http://2006.igem.org/wiki/index.php?title=Special:Contributions/Petergoldstein&feed=atom&limit=50&target=Petergoldstein&year=&month=2006.igem.org - User contributions [en]2020-11-23T21:52:44ZFrom 2006.igem.orgMediaWiki 1.16.5http://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T22:43:56Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.jpg|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
[[Image:Registry_tristable.jpg|Our implementation]]<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. Note that the equation describing the temporal evolution of AraC includes the term "Aend." This term represents the endogenous expression of AraC in dH5alpha's. Our preliminary work suggests that this endogenous AraC has very little effect on our pBad promoter.<br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protein monomers per time====<br />
Next we can rewrite the equations describing the temporal evolution of the total number inhibitor molecules (5) in terms of equations (10) and (11). This yields the somewhat complex equations (12) which are solely in terms of monomer protein concentration. <br />
<br />
[[Image:dzdt_eqs.png]]<br />
<br />
====Equations for the change in protein monomers per time====<br />
By applying the simple mathematical manipulation (13) to equations (12) and the X derivative of equations (9) ((9) can be written in terms of X by plugging in equations (10) and (11)) we can solve for the following equations for the evolution of protein monomers as a function of time (14). I will spare you the dZi/dXi derivative equations of equation (9).<br />
<br />
[[Image:simp_mat_man_eq.png]]<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of preliminary model constants==<br />
<br />
Coming Soon...<br />
<br />
==Preliminary modeling results==<br />
<br />
Coming Soon...<br />
<br />
Link to MATLAB code for tri-stable model [[Media:tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T22:43:40Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
[[Image:Registry_tristable.jpg|Our implementation]]<br />
<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.jpg|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. Note that the equation describing the temporal evolution of AraC includes the term "Aend." This term represents the endogenous expression of AraC in dH5alpha's. Our preliminary work suggests that this endogenous AraC has very little effect on our pBad promoter.<br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protein monomers per time====<br />
Next we can rewrite the equations describing the temporal evolution of the total number inhibitor molecules (5) in terms of equations (10) and (11). This yields the somewhat complex equations (12) which are solely in terms of monomer protein concentration. <br />
<br />
[[Image:dzdt_eqs.png]]<br />
<br />
====Equations for the change in protein monomers per time====<br />
By applying the simple mathematical manipulation (13) to equations (12) and the X derivative of equations (9) ((9) can be written in terms of X by plugging in equations (10) and (11)) we can solve for the following equations for the evolution of protein monomers as a function of time (14). I will spare you the dZi/dXi derivative equations of equation (9).<br />
<br />
[[Image:simp_mat_man_eq.png]]<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of preliminary model constants==<br />
<br />
Coming Soon...<br />
<br />
==Preliminary modeling results==<br />
<br />
Coming Soon...<br />
<br />
Link to MATLAB code for tri-stable model [[Media:tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T22:43:30Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
[[Image:Registry_tristable.jpg|Our implementation]]<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.jpg|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. Note that the equation describing the temporal evolution of AraC includes the term "Aend." This term represents the endogenous expression of AraC in dH5alpha's. Our preliminary work suggests that this endogenous AraC has very little effect on our pBad promoter.<br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protein monomers per time====<br />
Next we can rewrite the equations describing the temporal evolution of the total number inhibitor molecules (5) in terms of equations (10) and (11). This yields the somewhat complex equations (12) which are solely in terms of monomer protein concentration. <br />
<br />
[[Image:dzdt_eqs.png]]<br />
<br />
====Equations for the change in protein monomers per time====<br />
By applying the simple mathematical manipulation (13) to equations (12) and the X derivative of equations (9) ((9) can be written in terms of X by plugging in equations (10) and (11)) we can solve for the following equations for the evolution of protein monomers as a function of time (14). I will spare you the dZi/dXi derivative equations of equation (9).<br />
<br />
[[Image:simp_mat_man_eq.png]]<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of preliminary model constants==<br />
<br />
Coming Soon...<br />
<br />
==Preliminary modeling results==<br />
<br />
Coming Soon...<br />
<br />
Link to MATLAB code for tri-stable model [[Media:tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/File:Registry_tristable.jpgFile:Registry tristable.jpg2006-10-28T22:42:33Z<p>Petergoldstein: </p>
<hr />
<div></div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T22:42:11Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.jpg|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
[[Image:Registry_tristable.jpg|Our implementation]]<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. Note that the equation describing the temporal evolution of AraC includes the term "Aend." This term represents the endogenous expression of AraC in dH5alpha's. Our preliminary work suggests that this endogenous AraC has very little effect on our pBad promoter.<br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protein monomers per time====<br />
Next we can rewrite the equations describing the temporal evolution of the total number inhibitor molecules (5) in terms of equations (10) and (11). This yields the somewhat complex equations (12) which are solely in terms of monomer protein concentration. <br />
