORIES TO PHENOTYPES STOCHASTICITY IN GENE EXPRESSION: FROM THEORIES TO PHENOTYPES Mads Kærn*, Timothy C. Elston, William J. Blake and James J. Collins Abstract Genetically identical cells exposed to the same environmental

More information

2. Mathematical descriptions. (i) the master equation (ii) Langevin theory. 3. Single cell measurements

2. Mathematical descriptions. (i) the master equation (ii) Langevin theory. 3. Single cell measurements 1. Why stochastic?. Mathematical descriptions (i) the master equation (ii) Langevin theory 3. Single cell measurements 4. Consequences Any chemical reaction is stochastic. k P d φ dp dt = k d P deterministic

More information

Stochastic dynamics of small gene regulation networks. Lev Tsimring BioCircuits Institute University of California, San Diego

Stochastic dynamics of small gene regulation networks. Lev Tsimring BioCircuits Institute University of California, San Diego Stochastic dynamics of small gene regulation networks Lev Tsimring BioCircuits Institute University of California, San Diego Nizhni Novgorod, June, 2011 Central dogma Activator Gene mrna Protein Repressor

More information

A synthetic oscillatory network of transcriptional regulators

A synthetic oscillatory network of transcriptional regulators A synthetic oscillatory network of transcriptional regulators Michael B. Elowitz & Stanislas Leibler, Nature, 403, 2000 igem Team Heidelberg 2008 Journal Club Andreas Kühne Introduction Networks of interacting

More information

Measuring TF-DNA interactions

Measuring TF-DNA interactions Measuring TF-DNA interactions How is Biological Complexity Achieved? Mediated by Transcription Factors (TFs) 2 Regulation of Gene Expression by Transcription Factors TF trans-acting factors TF TF TF TF

More information

Introduction. Gene expression is the combined process of :

Introduction. Gene expression is the combined process of : 1 To know and explain: Regulation of Bacterial Gene Expression Constitutive ( house keeping) vs. Controllable genes OPERON structure and its role in gene regulation Regulation of Eukaryotic Gene Expression

More information

Lecture 7: Simple genetic circuits I

Lecture 7: Simple genetic circuits I Lecture 7: Simple genetic circuits I Paul C Bressloff (Fall 2018) 7.1 Transcription and translation In Fig. 20 we show the two main stages in the expression of a single gene according to the central dogma.

More information

Chapter 15 Active Reading Guide Regulation of Gene Expression

Chapter 15 Active Reading Guide Regulation of Gene Expression Name: AP Biology Mr. Croft Chapter 15 Active Reading Guide Regulation of Gene Expression The overview for Chapter 15 introduces the idea that while all cells of an organism have all genes in the genome,

More information

Multistability in the lactose utilization network of Escherichia coli

Multistability in the lactose utilization network of Escherichia coli Multistability in the lactose utilization network of Escherichia coli Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J. Ruby Abrams Agenda Motivation Intro to multistability Purpose

More information

Progress in Biophysics and Molecular Biology

Progress in Biophysics and Molecular Biology Progress in Biophysics and Molecular Biology 100 (2009) 57 66 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio

More information

56:198:582 Biological Networks Lecture 8

56:198:582 Biological Networks Lecture 8 56:198:582 Biological Networks Lecture 8 Course organization Two complementary approaches to modeling and understanding biological networks Constraint-based modeling (Palsson) System-wide Metabolism Steady-state

More information

REVIEW SESSION. Wednesday, September 15 5:30 PM SHANTZ 242 E

REVIEW SESSION. Wednesday, September 15 5:30 PM SHANTZ 242 E REVIEW SESSION Wednesday, September 15 5:30 PM SHANTZ 242 E Gene Regulation Gene Regulation Gene expression can be turned on, turned off, turned up or turned down! For example, as test time approaches,

More information

Warm-Up. Explain how a secondary messenger is activated, and how this affects gene expression. (LO 3.22)

