CellularMemory:Main Page - Revision history

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‎Introduction

Wideloache at 19:00, 29 November 2007

2007-11-29T19:00:56Z

Wideloache at 17:15, 20 November 2007

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Wideloache at 17:15, 20 November 2007

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 From there, three different papers will be discussed in detail:
-The [[CellularMemory:Toggle Switch | first paper]] describes the construction of a genetic toggle switch in ''E. coli'' ([[CellularMemory:References |Gardner, 2000]]). Published in 2000, this was a groundbreaking paper that laid the foundation for much of the research that has since been done on synthetic gene networks. While the genetic toggle switch is one of the most simplistic forms of synthetic memory, the establishment of a predictive mathematical model and a functional biological device set the stage for more complex networks to be constructed in more complex organisms.
+The [[CellularMemory:Toggle Switch | first paper]] describes the construction of a genetic toggle switch in ''E. coli'' ([[CellularMemory:References |Gardner, 2000]]). This was a groundbreaking paper that laid the foundation for much of the research that has since been done on synthetic gene networks. While the genetic toggle switch is one of the most simplistic forms of synthetic memory, the establishment of a predictive mathematical model and a functional biological device set the stage for more complex networks to be constructed in more complex organisms.
 The [[CellularMemory:Hysteresis in Mammalian Cells | second paper]] was published five years later and discusses the construction of a [http://en.wikipedia.org/wiki/Hysteresis hysteretic] memory switch in mammalian cells ([[CellularMemory:References |Kramer, 2005]]). This circuit improves upon the bistable toggle switch by adjusting the toggle-point based on the history of the cell. This work also demonstrates the feasibility of incorporating synthetic cellular memory into eukaryotic cells.

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 ==Introduction==
-Synthetic cellular memory refers to the engineering of living organisms to produce a "protracted response to a transient stimulus" ([[CellularMemory:References |Gardner, 2000; Ajo-Franklin, 2007]]). Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
+Synthetic cellular memory refers to the engineering of living organisms to produce a "protracted response to a transient stimulus" ([[CellularMemory:References |Gardner, 2000; Ajo-Franklin, 2007]]). Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described on this wiki site ([[CellularMemory:References |Gardner, 2000; Ajo-Franklin, 2007]]).
 [[Image:Memorycartoon.png|center]]

@@ Line 4: / Line 4: @@
 ==Introduction==
-Synthetic cellular memory refers to the engineering of living organisms to produce a "protracted response to a transient stimulus" ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]). Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
+Synthetic cellular memory refers to the engineering of living organisms to produce a "protracted response to a transient stimulus" ([[CellularMemory:References |Gardner, 2000; Ajo-Franklin, 2007]]). Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
 [[Image:Memorycartoon.png|center]]

@@ Line 4: / Line 4: @@
 ==Introduction==
-Synthetic cellular memory refers to the engineering of living organisms to produce a protracted response to a transient stimulus. Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
+Synthetic cellular memory refers to the engineering of living organisms to produce a "protracted response to a transient stimulus" ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]). Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
 [[Image:Memorycartoon.png|center]]

@@ Line 4: / Line 4: @@
 ==Introduction==
-Synthetic cellular memory refers to the engineering of living organisms to produce a protracted response to a transient stimulus. Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper.
+Synthetic cellular memory refers to the engineering of living organisms to produce a protracted response to a transient stimulus. Research in this area thus far has produced simple genetic circuits that change a cell's phenotype in response to a change in environment. In the short term, construction of such gene networks provides a more thorough understanding of natural systems. By matching experimental results with mathematical models, we can put our knowledge of systems biology to the test. In the long run, cellular memory promises to be a key component of synthetic biological design. While current research efforts have been directed at the production of a reporter protein in response to some input, memory circuits hold the potential to be incorporated into more complex gene networks. Engineered cell differentiation, detection of hazardous materials in drinking water, biocomputing, gene therapy, and other such applications of synthetic devices could all one day depend on modular memory circuits similar to the ones described in this paper ([[CellularMemory:References |Gardner, 2000 and Ajo-Franklin, 2007]]).
 [[Image:Memorycartoon.png|center]]

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 <hr>
 <center>
-<Previous Section | [[CellularMemory:Biological Desgins | Next Section>]]
+<Previous Section | [[CellularMemory:Biological Designs | Next Section>]]
 </center>