<br />
[[Image:dzdt_eqs.png]]<br />
<br />
====Equations for the change in protein monomers per time====<br />
By applying the simple mathematical manipulation (13) to equations (12) and the X derivative of equations (9) ((9) can be written in terms of X by plugging in equations (10) and (11)) we can solve for the following equations for the evolution of protein monomers as a function of time (14). I will spare you the dZi/dXi derivative equations of equation (9).<br />
<br />
[[Image:simp_mat_man_eq.png]]<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of preliminary model constants==<br />
<br />
Coming Soon...<br />
<br />
==Preliminary modeling results==<br />
<br />
Coming Soon...<br />
<br />
Link to MATLAB code for tri-stable model [[Media:tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/File:Tristable_Toggle.jpgFile:Tristable Toggle.jpg2006-10-28T22:28:29Z<p>Petergoldstein: </p>
<hr />
<div></div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T22:28:16Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.jpg|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. Note that the equation describing the temporal evolution of AraC includes the term "Aend." This term represents the endogenous expression of AraC in dH5alpha's. Our preliminary work suggests that this endogenous AraC has very little effect on our pBad promoter.<br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protein monomers per time====<br />
Next we can rewrite the equations describing the temporal evolution of the total number inhibitor molecules (5) in terms of equations (10) and (11). This yields the somewhat complex equations (12) which are solely in terms of monomer protein concentration. <br />
<br />
[[Image:dzdt_eqs.png]]<br />
<br />
====Equations for the change in protein monomers per time====<br />
By applying the simple mathematical manipulation (13) to equations (12) and the X derivative of equations (9) ((9) can be written in terms of X by plugging in equations (10) and (11)) we can solve for the following equations for the evolution of protein monomers as a function of time (14). I will spare you the dZi/dXi derivative equations of equation (9).<br />
<br />
[[Image:simp_mat_man_eq.png]]<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of preliminary model constants==<br />
<br />
Coming Soon...<br />
<br />
==Preliminary modeling results==<br />
<br />
Coming Soon...<br />
<br />
Link to MATLAB code for tri-stable model [[Media:tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:07:51Z<p>Petergoldstein: /* Brown's iGEM Beginnings */</p>
<hr />
<div>{{Brown navigation bar}}<br />
=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[User:Johncumbers|John]] and [[User:Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two? If we could construct and characterize a three-way toggle switch, we could begin to get a sense of the issues associated with building an n-stable toggle switch, possibly proving that there is a limit to the feasible size of such a device or suggesting scalability.<br />
<br />
== Practical Concerns==<br />
During the course of the summer, two students were funded for full-time labwork and the remaining six were on part time.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:07:33Z<p>Petergoldstein: /* Brown's iGEM Beginnings */</p>
<hr />
<div>{{Brown navigation bar}}<br />
=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Users/Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two? If we could construct and characterize a three-way toggle switch, we could begin to get a sense of the issues associated with building an n-stable toggle switch, possibly proving that there is a limit to the feasible size of such a device or suggesting scalability.<br />
<br />
== Practical Concerns==<br />
During the course of the summer, two students were funded for full-time labwork and the remaining six were on part time.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:06:39Z<p>Petergoldstein: </p>
<hr />
<div>{{Brown navigation bar}}<br />
=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two? If we could construct and characterize a three-way toggle switch, we could begin to get a sense of the issues associated with building an n-stable toggle switch, possibly proving that there is a limit to the feasible size of such a device or suggesting scalability.<br />
<br />
== Practical Concerns==<br />
During the course of the summer, two students were funded for full-time labwork and the remaining six were on part time.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:06:03Z<p>Petergoldstein: </p>
<hr />
<div>=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two? If we could construct and characterize a three-way toggle switch, we could begin to get a sense of the issues associated with building an n-stable toggle switch, possibly proving that there is a limit to the feasible size of such a device or suggesting scalability.<br />
<br />
== Practical Concerns==<br />
During the course of the summer, two students were funded for full-time labwork and the remaining six were on part time.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:04:51Z<p>Petergoldstein: </p>
<hr />
<div>=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two? If we could construct and characterize a three-way toggle switch, we could begin to get a sense of the issues associated with building an n-stable toggle switch, possibly proving that there is a limit to the feasible size of such a device or suggesting scalability.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T18:03:43Z<p>Petergoldstein: </p>
<hr />
<div>=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
==Ideas==<br />
Our initial ideas were very optimistic and we knew it at the time. Ideas that were floated included<br />
<br />
===Cell counter===<br />
If we could engineer a pathway whereby a cell could have a different behavior each generation, we could easily track varying growth rates, encourage long-period behavior change and produce many other desired effects. We got in contact with other labs working on the problem and, after they appraised us of their years of fruitless efforts, we went back to the drawing board.<br />
<br />
===Free radical detector===<br />