Warm-Up. Explain how a secondary messenger is activated, and how this affects gene expression. (LO 3.22) Warm-Up Explain how a secondary messenger is activated, and how this affects gene expression. (LO 3.22) Yesterday s Picture The first cell on Earth (approx. 3.5 billion years ago) was simple and prokaryotic,

More information

Eukaryotic Gene Expression

Eukaryotic Gene Expression Eukaryotic Gene Expression Lectures 22-23 Several Features Distinguish Eukaryotic Processes From Mechanisms in Bacteria 123 Eukaryotic Gene Expression Several Features Distinguish Eukaryotic Processes

More information

The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective

The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective The Effect of Stochasticity on the Lac Operon: An Evolutionary Perspective Milan van Hoek *, Paulien Hogeweg Theoretical Biology/Bioinformatics Group, Utrecht University, Utrecht, The Netherlands The role

More information

Bi 8 Lecture 11. Quantitative aspects of transcription factor binding and gene regulatory circuit design. Ellen Rothenberg 9 February 2016

Bi 8 Lecture 11. Quantitative aspects of transcription factor binding and gene regulatory circuit design. Ellen Rothenberg 9 February 2016 Bi 8 Lecture 11 Quantitative aspects of transcription factor binding and gene regulatory circuit design Ellen Rothenberg 9 February 2016 Major take-home messages from λ phage system that apply to many

More information

CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON

CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON PROKARYOTE GENES: E. COLI LAC OPERON CHAPTER 13 CHAPTER 13 PROKARYOTE GENES: E. COLI LAC OPERON Figure 1. Electron micrograph of growing E. coli. Some show the constriction at the location where daughter

More information

Prokaryotic Regulation

Prokaryotic Regulation Prokaryotic Regulation Control of transcription initiation can be: Positive control increases transcription when activators bind DNA Negative control reduces transcription when repressors bind to DNA regulatory

More information

Name Period The Control of Gene Expression in Prokaryotes Notes

Name Period The Control of Gene Expression in Prokaryotes Notes Bacterial DNA contains genes that encode for many different proteins (enzymes) so that many processes have the ability to occur -not all processes are carried out at any one time -what allows expression

More information

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization.

3.B.1 Gene Regulation. Gene regulation results in differential gene expression, leading to cell specialization. 3.B.1 Gene Regulation Gene regulation results in differential gene expression, leading to cell specialization. We will focus on gene regulation in prokaryotes first. Gene regulation accounts for some of

More information

Cybergenetics: Control theory for living cells

Cybergenetics: Control theory for living cells Department of Biosystems Science and Engineering, ETH-Zürich Cybergenetics: Control theory for living cells Corentin Briat Joint work with Ankit Gupta and Mustafa Khammash Introduction Overview Cybergenetics:

More information

CS-E5880 Modeling biological networks Gene regulatory networks

CS-E5880 Modeling biological networks Gene regulatory networks CS-E5880 Modeling biological networks Gene regulatory networks Jukka Intosalmi (based on slides by Harri Lähdesmäki) Department of Computer Science Aalto University January 12, 2018 Outline Modeling gene

More information

Regulation of Gene Expression

Regulation of Gene Expression Chapter 18 Regulation of Gene Expression Edited by Shawn Lester PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley

More information

INVESTIGATION OF STOCHASTICITY IN GENE EXPRESSION IN RESPONSE TO OSMOTIC STRESS

INVESTIGATION OF STOCHASTICITY IN GENE EXPRESSION IN RESPONSE TO OSMOTIC STRESS INVESTIGATION OF STOCHASTICITY IN GENE EXPRESSION IN RESPONSE TO OSMOTIC STRESS By GAYATHRI BALANDARAM A thesis submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE

More information

Boulder 07: Modelling Stochastic Gene Expression

Boulder 07: Modelling Stochastic Gene Expression Boulder 7: Modelling Stochastic Gene Expression Peter Swain, Physiology, McGill University swain@cnd.mcgill.ca The whys and wherefores of stochasticity A system evolves stochastically if its dynamics is