← Older revision		Revision as of 17:14, 20 November 2007
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	==Description of Wiki-Paper Contents==		==Description of Wiki-Paper Contents==
−	In order to examine the current state of the field of synthetic cellular memory, I will first look at common [[CellularMemory:Biological ~~Models~~ \| biological ~~models~~]] that are used to construct simple memory circuits ''in vivo''. Memory circuits typically fall into one of two categories: [[CellularMemory:Biological ~~Models~~#Mutual Repression \| mutual repression]] and [[CellularMemory:Biological ~~Models~~#Autoregulatory Positive Feedback \| autoregulatory positive feedback]]. Each of these networks will be described in detail. I will then present a few different [[CellularMemory:Mathematical Models \| mathematical models]] that are used to describe how these biological circuits function.	+	In order to examine the current state of the field of synthetic cellular memory, I will first look at common [[CellularMemory:Biological Designs \| biological designs]] that are used to construct simple memory circuits ''in vivo''. Memory circuits typically fall into one of two categories: [[CellularMemory:Biological Designs#Mutual Repression \| mutual repression]] and [[CellularMemory:Biological Designs#Autoregulatory Positive Feedback \| autoregulatory positive feedback]]. Each of these networks will be described in detail. I will then present a few different [[CellularMemory:Mathematical Models \| mathematical models]] that are used to describe how these biological circuits function.

@@ Line 9: / Line 9: @@
 ==Description of Wiki-Paper Contents==
-In order to examine the current state of the field of synthetic cellular memory, we will first look at common [[CellularMemory:Biological Models | biological models]] that are used to construct simple memory circuits ''in vivo''. Memory circuits typically fall into one of two categories: [[CellularMemory:Biological Models#Mutual Repression | mutual repression]] and [[CellularMemory:Biological Models#Autoregulatory Positive Feedback | autoregulatory positive feedback]]. Each of these networks will be described in detail. We will then look at a few different [[CellularMemory:Mathematical Models | mathematical models]] that are used to describe how these biological circuits function.
+In order to examine the current state of the field of synthetic cellular memory, I will first look at common [[CellularMemory:Biological Models | biological models]] that are used to construct simple memory circuits ''in vivo''. Memory circuits typically fall into one of two categories: [[CellularMemory:Biological Models#Mutual Repression | mutual repression]] and [[CellularMemory:Biological Models#Autoregulatory Positive Feedback | autoregulatory positive feedback]]. Each of these networks will be described in detail. I will then present a few different [[CellularMemory:Mathematical Models | mathematical models]] that are used to describe how these biological circuits function.
 From there, three different papers will be discussed in detail:
-The [[CellularMemory:Toggle Switch | first paper]] describes the construction of a genetic toggle switch in ''E. coli'' (Gardner, 2000). Published in 2000, this was a groundbreaking paper that laid the foundation for much of the research that has since been done on synthetic gene networks. While the genetic toggle switch is one of the most simplistic forms of synthetic memory, the establishment of a predictive mathematical model and a functional biological device set the stage for more complex networks in more complex organisms.
+The [[CellularMemory:Toggle Switch | first paper]] describes the construction of a genetic toggle switch in ''E. coli'' ([[CellularMemory:References |Gardner, 2000]]). Published in 2000, this was a groundbreaking paper that laid the foundation for much of the research that has since been done on synthetic gene networks. While the genetic toggle switch is one of the most simplistic forms of synthetic memory, the establishment of a predictive mathematical model and a functional biological device set the stage for more complex networks in more complex organisms.
-The [[CellularMemory:Hysteresis in Mammalian Cells | second paper]] was published five years later and discusses the construction of a [http://en.wikipedia.org/wiki/Hysteresis hysteretic] memory switch in mammalian cells (Kramer, 2005). This circuit improves upon the bistable toggle switch by adjusting the toggle-point based on the history of the cell. This work also demonstrates the feasibility of incorporating synthetic cellular memory into eukaryotic cells.
+The [[CellularMemory:Hysteresis in Mammalian Cells | second paper]] was published five years later and discusses the construction of a [http://en.wikipedia.org/wiki/Hysteresis hysteretic] memory switch in mammalian cells ([[CellularMemory:References |Kramer, 2005]]). This circuit improves upon the bistable toggle switch by adjusting the toggle-point based on the history of the cell. This work also demonstrates the feasibility of incorporating synthetic cellular memory into eukaryotic cells.
-The [[CellularMemory:Permanent Memory in Eukaryotes| final paper]], published in September of 2007, details a "permanent" memory network in yeast cells (Ajo-Franklin, 2007). Yeast were engineered to fluoresce indefinitely after sensing an input. This system is a move towards non-rewritable synthetic cellular memory. After the cells have sensed an input, their "memory" state is retained in all environments (as opposed to toggling back and forth between two different states), even through multiple cell divisions. An accurate mathematical model was also developed to predict network behavior in this eukaryotic system based on quantitative part characterization.
+The [[CellularMemory:Permanent Memory in Eukaryotes| final paper]], published in September of 2007, details a "permanent" memory network in yeast cells ([[CellularMemory:References |Ajo-Franklin, 2007]]). Yeast were engineered to fluoresce indefinitely after sensing an input. This system is a move towards non-rewritable synthetic cellular memory. After the cells have sensed an input, their "memory" state is retained in all environments (as opposed to toggling back and forth between two different states), even through multiple cell divisions. An accurate mathematical model was also developed to predict network behavior in this eukaryotic system based on quantitative part characterization.