Free radicals have a profound impact on the workings of biological systems. As such, if we could engineer a part that uptook and reported the presence of such radicals, this could have medical applications.<br />
<br />
===Magnetic bacteria===<br />
Magnetospirillum have an extra organelle called a magnetosome which contains magnetic nanoparticals. These bacteria are often found in sewers and other metal-rich damp places aligned to the earth's magnetic poles. These bacteria are exciting to synthetic biology because it is possibe to tag the magnetic particles with proteins and so magnetize the desired protein. This has medical applications because applying a magnetic field to the nanoparticles causes them to heat up and eventually destroy whatever cell in which they reside.<br />
<br />
===Bacterial Freeze tag===<br />
The first purely iGEM-related idea we had, the freeze tag project was a concession to the observation that our team worked better split into smaller groups. The project is made up of four modular devices: an AHL-producing cell, an AHL-PoPS device, a bi-stable switch turning off motility and finally a gene responsible for switching the toggle back. Expected behavior: the sender cell comes near another cell, floods it with AHL. The AHL causes the second cell to cease producing motB, a protein necessary for motility. Another cell comes along later and reactivates the second cell's motility by virtue of the unfreezing device. This is a work in progress.<br />
<br />
===Tri-stable toggle switch===<br />
The bi-stable toggle swich was a hit but why stop at two?</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Team_logisticsBrown:Team logistics2006-10-28T17:52:48Z<p>Petergoldstein: </p>
<hr />
<div>=Brown's iGEM Beginnings=<br />
In early 2006, a small group of interested persons, most notably [[Johncumbers|John]] and [[Brendanhickey|Brendan]], got together and decided that they wanted to get involved with the iGEM project. They put the word out that we wanted a team of 8 undergraduates for innovative synthetic biology labwork over the summer. Students from many different departments, including engineering, biology, and computer science, responded to this first call and started the Journal club. The purpose of the journal club was to go through seminal papers in synthetic biology to bring us up to speed on the state of the art, to give us ideas for our summer's project, and to bring our number down to eight undergraduates. In April, the team was set and we were brainstorming projects.<br />
<br />
=Ideas=</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/File:Tristable_Toggle.pngFile:Tristable Toggle.png2006-10-28T17:42:41Z<p>Petergoldstein: </p>
<hr />
<div></div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:42:11Z<p>Petergoldstein: /* A tri-stable toggle switch */</p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable_Toggle.png|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:35:31Z<p>Petergoldstein: /* A tri-stable toggle switch */</p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable.png|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes. By characterizing each of the three pathways without following genes and terminators, we enable a tri-stable switching network of any three biobricks to be constructed with minimal cloning.<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:32:14Z<p>Petergoldstein: /* A tri-stable toggle switch */</p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
<br />
[[Image:Tristable.png|A general tri-stable toggle]]<br />
<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes.<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:31:53Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. The general idea is that when a selected promoter is activated, it represses the other two. As such each of the three states of our network are self-stabilizing.<br />
[[Image:Tristable.png|A general tri-stable toggle]]<br />
Our implementation uses the pLac, pTet, and pBad/AraC promoters and their respective inhibiting proteins. We chose these because of the relative ease with which each promoter is induced: by adding IPTG for the pLac-promoted region, tetracycline for the PTet-promoted region, and arabinose for the pBad/Ara genes.<br />
<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/File:Tristable.pngFile:Tristable.png2006-10-28T17:22:41Z<p>Petergoldstein: </p>
<hr />
<div></div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:22:14Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. <br />
[[Image:Tristable.png]]<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Tri-Stable_toggle_switchBrown:Tri-Stable toggle switch2006-10-28T17:21:05Z<p>Petergoldstein: </p>
<hr />
<div>=A tri-stable toggle switch=<br />
Pursuant to the the 1999 paper "Construction of a genetic toggle switch in Escherichia coli," by Timothy S. Gardner, Charles R. Cantor and James J. Collins, we wondered if the bi-stable toggle switch could be generalized to an n-stable switch. To that end, we conceived and began construction of the tri-stable toggle switch. <br />
[[Image:Tristable.pict]]<br />
=Modeling the tri-stable toggle switch=<br />
While the tri-stable switch is seemingly simple in design, just like any other system it is subject to potentially comprising factors such as promoter leakiness and other stochastic fluctuations. In an attempt to predict the behavior of the tri-stable switch, we created a deterministic model of the system taking into account these factors. The model structure is based on that described in "Prediction and measurement of an autoregulatory genetic module" by Farren Isaacs, et al. This paper features an excellent supplement that takes you hand-in-hand through the derivation of model equations. I will attempt to emulate this derivation with our model below. It is important to note that while we have some preliminary results, our model is very much a work in progress. In order to model the system accurately, many of the fundamental constants governing the model will need to be determined experimentally. For now we have used some constants from the literature and estimated some based on similar the values of similar constants also from the literature. <br />
<br />