More information

Noise is often perceived as being undesirable and unpredictable;

Noise is often perceived as being undesirable and unpredictable; Intrinsic noise in gene regulatory networks Mukund Thattai and Alexander van Oudenaarden* Department of Physics, Room 13-2010, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge,

More information

Prokaryotic Gene Expression (Learning Objectives)

Prokaryotic Gene Expression (Learning Objectives) Prokaryotic Gene Expression (Learning Objectives) 1. Learn how bacteria respond to changes of metabolites in their environment: short-term and longer-term. 2. Compare and contrast transcriptional control

More information

A Synthetic Oscillatory Network of Transcriptional Regulators

A Synthetic Oscillatory Network of Transcriptional Regulators A Synthetic Oscillatory Network of Transcriptional Regulators Michael Elowitz & Stanislas Leibler Nature, 2000 Presented by Khaled A. Rahman Background Genetic Networks Gene X Operator Operator Gene Y

More information

Induction Level Determines Signature of Gene Expression Noise in Cellular Systems

Induction Level Determines Signature of Gene Expression Noise in Cellular Systems Induction Level Determines Signature of Gene Expression Noise in Cellular Systems Julia Rausenberger Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany and Center for Biological

More information

Regulation of Gene Expression in Bacteria and Their Viruses

Regulation of Gene Expression in Bacteria and Their Viruses 11 Regulation of Gene Expression in Bacteria and Their Viruses WORKING WITH THE FIGURES 1. Compare the structure of IPTG shown in Figure 11-7 with the structure of galactose shown in Figure 11-5. Why is

More information

Biomolecular Feedback Systems

Biomolecular Feedback Systems Biomolecular Feedback Systems Domitilla Del Vecchio MIT Richard M. Murray Caltech Version 1.0b, September 14, 2014 c 2014 by Princeton University Press All rights reserved. This is the electronic edition

More information

CHAPTER : Prokaryotic Genetics

CHAPTER : Prokaryotic Genetics CHAPTER 13.3 13.5: Prokaryotic Genetics 1. Most bacteria are not pathogenic. Identify several important roles they play in the ecosystem and human culture. 2. How do variations arise in bacteria considering

More information

Multistability in the lactose utilization network of E. coli. Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J.

Multistability in the lactose utilization network of E. coli. Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J. Multistability in the lactose utilization network of E. coli Lauren Nakonechny, Katherine Smith, Michael Volk, Robert Wallace Mentor: J. Ruby Abrams Motivation Understanding biological switches in the

More information

Lecture 18 June 2 nd, Gene Expression Regulation Mutations

Lecture 18 June 2 nd, Gene Expression Regulation Mutations Lecture 18 June 2 nd, 2016 Gene Expression Regulation Mutations From Gene to Protein Central Dogma Replication DNA RNA PROTEIN Transcription Translation RNA Viruses: genome is RNA Reverse Transcriptase

More information

Bi 1x Spring 2014: LacI Titration

Bi 1x Spring 2014: LacI Titration Bi 1x Spring 2014: LacI Titration 1 Overview In this experiment, you will measure the effect of various mutated LacI repressor ribosome binding sites in an E. coli cell by measuring the expression of a

More information

Computational Cell Biology Lecture 4

Computational Cell Biology Lecture 4 Computational Cell Biology Lecture 4 Case Study: Basic Modeling in Gene Expression Yang Cao Department of Computer Science DNA Structure and Base Pair Gene Expression Gene is just a small part of DNA.

More information

Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Tuesday, December 27, 16

Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Tuesday, December 27, 16 Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Enduring understanding 3.B: Expression of genetic information involves cellular and molecular

More information

Stochastically driven genetic circuits

Stochastically driven genetic circuits Stochastically driven genetic circuits CHAOS 16, 026103 2006 L. S. Tsimring Institute for Nonlinear Science, University of California, San Diego, La Jolla, California 92093-0402 D. Volfson Institute for

More information

Modelling Stochastic Gene Expression

Modelling Stochastic Gene Expression Modelling Stochastic Gene Expression Peter Swain Centre for Systems Biology at Edinburgh University of Edinburgh peter.swain@ed.ac.uk The whys and wherefores of stochasticity A system evolves stochastically

More information

Controlling Gene Expression

Controlling Gene Expression Controlling Gene Expression Control Mechanisms Gene regulation involves turning on or off specific genes as required by the cell Determine when to make more proteins and when to stop making more Housekeeping

More information

32 Gene regulation, continued Lecture Outline 11/21/05

32 Gene regulation, continued Lecture Outline 11/21/05 32 Gene regulation, continued Lecture Outline 11/21/05 Review the operon concept Repressible operons (e.g. trp) Inducible operons (e.g. lac) Positive regulation of lac () Practice applying the operon concept

More information

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes

Chapter 16 Lecture. Concepts Of Genetics. Tenth Edition. Regulation of Gene Expression in Prokaryotes Chapter 16 Lecture Concepts Of Genetics Tenth Edition Regulation of Gene Expression in Prokaryotes Chapter Contents 16.1 Prokaryotes Regulate Gene Expression in Response to Environmental Conditions 16.2

More information

Name: SBI 4U. Gene Expression Quiz. Overall Expectation:

Name: SBI 4U. Gene Expression Quiz. Overall Expectation: Gene Expression Quiz Overall Expectation: - Demonstrate an understanding of concepts related to molecular genetics, and how genetic modification is applied in industry and agriculture Specific Expectation(s):

More information

Lecture 4: Transcription networks basic concepts

Lecture 4: Transcription networks basic concepts Lecture 4: Transcription networks basic concepts - Activators and repressors - Input functions; Logic input functions; Multidimensional input functions - Dynamics and response time 2.1 Introduction The

More information

Written Exam 15 December Course name: Introduction to Systems Biology Course no

Written Exam 15 December Course name: Introduction to Systems Biology Course no Technical University of Denmark Written Exam 15 December 2008 Course name: Introduction to Systems Biology Course no. 27041 Aids allowed: Open book exam Provide your answers and calculations on separate

More information

Promoter Sequence Determines the Relationship between Expression Level and Noise

Promoter Sequence Determines the Relationship between Expression Level and Noise Promoter Sequence Determines the Relationship between Expression Level and Noise Lucas. Carey 1., David van Dijk 1,3., Peter M. A. Sloot 2,3, Jaap A. Kaandorp 3, Eran Segal 1 * 1 Department of Computer

More information

REGULATION OF GENE EXPRESSION. Bacterial Genetics Lac and Trp Operon

REGULATION OF GENE EXPRESSION. Bacterial Genetics Lac and Trp Operon REGULATION OF GENE EXPRESSION Bacterial Genetics Lac and Trp Operon Levels of Metabolic Control The amount of cellular products can be controlled by regulating: Enzyme activity: alters protein function

More information

L3.1: Circuits: Introduction to Transcription Networks. Cellular Design Principles Prof. Jenna Rickus

L3.1: Circuits: Introduction to Transcription Networks. Cellular Design Principles Prof. Jenna Rickus L3.1: Circuits: Introduction to Transcription Networks Cellular Design Principles Prof. Jenna Rickus In this lecture Cognitive problem of the Cell Introduce transcription networks Key processing network

More information

Regulation of Gene Expression

Regulation of Gene Expression Chapter 18 Regulation of Gene Expression PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from

More information

Gene regulation I Biochemistry 302. Bob Kelm February 25, 2005

Gene regulation I Biochemistry 302. Bob Kelm February 25, 2005 Gene regulation I Biochemistry 302 Bob Kelm February 25, 2005 Principles of gene regulation (cellular versus molecular level) Extracellular signals Chemical (e.g. hormones, growth factors) Environmental