==Derivation of the Model Equations==<br />
The chemical reactions describing the tri-stable switch can be divided into the two catagories of fast and slow reactions. Fast reactions such as dimer formation and promoter-binding occur in the scale of seconds and are therefore modeled to be in equilibrium. Conversely, slow reactions including the likes of transcription, translation, and protein degradation occur on the scale of minutes and are thus modeled to be evolving with time. <br />
<br />
====Fast reversible reaction equations====<br />
The following equations (1) describe the fast reactions. The characters L,T,A denote molecules of LacI, TetR, and, AraC, respectively while the subscripts denote whether the molecule is a monomer (blank), dimer(2), tri-mer(3), etc. The k's denote reaction rates.<br />
<br />
[[Image:Fast_rxn_eqs1.png]]<br />
<br />
Note that the equations include volume explicitly. Cell volume is modeled in this way as it is a slowly evolving function of time.<br />
<br />
====Slow irreversible reaction equations====<br />
The following equations (2) describe the slow irreversible reactions of transcription and translation (both taken into account with the reaction rate kti) and protein degradation (reaction constant kdi). The coefficients eta-ij take into account the relative translation rates of proteins from the same transcripts. For eta-ij, "i" represents the promoter responsible for producing the molecule and "j" represents the molecule being translated [ex: eta-LA corresponds to the relative rate of AraC production from the trascript produced by the LacI promoter]. To establish a convention, eta's are relative to the translation rate of the first gene on a particular transcript. Thus eta for the first gene on the mRNA transcript = 1. The alpha-i coefficients represent relative transcription rates. In this case, "i" denotes the promoter from which the mRNA is transcribed.<br />
<br />
[[Image:slow_rxn_eqs.png]]<br />
====Equations governing cell volume====<br />
The following two equations (3) describing cellular growth and division are taken directly from the aforementioned paper by Isaacs et al. The first equation describes the volume increase from the time immediately following cell division to the time immediately before it. In this equation, V0 denotes the volume of the cell at the beginning of growth and T0 denotes the time of cell division. In our model at times T=q*t0 in which q is an integer, we have volume V and protein concentration n halve - thus modeling volume division and the resulting protein redistribution. The second equation describes the dimensionless equation in which t is measured in terms of fcell-division time and the cell volume changes between 1 and 2.<br />
<br />
[[Image:vol_eq.png]]<br />
====Equations for the total number of molecules====<br />
The following equations (4) describe the total number of inhibitor protein molecules zi. d#i represents the number, "#", of molecules bound to the "i" promoter. (ex: all of the LacI tetramers bound to pLacI promoters are accounted for by the 4d1L term.)<br />
[[Image:Tot_mol_eq.png]]<br />
<br />
====Equations describing the temporal evolution of the total number inhibitor molecules====<br />
The following equations (5) describe the temporal evolution of the total number of inhibitor molecules. Beta-i = the cell division time multiplied by the combined transcription and tranlation rates from a given promoter "i" (t0*kti), thus representing the total number of protein molecules maximally produced by a given promoter. Similarly, Gamma-i = the cell division time multipled by the degradation rate of protein i (t0*kdi), thus representing the total number of protein i destabilized over one cell division time. The eta and alpha terms are described in the section above describing the equations for the slow reactions. <br />
<br />
[[Image:Ev_tot_mol_eqs.png]]<br />
====Fast reaction equilibrium equations====<br />
Compared to the slowly evolving reactions(2) described by the above equations (5), the fast reactions (1) can be considered to be in equilibrium. Thus the following equilibrium relations (6) hold.<br />
[[Image:Fast_eq_eqs.png]]<br />
<br />
====Equations modeling the presence of the inducers====<br />
The following equations (7) model the effect of the chemical inducers on the system. The model regards the proteins bound to the inducers as having increased dissociation rates (ki-#) as specified below. The reation rate with the apostrophe denotes the original reaction rate in the absence of inducer inclusion. In these equations "I" denotes IPTG, "a" denotes arabinose, and "Tc" denotes tetracycline (or analogue aTc). The concept for and the form of these equations are based on equations described in the supplementary Information for "A bottom-up approach to gene regulation" by Guido et al. Much like the aforementioned paper by Isaacs et al., 'Bottom-up' has an extensive and brilliantly articulate derviation supplement. <br />
<br />
[[Image:inducer_eqs.png]]<br />
<br />
====Equations relating plasmid copy number to operator sites====<br />
The following equations (8) relate the plasmid copy number, "m", to the number of promoters with bound and unbound operators. As each plasmid contains 1 of each promoter, m is constant for all three promoter types. <br />
<br />
[[Image:cop_num_eqs.png]]<br />
<br />
====Simplified fast reaction equilibrium equations====<br />
The equilibrium equations governing the fast reactions (6) can be simplified by defining dimensionless equilibrium constants in the form of cij=kij/(k(-ij)*V0*A) in which A is Avogadro's number. The cL's are further simplified by defining the constant cL=c1L*c2L*c3L*c4L. Additionally by plugging in successive terms we were able to write the operator equations in terms of d0L. <br />
<br />
[[Image:Simp_fast_eq_eqs.png]]<br />
<br />
====Equations for the number of unbound operators====<br />
Combining equations (8) and the above simplified equilibrium equations(9), we are able to solve for the number of unbound operators d0i. <br />
<br />
[[Image:Unbound_eqs.png]]<br />
<br />
====Equations for the number of bound operators====<br />
By plugging the d0i's (10) back into the equations for bound operators (9), we can solve for these equations in terms of monomer concentrations.<br />