More information

Regulation of Transcription in Eukaryotes. Nelson Saibo

Regulation of Transcription in Eukaryotes. Nelson Saibo Regulation of Transcription in Eukaryotes Nelson Saibo saibo@itqb.unl.pt In eukaryotes gene expression is regulated at different levels 1 - Transcription 2 Post-transcriptional modifications 3 RNA transport

More information

GENE REGULATION AND PROBLEMS OF DEVELOPMENT

GENE REGULATION AND PROBLEMS OF DEVELOPMENT GENE REGULATION AND PROBLEMS OF DEVELOPMENT By Surinder Kaur DIET Ropar Surinder_1998@ yahoo.in Mob No 9988530775 GENE REGULATION Gene is a segment of DNA that codes for a unit of function (polypeptide,

More information

UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11

UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11 UNIT 6 PART 3 *REGULATION USING OPERONS* Hillis Textbook, CH 11 REVIEW: Signals that Start and Stop Transcription and Translation BUT, HOW DO CELLS CONTROL WHICH GENES ARE EXPRESSED AND WHEN? First of

More information

56:198:582 Biological Networks Lecture 9

56:198:582 Biological Networks Lecture 9 56:198:582 Biological Networks Lecture 9 The Feed-Forward Loop Network Motif Subgraphs in random networks We have discussed the simplest network motif, self-regulation, a pattern with one node We now consider

More information

4. Why not make all enzymes all the time (even if not needed)? Enzyme synthesis uses a lot of energy.

4. Why not make all enzymes all the time (even if not needed)? Enzyme synthesis uses a lot of energy. 1 C2005/F2401 '10-- Lecture 15 -- Last Edited: 11/02/10 01:58 PM Copyright 2010 Deborah Mowshowitz and Lawrence Chasin Department of Biological Sciences Columbia University New York, NY. Handouts: 15A

More information

Biology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall

Biology. Biology. Slide 1 of 26. End Show. Copyright Pearson Prentice Hall Biology Biology 1 of 26 Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 2 of 26 Gene Regulation: An Example Gene Regulation: An Example

More information

Welcome to Class 21!

Welcome to Class 21! Welcome to Class 21! Introductory Biochemistry! Lecture 21: Outline and Objectives l Regulation of Gene Expression in Prokaryotes! l transcriptional regulation! l principles! l lac operon! l trp attenuation!

More information

Genetic transcription and regulation

Genetic transcription and regulation Genetic transcription and regulation Central dogma of biology DNA codes for DNA DNA codes for RNA RNA codes for proteins not surprisingly, many points for regulation of the process DNA codes for DNA replication

More information

Bacterial Genetics & Operons

Bacterial Genetics & Operons Bacterial Genetics & Operons The Bacterial Genome Because bacteria have simple genomes, they are used most often in molecular genetics studies Most of what we know about bacterial genetics comes from the

More information

Regulation of gene expression. Premedical - Biology

Regulation of gene expression. Premedical - Biology Regulation of gene expression Premedical - Biology Regulation of gene expression in prokaryotic cell Operon units system of negative feedback positive and negative regulation in eukaryotic cell - at any

More information

Analog Electronics Mimic Genetic Biochemical Reactions in Living Cells

Analog Electronics Mimic Genetic Biochemical Reactions in Living Cells Analog Electronics Mimic Genetic Biochemical Reactions in Living Cells Dr. Ramez Daniel Laboratory of Synthetic Biology & Bioelectronics (LSB 2 ) Biomedical Engineering, Technion May 9, 2016 Cytomorphic

More information

Complete all warm up questions Focus on operon functioning we will be creating operon models on Monday

Complete all warm up questions Focus on operon functioning we will be creating operon models on Monday Complete all warm up questions Focus on operon functioning we will be creating operon models on Monday 1. What is the Central Dogma? 2. How does prokaryotic DNA compare to eukaryotic DNA? 3. How is DNA

More information

Prokaryotic Gene Expression (Learning Objectives)

Prokaryotic Gene Expression (Learning Objectives) Prokaryotic Gene Expression (Learning Objectives) 1. Learn how bacteria respond to changes of metabolites in their environment: short-term and longer-term. 2. Compare and contrast transcriptional control

More information

Slide 1 / 7. Free Response

Slide 1 / 7. Free Response Slide 1 / 7 Free Response Slide 2 / 7 Slide 3 / 7 1 The above diagrams illustrate the experiments carried out by Griffith and Hershey and Chaserespectively. Describe the hypothesis or conclusion that each

More information

Lecture 8: Temporal programs and the global structure of transcription networks. Chap 5 of Alon. 5.1 Introduction

Lecture 8: Temporal programs and the global structure of transcription networks. Chap 5 of Alon. 5.1 Introduction Lecture 8: Temporal programs and the global structure of transcription networks Chap 5 of Alon 5. Introduction We will see in this chapter that sensory transcription networks are largely made of just four

More information

Development Team. Regulation of gene expression in Prokaryotes: Lac Operon. Molecular Cell Biology. Department of Zoology, University of Delhi

Development Team. Regulation of gene expression in Prokaryotes: Lac Operon. Molecular Cell Biology. Department of Zoology, University of Delhi Paper Module : 15 : 23 Development Team Principal Investigator : Prof. Neeta Sehgal Department of Zoology, University of Delhi Co-Principal Investigator : Prof. D.K. Singh Department of Zoology, University

More information

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus:

Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: m Eukaryotic mrna processing Newly made RNA is called primary transcript and is modified in three ways before leaving the nucleus: Cap structure a modified guanine base is added to the 5 end. Poly-A tail

More information

Regulation and signaling. Overview. Control of gene expression. Cells need to regulate the amounts of different proteins they express, depending on

Regulation and signaling. Overview. Control of gene expression. Cells need to regulate the amounts of different proteins they express, depending on Regulation and signaling Overview Cells need to regulate the amounts of different proteins they express, depending on cell development (skin vs liver cell) cell stage environmental conditions (food, temperature,

More information

There has been considerable interest in the modeling and

There has been considerable interest in the modeling and Frequency domain analysis of noise in autoregulated gene circuits Michael L. Simpson, Chris D. Cox, and Gary S. Sayler Molecular Scale Engineering and Nanoscale Technologies Research Group, Oak Ridge National

More information

Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks

Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks Biophysical Journal Volume 96 May 009 4013 403 4013 Optimal Feedback Strength for Noise Suppression in Autoregulatory Gene Networks Abhyudai Singh* and Joao P. Hespanha Department of Electrical and Computer

More information

Topic 4 - #14 The Lactose Operon

Topic 4 - #14 The Lactose Operon Topic 4 - #14 The Lactose Operon The Lactose Operon The lactose operon is an operon which is responsible for the transport and metabolism of the sugar lactose in E. coli. - Lactose is one of many organic

More information

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005

Gene regulation II Biochemistry 302. Bob Kelm February 28, 2005 Gene regulation II Biochemistry 302 Bob Kelm February 28, 2005 Catabolic operons: Regulation by multiple signals targeting different TFs Catabolite repression: Activity of lac operon is restricted when

More information

Peter Pristas. Gene regulation in eukaryotes

Peter Pristas. Gene regulation in eukaryotes Peter Pristas BNK1 Gene regulation in eukaryotes Gene Expression in Eukaryotes Only about 3-5% of all the genes in a human cell are expressed at any given time. The genes expressed can be specific for

More information

Unit 3: Control and regulation Higher Biology

Unit 3: Control and regulation Higher Biology Unit 3: Control and regulation Higher Biology To study the roles that genes play in the control of growth and development of organisms To be able to Give some examples of features which are controlled