<br />
<br />
[[Image:bound_eqs.png]]<br />
<br />
====Equation manipulations to determine change in protien monomers per time====<br />
<br />
====Equations for the change in protein monomers per time====<br />
<br />
====Equations describing stochastic variation====<br />
<br />
====Equations for the evolution of fluorescent reporters====<br />
<br />
==Table of constants==<br />
<br />
==Preliminary modeling results==<br />
<br />
Link to MATLAB code of model [[tristable1.m]]<br />
<br />
--[[User:Jlohmuel|Jlohmuel]] 03:59, 28 October 2006 (EDT)</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:48:37Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg|thumb|As a pirate...]] <br />
[[Image:pgoldste.jpg|thumb|As a teacher...]] [[Image:wolverine.jpg|thumb|The next step]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:47:55Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg|left]] <br />
[[Image:pgoldste.jpg|left ]] Next step: [[Image:wolverine.jpg|thumb|The next step]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:47:28Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg | left]] <br />
[[Image:pgoldste.jpg | left ]] Next step: [[Image:wolverine.jpg | thumb |The next step]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:44:39Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]] Next step: [[Image:wolverine.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/File:Wolverine.jpgFile:Wolverine.jpg2006-07-25T15:44:07Z<p>Petergoldstein: </p>
<hr />
<div></div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:43:45Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]] Goal: [[Image:wolverine.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:41:06Z<p>Petergoldstein: /* Weekly Reports */</p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<Br><br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<Br><br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-25T15:40:46Z<p>Petergoldstein: /* Weekly Reports */</p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.<br />
'''Week Six'''<Br>We regrew our parts as the suspicious results of before led us to repeat the process. By the end of the week we'd done our first ligation. This week's journal club was Jason discussing a paper about invasin.<br />
'''Week Seven'''<Br>Came in at night every day during the weekend to either start or finish an overnight growth. At this point we've miniprepped car and cdr of our final device so should be running the ligation to produce the sender cell soon.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pages/dessertBrown:Calendar pages/dessert2006-07-19T16:51:13Z<p>Petergoldstein: /* What you bringing? */</p>
<hr />
<div>{{Brown navigation bar}}<br />
<br />
==What you bringing?==<br />
Annie: Cookies- any preferences?<br />
<br />
Azeem: Chocolate chip cookies</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pages/dessertBrown:Calendar pages/dessert2006-07-19T16:51:05Z<p>Petergoldstein: /* What you bringing? */</p>
<hr />
<div>{{Brown navigation bar}}<br />
<br />
==What you bringing?==<br />
Annie: Cookies- any preferences?<br />
Azeem: Chocolate chip cookies</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pages/dessertBrown:Calendar pages/dessert2006-07-14T18:08:44Z<p>Petergoldstein: </p>
<hr />
<div>{{Brown navigation bar}}<br />
<br />
==What you bringing?==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pages/dessertBrown:Calendar pages/dessert2006-07-14T18:08:20Z<p>Petergoldstein: </p>
<hr />
<div>{Brown navigation bar}<br />
<br />
==What you bringing?==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pages/dessertBrown:Calendar pages/dessert2006-07-14T18:07:50Z<p>Petergoldstein: </p>
<hr />
<div>==What you bringing?==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pagesBrown:Calendar pages2006-07-14T18:07:14Z<p>Petergoldstein: /* "Summer calendar" */</p>
<hr />
<div>{{Brown navigation bar}}<br />
<br />
<br />
==Week Six==<br />
Mon 07/10/06: <br><br />
Tue 07/11/06: Journal Club, Time TBA<br> <br />
Wed 07/12/06: [[Samantha Sutton, 12PM Walter Hall]]<br> <br />
Thu 07/13/06: <br><br />
Fri 07/14/06: 1PM Weekly Meeting, JWW 260 <br><br />
<br />
==Week Seven==<br />
Mon 07/17/06:<br><br />
Tue 07/18/06: Journal Club, Time TBA <br><br />
Wed 07/19/06: <br><br />
Thu 07/20/06:<br><br />
Fri 07/21/06: 1PM Weekly Meeting, JWW 260<br><br />
<br />
=="Summer calendar"==<br />
{| style="height:1000px" border="1"<br />
!valign="top" width="100" height="10"| Week <br />
! valign="top" width="100"| Sun <br />
! valign="top" width="100"| Mon <br />
! valign="top" width="100"| Tue <br />
! valign="top" width="100"| Wed <br />
! valign="top" width="100"| Thu <br />
! valign="top" width="100"| Fri <br />
! valign="top" width="100"| Sat<br />
<br />
|-<br />
!1<br />
|4<br />
|5<br />
|6<br />
|7<br> 1PM: Meeting with faculty in JWW conference room<br />
|8<br> 1PM: Bacteria tutorial led by Jamie Gagnon<br />
|9<br> 10AM: APE tutorial led by Azeem and Jason<br />
|10<br />
|-<br />
!2<br />
|11<br />
|12 <br />
|13<br />
|14<br />
|15<br />
|16<br />
|17<br />
|-<br />
!3<br />
|18<br />
|19 <br> 11-1 meeting with Pfizer<br />
|20<br />
|21 <br> 10AM Meeting with Jay Tang (Bacterial Super Glue)<br />
|22 <br> 10AM-12PM Modeling Tutorial<br />
|23 <br> 10AM BioHazard Training?<br />
1PM Weekly Update, JWW 260<br />
|24<br />
|-<br />
!4<br />
|25<br />
|26<br />
|27<br />
|28 Mac Cowell speak, 2(?)pm WH<br />
|29<br />
|30<br />
|1 July<br />
|-<br />
!5<br />
|2<br />
|3<br />
|4<br />
|5<br />
|6<br />
|7<br />
|8<br />
|-<br />
<br />
!6<br />
|9<br />
|10<br />
|11<br />
|12 [[Samantha Sutton, 12PM Walter Hall]]<br><br />
|13<br />
|14<br />
|15<br />
|-<br />
<br />
!7<br />
|16<br />
|17<br />
|18<br />
|19 Barbecue at Gary's: bring [[Brown:Calendar pages/dessert|dessert]]!<br />
|20<br />
|21<br />
|22<br />
|-<br />
<br />
!8<br />
|23<br />
|24<br />
|25<br />
|26<br />
|27<br />
|28<br />
|29<br />
|-<br />
<br />
!9<br />
|30<br />
|31<br />
|1 Aug <br />
|2<br />
|3 Annie gone for vacation<br />
|4<br />
|5<br />
|-<br />
<br />
!10<br />
|6<br />
|7<br />
|8 Annie back from vacation<br />
|9<br />
|10<br />
|11<br />
|12<br />
|-<br />
<br />
!11<br />
|13 Jamie L. gone home<br />
|14 Annie gone for the day<br />
|15<br />
|16<br />
|17<br />
|18<br />
|19<br />
|-<br />
<br />
!12<br />
|20<br />
|21<br />
|22<br />
|23<br />
|24<br />
|25<br />
|26<br />
|}<br />
<br />
<h2>Personal calendars</h2><br />
- [[calendar:johncumbers|John Cumbers]]<br><br />
- [[calendar:petergoldstein|Peter Goldstein]]<br><br />
- [[calendar:bhickey|Brendan Hickey]]<br><br />
- [[calendar:anniegao|Annie Gao]] <br><br />
- [[calendar:meganschmidt|Megan Schmidt]]<br><br />
<br />
- Add your name here and copy my page for a template.<br />
<br />
<br />
<br />
==Calendar Archive==<br />
'''Week Five''' <br><br />
Mon 07/03/06: <br><br />
Tue 07/04/06: <br><br />
Wed 07/05/06: Journal club 1.30 PM Walter hall <br><br />
Thu 07/06/06: <br><br />
Fri 07/07/06: 1PM - Weekly Update, JWW 260<br><br />
'''Week Three''' <Br><br />
Mon 06/19/06: Pfizer meeting 11-1 at Walter Hall <br><br />
Tue 06/20/06: Journal club 6pm Walter hall <br><br />
Wed 06/21/06: 10am Jay Tang to speak on Bacterial SuperGlue <br><br />
Thu 06/22/06: 10AM-12PM Modeling Tutorial, Walter Hall <br><br />
Fri 06/23/06: health and safety 10.15am, 4th floor conference room Brown office building 1PM - Weekly Update, JWW 260<br />
<br />
'''Week Two''' <Br><br />
Mon 06/12/06: <br />
*john back from vacation, 9.30pm<br />
Tue 06/13/06 <br><br />
*James Brown to visit, arrive ~lunchtime, talk 3-5pm, dinner for all at John's 7pm<br />
Wed 06/14/06 <br><br />
*James Brown to give second talk , 10-12 before leaving for Princeton<br />
<br />
'''Week One''' <br><br />
Mon 06/05/06: <br />
* Morning meeting, plan for this week<br />
* Lab safety training <br><br />
Tue 06/06/06 <br><br />
*11am - 12pm Group meeting. Location: JWW rm. 228 <br><br />
Wed<br><br />
*Mid-week progress talk with faculty- 1pm - 2pm JWW rm. 260<br />
Thu <br><br />
Fri <br><br />
* afternoon meeting, wrap up the week, plan for next week</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Calendar_pagesBrown:Calendar pages2006-07-14T18:06:08Z<p>Petergoldstein: /* "Summer calendar" */</p>
<hr />
<div>{{Brown navigation bar}}<br />
<br />
<br />
==Week Six==<br />
Mon 07/10/06: <br><br />
Tue 07/11/06: Journal Club, Time TBA<br> <br />
Wed 07/12/06: [[Samantha Sutton, 12PM Walter Hall]]<br> <br />
Thu 07/13/06: <br><br />
Fri 07/14/06: 1PM Weekly Meeting, JWW 260 <br><br />
<br />
==Week Seven==<br />
Mon 07/17/06:<br><br />
Tue 07/18/06: Journal Club, Time TBA <br><br />
Wed 07/19/06: <br><br />
Thu 07/20/06:<br><br />
Fri 07/21/06: 1PM Weekly Meeting, JWW 260<br><br />
<br />
=="Summer calendar"==<br />
{| style="height:1000px" border="1"<br />
!valign="top" width="100" height="10"| Week <br />
! valign="top" width="100"| Sun <br />
! valign="top" width="100"| Mon <br />
! valign="top" width="100"| Tue <br />
! valign="top" width="100"| Wed <br />
! valign="top" width="100"| Thu <br />
! valign="top" width="100"| Fri <br />
! valign="top" width="100"| Sat<br />
<br />
|-<br />
!1<br />
|4<br />
|5<br />
|6<br />
|7<br> 1PM: Meeting with faculty in JWW conference room<br />
|8<br> 1PM: Bacteria tutorial led by Jamie Gagnon<br />
|9<br> 10AM: APE tutorial led by Azeem and Jason<br />
|10<br />
|-<br />
!2<br />
|11<br />
|12 <br />
|13<br />
|14<br />
|15<br />
|16<br />
|17<br />
|-<br />
!3<br />
|18<br />
|19 <br> 11-1 meeting with Pfizer<br />
|20<br />
|21 <br> 10AM Meeting with Jay Tang (Bacterial Super Glue)<br />
|22 <br> 10AM-12PM Modeling Tutorial<br />
|23 <br> 10AM BioHazard Training?<br />
1PM Weekly Update, JWW 260<br />
|24<br />
|-<br />
!4<br />
|25<br />
|26<br />
|27<br />
|28 Mac Cowell speak, 2(?)pm WH<br />
|29<br />
|30<br />
|1 July<br />
|-<br />
!5<br />
|2<br />
|3<br />
|4<br />
|5<br />
|6<br />
|7<br />
|8<br />
|-<br />
<br />
!6<br />
|9<br />
|10<br />
|11<br />
|12 [[Samantha Sutton, 12PM Walter Hall]]<br><br />
|13<br />
|14<br />
|15<br />
|-<br />
<br />
!7<br />
|16<br />
|17<br />
|18<br />
|19 Barbecue at Gary's: bring dessert!<br />
|20<br />
|21<br />
|22<br />
|-<br />
<br />
!8<br />
|23<br />
|24<br />
|25<br />
|26<br />
|27<br />
|28<br />
|29<br />
|-<br />
<br />
!9<br />
|30<br />
|31<br />
|1 Aug <br />
|2<br />
|3 Annie gone for vacation<br />
|4<br />
|5<br />
|-<br />
<br />
!10<br />
|6<br />
|7<br />
|8 Annie back from vacation<br />
|9<br />
|10<br />
|11<br />
|12<br />
|-<br />
<br />
!11<br />
|13 Jamie L. gone home<br />
|14 Annie gone for the day<br />
|15<br />
|16<br />
|17<br />
|18<br />
|19<br />
|-<br />
<br />
!12<br />
|20<br />
|21<br />
|22<br />
|23<br />
|24<br />
|25<br />
|26<br />
|}<br />
<br />
<h2>Personal calendars</h2><br />
- [[calendar:johncumbers|John Cumbers]]<br><br />
- [[calendar:petergoldstein|Peter Goldstein]]<br><br />
- [[calendar:bhickey|Brendan Hickey]]<br><br />
- [[calendar:anniegao|Annie Gao]] <br><br />
- [[calendar:meganschmidt|Megan Schmidt]]<br><br />
<br />
- Add your name here and copy my page for a template.<br />
<br />
<br />
<br />
==Calendar Archive==<br />
'''Week Five''' <br><br />
Mon 07/03/06: <br><br />
Tue 07/04/06: <br><br />
Wed 07/05/06: Journal club 1.30 PM Walter hall <br><br />
Thu 07/06/06: <br><br />
Fri 07/07/06: 1PM - Weekly Update, JWW 260<br><br />
'''Week Three''' <Br><br />
Mon 06/19/06: Pfizer meeting 11-1 at Walter Hall <br><br />
Tue 06/20/06: Journal club 6pm Walter hall <br><br />
Wed 06/21/06: 10am Jay Tang to speak on Bacterial SuperGlue <br><br />
Thu 06/22/06: 10AM-12PM Modeling Tutorial, Walter Hall <br><br />
Fri 06/23/06: health and safety 10.15am, 4th floor conference room Brown office building 1PM - Weekly Update, JWW 260<br />
<br />
'''Week Two''' <Br><br />
Mon 06/12/06: <br />
*john back from vacation, 9.30pm<br />
Tue 06/13/06 <br><br />
*James Brown to visit, arrive ~lunchtime, talk 3-5pm, dinner for all at John's 7pm<br />
Wed 06/14/06 <br><br />
*James Brown to give second talk , 10-12 before leaving for Princeton<br />
<br />
'''Week One''' <br><br />
Mon 06/05/06: <br />
* Morning meeting, plan for this week<br />
* Lab safety training <br><br />
Tue 06/06/06 <br><br />
*11am - 12pm Group meeting. Location: JWW rm. 228 <br><br />
Wed<br><br />
*Mid-week progress talk with faculty- 1pm - 2pm JWW rm. 260<br />
Thu <br><br />
Fri <br><br />