More information

Principles of Genetics

Principles of Genetics Principles of Genetics Snustad, D ISBN-13: 9780470903599 Table of Contents C H A P T E R 1 The Science of Genetics 1 An Invitation 2 Three Great Milestones in Genetics 2 DNA as the Genetic Material 6 Genetics

More information

Initiation of translation in eukaryotic cells:connecting the head and tail

Initiation of translation in eukaryotic cells:connecting the head and tail Initiation of translation in eukaryotic cells:connecting the head and tail GCCRCCAUGG 1: Multiple initiation factors with distinct biochemical roles (linking, tethering, recruiting, and scanning) 2: 5

More information

GLOBEX Bioinformatics (Summer 2015) Genetic networks and gene expression data

GLOBEX Bioinformatics (Summer 2015) Genetic networks and gene expression data GLOBEX Bioinformatics (Summer 2015) Genetic networks and gene expression data 1 Gene Networks Definition: A gene network is a set of molecular components, such as genes and proteins, and interactions between

More information

Gene Regulation and Expression

Gene Regulation and Expression THINK ABOUT IT Think of a library filled with how-to books. Would you ever need to use all of those books at the same time? Of course not. Now picture a tiny bacterium that contains more than 4000 genes.

More information

The Gene The gene; Genes Genes Allele;

The Gene The gene; Genes Genes Allele; Gene, genetic code and regulation of the gene expression, Regulating the Metabolism, The Lac- Operon system,catabolic repression, The Trp Operon system: regulating the biosynthesis of the tryptophan. Mitesh

More information

Translation - Prokaryotes

Translation - Prokaryotes 1 Translation - Prokaryotes Shine-Dalgarno (SD) Sequence rrna 3 -GAUACCAUCCUCCUUA-5 mrna...ggagg..(5-7bp)...aug Influences: Secondary structure!! SD and AUG in unstructured region Start AUG 91% GUG 8 UUG

More information

PROTEIN SYNTHESIS INTRO

PROTEIN SYNTHESIS INTRO MR. POMERANTZ Page 1 of 6 Protein synthesis Intro. Use the text book to help properly answer the following questions 1. RNA differs from DNA in that RNA a. is single-stranded. c. contains the nitrogen

More information

Molecular Biology, Genetic Engineering & Biotechnology Operons ???

Molecular Biology, Genetic Engineering & Biotechnology Operons ??? 1 Description of Module Subject Name?? Paper Name Module Name/Title XV- 04: 2 OPERONS OBJECTIVES To understand how gene is expressed and regulated in prokaryotic cell To understand the regulation of Lactose

More information

13.4 Gene Regulation and Expression

13.4 Gene Regulation and Expression 13.4 Gene Regulation and Expression Lesson Objectives Describe gene regulation in prokaryotes. Explain how most eukaryotic genes are regulated. Relate gene regulation to development in multicellular organisms.

More information

Control of Gene Expression in Prokaryotes

Control of Gene Expression in Prokaryotes Why? Control of Expression in Prokaryotes How do prokaryotes use operons to control gene expression? Houses usually have a light source in every room, but it would be a waste of energy to leave every light

More information

arxiv: v4 [q-bio.mn] 24 Oct 2017

arxiv: v4 [q-bio.mn] 24 Oct 2017 Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level Chen Jia 1, Peng Xie 2, Min Chen 1,, Michael Q. Zhang 2,3, 1 Department of Mathematical Sciences,

More information

Modeling and Systems Analysis of Gene Regulatory Networks

Modeling and Systems Analysis of Gene Regulatory Networks Modeling and Systems Analysis of Gene Regulatory Networks Mustafa Khammash Center for Control Dynamical-Systems and Computations University of California, Santa Barbara Outline Deterministic A case study:

More information

APGRU6L2. Control of Prokaryotic (Bacterial) Genes

APGRU6L2. Control of Prokaryotic (Bacterial) Genes APGRU6L2 Control of Prokaryotic (Bacterial) Genes 2007-2008 Bacterial metabolism Bacteria need to respond quickly to changes in their environment STOP u if they have enough of a product, need to stop production