* afternoon meeting, wrap up the week, plan for next week</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-10T14:00:12Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
==My Part==<br />
I was brought onboard as a computer science-type gent so I'm responsible for a number of the more technical/less liquidy portions of the team's work. I run the journal club, keep the chemical database managed, and work with others on modeling the systems we're assembling in the lab. I am also working with Brendan on assembling the parts necessary for the sender cell portion of the freeze tag project.<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-10T13:57:07Z<p>Petergoldstein: /* Weekly Reports */</p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.<br />
'''Week Five'''<Br>Came in during the weekend with Brendan to grow up and then miniprep our parts. One of them is suspiciously yellow and it turns out that one was expressing GFP. Pity the part as which we had it labled doesn't have GFP... I ran the journal club this week, discussing the repressilator. I met with Azeem and LK to build a model for the freeze circuit in the receiver cell on Friday.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:21:38Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator. The article is [http://sas.epnet.com/externalframe.asp?tb=0&_ug=sid+22B5129D%2D5B8E%2D4F95%2D8DF7%2D47E076627D12%40sessionmgr6+812C&_us=SLsrc+ext+or+Date+034D&_usmtl=ftv+True+137E&_uso=hd+False+db%5B0+%2Daph+1BEE&fi=aph_2752232_AN&lpdf=true&pdfs=&tn=&tp=PC&es=cs%5Fclient%2Easp%3FT%3DP%26P%3DAN%26K%3D2752232%26rn%3D1%26db%3Daph%26is%3D0028%2D0836%26sc%3D%26S%3D%26D%3Daph%26title%3DNature%26year%3D2000%26bk%3DS&fn=1&rn=1&bk=S&EBSCOContent=ZWJjY8bb43ePprRruevra6Gmr4GPprOFoaa5fKaWxpjDpfG60uGtuNDf7XnU3u6+4wAA&an=2752232&db=aph& here]<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:21:04Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator.[http://sas.epnet.com/externalframe.asp?tb=0&_ug=sid+22B5129D%2D5B8E%2D4F95%2D8DF7%2D47E076627D12%40sessionmgr6+812C&_us=SLsrc+ext+or+Date+034D&_usmtl=ftv+True+137E&_uso=hd+False+db%5B0+%2Daph+1BEE&fi=aph_2752232_AN&lpdf=true&pdfs=&tn=&tp=PC&es=cs%5Fclient%2Easp%3FT%3DP%26P%3DAN%26K%3D2752232%26rn%3D1%26db%3Daph%26is%3D0028%2D0836%26sc%3D%26S%3D%26D%3Daph%26title%3DNature%26year%3D2000%26bk%3DS&fn=1&rn=1&bk=S&EBSCOContent=ZWJjY8bb43ePprRruevra6Gmr4GPprOFoaa5fKaWxpjDpfG60uGtuNDf7XnU3u6+4wAA&an=2752232&db=aph& here]<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:19:42Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator.<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:19:07Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator. The article is [[Media:Repressilator|here]].<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:18:44Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator. The article is [[PDF:Repressilator|here]].<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:12:12Z<p>Petergoldstein: /* 5 July */</p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator. The article is [[Media:Repressilator|here]].<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:03:36Z<p>Petergoldstein: </p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]==<br />
Peter presents an article about transcriptional regulators used to form an oscillator.<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-07-05T04:03:18Z<p>Petergoldstein: </p>
<hr />
<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/07.05.06|5 July]]<br />
Peter presents an article about transcriptional regulators used to form an oscillator.<br />
<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
<br />
6pm Walter Hall<br />
<br />
==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
<br />
==[[Brown:Journal club/5.09.06|9th May]]==<br />
<br />
Journal Club is in Walter Hall, 80 Waterman<br />
<br />
Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
<br />
Matthias Seydack<br />
<br />
<br />
==Tuesday 2nd May, 6-7pm, == <br />
<br />
==[[Brown:Journal club/5.02.06|2nd May]]==<br />
<br />
[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
<br />
==[[Brown:Journal club/4.25.06|25th April]]==<br />
<br />
John to present, + overview of Biobricks<br />
<br />
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
<br />
==[[Brown:Journal club/4.18.06|18th April]]==<br />
<br />
Kara and Jesse<br />
<br />
http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
<br />
Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
<br />
Bayer TS, Smolke CD.<br />
<br />
==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
<br />
The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
<br />
Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
<br />
<br />
==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
<br />
Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
<br />
It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
<Br><br />
<br />
==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
<br />
Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
<br />
==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
<br />
<br />
==please add future weeks==</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-02T09:10:19Z<p>Petergoldstein: /* Weekly Reports */</p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<Br><br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<Br><br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<Br><br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-02T09:09:58Z<p>Petergoldstein: </p>
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<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
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Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
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I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
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== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br> Arrived and set myself up. Took lab safety and hazardous waste training minicourses. Learned about transformation, running gels, and ethanol precipitation. Made plates with Annie (later turned out to be faulty as we omitted LB broth. Live and learn)<br />