More information

Random Boolean Networks

Random Boolean Networks Random Boolean Networks Boolean network definition The first Boolean networks were proposed by Stuart A. Kauffman in 1969, as random models of genetic regulatory networks (Kauffman 1969, 1993). A Random

More information

Limitations of Quantitative Gene Regulation Models: A Case Study

Limitations of Quantitative Gene Regulation Models: A Case Study Article Limitations of Quantitative Gene Regulation Models: A Case Study Philip M. Kim 1,2 and Bruce Tidor 1,3,4,5 1 Computer Science and Artificial Intelligence Laboratory, 2 Department of Chemistry,

More information

Principles of Synthetic Biology: Midterm Exam

Principles of Synthetic Biology: Midterm Exam Principles of Synthetic Biology: Midterm Exam October 28, 2010 1 Conceptual Simple Circuits 1.1 Consider the plots in figure 1. Identify all critical points with an x. Put a circle around the x for each

More information

GENETICS - CLUTCH CH.12 GENE REGULATION IN PROKARYOTES.

GENETICS - CLUTCH CH.12 GENE REGULATION IN PROKARYOTES. GEETICS - CLUTCH CH.12 GEE REGULATIO I PROKARYOTES!! www.clutchprep.com GEETICS - CLUTCH CH.12 GEE REGULATIO I PROKARYOTES COCEPT: LAC OPERO An operon is a group of genes with similar functions that are

More information

12-5 Gene Regulation

12-5 Gene Regulation 12-5 Gene Regulation Fruit fly chromosome 12-5 Gene Regulation Mouse chromosomes Fruit fly embryo Mouse embryo Adult fruit fly Adult mouse 1 of 26 12-5 Gene Regulation Gene Regulation: An Example Gene

More information

Introduction. ECE/CS/BioEn 6760 Modeling and Analysis of Biological Networks. Adventures in Synthetic Biology. Synthetic Biology.

Introduction. ECE/CS/BioEn 6760 Modeling and Analysis of Biological Networks. Adventures in Synthetic Biology. Synthetic Biology. Introduction ECE/CS/BioEn 6760 Modeling and Analysis of Biological Networks Chris J. Myers Lecture 17: Genetic Circuit Design Electrical engineering principles can be applied to understand the behavior

More information

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences Leading Edge Review Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences Arjun Raj 1 and Alexander van Oudenaarden 1, * 1 Department of Physics, Massachusetts Institute of Technology,

More information

56:198:582 Biological Networks Lecture 10

56:198:582 Biological Networks Lecture 10 56:198:582 Biological Networks Lecture 10 Temporal Programs and the Global Structure The single-input module (SIM) network motif The network motifs we have studied so far all had a defined number of nodes.

More information

Testing the transition state theory in stochastic dynamics of a. genetic switch

Testing the transition state theory in stochastic dynamics of a. genetic switch Testing the transition state theory in stochastic dynamics of a genetic switch Tomohiro Ushikubo 1, Wataru Inoue, Mitsumasa Yoda 1 1,, 3, and Masaki Sasai 1 Department of Computational Science and Engineering,

More information

Control of Prokaryotic (Bacterial) Gene Expression. AP Biology

Control of Prokaryotic (Bacterial) Gene Expression. AP Biology Control of Prokaryotic (Bacterial) Gene Expression Figure 18.1 How can this fish s eyes see equally well in both air and water? Aka. Quatro ojas Regulation of Gene Expression: Prokaryotes and eukaryotes

More information

Designer gene networks: Towards fundamental cellular control

Designer gene networks: Towards fundamental cellular control CHAOS VOLUME 11, NUMBER 1 MARCH 2001 Designer gene networks: Towards fundamental cellular control Jeff Hasty a) and Farren Isaacs Center for BioDynamics and Department of Biomedical Engineering, Boston

More information