'''Week Two'''<Br> More tranformations carried out on better plates than the ones we made. Met James Brown, our iGEM ambassador. The concept of iGEM as a project intending to turn genetic engineering into a well-defined standardized system becomes clear to me.<br />
'''Week Three'''<Br> Arranged the journal club, which met in the evening. Hayato's paper is about binding luciferace to the magnetic particles in our magnetotactic bacteria. Attended numerous meetings including a visit from Pfizer's outreach team.<br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/User:PetergoldsteinUser:Petergoldstein2006-07-02T09:02:50Z<p>Petergoldstein: </p>
<hr />
<div>[[Image:petah.jpg]] [[Image:pgoldste.jpg]]<br />
<br />
Peter Goldstein<p><br />
<br />
Brown Undergrad, class of 2008.<br><br />
Brown PO Box 4209<br><br><br />
Click here to view my [[Calendar:petergoldstein|calendar]]<br><br><br />
<br />
<br />
Concentration history: I came in as a Math major and changed to Math/Computer Science after a semester. After three days of believing I was a Computer Science concentrator, I decided on computational biology, where I have remained to this day.<br><br><br />
<br />
I play the viola (as loudly as possible), sing in Gilbert and Sullivan operas, whistle with Lip Service (whistling choir) and am a brother in the Alpha Delta Phi society.<br />
<br />
<br />
== Weekly Reports==<br />
<Br><br />
'''Week One'''<Br><br />
'''Week Two'''<Br><br />
'''Week Three'''<Br> <br />
'''Week Four'''<Br>I arranged the journal club, at which Azeem presented his paper about the bacterial bull's-eye. The following day I modeled the bacterial bull's-eye in JDesigner as an exercise in the program's use and to get a better handle on how computaitonal analysis can help the project. The remainder of the week I spent transforming the various parts necessary for the sender cell for the freeze tag project. All three parts transformed and we are now growing them up.</div>Petergoldsteinhttp://2006.igem.org/wiki/index.php/Brown:Journal_club:Synthetic_biology_journal_clubBrown:Journal club:Synthetic biology journal club2006-06-20T05:05:23Z<p>Petergoldstein: </p>
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<div>{{Brown navigation bar}}<br />
==[[Brown:Journal club/06.20.06|20 June]]==<br />
Hayato presents an article on producing the luciferace-magnetic particle complex.<br />
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==[[Brown:Journal club/05.16.06|16th May]]==<br />
This is the last journal club until the summer. This week will be a meeting to discuss the lab and the first few weeks of the summer. In Walter Hall, 80 Waterman, 6-7pm<br />
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==[[Brown:Journal club/5.09.06|9th May]]==<br />
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Journal Club is in Walter Hall, 80 Waterman<br />
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Hiyato to present: Nanoparticle labels in immunosensing using optical detection methods<br />
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Matthias Seydack<br />
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==Tuesday 2nd May, 6-7pm, == <br />
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==[[Brown:Journal club/5.02.06|2nd May]]==<br />
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[http://openwetware.org/wiki/Sriram_Kosuri Sri Kosuri] from MIT to come and talk about his paper from the previous week.<br />
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==[[Brown:Journal club/4.25.06|25th April]]==<br />
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John to present, + overview of Biobricks<br />
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[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7]<br />
Leon Y Chan1,a, Sriram Kosuri2,a and Drew Endy2<br />
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==[[Brown:Journal club/4.18.06|18th April]]==<br />
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Kara and Jesse<br />
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http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html<br />
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Programmable ligand-controlled riboregulators of eukaryotic gene expression.<br />
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Bayer TS, Smolke CD.<br />
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==[[Brown:Journal club/4.04.06|11th April]]==<br />
Annie and Angela will present the article: "Design of artificial cell–cell communication using gene and metabolic networks".<br />
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The paper can be found at: http://www.pnas.org/cgi/content/short/101/8/2299<br />
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Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal).<br />
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==[[Brown:Journal club/4.04.06|4th April]]==<br />
Brendan and Peter will be presenting the article entitled "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids".<br />
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Vincent J J Martin, Douglas J Pitera1, Sydnor T Withers1, Jack D Newman & Jay D Keasling. "Engineering a<br />
mevalonate pathway in Escherichia coli for production of terpenoids." Nature Biotechnology 21, 796 - 802 (2003).<br />
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It can be found online at http://www.nature.com/nbt/journal/v21/n7/abs/nbt833.html<br />
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==[[Brown:Journal club/3.21.06|21st March]]==<br />
Megan and Victoria will present the article handed out in last meeting. Article is entitled: "Construction of a genetic toggle switch in Escherichia coli" <br><br />
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Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory) [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Download the paper here]<br />
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==Archive==<br />
==14th March==<br />
John to give overview of last year's competition and to hand out readings<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html Download paper here]<br />
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==please add future weeks==</div>Petergoldstein